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Volume 19
Issue 4
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Int. J. Mol. Sci., Volume 19, Issue 4 (April 2018) – 343 articles

Cover Story (view full-size image): GTPases control cellular processes by toggling between an active and an inactive state. The most prominent family members—H-Ras, N-Ras, and K-Ras isoforms—are frequently mutated in cancer. As plasticisers, bisphenols are widespread in modern life. BPA, BPAF, BPB, BPE, BPF, and BPNH2 interact with GDP-bound Ras through binding to a common site. This study reveals a new bisphenol-induced, allosterically activated GDP-bound Ras conformation that defines these plasticisers as Ras allosteric agonists. View the paper here.
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Editorial

Jump to: Research, Review, Other

10 pages, 6168 KiB  
Editorial
Oxidative Stress and Space Biology: An Organ-Based Approach
by Thomas J. Goodwin and Melpo Christofidou-Solomidou
Int. J. Mol. Sci. 2018, 19(4), 959; https://doi.org/10.3390/ijms19040959 - 23 Mar 2018
Cited by 41 | Viewed by 5782
Abstract
The environment of space provides many challenges to the human physiology and therefore to extended habitation and exploration[...] Full article
(This article belongs to the Special Issue Oxidative Stress and Space Biology: An Organ-Based Approach)
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5 pages, 170 KiB  
Editorial
Role of the Hypothalamic–Pituitary–Adrenal Axis in Health and Disease
by Sharon DeMorrow
Int. J. Mol. Sci. 2018, 19(4), 986; https://doi.org/10.3390/ijms19040986 - 26 Mar 2018
Cited by 52 | Viewed by 12443
Abstract
The Hypothalamic–Pituitary–adrenal (HPA) axis describes a complex set of positive and negative feedback influences between the hypothalamus, pituitary gland, and adrenal gland.[...] Full article
(This article belongs to the Special Issue Role of the Hypothalamo–Pituitary–Adrenal (HPA) Axis in Health and Disease)
7 pages, 211 KiB  
Editorial
Emerging Non-Canonical Functions and Regulation of p53
by Atul Ranjan and Tomoo Iwakuma
Int. J. Mol. Sci. 2018, 19(4), 1015; https://doi.org/10.3390/ijms19041015 - 28 Mar 2018
Cited by 7 | Viewed by 3278
Abstract
The tumor suppressor p53 induces cell cycle arrest and/or apoptosis by transactivating numerous downstream target genes and also translocating to the mitochondrial outer membrane. Full article
(This article belongs to the Special Issue Emerging Non-Canonical Functions and Regulation of p53)
5 pages, 223 KiB  
Editorial
Ubiquitin System
by Nobuhiro Nakamura
Int. J. Mol. Sci. 2018, 19(4), 1080; https://doi.org/10.3390/ijms19041080 - 4 Apr 2018
Cited by 55 | Viewed by 7895
Abstract
Ever since the discovery of ubiquitin in 1975[...] Full article
(This article belongs to the Special Issue Ubiquitin System)
3 pages, 179 KiB  
Editorial
Editorial—Special Issue “Nutraceuticals in Human Health and Disease”
by Leticia M. Estevinho
Int. J. Mol. Sci. 2018, 19(4), 1213; https://doi.org/10.3390/ijms19041213 - 17 Apr 2018
Cited by 6 | Viewed by 3245
Abstract
n/a Full article
(This article belongs to the Special Issue Nutraceuticals in Human Health and Disease)

Research

Jump to: Editorial, Review, Other

18 pages, 6296 KiB  
Article
Transcriptome Analysis Reveals Candidate Genes Associated with Leaf Etiolation of a Cytoplasmic Male Sterility Line in Chinese Cabbage (Brassica Rapa L. ssp. Pekinensis)
by Fei Xie, Jia-Lan Yuan, Yi-Xiao Li, Can-Jie Wang, Hong-Yu Tang, Jun-Hui Xia, Qing-Yong Yang and Zheng-Jie Wan
Int. J. Mol. Sci. 2018, 19(4), 922; https://doi.org/10.3390/ijms19040922 - 21 Mar 2018
Cited by 10 | Viewed by 5855
Abstract
Cytoplasmic male sterility (CMS) is universally utilized in cruciferous vegetables. However, the Chinese cabbage hau CMS lines, obtained by interspecific hybridization and multiple backcrosses of the Brassica juncea (B. juncea) CMS line and Chinese cabbage, show obvious leaf etiolation, and the [...] Read more.
Cytoplasmic male sterility (CMS) is universally utilized in cruciferous vegetables. However, the Chinese cabbage hau CMS lines, obtained by interspecific hybridization and multiple backcrosses of the Brassica juncea (B. juncea) CMS line and Chinese cabbage, show obvious leaf etiolation, and the molecular mechanism of etiolation remains elusive. Here, the ultrastructural and phenotypic features of leaves from the Chinese cabbage CMS line 1409A and maintainer line 1409B are analyzed. The results show that chloroplasts of 1409A exhibit abnormal morphology and distribution. Next, RNA-sequencing (RNA-Seq) is used to identify 485 differentially expressed genes (DEGs) between 1409A and 1409B, and 189 up-regulated genes and 296 down-regulated genes are found. Genes that affect chloroplasts development, such as GLK1 and GLK2, and chlorophyll biosynthesis, such as PORB, are included in the down-regulated DEGs. Quantitative real-time PCR (qRT-PCR) analysis validate that the expression levels of these genes are significantly lower in 1409A than in 1409B. Taken together, these results demonstrate that leaf etiolation is markedly affected by chloroplast development and pigment biosynthesis. This study provides an effective foundation for research on the molecular mechanisms of leaf etiolation of the hau CMS line in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Full article
(This article belongs to the Section Molecular Plant Sciences)
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16 pages, 7261 KiB  
Article
Characterization of an Integrated Active Glu-1Ay Allele in Common Wheat from Wild Emmer and Its Potential Role in Flour Improvement
by Zhenzhen Wang, Lin Huang, Bihua Wu, Jiliang Hu, Zilong Jiang, Pengfei Qi, Youliang Zheng and Dengcai Liu
Int. J. Mol. Sci. 2018, 19(4), 923; https://doi.org/10.3390/ijms19040923 - 21 Mar 2018
Cited by 20 | Viewed by 4565
Abstract
Glu-1Ay, one of six genes encoding a high molecular weight glutenin subunit (HMW-GS), is frequently silenced in hexaploid common wheat. Here, an active allele of Glu-1Ay was integrated from wild emmer wheat (Triticum turgidum ssp. dicoccoides) accession D97 into the [...] Read more.
Glu-1Ay, one of six genes encoding a high molecular weight glutenin subunit (HMW-GS), is frequently silenced in hexaploid common wheat. Here, an active allele of Glu-1Ay was integrated from wild emmer wheat (Triticum turgidum ssp. dicoccoides) accession D97 into the common wheat (Triticum aestivum) cultivar Chuannong 16 via the repeated self-fertilization of the pentaploid interspecific hybrid, culminating in the selection of a line TaAy7-40 shown to express the wild emmer Glu-1Ay allele. The open reading frame of this allele was a 1830 bp long sequence, demonstrated by its heterologous expression in Escherichia coli to encode a 608-residue polypeptide. Its nucleotide sequence was 99.2% identical to that of the sequence within the wild emmer parent. The TaAy7-40 introgression line containing the active Glu-1Ay allele showed higher protein content, higher sodium dodecyl sulfate (SDS) sedimentation value, higher content of wet gluten in the flour, higher grain weight, and bigger grain size than Chuannong 16. The end-use quality parameters of the TaAy7-40 were superior to those of the medium gluten common wheat cultivars Mianmai 37 and Neimai 9. Thus, the active Glu-1Ay allele might be of potential value in breeding programs designed to improve wheat flour quality. Full article
(This article belongs to the Section Molecular Plant Sciences)
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13 pages, 1243 KiB  
Article
PKC-Mediated Modulation of Astrocyte SNAT3 Glutamine Transporter Function at Synapses in Situ
by Wuxing Dong, Alison C. Todd, Angelika Bröer, Sarah R. Hulme, Stefan Bröer and Brian Billups
Int. J. Mol. Sci. 2018, 19(4), 924; https://doi.org/10.3390/ijms19040924 - 21 Mar 2018
Cited by 5 | Viewed by 4493
Abstract
Astrocytes are glial cells that have an intimate physical and functional association with synapses in the brain. One of their main roles is to recycle the neurotransmitters glutamate and gamma-aminobutyric acid (GABA), as a component of the glutamate/GABA-glutamine cycle. They perform this function [...] Read more.
Astrocytes are glial cells that have an intimate physical and functional association with synapses in the brain. One of their main roles is to recycle the neurotransmitters glutamate and gamma-aminobutyric acid (GABA), as a component of the glutamate/GABA-glutamine cycle. They perform this function by sequestering neurotransmitters and releasing glutamine via the neutral amino acid transporter SNAT3. In this way, astrocytes regulate the availability of neurotransmitters and subsequently influence synaptic function. Since many plasma membrane transporters are regulated by protein kinase C (PKC), the aim of this study was to understand how PKC influences SNAT3 glutamine transport in astrocytes located immediately adjacent to synapses. We studied SNAT3 transport by whole-cell patch-clamping and fluorescence pH imaging of single astrocytes in acutely isolated brainstem slices, adjacent to the calyx of the Held synapse. Activation of SNAT3-mediated glutamine transport in these astrocytes was reduced to 77 ± 6% when PKC was activated with phorbol 12-myristate 13-acetate (PMA). This effect was very rapid (within ~20 min) and eliminated by application of bisindolylmaleimide I (Bis I) or 7-hydroxystaurosporine (UCN-01), suggesting that activation of conventional isoforms of PKC reduces SNAT3 function. In addition, cell surface biotinylation experiments in these brain slices show that the amount of SNAT3 in the plasma membrane is reduced by a comparable amount (to 68 ± 5%) upon activation of PKC. This indicates a role for PKC in dynamically controlling the trafficking of SNAT3 transporters in astrocytes in situ. These data demonstrate that PKC rapidly regulates the astrocytic glutamine release mechanism, which would influence the glutamine availability for adjacent synapses and control levels of neurotransmission. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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16 pages, 1359 KiB  
Article
212Pb-Labeled Antibody 225.28 Targeted to Chondroitin Sulfate Proteoglycan 4 for Triple-Negative Breast Cancer Therapy in Mouse Models
by Benjamin B. Kasten, Patsy G. Oliver, Harrison Kim, Jinda Fan, Soldano Ferrone, Kurt R. Zinn and Donald J. Buchsbaum
Int. J. Mol. Sci. 2018, 19(4), 925; https://doi.org/10.3390/ijms19040925 - 21 Mar 2018
Cited by 31 | Viewed by 5158
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis. There is a clinical need for effective, targeted therapy strategies that destroy both differentiated TNBC cells and TNBC cancer initiating cells (CICs), as the latter are implicated in [...] Read more.
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis. There is a clinical need for effective, targeted therapy strategies that destroy both differentiated TNBC cells and TNBC cancer initiating cells (CICs), as the latter are implicated in the metastasis and recurrence of TNBC. Chondroitin sulfate proteoglycan 4 (CSPG4) is overexpressed on differentiated tumor cells and CICs obtained from TNBC patient specimens, suggesting that CSPG4 may be a clinically relevant target for the imaging and therapy of TNBC. The purpose of this study was to determine whether α-particle radioimmunotherapy (RIT) targeting TNBC cells using the CSPG4-specific monoclonal antibody (mAb) 225.28 as a carrier was effective at eliminating TNBC tumors in preclinical models. To this end, mAb 225.28 labeled with 212Pb (212Pb-225.28) as a source of α-particles for RIT was used for in vitro Scatchard assays and clonogenic survival assays with human TNBC cells (SUM159 and 2LMP) grown as adherent cells or non-adherent CIC-enriched mammospheres. Immune-deficient mice bearing orthotopic SUM159 or 2LMP xenografts were injected i.v. with the targeted (225.28) or irrelevant isotype-matched control (F3-C25) mAbs, labeled with 99mTc, 125I, or 212Pb for in vivo imaging, biodistribution, or tumor growth inhibition studies. 212Pb-225.28 bound to adherent SUM159 and 2LMP cells and to CICs from SUM159 and 2LMP mammospheres with a mean affinity of 0.5 nM. Nearly ten times more binding sites per cell were present on SUM159 cells and CICs compared with 2LMP cells. 212Pb-225.28 was six to seven times more effective than 212Pb-F3-C25 at inhibiting SUM159 cell and CIC clonogenic survival (p < 0.05). Radiolabeled mAb 225.28 showed significantly higher uptake than radiolabeled mAb F3-C25 in SUM159 and 2LMP xenografts (p < 0.05), and the uptake of 212Pb-225.28 in TNBC xenografts was correlated with target epitope expression. 212Pb-225.28 caused dose-dependent growth inhibition of SUM159 xenografts; 0.30 MBq 212Pb-225.28 was significantly more effective than 0.33 MBq 212Pb-F3-C25 at inhibiting tumor growth (p < 0.01). These results suggest that CSPG4-specific 212Pb-225.28 is a useful reagent for RIT of CSPG4-expressing tumors, including metastatic TNBC. Full article
(This article belongs to the Special Issue Receptor-Targeted Cancer Therapy)
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17 pages, 1824 KiB  
Article
The Role of Potassium Channels in Arabidopsis thaliana Long Distance Electrical Signalling: AKT2 Modulates Tissue Excitability While GORK Shapes Action Potentials
by Tracey Ann Cuin, Ingo Dreyer and Erwan Michard
Int. J. Mol. Sci. 2018, 19(4), 926; https://doi.org/10.3390/ijms19040926 - 21 Mar 2018
Cited by 65 | Viewed by 6804
Abstract
Fast responses to an external threat depend on the rapid transmission of signals through a plant. Action potentials (APs) are proposed as such signals. Plant APs share similarities with their animal counterparts; they are proposed to depend on the activity of voltage-gated ion [...] Read more.
Fast responses to an external threat depend on the rapid transmission of signals through a plant. Action potentials (APs) are proposed as such signals. Plant APs share similarities with their animal counterparts; they are proposed to depend on the activity of voltage-gated ion channels. Nonetheless, despite their demonstrated role in (a)biotic stress responses, the identities of the associated voltage-gated channels and transporters remain undefined in higher plants. By demonstrating the role of two potassium-selective channels in Arabidopsis thaliana in AP generation and shaping, we show that the plant AP does depend on similar Kv-like transport systems to those of the animal signal. We demonstrate that the outward-rectifying potassium-selective channel GORK limits the AP amplitude and duration, while the weakly-rectifying channel AKT2 affects membrane excitability. By computational modelling of plant APs, we reveal that the GORK activity not only determines the length of an AP but also the steepness of its rise and the maximal amplitude. Thus, outward-rectifying potassium channels contribute to both the repolarisation phase and the initial depolarisation phase of the signal. Additionally, from modelling considerations we provide indications that plant APs might be accompanied by potassium waves, which prime the excitability of the green cable. Full article
(This article belongs to the Special Issue Plasma-Membrane Transport)
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18 pages, 3442 KiB  
Article
The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree
by Josphat K. Saina, Zhi-Zhong Li, Andrew W. Gichira and Yi-Ying Liao
Int. J. Mol. Sci. 2018, 19(4), 929; https://doi.org/10.3390/ijms19040929 - 21 Mar 2018
Cited by 65 | Viewed by 6132
Abstract
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until [...] Read more.
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family. Full article
(This article belongs to the Special Issue Chloroplast)
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12 pages, 1450 KiB  
Article
Mutagenesis Study of the Cytochrome c Subunit Responsible for the Direct Electron Transfer-Type Catalytic Activity of FAD-Dependent Glucose Dehydrogenase
by Yuki Yamashita, Nanoha Suzuki, Nana Hirose, Katsuhiro Kojima, Wakako Tsugawa and Koji Sode
Int. J. Mol. Sci. 2018, 19(4), 931; https://doi.org/10.3390/ijms19040931 - 21 Mar 2018
Cited by 14 | Viewed by 3828
Abstract
The FAD-dependent glucose dehydrogenase from Burkholderia cepacia (FADGDH) is a hetero-oligomeric enzyme that is capable of direct electron transfer (DET) with an electrode. The cytochrome c (cyt c) subunit, which possesses three hemes (heme 1, heme 2, and heme 3, from the [...] Read more.
The FAD-dependent glucose dehydrogenase from Burkholderia cepacia (FADGDH) is a hetero-oligomeric enzyme that is capable of direct electron transfer (DET) with an electrode. The cytochrome c (cyt c) subunit, which possesses three hemes (heme 1, heme 2, and heme 3, from the N-terminal sequence), is known to enable DET; however, details of the electron transfer pathway remain unknown. A mutagenesis investigation of the heme axial ligands was carried out to elucidate the electron transfer pathway to the electron mediators and/or the electrode. The sixth axial ligand for each of the three heme irons, Met109, Met263, and Met386 were substituted with His. The catalytic activities of the wild-type (WT) and mutant enzymes were compared by investigating their dye-mediated dehydrogenase activities and their DET abilities toward the electrode. The results suggested that (1) heme 1 with Met109 as an axial ligand is mainly responsible for the electron transfer with electron acceptors in the solution, but not for the DET with the electrode; (2) heme 2 with Met263 is responsible for the DET-type reaction with the electrode; and (3) heme 3 with Met386 seemed to be the electron acceptor from the catalytic subunit. From these results, two electron transfer pathways were proposed depending on the electron acceptors. Electrons are transferred from the catalytic subunit to heme 3, then to heme 2, to heme 1 and, finally, to electron acceptors in solution. However, if the enzyme complex is immobilized on the electrode and is used as electron acceptors, electrons are passed to the electrode from heme 2. Full article
(This article belongs to the Section Biochemistry)
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18 pages, 2277 KiB  
Article
Immune-Specific Expression and Estrogenic Regulation of the Four Estrogen Receptor Isoforms in Female Rainbow Trout (Oncorhynchus mykiss)
by Ayako Casanova-Nakayama, Elena Wernicke von Siebenthal, Christian Kropf, Elisabeth Oldenberg and Helmut Segner
Int. J. Mol. Sci. 2018, 19(4), 932; https://doi.org/10.3390/ijms19040932 - 21 Mar 2018
Cited by 22 | Viewed by 3893
Abstract
Genomic actions of estrogens in vertebrates are exerted via two intracellular estrogen receptor (ER) subtypes, ERα and ERβ, which show cell- and tissue-specific expression profiles. Mammalian immune cells express ERs and are responsive to estrogens. More recently, evidence became available that ERs are [...] Read more.
Genomic actions of estrogens in vertebrates are exerted via two intracellular estrogen receptor (ER) subtypes, ERα and ERβ, which show cell- and tissue-specific expression profiles. Mammalian immune cells express ERs and are responsive to estrogens. More recently, evidence became available that ERs are also present in the immune organs and cells of teleost fish, suggesting that the immunomodulatory function of estrogens has been conserved throughout vertebrate evolution. For a better understanding of the sensitivity and the responsiveness of the fish immune system to estrogens, more insight is needed on the abundance of ERs in the fish immune system, the cellular ratios of the ER subtypes, and their autoregulation by estrogens. Consequently, the aims of the present study were (i) to determine the absolute mRNA copy numbers of the four ER isoforms in the immune organs and cells of rainbow trout, Oncorhynchus mykiss, and to compare them to the hepatic ER numbers; (ii) to analyse the ER mRNA isoform ratios in the immune system; and, (iii) finally, to examine the alterations of immune ER mRNA expression levels in sexually immature trout exposed to 17β-estradiol (E2), as well as the alterations of immune ER mRNA expression levels in sexually mature trout during the reproductive cycle. All four ER isoforms were present in immune organs—head kidney, spleen-and immune cells from head kidney and blood of rainbow trout, but their mRNA levels were substantially lower than in the liver. The ER isoform ratios were tissue- and cell-specific, both within the immune system, but also between the immune system and the liver. Short-term administration of E2 to juvenile female trout altered the ER mRNA levels in the liver, but the ERs of the immune organs and cells were not responsive. Changes of ER gene transcript numbers in immune organs and cells occurred during the reproductive cycle of mature female trout, but the changes in the immune ER profiles differed from those in the liver and gonads. The correlation between ER gene transcript numbers and serum E2 concentrations was only moderate to low. In conclusion, the low mRNA numbers of nuclear ER in the trout immune system, together with their limited estrogen-responsiveness, suggest that the known estrogen actions on trout immunity may be not primarily mediated through genomic actions, but may involve other mechanisms, such as non-genomic pathways or indirect effects. Full article
(This article belongs to the Special Issue Molecular Pathways of Estrogen Receptor Action)
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16 pages, 2354 KiB  
Article
Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori
by Songzhen He, Xiaoling Tong, Minjin Han, Yanmin Bai and Fangyin Dai
Int. J. Mol. Sci. 2018, 19(4), 934; https://doi.org/10.3390/ijms19040934 - 21 Mar 2018
Cited by 10 | Viewed by 4190
Abstract
The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. [...] Read more.
The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO) analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions. Full article
(This article belongs to the Special Issue Molecular Entomology of Insects of Economic Importance)
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15 pages, 6765 KiB  
Article
Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
by Yuki Mitsuta, Takashi Kawakami, Mitsutaka Okumura and Shusuke Yamanaka
Int. J. Mol. Sci. 2018, 19(4), 937; https://doi.org/10.3390/ijms19040937 - 21 Mar 2018
Cited by 10 | Viewed by 3984
Abstract
We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) [...] Read more.
We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values. Full article
(This article belongs to the Special Issue Computational Studies of Structure-Dynamics-Function Relationships in Biomolecules)
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13 pages, 6372 KiB  
Article
Hinokitiol Inhibits Migration of A549 Lung Cancer Cells via Suppression of MMPs and Induction of Antioxidant Enzymes and Apoptosis
by Thanasekaran Jayakumar, Chao-Hong Liu, Guan-Yi Wu, Tzu-Yin Lee, Manjunath Manubolu, Cheng-Ying Hsieh, Chih-Hao Yang and Joen-Rong Sheu
Int. J. Mol. Sci. 2018, 19(4), 939; https://doi.org/10.3390/ijms19040939 - 22 Mar 2018
Cited by 32 | Viewed by 6710
Abstract
Hinokitiol, a natural monoterpenoid from the heartwood of Calocedrus formosana, has been reported to have anticancer effects against various cancer cell lines. However, the detailed molecular mechanisms and the inhibiting roles of hinokitiol on adenocarcinoma A549 cells remain to be fully elucidated. [...] Read more.
Hinokitiol, a natural monoterpenoid from the heartwood of Calocedrus formosana, has been reported to have anticancer effects against various cancer cell lines. However, the detailed molecular mechanisms and the inhibiting roles of hinokitiol on adenocarcinoma A549 cells remain to be fully elucidated. Thus, the current study was designed to evaluate the effect of hinokitiol on the migration of human lung adenocarcinoma A549 cells in vitro. The data demonstrates that hinokitiol does not effectively inhibit the viability of A549 cells at up to a 10 µM concentration. When treated with non-toxic doses (1–5 µM) of hinokitiol, the cell migration is markedly suppressed at 5 µM. Hinokitiol significantly reduced p53 expression, followed by attenuation of Bax in A549 cells. A dose-dependent inhibition of activated caspase-9 and -3 was observed in the presence of hinokitiol. An observed increase in protein expression of matrix metalloproteinases (MMPs) -2/-9 in A549 cells was significantly inhibited by hinokitiol. Remarkably, when A549 cells were subjected to hinokitiol (1–5 µM), there was an increase in the activities of antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD) from the reduction in cells. In addition, the incubation of A549 cells with hinokitiol significantly activated the cytochrome c expression, which may be triggered by activation of caspase-9 followed by caspase-3. These observations indicate that hinokitiol inhibited the migration of lung cancer A549 cells through several mechanisms, including the activation of caspases-9 and -3, induction of p53/Bax and antioxidant CAT and SOD, and reduction of MMP-2 and -9 activities. It also induces cytochrome c expression. These findings demonstrate a new therapeutic potential for hinokitiol in lung cancer chemoprevention. Full article
(This article belongs to the Special Issue Plant Natural Products for Human Health)
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17 pages, 14069 KiB  
Article
Overexpression of a SBP-Box Gene (VpSBP16) from Chinese Wild Vitis Species in Arabidopsis Improves Salinity and Drought Stress Tolerance
by Hongmin Hou, Hui Jia, Qin Yan and Xiping Wang
Int. J. Mol. Sci. 2018, 19(4), 940; https://doi.org/10.3390/ijms19040940 - 22 Mar 2018
Cited by 55 | Viewed by 5619
Abstract
Salinity and drought are two major abiotic stresses that limit grape productivity. Responses to stress in grape are known to be regulated by several families of transcription factors. However, little is known about the role of grape Squamosa promoter binding protein (SBP)-box transcription [...] Read more.
Salinity and drought are two major abiotic stresses that limit grape productivity. Responses to stress in grape are known to be regulated by several families of transcription factors. However, little is known about the role of grape Squamosa promoter binding protein (SBP)-box transcription factor genes in response to abiotic stress. To better understand the functions of the grape SBP-box genes in abiotic stress tolerance, a full-length complementary DNA (cDNA) sequence of the putative SBP-box transcription factor gene, VpSBP16 was amplified from Chinese wild grapevine Vitis pseudoreticulata clone “Baihe-35-1”. We observed that the VpSBP16 protein fused to the green fluorescent protein (GFP) reporter accumulated in the nucleus when transiently expressed in onion epidermal cells. Moreover, VpSBP16 was shown to have transcriptional activation activity using a yeast trans-activation assay. We performed a VpSBP16 functional analysis through the characterization of transgenic Arabidopsis thaliana plants constitutively over-expressing VpSBP16. The transgenic lines had longer roots and the seeds had a higher germination rate than the wild type (WT) under osmotic stress. In addition, the accumulation of reactive oxygen species (ROS) of transgenic seedlings was significantly lower than WT in the transgenic lines, as was electrolyte leakage. VpSBP16 overexpression also elevated expression levels of stress-response genes involved in the salt overly sensitive (SOS) pathway. These results indicate that overexpression VpSBP16 in A. thaliana enhances tolerance of salt and drought stress during seed germination, as well in seedlings and mature plants, by regulating SOS and ROS signaling cascades. Full article
(This article belongs to the Section Molecular Plant Sciences)
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20 pages, 5134 KiB  
Article
α-Ketoglutarate Promotes Pancreatic Progenitor-Like Cell Proliferation
by Jing Song, Dongshen Ma, Yun Xing, Shanshan Tang, Murad Alahdal, Jiamin Guo, Yi Pan, Yanfeng Zhang, Yumeng Shen, Qiong Wu, Zhou Lu and Liang Jin
Int. J. Mol. Sci. 2018, 19(4), 943; https://doi.org/10.3390/ijms19040943 - 22 Mar 2018
Cited by 2 | Viewed by 4749
Abstract
A major source of β cell generation is pancreatic progenitor-like cell differentiation. Multiple studies have confirmed that stem cell metabolism plays important roles in self-renewal and proliferation. In the absence of glucose, glutamine provides the energy for cell division and growth. Furthermore, α-ketoglutarate [...] Read more.
A major source of β cell generation is pancreatic progenitor-like cell differentiation. Multiple studies have confirmed that stem cell metabolism plays important roles in self-renewal and proliferation. In the absence of glucose, glutamine provides the energy for cell division and growth. Furthermore, α-ketoglutarate (αKG), a precursor for glutamine synthesis, is sufficient for enabling glutamine-independent cell proliferation. We have demonstrated that αKG contributes to the large-scale proliferation of pancreatic progenitor-like cells that can provide an ample amount of clinically relevant β cells. We compared the mRNA expression of a subset of genes, the abundance of ATP, reactive oxide species, mitochondrial number, and the colony-forming frequency between mouse pancreatic CD133+ and CD133− cells. We employed Real-Time PCR, immunostaining and passage assays to investigate self-renewal and proliferation of pancreatic progenitor-like cells in a 3D culture system in the presence and absence of αKG. The energy metabolism of CD133+ cells was more prone to oxidative phosphorylation. However, in the 3D culture system, when αKG was supplemented to the culture medium, the proliferation of the pancreatic progenitor-like cells was significantly elevated. We confirmed that the presence of αKG correlated with the up-regulation of Ten-Eleven Translocation (Tet). αKG can promote the proliferation of pancreatic progenitor-like cells via the up-regulation of Tet. Full article
(This article belongs to the Section Biochemistry)
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19 pages, 2432 KiB  
Article
Imine Deaminase Activity and Conformational Stability of UK114, the Mammalian Member of the Rid Protein Family Active in Amino Acid Metabolism
by Genny Degani, Alberto Barbiroli, Luca Regazzoni, Laura Popolo and Maria Antonietta Vanoni
Int. J. Mol. Sci. 2018, 19(4), 945; https://doi.org/10.3390/ijms19040945 - 22 Mar 2018
Cited by 17 | Viewed by 4607
Abstract
Reactive intermediate deaminase (Rid) protein family is a recently discovered group of enzymes that is conserved in all domains of life and is proposed to play a role in the detoxification of reactive enamines/imines. UK114, the mammalian member of RidA subfamily, was identified [...] Read more.
Reactive intermediate deaminase (Rid) protein family is a recently discovered group of enzymes that is conserved in all domains of life and is proposed to play a role in the detoxification of reactive enamines/imines. UK114, the mammalian member of RidA subfamily, was identified in the early 90s as a component of perchloric acid-soluble extracts from goat liver and exhibited immunomodulatory properties. Multiple activities were attributed to this protein, but its function is still unclear. This work addressed the question of whether UK114 is a Rid enzyme. Biochemical analyses demonstrated that UK114 hydrolyzes α-imino acids generated by l- or d-amino acid oxidases with a preference for those deriving from Ala > Leu = l-Met > l-Gln, whereas it was poorly active on l-Phe and l-His. Circular Dichroism (CD) analyses of UK114 conformational stability highlighted its remarkable resistance to thermal unfolding, even at high urea concentrations. The half-life of heat inactivation at 95 °C, measured from CD and activity data, was about 3.5 h. The unusual conformational stability of UK114 could be relevant in the frame of a future evaluation of its immunogenic properties. In conclusion, mammalian UK114 proteins are RidA enzymes that may play an important role in metabolism homeostasis also in these organisms. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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20 pages, 4633 KiB  
Article
CRISPR/Cas9-Based Cellular Engineering for Targeted Gene Overexpression
by Mark J. Osborn, Christopher J. Lees, Amber N. McElroy, Sarah C. Merkel, Cindy R. Eide, Wendy Mathews, Colby J. Feser, Madison Tschann, Ron T. McElmury, Beau R. Webber, Chong Jai Kim, Bruce R. Blazar and Jakub Tolar
Int. J. Mol. Sci. 2018, 19(4), 946; https://doi.org/10.3390/ijms19040946 - 22 Mar 2018
Cited by 17 | Viewed by 9659
Abstract
Gene and cellular therapies hold tremendous promise as agents for treating genetic disorders. However, the effective delivery of genes, particularly large ones, and expression at therapeutic levels can be challenging in cells of clinical relevance. To address this engineering hurdle, we sought to [...] Read more.
Gene and cellular therapies hold tremendous promise as agents for treating genetic disorders. However, the effective delivery of genes, particularly large ones, and expression at therapeutic levels can be challenging in cells of clinical relevance. To address this engineering hurdle, we sought to employ the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system to insert powerful regulatory elements upstream of an endogenous gene. We achieved robust activation of the COL7A1 gene in primary human umbilical cord blood CD34+ hematopoietic stem cells and peripheral blood T-cells. CD34+ cells retained their colony forming potential and, in a second engineering step, we disrupted the T-cell receptor complex in T-cells. These cellular populations are of high translational impact due to their engraftment potential, broad circulatory properties, and favorable immune profile that supports delivery to multiple recipients. This study demonstrates the feasibility of targeted knock in of a ubiquitous chromatin opening element, promoter, and marker gene that doubles as a suicide gene for precision gene activation. This system merges the specificity of gene editing with the high level, sustained gene expression achieved with gene therapy vectors. We predict that this design concept will be highly transferrable to most genes in multiple model systems representing a facile cellular engineering platform for promoting gene expression. Full article
(This article belongs to the Special Issue Genome Editing 2018)
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15 pages, 25188 KiB  
Article
Calcium-Dependent Protein Kinase Family Genes Involved in Ethylene-Induced Natural Rubber Production in Different Hevea brasiliensis Cultivars
by Liping Zhu, Xiang Jin, Quanliang Xie, Qi Yao, Xuchu Wang and Hongbin Li
Int. J. Mol. Sci. 2018, 19(4), 947; https://doi.org/10.3390/ijms19040947 - 22 Mar 2018
Cited by 10 | Viewed by 4055
Abstract
Natural rubber latex production can be improved by ethylene stimulation in the rubber tree (Hevea brasiliensis). However, the expression levels of most functional proteins for natural rubber biosynthesis are not induced after ethylene application, indicating that post-translational modifications, especially protein phosphorylation, [...] Read more.
Natural rubber latex production can be improved by ethylene stimulation in the rubber tree (Hevea brasiliensis). However, the expression levels of most functional proteins for natural rubber biosynthesis are not induced after ethylene application, indicating that post-translational modifications, especially protein phosphorylation, may play important roles in ethylene signaling in Hevea. Here, we performed a comprehensive investigation on evolution, ethylene-induced expression and protein–protein interaction of calcium-dependent protein kinases (CPKs), an important serine/threonine protein kinase family, in Hevea. Nine duplication events were determined in the 30 identified HbCPK genes. Expression profiling of HbCPKs in three rubber tree cultivars with low, medium and high ethylene sensitivity showed that HbCPK6, 17, 20, 22, 24, 28 and 30 are induced by ethylene in at least one cultivar. Evolution rate analysis suggested accelerated evolution rates in two paralogue pairs, HbCPK9/18 and HbCPK19/20. Analysis of proteomic data for rubber latex after ethylene treatment showed that seven HbCPK proteins could be detected, including six ethylene-induced ones. Protein–protein interaction analysis of the 493 different abundant proteins revealed that protein kinases, especially calcium-dependent protein kinases, possess most key nodes of the interaction network, indicating that protein kinase and protein phosphorylation play important roles in ethylene signaling in latex of Hevea. In summary, our data revealed the expression patterns of HbCPK family members and functional divergence of two HbCPK paralogue pairs, as well as the potential important roles of HbCPKs in ethylene-induced rubber production improvement in Hevea. Full article
(This article belongs to the Section Molecular Plant Sciences)
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10 pages, 2596 KiB  
Article
Renoprotective Effects of Hypoxylonol C and F Isolated from Hypoxylon truncatum against Cisplatin-Induced Cytotoxicity in LLC-PK1 Cells
by Buyng Su Hwang, Dahae Lee, Pilju Choi, Kyu Sun Kim, Seon-Jun Choi, Bong Geun Song, Taejung Kim, Ji Hoon Song, Ki Sung Kang and Jungyeob Ham
Int. J. Mol. Sci. 2018, 19(4), 948; https://doi.org/10.3390/ijms19040948 - 22 Mar 2018
Cited by 8 | Viewed by 3307
Abstract
Although cisplatin is the standard platinum-based anticancer drug used to treat various solid tumors, it can cause damage in normal kidney cells. Protective strategies against cisplatin-induced nephrotoxicity are, therefore, clinically important and urgently required. To address this challenge, we investigated the renoprotective effects [...] Read more.
Although cisplatin is the standard platinum-based anticancer drug used to treat various solid tumors, it can cause damage in normal kidney cells. Protective strategies against cisplatin-induced nephrotoxicity are, therefore, clinically important and urgently required. To address this challenge, we investigated the renoprotective effects of Hypoxylon truncatum, a ball-shaped wood-rotting fungus. Chemical investigation of the active fraction from the methanol extract of H. truncatum resulted in the isolation and identification of the renoprotective compounds, hypoxylonol C and F, which ameliorated cisplatin-induced nephrotoxicity to approximately 80% of the control value at 5 μM. The mechanism of this effect was further investigated using hypoxylonol F, which showed a protective effect at the lowest concentration. Upregulated phosphorylation of p38, extracellular signal-regulated kinases, and c-Jun N-terminal kinases following cisplatin treatment were markedly decreased after pre-treatment with hypoxylonol F. In addition, the protein expression level of cleaved caspase-3 was significantly reduced after co-treatment with hypoxylonol F. These results show that blocking the mitogen-activated protein kinase signaling cascade plays a critical role in mediating the renoprotective effect of hypoxylonol F isolated from H. truncatum fruiting bodies. Full article
(This article belongs to the Section Molecular Toxicology)
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10 pages, 16954 KiB  
Article
Time-Resolved Measurement of the ATP-Dependent Motion of the Group II Chaperonin by Diffracted Electron Tracking
by Naoki Ogawa, Yohei Y. Yamamoto, Keisuke Abe, Hiroshi Sekiguchi, Yuji C. Sasaki, Akira Ishikawa, Judith Frydman and Masafumi Yohda
Int. J. Mol. Sci. 2018, 19(4), 950; https://doi.org/10.3390/ijms19040950 - 22 Mar 2018
Cited by 2 | Viewed by 3898
Abstract
Previously, we demonstrated the ATP-dependent dynamics of a group II chaperonin at the single-molecule level by diffracted X-ray tracking (DXT). The disadvantage of DXT is that it requires a strong X-ray source and also perfect gold nano-crystals. To resolve this problem, we developed [...] Read more.
Previously, we demonstrated the ATP-dependent dynamics of a group II chaperonin at the single-molecule level by diffracted X-ray tracking (DXT). The disadvantage of DXT is that it requires a strong X-ray source and also perfect gold nano-crystals. To resolve this problem, we developed diffracted electron tracking (DET). Electron beams have scattering cross-sections that are approximately 1000 times larger than those of X-rays. Thus, DET enables us to perform super-accurate measurements of the time-resolved 3D motion of proteins labeled with commercially available gold nanorods using a scanning electron microscope. In this study, we compared DXT and DET using the group II chaperonin from Methanococcus maripaludis (MmCpn) as a model protein. In DET, the samples are prepared in an environmental cell (EC). To reduce the electron beam-induced protein damage, we immobilized MmCpn on the bottom of the EC to expose gold nanorods close to the carbon thin film. The sample setup worked well, and the motions of gold nanorods were clearly traced. Compared with the results of DXT, the mobility in DET was significantly higher, which is probably due to the difference in the method for immobilization. In DET, MmCpn was immobilized on a film of triacetyl cellulose. Whereas proteins are directly attached on the surface of solid support in DXT. Therefore, MmCpn could move relatively freely in DET. DET will be a state-of-the-art technology for analyzing protein dynamics. Full article
(This article belongs to the Special Issue Molecular Chaperones)
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13 pages, 77351 KiB  
Article
Antioxidative Effect of Quetiapine on Acute Ultraviolet-B-Induced Skin and HaCaT Cell Damage
by Pengcheng Xu, Min Zhang, Xueer Wang, Yuan Yan, Yinghua Chen, Wei Wu, Lu Zhang and Lin Zhang
Int. J. Mol. Sci. 2018, 19(4), 953; https://doi.org/10.3390/ijms19040953 - 23 Mar 2018
Cited by 11 | Viewed by 5506
Abstract
Quetiapine is a new type of antipsychotic drug, with effective protection of pheochromocytoma PC12 cells from oxidative stress-induced apoptosis. Ultraviolet-B radiation can increase reactive oxygen species (ROS) production, resulting in significant inflammatory responses in damaged skin. Thus, the purpose of this study is [...] Read more.
Quetiapine is a new type of antipsychotic drug, with effective protection of pheochromocytoma PC12 cells from oxidative stress-induced apoptosis. Ultraviolet-B radiation can increase reactive oxygen species (ROS) production, resulting in significant inflammatory responses in damaged skin. Thus, the purpose of this study is to explore whether quetiapine protects the skin from intermediate-wave ultraviolet (UVB)-induced damage through antioxidant stress. In vivo, we found quetiapine treatment was able to significantly decrease skin thickness, erythema, and edema, as well as inflammation compared to control group. Moreover, quetiapine treatment increased the activities of antioxidant enzymes, including superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px). In addition, it reduced the production of malondialdehyde (MDA), a kind of oxidized lipid. In vitro, we found that quetiapine blocked UVB-induced intracellular ROS generation and maintained the cell activity at a normal level. Furthermore, we tested the phosphorylation of p38 both in vivo and in vitro, and we found that quetiapine could inhibit phosphorylation of p38, which is caused by UVB irradiation. We concluded that quetiapine was able to relieve UVB-induced skin damage through its antioxidative properties. These effects might be associated with p38 MAPK signaling pathway. Full article
(This article belongs to the Section Biochemistry)
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15 pages, 3656 KiB  
Article
Transcriptomic and GC-MS Metabolomic Analyses Reveal the Sink Strength Changes during Petunia Anther Development
by Yuanzheng Yue, Shaoze Tian, Yu Wang, Hui Ma, Siyu Liu, Yuqiao Wang and Huirong Hu
Int. J. Mol. Sci. 2018, 19(4), 955; https://doi.org/10.3390/ijms19040955 - 23 Mar 2018
Cited by 15 | Viewed by 4202
Abstract
Petunia, which has been prevalently cultivated in landscaping, is a dicotyledonous herbaceous flower of high ornamental value. Annually, there is a massive worldwide market demand for petunia seeds. The normal development of anther is the necessary prerequisite for the plants to generate [...] Read more.
Petunia, which has been prevalently cultivated in landscaping, is a dicotyledonous herbaceous flower of high ornamental value. Annually, there is a massive worldwide market demand for petunia seeds. The normal development of anther is the necessary prerequisite for the plants to generate seeds. However, the knowledge of petunia anther development processes is still limited. To better understand the mechanisms of petunia anther development, the transcriptomes and metabolomes of petunia anthers at three typical development stages were constructed and then used to detect the gene expression patterns and primary metabolite profiles during the anther development processes. Results suggested that there were many differentially-expressed genes (DEGs) that mainly participated in photosynthesis and starch and sucrose metabolism when DEGs were compared between the different development stages of anthers. In this study, fructose and glucose, which were involved in starch and sucrose metabolism, were taken as the most important metabolites by partial least-squares discriminate analysis (PLS-DA). Additionally, the qRT-PCR analysis of the photosynthetic-related genes all showed decreased expression trends along with the anther development. These pieces of evidence indicated that the activities of energy and carbohydrate metabolic pathways were gradually reduced during all the development stages of anther, which affects the sink strength. Overall, this work provides a novel and comprehensive understanding of the metabolic processes in petunia anthers. Full article
(This article belongs to the Special Issue Pollen Tube and Plant Reproduction)
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19 pages, 19470 KiB  
Article
Angiotensin II-Induced Mesangial Cell Damage Is Preceded by Cell Membrane Permeabilization Due to Upregulation of Non-Selective Channels
by Gonzalo I. Gómez, Paola Fernández, Victoria Velarde and Juan C. Sáez
Int. J. Mol. Sci. 2018, 19(4), 957; https://doi.org/10.3390/ijms19040957 - 23 Mar 2018
Cited by 16 | Viewed by 5690
Abstract
Connexin43 (Cx43), pannexin1 (Panx1) and P2X7 receptor (P2X7R) are expressed in kidneys and are known to constitute a feedforward mechanism leading to inflammation in other tissues. However, the possible functional relationship between these membrane channels and their role in damaged [...] Read more.
Connexin43 (Cx43), pannexin1 (Panx1) and P2X7 receptor (P2X7R) are expressed in kidneys and are known to constitute a feedforward mechanism leading to inflammation in other tissues. However, the possible functional relationship between these membrane channels and their role in damaged renal cells remain unknown. In the present work, we found that MES-13 cells, from a cell line derived from mesangial cells, stimulated with angiotensin II (AngII) developed oxidative stress (OS, thiobarbituric acid reactive species (TBARS) and generated pro-inflammatory cytokines (ELISA; IL-1β and TNF-α). The membrane permeability increased progressively several hours before the latter outcome, which was a response prevented by Losartan, indicating the involvement of AT1 receptors. Western blot analysis showed that the amount of phosphorylated MYPT (a substrate of RhoA/ROCK) and Cx43 increased progressively and in parallel in cells treated with AngII, a response followed by an increase in the amount in Panx1 and P2X7R. Greater membrane permeability was partially explained by opening of Cx43 hemichannels (Cx43 HCs) and Panx1 channels (Panx1 Chs), as well as P2X7Rs activation by extracellular ATP, which was presumably released via Cx HCs and Panx1 Chs. Additionally, inhibition of RhoA/ROCK blocked the progressive increase in membrane permeability, and the remaining response was explained by the other non-selective channels. The rise of activity in the RhoA/ROCK-dependent pathway, as well as in Cx HCs, P2X7R, and to a minor extent in Panx1 Chs led to higher amounts of TBARS and pro-inflammatory cytokines. We propose that AngII-induced mesangial cell damage could be effectively inhibited by concomitantly inhibiting the RhoA/ROCK-dependent pathway and one or more non-selective channel(s) activated through this pathway. Full article
(This article belongs to the Special Issue Involvement of Connexin Hemichannels in the Inflammatory Response of Chronic Diseases)
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8 pages, 989 KiB  
Article
Differential Tissue Fatty Acids Profiling between Colorectal Cancer Patients with and without Synchronous Metastasis
by Maria Notarnicola, Dionigi Lorusso, Valeria Tutino, Valentina De Nunzio, Giampiero De Leonardis, Gisella Marangelli, Vito Guerra, Nicola Veronese, Maria Gabriella Caruso and Gianluigi Giannelli
Int. J. Mol. Sci. 2018, 19(4), 962; https://doi.org/10.3390/ijms19040962 - 23 Mar 2018
Cited by 28 | Viewed by 4263
Abstract
The early detection of colorectal cancer and determination of its metastatic potential are important factors to set up more efficacious therapeutic strategies. In the present study, we hypothesize that fatty acids analysis in colorectal cancer patients can discriminate between metastatic and non-metastatic patients. [...] Read more.
The early detection of colorectal cancer and determination of its metastatic potential are important factors to set up more efficacious therapeutic strategies. In the present study, we hypothesize that fatty acids analysis in colorectal cancer patients can discriminate between metastatic and non-metastatic patients. Fifty-one consecutive patients with histologically proven colorectal cancer were enrolled in the study and the presence of synchronous metastasis was detected in 25 of these 51 patients. Fatty acid profile analysis in red blood cell membranes was not able to discriminate the metastatic colorectal cancer patients from those without metastasis. However, significant differences in the tumor tissue fatty acid profile were found in metastatic cancer patients when compared to patients without metastasis. Metastatic patients showed significantly lower percentages of Eicosapentaenoic acid (EPA) and higher levels of γ-linolenic acid (GLA), a n-3- and n-6-Polyunsaturated fatty acid (PUFA), respectively. Our findings, suggesting that membrane lipid rearrangement could influence the cellular function and make the cell more prone to metastasis, offer the opportunity to develop nutritional strategies that may be helpful in the prevention and treatment of colorectal cancer. Full article
(This article belongs to the Special Issue Basic and Translational Research in Colorectal Cancer)
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17 pages, 7821 KiB  
Article
Oxymatrine Inhibits Influenza A Virus Replication and Inflammation via TLR4, p38 MAPK and NF-κB Pathways
by Jian-Ping Dai, Qian-Wen Wang, Yun Su, Li-Ming Gu, Hui-Xiong Deng, Xiao-Xuan Chen, Wei-Zhong Li and Kang-Sheng Li
Int. J. Mol. Sci. 2018, 19(4), 965; https://doi.org/10.3390/ijms19040965 - 23 Mar 2018
Cited by 58 | Viewed by 7042
Abstract
Oxymatrine (OMT) is a strong immunosuppressive agent that has been used in the clinic for many years. In the present study, by using plaque inhibition, luciferase reporter plasmids, qRT-PCR, western blotting, and ELISA assays, we have investigated the effect and mechanism of OMT [...] Read more.
Oxymatrine (OMT) is a strong immunosuppressive agent that has been used in the clinic for many years. In the present study, by using plaque inhibition, luciferase reporter plasmids, qRT-PCR, western blotting, and ELISA assays, we have investigated the effect and mechanism of OMT on influenza A virus (IAV) replication and IAV-induced inflammation in vitro and in vivo. The results showed that OMT had excellent anti-IAV activity on eight IAV strains in vitro. OMT could significantly decrease the promoter activity of TLR3, TLR4, TLR7, MyD88, and TRAF6 genes, inhibit IAV-induced activations of Akt, ERK1/2, p38 MAPK, and NF-κB pathways, and suppress the expressions of inflammatory cytokines and MMP-2/-9. Activators of TLR4, p38 MAPK and NF-κB pathways could significantly antagonize the anti-IAV activity of OMT in vitro, including IAV replication and IAV-induced cytopathogenic effect (CPE). Furthermore, OMT could reduce the loss of body weight, significantly increase the survival rate of IAV-infected mice, decrease the lung index, pulmonary inflammation and lung viral titter, and improve pulmonary histopathological changes. In conclusion, OMT possesses anti-IAV and anti-inflammatory activities, the mechanism of action may be linked to its ability to inhibit IAV-induced activations of TLR4, p38 MAPK, and NF-κB pathways. Full article
(This article belongs to the Special Issue Nutraceuticals in Human Health and Disease)
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14 pages, 13497 KiB  
Article
St. John’s Wort Regulates Proliferation and Apoptosis in MCF-7 Human Breast Cancer Cells by Inhibiting AMPK/mTOR and Activating the Mitochondrial Pathway
by Mi-Kyoung You, Hwa-Jin Kim, Ji Hyun Kook and Hyeon-A Kim
Int. J. Mol. Sci. 2018, 19(4), 966; https://doi.org/10.3390/ijms19040966 - 23 Mar 2018
Cited by 31 | Viewed by 6149
Abstract
St. John’s Wort (SJW) has been used as an estrogen agonist in the systems affected by menopause. Also, hypericin, a bioactive compound of SJW, has been used as a photosensitizer in photodynamic therapy. In the present study, we investigate the anti-proliferative and pro-apoptotic [...] Read more.
St. John’s Wort (SJW) has been used as an estrogen agonist in the systems affected by menopause. Also, hypericin, a bioactive compound of SJW, has been used as a photosensitizer in photodynamic therapy. In the present study, we investigate the anti-proliferative and pro-apoptotic effects of SJW to demonstrate the chemo-preventive effect in human breast cancer cells. MCF-7 cells were cultured with DMSO or various concentrations of SJW ethanol extract (SJWE). Cell viability, proliferation, apoptosis, the expression of proteins involved in cell growth and apoptosis, and caspase-3/7 activity were examined. SJWE dose-dependently suppressed cell growth and induced apoptosis of MCF-7 cells. Mechanistically, SJWE enhanced the phosphorylation of AMP-activated protein kinase (AMPK) and decreased the expression of p-mammalian target of rapamycin (p-mTOR) and p-eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1). Also, SJWE inhibited the phosphorylation of protein kinase B (Akt) and showed increases in the expression of pro-apoptotic proteins Bax and Bad with decreases in the expression of anti-apoptotic proteins including B-cell lymphoma 2 (Bcl-2), B-cell lymphoma-extra large (Bcl-xL), and p-Bcl-2-associated death promoter (p-Bad). SJWE at 50 μg/mL showed markedly enhanced caspase-7 activation. Taken together, our results provide evidence that SJWE shows anti-proliferative and pro-apoptotic effects via inhibition of AMPK/mTOR and activation of a mitochondrial pathway. Therefore, SJWE can be used as a chemo-preventive agent without photo-activation. Full article
(This article belongs to the Special Issue Natural Bioactives and Phytochemicals in Cancer Prevention)
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12 pages, 13326 KiB  
Article
Impact of the NO-Sensitive Guanylyl Cyclase 1 and 2 on Renal Blood Flow and Systemic Blood Pressure in Mice
by Evanthia Mergia, Manuel Thieme, Henning Hoch, Georgios Daniil, Lydia Hering, Mina Yakoub, Christina Rebecca Scherbaum, Lars Christian Rump, Doris Koesling and Johannes Stegbauer
Int. J. Mol. Sci. 2018, 19(4), 967; https://doi.org/10.3390/ijms19040967 - 23 Mar 2018
Cited by 5 | Viewed by 3649
Abstract
Nitric oxide (NO) modulates renal blood flow (RBF) and kidney function and is involved in blood pressure (BP) regulation predominantly via stimulation of the NO-sensitive guanylyl cyclase (NO-GC), existing in two isoforms, NO-GC1 and NO-GC2. Here, we used isoform-specific knockout (KO) mice and [...] Read more.
Nitric oxide (NO) modulates renal blood flow (RBF) and kidney function and is involved in blood pressure (BP) regulation predominantly via stimulation of the NO-sensitive guanylyl cyclase (NO-GC), existing in two isoforms, NO-GC1 and NO-GC2. Here, we used isoform-specific knockout (KO) mice and investigated their contribution to renal hemodynamics under normotensive and angiotensin II-induced hypertensive conditions. Stimulation of the NO-GCs by S-nitrosoglutathione (GSNO) reduced BP in normotensive and hypertensive wildtype (WT) and NO-GC2-KO mice more efficiently than in NO-GC1-KO. NO-induced increase of RBF in normotensive mice did not differ between the genotypes, but the respective increase under hypertensive conditions was impaired in NO-GC1-KO. Similarly, inhibition of endogenous NO increased BP and reduced RBF to a lesser extent in NO-GC1-KO than in NO-GC2-KO. These findings indicate NO-GC1 as a target of NO to normalize RBF in hypertension. As these effects were not completely abolished in NO-GC1-KO and renal cyclic guanosine monophosphate (cGMP) levels were decreased in both NO-GC1-KO and NO-GC2-KO, the results suggest an additional contribution of NO-GC2. Hence, NO-GC1 plays a predominant role in the regulation of BP and RBF, especially in hypertension. However, renal NO-GC2 appears to compensate the loss of NO-GC1, and is able to regulate renal hemodynamics under physiological conditions. Full article
(This article belongs to the Special Issue cGMP-Signalling in Cells: Molecular and Functional Features)
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12 pages, 1810 KiB  
Article
Protective Effects of Gomisin N against Hepatic Cannabinoid Type 1 Receptor-Induced Insulin Resistance and Gluconeogenesis
by Arulkumar Nagappan, Dae Young Jung, Ji-Hyun Kim and Myeong Ho Jung
Int. J. Mol. Sci. 2018, 19(4), 968; https://doi.org/10.3390/ijms19040968 - 23 Mar 2018
Cited by 7 | Viewed by 4352
Abstract
Activation of the hepatic cannabinoid type 1 receptor (CB1R) induces insulin resistance and gluconeogenesis via endoplasmic reticulum (ER) stress, thereby contributing to hyperglycemia. Gomisin N (GN) is a phytochemical derived from Schisandra chinensis. In the current study, we investigated the inhibitory effects [...] Read more.
Activation of the hepatic cannabinoid type 1 receptor (CB1R) induces insulin resistance and gluconeogenesis via endoplasmic reticulum (ER) stress, thereby contributing to hyperglycemia. Gomisin N (GN) is a phytochemical derived from Schisandra chinensis. In the current study, we investigated the inhibitory effects of GN on hepatic CB1R-mediated insulin resistance and gluconeogenesis in 2-arachidonoylglycerol (AG; an agonist of CB1R)-treated HepG2 cells and in high-fat diet (HFD)-induced obese mice. Treatment with 2-AG induced the expression of ER stress markers, serine/threonine phosphatase PHLPP1, Lipin1, and ceramide synthesis genes, but reduced the expression of ceramide degradation genes in HepG2 cells. However, GN reversed 2-AG-mediated effects and improved the 2-AG-mediated impairment of insulin signaling. Furthermore, GN inhibited 2-AG-induced intracellular triglyceride accumulation and glucose production in HepG2 cells by downregulation of lipogenesis and gluconeogenesis genes, respectively. In vivo, GN administration to HFD obese mice reduced the HFD-induced increase in fasting blood glucose and insulin levels, which was accompanied with downregulation of HFD-induced expression of CB1R, ER stress markers, ceramide synthesis gene, and gluconeogenesis genes in the livers of HFD obese mice. These findings demonstrate that GN protects against hepatic CB1-mediated impairment of insulin signaling and gluconeogenesis, thereby contributing to the amelioration of hyperglycemia. Full article
(This article belongs to the Special Issue Plant Natural Products for Human Health)
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15 pages, 4301 KiB  
Article
Preclinical Evaluation of Vemurafenib as Therapy for BRAFV600E Mutated Sarcomas
by Sarina Gouravan, Leonardo A. Meza-Zepeda, Ola Myklebost, Eva W. Stratford and Else Munthe
Int. J. Mol. Sci. 2018, 19(4), 969; https://doi.org/10.3390/ijms19040969 - 23 Mar 2018
Cited by 12 | Viewed by 4880
Abstract
The BRAFV600E mutation, which in melanoma is targetable with vemurafenib, is also found in sarcomas and we here evaluate the therapeutic potential in sarcoma cell lines. Methods: Four sarcoma cell lines harboring the BRAFV600E mutation, representing liposarcomas (SA-4 and SW872), Ewing sarcoma [...] Read more.
The BRAFV600E mutation, which in melanoma is targetable with vemurafenib, is also found in sarcomas and we here evaluate the therapeutic potential in sarcoma cell lines. Methods: Four sarcoma cell lines harboring the BRAFV600E mutation, representing liposarcomas (SA-4 and SW872), Ewing sarcoma (A673) and atypical synovial sarcoma (SW982), were treated with vemurafenib and the effects on cell growth, apoptosis, cell cycle progression and cell signaling were determined. Results: Vemurafenib induced a strong cytostatic effect in SA-4 cells, mainly due to cell cycle arrest, whereas only moderate levels of apoptosis were observed. However, a high dose was required compared to BRAFV600E mutated melanoma cells, and removal of vemurafenib demonstrated that the continuous presence of drug was required for sustained growth inhibition. A limited growth inhibition was observed in the other three cell lines. Protein analyses demonstrated reduced phosphorylation of ERK during treatment with vemurafenib in all the four sarcoma cell lines confirming that the MAPK pathway is active in these cell lines, and that the pathway can be inhibited by vemurafenib, but also that these cells can proliferate despite this. Conclusions: These findings indicate that vemurafenib alone would not be an efficient therapy against BRAFV600E mutated sarcomas. However, further investigations of combination with other drugs are warranted. Full article
(This article belongs to the Special Issue Current Advances in Soft Tissue and Bone Sarcoma)
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19 pages, 5813 KiB  
Article
Evaluation of Two Liver Treatment Strategies in a Mouse Model of Niemann–Pick-Disease Type C1
by Lynn Ebner, Anne Gläser, Anja Bräuer, Martin Witt, Andreas Wree, Arndt Rolfs, Marcus Frank, Brigitte Vollmar and Angela Kuhla
Int. J. Mol. Sci. 2018, 19(4), 972; https://doi.org/10.3390/ijms19040972 - 24 Mar 2018
Cited by 18 | Viewed by 5058
Abstract
Niemann–Pick-disease type C1 (NPC1) is an autosomal-recessive cholesterol-storage disorder. Besides other symptoms, NPC1 patients develop liver dysfunction and hepatosplenomegaly. The mechanisms of hepatomegaly and alterations of lipid metabolism-related genes in NPC1 disease are still poorly understood. Here, we used an NPC1 mouse model [...] Read more.
Niemann–Pick-disease type C1 (NPC1) is an autosomal-recessive cholesterol-storage disorder. Besides other symptoms, NPC1 patients develop liver dysfunction and hepatosplenomegaly. The mechanisms of hepatomegaly and alterations of lipid metabolism-related genes in NPC1 disease are still poorly understood. Here, we used an NPC1 mouse model to study an additive hepatoprotective effect of a combination of 2-hydroxypropyl-β-cyclodextrin (HPβCD), miglustat and allopregnanolone (combination therapy) with the previously established monotherapy using HPβCD. We examined transgene effects as well as treatment effects on liver morphology and hepatic lipid metabolism, focusing on hepatic cholesterol transporter genes. Livers of Npc1−/− mice showed hepatic cholesterol sequestration with consecutive liver injury, an increase of lipogenetic gene expression, e.g., HMG-CoA, a decrease of lipolytic gene expression, e.g., pparα and acox1, and a decrease of lipid transporter gene expression, e.g., acat1, abca1 and fatp2. Both, combination therapy and monotherapy, led to a reduction of hepatic lipids and an amelioration of NPC1 liver disease symptoms. Monotherapy effects were related to pparα- and acox1-associated lipolysis/β-oxidation and to fatp2-induced fatty acid transport, whereas the combination therapy additionally increased the cholesterol transport via abca1 and apoE. However, HPβCD monotherapy additionally increased cholesterol synthesis as indicated by a marked increase of the HMG-CoA and srebp-2 mRNA expression, probably as a result of increased hepatocellular proliferation. Full article
(This article belongs to the Special Issue Rare Diseases: Molecular Mechanisms and Therapeutic Strategies)
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13 pages, 5918 KiB  
Article
Baicalein Rescues Delayed Cooling via Preservation of Akt Activation and Akt-Mediated Phospholamban Phosphorylation
by Zuohui Shao, Sy-Jou Chen, Xiangdong Zhu, Chunpei Lee, Hsien-Hao Huang, Angelo Meliton, Changqing Li, Terry L. Vanden Hoek and Jing Li
Int. J. Mol. Sci. 2018, 19(4), 973; https://doi.org/10.3390/ijms19040973 - 24 Mar 2018
Cited by 4 | Viewed by 3591
Abstract
Cooling reduces the ischemia/reperfusion (I/R) injury seen in sudden cardiac arrest (SCA) by decreasing the burst of reactive oxygen species (ROS). Its cardioprotection is diminished when delay in reaching the target temperature occurs. Baicalein, a flavonoid derived from the root of Scutellaria baicalensis [...] Read more.
Cooling reduces the ischemia/reperfusion (I/R) injury seen in sudden cardiac arrest (SCA) by decreasing the burst of reactive oxygen species (ROS). Its cardioprotection is diminished when delay in reaching the target temperature occurs. Baicalein, a flavonoid derived from the root of Scutellaria baicalensis Georgi, possesses antioxidant properties. Therefore, we hypothesized that baicalein can rescue cooling cardioprotection when cooling is delayed. Two murine cardiomyocyte models, an I/R model (90 min ischemia/3 h reperfusion) and stunning model (30 min ischemia/90 min reperfusion), were used to assess cell survival and contractility, respectively. Cooling (32 °C) was initiated either during ischemia or during reperfusion. Cell viability and ROS generation were measured. Cell contractility was evaluated by real-time phase-contrast imaging. Our results showed that cooling reduced cell death and ROS generation, and this effect was diminished when cooling was delayed. Baicalein (25 µM), given either at the start of reperfusion or start of cooling, resulted in a comparable reduction of cell death and ROS production. Baicalein improved phospholamban phosphorylation, contractility recovery, and cell survival. These effects were Akt-dependent. In addition, no synergistic effect was observed with the combined treatments of cooling and baicalein. Our data suggest that baicalein may serve as a novel adjunct therapeutic strategy for SCA resuscitation. Full article
(This article belongs to the Special Issue Oxidative Stress in Cardiovascular Disease 2018)
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11 pages, 6297 KiB  
Article
An SCFFBXO28 E3 Ligase Protects Pancreatic β-Cells from Apoptosis
by Kanaka Durga Devi Gorrepati, Wei He, Blaz Lupse, Ting Yuan, Kathrin Maedler and Amin Ardestani
Int. J. Mol. Sci. 2018, 19(4), 975; https://doi.org/10.3390/ijms19040975 - 24 Mar 2018
Cited by 11 | Viewed by 3672
Abstract
Loss of pancreatic β-cell function and/or mass is a central hallmark of all forms of diabetes but its molecular basis is incompletely understood. β-cell apoptosis contributes to the reduced β-cell mass in diabetes. Therefore, the identification of important signaling molecules that promote β-cell [...] Read more.
Loss of pancreatic β-cell function and/or mass is a central hallmark of all forms of diabetes but its molecular basis is incompletely understood. β-cell apoptosis contributes to the reduced β-cell mass in diabetes. Therefore, the identification of important signaling molecules that promote β-cell survival in diabetes could lead to a promising therapeutic intervention to block β-cell decline during development and progression of diabetes. In the present study, we identified F-box protein 28 (FBXO28), a substrate-recruiting component of the Skp1-Cul1-F-box (SCF) ligase complex, as a regulator of pancreatic β-cell survival. FBXO28 was down-regulated in β-cells and in isolated human islets under diabetic conditions. Consistently, genetic silencing of FBXO28 impaired β-cell survival, and restoration of FBXO28 protected β-cells from the harmful effects of the diabetic milieu. Although FBXO28 expression positively correlated with β-cell transcription factor NEUROD1 and FBXO28 depletion also reduced insulin mRNA expression, neither FBXO28 overexpression nor depletion had any significant impact on insulin content, glucose-stimulated insulin secretion (GSIS) or on other genes involved in glucose sensing and metabolism or on important β-cell transcription factors in isolated human islets. Consistently, FBXO28 overexpression did not further alter insulin content and GSIS in freshly isolated islets from patients with type 2 diabetes (T2D). Our data show that FBXO28 improves pancreatic β-cell survival under diabetogenic conditions without affecting insulin secretion, and its restoration may be a novel therapeutic tool to promote β-cell survival in diabetes. Full article
(This article belongs to the Section Biochemistry)
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16 pages, 21424 KiB  
Article
Functional Characterization of Novel Atrial Fibrillation-Linked GJA5 (Cx40) Mutants
by Mahmoud Noureldin, Honghong Chen and Donglin Bai
Int. J. Mol. Sci. 2018, 19(4), 977; https://doi.org/10.3390/ijms19040977 - 25 Mar 2018
Cited by 24 | Viewed by 4178
Abstract
Atrial fibrillation (AF) is the most common form of cardiac arrhythmia. Recently, four novel heterozygous Cx40 mutations—K107R, L223M, Q236H, and I257L—were identified in 4 of 310 unrelated AF patients and a followup genetic analysis of the mutant carriers’ families showed that the mutants [...] Read more.
Atrial fibrillation (AF) is the most common form of cardiac arrhythmia. Recently, four novel heterozygous Cx40 mutations—K107R, L223M, Q236H, and I257L—were identified in 4 of 310 unrelated AF patients and a followup genetic analysis of the mutant carriers’ families showed that the mutants were present in all the affected members. To study possible alterations associated with these Cx40 mutants, including their cellular localization and gap junction (GJ) function, we expressed GFP-tagged and untagged mutants in connexin-deficient model cells. All four Cx40 mutants showed clustered localization at cell–cell junctions similar to that observed of wildtype Cx40. However, cell pairs expressing Cx40 Q236H, but not the other individual mutants, displayed a significantly lower GJ coupling conductance (Gj) than wildtype Cx40. Similarly, co-expression of Cx40 Q236H with Cx43 resulted in a significantly lower Gj. Transjunctional voltage-dependent gating (Vj gating) properties were also altered in the GJs formed by Q236H. Reduced GJ function and altered Vj gating may play a role in promoting the Q236H carriers to AF. Full article
(This article belongs to the Special Issue Interplay of Connexins and Pannexins in Tissue Function and Disease)
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17 pages, 8751 KiB  
Article
Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome
by Torbjörn Ramqvist, Anders Näsman, Bo Franzén, Cinzia Bersani, Andrey Alexeyenko, Susanne Becker, Linnea Haeggblom, Aeneas Kolev, Tina Dalianis and Eva Munck-Wikland
Int. J. Mol. Sci. 2018, 19(4), 978; https://doi.org/10.3390/ijms19040978 - 25 Mar 2018
Cited by 12 | Viewed by 5999
Abstract
Human papillomavirus (HPV) is a major etiological factor for tonsillar and the base of tongue cancer (TSCC/BOTSCC). HPV-positive and HPV-negative TSCC/BOTSCC present major differences in mutations, mRNA expression and clinical outcome. Earlier protein studies on TSCC/BOTSCC have mainly analyzed individual proteins. Here, the [...] Read more.
Human papillomavirus (HPV) is a major etiological factor for tonsillar and the base of tongue cancer (TSCC/BOTSCC). HPV-positive and HPV-negative TSCC/BOTSCC present major differences in mutations, mRNA expression and clinical outcome. Earlier protein studies on TSCC/BOTSCC have mainly analyzed individual proteins. Here, the aim was to compare a larger set of cancer and immune related proteins in HPV-positive and HPV-negative TSCC/BOTSCC in relation to normal tissue, presence of HPV, and clinical outcome. Fresh frozen tissue from 42 HPV-positive and 17 HPV-negative TSCC/BOTSCC, and corresponding normal samples, were analyzed for expression of 167 proteins using two Olink multiplex immunoassays. Major differences in protein expression between TSCC/BOTSCC and normal tissue were identified, especially in chemo- and cytokines. Moreover, 34 proteins, mainly immunoregulatory proteins and chemokines, were differently expressed in HPV-positive vs HPV-negative TSCC/BOTSCC. Several proteins were potentially related to clinical outcome for HPV-positive or HPV-negative tumors. For HPV-positive tumors, these were mostly related to angiogenesis and hypoxia. Correlation with clinical outcome of one of these, VEGFA, was validated by immunohistochemistry. Differences in immune related proteins between HPV-positive and HPV-negative TSCC/BOTSCC reflect the stronger activity of the immune defense in the former. Angiogenesis related proteins might serve as potential targets for therapy in HPV-positive TSCC/BOTSCC. Full article
(This article belongs to the Special Issue Human Polyomaviruses and Papillomaviruses)
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26 pages, 5106 KiB  
Article
Inactivation of SREBP-1a Phosphorylation Prevents Fatty Liver Disease in Mice: Identification of Related Signaling Pathways by Gene Expression Profiles in Liver and Proteomes of Peroxisomes
by Birgit Knebel, Sonja Hartwig, Sylvia Jacob, Ulrike Kettel, Martina Schiller, Waltraud Passlack, Cornelia Koellmer, Stefan Lehr, Dirk Müller-Wieland and Jorg Kotzka
Int. J. Mol. Sci. 2018, 19(4), 980; https://doi.org/10.3390/ijms19040980 - 25 Mar 2018
Cited by 20 | Viewed by 5939
Abstract
The key lipid metabolism transcription factor sterol regulatory element-binding protein (SREBP)-1a integrates gene regulatory effects of hormones, cytokines, nutrition and metabolites as lipids, glucose, or cholesterol via phosphorylation by different mitogen activated protein kinase (MAPK) cascades. We have previously reported the impact of [...] Read more.
The key lipid metabolism transcription factor sterol regulatory element-binding protein (SREBP)-1a integrates gene regulatory effects of hormones, cytokines, nutrition and metabolites as lipids, glucose, or cholesterol via phosphorylation by different mitogen activated protein kinase (MAPK) cascades. We have previously reported the impact of SREBP-1a phosphorylation on the phenotype in transgenic mouse models with liver-specific overexpression of the N-terminal transcriptional active domain of SREBP-1a (alb-SREBP-1a) or a MAPK phosphorylation site-deficient variant (alb-SREBP-1a∆P; (S63A, S117A, T426V)), respectively. In this report, we investigated the molecular basis of the systemic observations by holistic analyses of gene expression in liver and of proteome patterns in lipid-degrading organelles involved in the pathogenesis of metabolic syndrome, i.e., peroxisomes, using 2D-DIGE and mass spectrometry. The differences in hepatic gene expression and peroxisomal protein patterns were surprisingly small between the control and alb-SREBP-1a mice, although the latter develop a severe phenotype with visceral obesity and fatty liver. In contrast, phosphorylation site-deficient alb-SREBP-1a∆P mice, which are protected from fatty liver disease, showed marked differences in hepatic gene expression and peroxisomal proteome patterns. Further knowledge-based analyses revealed that disruption of SREBP-1a phosphorylation resulted in massive alteration of cellular processes, including signs for loss of targeting lipid pathways. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Lipid Metabolism)
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20 pages, 8666 KiB  
Article
Identification of Dysregulated microRNA Networks in Schwann Cell-Like Cultures Exposed to Immune Challenge: Potential Crosstalk with the Protective VIP/PACAP Neuropeptide System
by Giuseppe Musumeci, Gian Marco Leggio, Rubina Marzagalli, Ghaith Al-Badri, Filippo Drago and Alessandro Castorina
Int. J. Mol. Sci. 2018, 19(4), 981; https://doi.org/10.3390/ijms19040981 - 25 Mar 2018
Cited by 10 | Viewed by 4964
Abstract
Following peripheral nerve injury, dysregulations of certain non-coding microRNAs (miRNAs) occur in Schwann cells. Whether these alterations are the result of local inflammation and/or correlate with perturbations in the expression profile of the protective vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating polypeptide (PACAP) system [...] Read more.
Following peripheral nerve injury, dysregulations of certain non-coding microRNAs (miRNAs) occur in Schwann cells. Whether these alterations are the result of local inflammation and/or correlate with perturbations in the expression profile of the protective vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating polypeptide (PACAP) system is currently unknown. To address these issues, we aimed at profiling the expression of selected miRNAs in the rat RT4 Schwann cell line. Cells exposed to lipopolysaccharide (LPS), to mimic the local inflammatory milieu, were appraised by real-time qPCR, Western blot and ELISAs. We found that upon LPS treatment, levels of pro-inflammatory cytokines (IL-1β, -6, -18, -17A, MCP-1 and TNFα) increased in a time-dependent manner. Unexpectedly, the expression levels of VIP and PACAP were also increased. Conversely, levels of VPAC1 and VPAC2 receptors were reduced. Downregulated miRNAs included miR-181b, -145, -27a, -340 and -132 whereas upregulated ones were miR-21, -206, -146a, -34a, -155, -204 and -29a, respectively. Regression analyses revealed that a subset of the identified miRNAs inversely correlated with the expression of VPAC1 and VPAC2 receptors. In conclusion, these findings identified a novel subset of miRNAs that are dysregulated by immune challenge whose activities might elicit a regulatory function on the VIP/PACAP system. Full article
(This article belongs to the Special Issue Peripheral Nerve Regeneration: From Bench to Bedside 2017)
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11 pages, 1026 KiB  
Article
Identification of Blueberry miRNAs and Their Targets Based on High-Throughput Sequencing and Degradome Analyses
by Guangping Li, Yun Wang, Xiaoming Lou, Hailing Li and Changqing Zhang
Int. J. Mol. Sci. 2018, 19(4), 983; https://doi.org/10.3390/ijms19040983 - 26 Mar 2018
Cited by 10 | Viewed by 3815
Abstract
miRNAs are important regulators of plant gene expression. To better characterize their functions, we applied high-throughput sequencing and degradome analyses to investigate three blueberry (Vaccinium ashei) tissues. A total of 127 known and 101 novel miRNAs were identified. Moreover, 141 targets [...] Read more.
miRNAs are important regulators of plant gene expression. To better characterize their functions, we applied high-throughput sequencing and degradome analyses to investigate three blueberry (Vaccinium ashei) tissues. A total of 127 known and 101 novel miRNAs were identified. Moreover, 141 targets for 42 known and 19 novel miRNAs were experimentally validated by degradome sequencing. A functional analysis of these miRNA targets revealed they were associated with diverse biological activities and several pathways, e.g., anthocyanin biosynthesis and cytokinin signal transduction. The data presented herein expand our understanding of the regulation of blueberry miRNAs during floral and fruit development stages. They may also provide new insights into the roles of miRNAs during anthocyanin biosynthesis in blueberry fruits. Full article
(This article belongs to the Section Molecular Plant Sciences)
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13 pages, 15755 KiB  
Article
Knocking down Insulin Receptor in Pancreatic Beta Cell lines with Lentiviral-Small Hairpin RNA Reduces Glucose-Stimulated Insulin Secretion via Decreasing the Gene Expression of Insulin, GLUT2 and Pdx1
by Jie Wang, Wenyi Gu and Chen Chen
Int. J. Mol. Sci. 2018, 19(4), 985; https://doi.org/10.3390/ijms19040985 - 26 Mar 2018
Cited by 16 | Viewed by 6756
Abstract
Type 2 diabetes (T2D) is a metabolic disorder characterized by beta cell dysfunction and insulin resistance in fat, muscle and liver cells. Recent studies have shown that the development of insulin resistance in pancreatic beta cell lines may contribute to beta cell dysfunction [...] Read more.
Type 2 diabetes (T2D) is a metabolic disorder characterized by beta cell dysfunction and insulin resistance in fat, muscle and liver cells. Recent studies have shown that the development of insulin resistance in pancreatic beta cell lines may contribute to beta cell dysfunction in T2D. However, there still is a lack of detailed investigations regarding the mechanisms by which insulin deficiency may contribute in diabetes. In this study, we firstly established a stable insulin receptor knockdown cell line in pancreatic beta cells INS-1 (InsRβKD cells) using anti InsRβ small hairpin RNA (InsRβ-shRNA) encoded by lentiviral vectors. The resultant InsRβKD cells demonstrated a significantly reduced expression of InsRβ as determined by real-time PCR and Western blotting analyses. Upon removing glucose from the medium, these cells exhibited a significant decrease in insulin gene expression and protein secretion in response to 20 mM glucose stimulation. In accordance with this insulin reduction, the glucose uptake efficiency as indicated by a 3[H]-2-deoxy-d-glucose assay also decreased. Furthermore, InsRβKD cells showed a dramatic decrease in glucose transporter 2 (GLUT2, encoded by SLC2A2) and pancreatic duodenal homeobox (Pdx1) mRNA expression compared to the controls. These data collectively suggest that pancreatic beta cell insulin resistance contributes to the development of beta cell dysfunction by impairing pancreatic beta cell glucose sensation through the Pdx1- GLUT2 pathway. InsRβKD cells provide a good model to further investigate the mechanism of β-cell dysfunction in T2D. Full article
(This article belongs to the Special Issue Cell and Molecular Biology of Pancreatic Disorders)
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18 pages, 3777 KiB  
Article
Genome-Wide Identification, Expression, and Functional Analysis of the Sugar Transporter Gene Family in Cassava (Manihot esculenta)
by Qin Liu, Huijie Dang, Zhijian Chen, Junzheng Wu, Yinhua Chen, Songbi Chen and Lijuan Luo
Int. J. Mol. Sci. 2018, 19(4), 987; https://doi.org/10.3390/ijms19040987 - 26 Mar 2018
Cited by 31 | Viewed by 6752
Abstract
The sugar transporter (STP) gene family encodes monosaccharide transporters that contain 12 transmembrane domains and belong to the major facilitator superfamily. STP genes play critical roles in monosaccharide distribution and participate in diverse plant metabolic processes. To investigate the potential roles [...] Read more.
The sugar transporter (STP) gene family encodes monosaccharide transporters that contain 12 transmembrane domains and belong to the major facilitator superfamily. STP genes play critical roles in monosaccharide distribution and participate in diverse plant metabolic processes. To investigate the potential roles of STPs in cassava (Manihot esculenta) tuber root growth, genome-wide identification and expression and functional analyses of the STP gene family were performed in this study. A total of 20 MeSTP genes (MeSTP1–20) containing the Sugar_tr conserved motifs were identified from the cassava genome, which could be further classified into four distinct groups in the phylogenetic tree. The expression profiles of the MeSTP genes explored using RNA-seq data showed that most of the MeSTP genes exhibited tissue-specific expression, and 15 out of 20 MeSTP genes were mainly expressed in the early storage root of cassava. qRT-PCR analysis further confirmed that most of the MeSTPs displayed higher expression in roots after 30 and 40 days of growth, suggesting that these genes may be involved in the early growth of tuber roots. Although all the MeSTP proteins exhibited plasma membrane localization, variations in monosaccharide transport activity were found through a complementation analysis in a yeast (Saccharomyces cerevisiae) mutant, defective in monosaccharide uptake. Among them, MeSTP2, MeSTP15, and MeSTP19 were able to efficiently complement the uptake of five monosaccharides in the yeast mutant, while MeSTP3 and MeSTP16 only grew on medium containing galactose, suggesting that these two MeSTP proteins are transporters specific for galactose. This study provides significant insights into the potential functions of MeSTPs in early tuber root growth, which possibly involves the regulation of monosaccharide distribution. Full article
(This article belongs to the Section Biochemistry)
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18 pages, 8779 KiB  
Article
Investigation of Linum flavum (L.) Hairy Root Cultures for the Production of Anticancer Aryltetralin Lignans
by Sullivan Renouard, Cyrielle Corbin, Samantha Drouet, Barbara Medvedec, Joël Doussot, Cyril Colas, Benoit Maunit, Avninder S. Bhambra, Eric Gontier, Nathalie Jullian, François Mesnard, Michèle Boitel, Bilal Haider Abbasi, Randolph R. J. Arroo, Eric Lainé and Christophe Hano
Int. J. Mol. Sci. 2018, 19(4), 990; https://doi.org/10.3390/ijms19040990 - 26 Mar 2018
Cited by 33 | Viewed by 6966
Abstract
Linum flavum hairy root lines were established from hypocotyl pieces using Agrobacterium rhizogenes strains LBA 9402 and ATCC 15834. Both strains were effective for transformation but induction of hairy root phenotype was more stable with strain ATCC 15834. Whereas similar accumulation patterns were [...] Read more.
Linum flavum hairy root lines were established from hypocotyl pieces using Agrobacterium rhizogenes strains LBA 9402 and ATCC 15834. Both strains were effective for transformation but induction of hairy root phenotype was more stable with strain ATCC 15834. Whereas similar accumulation patterns were observed in podophyllotoxin-related compounds (6-methoxy-podophyllotoxin, podophyllotoxin and deoxypodophyllotoxin), significant quantitative variations were noted between root lines. The influence of culture medium and various treatments (hormone, elicitation and precursor feeding) were evaluated. The highest accumulation was obtained in Gamborg B5 medium. Treatment with methyl jasmonate, and feeding using ferulic acid increased the accumulation of aryltetralin lignans. These results point to the use of hairy root culture lines of Linum flavum as potential sources for these valuable metabolites as an alternative, or as a complement to Podophyllum collected from wild stands. Full article
(This article belongs to the Special Issue Bioactive Phenolics and Polyphenols 2018)
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15 pages, 3864 KiB  
Article
Low Serum Levels of (Dihydro-)Ceramides Reflect Liver Graft Dysfunction in a Real-World Cohort of Patients Post Liver Transplantation
by Victoria Therese Mücke, Janis Gerharz, Katja Jakobi, Dominique Thomas, Nerea Ferreirós Bouzas, Marcus Maximilian Mücke, Sven Trötschler, Nina Weiler, Martin-Walter Welker, Stefan Zeuzem, Josef Pfeilschifter and Georgios Grammatikos
Int. J. Mol. Sci. 2018, 19(4), 991; https://doi.org/10.3390/ijms19040991 - 26 Mar 2018
Cited by 8 | Viewed by 4971
Abstract
Patients after orthopic liver transplantation (OLT) are at risk of developing graft dysfunction. Sphingolipids (SL’s) have been identified to play a pivotal role in the regulation of hepatocellular apoptosis, inflammation and immunity. We aimed to investigate the serum SL profile in a prospective [...] Read more.
Patients after orthopic liver transplantation (OLT) are at risk of developing graft dysfunction. Sphingolipids (SL’s) have been identified to play a pivotal role in the regulation of hepatocellular apoptosis, inflammation and immunity. We aimed to investigate the serum SL profile in a prospective real-world cohort of post-OLT patients. From October 2015 until July 2016, 149 well-characterized post-OLT patients were analyzed. SL’s were assessed in serum probes via Liquid Chromatography/Tandem Mass Spectrometry. Twenty-nine (20%) patients had a biopsy proven graft rejection with decreased C20-ceramide (Cer) (p = 0.042), C18-dihydroceramide (DHC) (p = 0.022) and C24DHC (p = 0.060) levels. Furthermore, C18DHC (p = 0.044) and C24DHC (p = 0.011) were significantly down-regulated in patients with ischemic type biliary lesions (ITBL; n = 15; 10%). One-hundred and thirty-three patients (89%) have so far received tacrolimus as the main immunosuppressive agent with observed elevations of C14Cer (p = 0.052), C18Cer (p = 0.049) and C18:1Cer (p = 0.024). Hepatocellular carcinoma (HCC) pre-OLT was associated with increases in C24:1Cer (p = 0.024) and C24:1DHC (p = 0.024). In this large prospective cross-sectional study of patients, post-OLT serum levels of (very-)long chain (dihydro-)ceramides associate with graft rejection, ITBL, tacrolimus intake and HCC pre-OLT. Hence, serum SL’s may be indicative of graft complications. Further research is necessary to identify their diverse mechanistic role in regulating immunity and inflammation in patients post-OLT. Full article
(This article belongs to the Special Issue Sphingolipids: Signals and Disease)
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18 pages, 3158 KiB  
Article
Seed Hydropriming and Smoke Water Significantly Improve Low-Temperature Germination of Lupinus angustifolius L.
by Agnieszka Płażek, Franciszek Dubert, Przemysław Kopeć, Michał Dziurka, Agnieszka Kalandyk, Jakub Pastuszak and Bogdan Wolko
Int. J. Mol. Sci. 2018, 19(4), 992; https://doi.org/10.3390/ijms19040992 - 26 Mar 2018
Cited by 34 | Viewed by 6416
Abstract
Seed imbibition under cold temperature is dangerous when dry seeds have relatively low water content. The aim of this study was to investigate germination of 20 lines/cultivars of narrow-leaf lupine at 7 °C (cold) and 13 °C (control) under the influence of smoke [...] Read more.
Seed imbibition under cold temperature is dangerous when dry seeds have relatively low water content. The aim of this study was to investigate germination of 20 lines/cultivars of narrow-leaf lupine at 7 °C (cold) and 13 °C (control) under the influence of smoke water and following seed hydropriming for 3 h at 20 °C. The efficacy of individual treatments was examined with regard to seed protection during low-temperature germination. Based on seed germination, vigour at cold was evaluated four days after sowing by means of hypocotyl length, the studied lines/cultivars were divided into three groups with low, high and very high germination rates. Germination vigour correlated with cell membrane permeability, dehydrogenase activity and abscisic acid (ABA) content and was analysed in the seeds one day after sowing. Gibberellin content did not correlate with germination vigour. The seeds of weakly germinating lines/cultivars had the highest cell permeability and ABA content as well as the lowest amylolytic activity at both studied temperatures. Additionally, the vigour of weakly germinating seeds at 7 °C correlated with dehydrogenase activity. Three-hour hydropriming was the most effective for seed germination under cold due to reduced cell membrane permeability and ABA level. Stimulating effects of smoke water on germination under cold could be explained by enhanced dehydrogenase activity. Full article
(This article belongs to the Special Issue Phytohormones and Their Crosstalk during Plant Growth, Development and Environmental Stress Adaptation)
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14 pages, 22989 KiB  
Article
MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota
by Chong-Tao Du, Wei Gao, Ke Ma, Shui-Xing Yu, Na Li, Shi-Qing Yan, Feng-Hua Zhou, Zhen-Zhen Liu, Wei Chen, Lian-Cheng Lei, Yong-Jun Yang and Wen-Yu Han
Int. J. Mol. Sci. 2018, 19(4), 993; https://doi.org/10.3390/ijms19040993 - 26 Mar 2018
Cited by 31 | Viewed by 5810
Abstract
The gut microbiota and microRNAs play important roles in the defense against infection. However, the role of miR-146a in L. monocytogenes infection and gut microbiota remains unclear. We tried to determine whether miR-146a controlled L. monocytogenes infection by regulating the gut microbiota. Wild-type [...] Read more.
The gut microbiota and microRNAs play important roles in the defense against infection. However, the role of miR-146a in L. monocytogenes infection and gut microbiota remains unclear. We tried to determine whether miR-146a controlled L. monocytogenes infection by regulating the gut microbiota. Wild-type and miR-146a-deficient mice or macrophages were used to characterize the impact of miR-146a on animal survival, cell death, bacterial clearance, and gut microbiota following L. monocytogenes challenge. We found that L. monocytogenes infection induced miR-146a expression both in vitro and in vivo. When compared to wild-type mice, miR-146a-deficient mice were more resistant to L. monocytogenes infection. MiR-146a deficiency in macrophages resulted in reduced invasion and intracellular survival of L. monocytogenes. High-throughput sequencing of 16S rRNA revealed that the gut microbiota composition differed between miR-146a-deficient and wild-type mice. Relative to wild-type mice, miR-146a-deficient mice had decreased levels of the Proteobacteria phylum, Prevotellaceae family, and Parasutterella genus, and significantly increased short-chain fatty acid producing bacteria, including the genera Alistipes, Blautia, Coprococcus_1, and Ruminococcus_1. Wild-type mice co-housed with miR-146a-deficient mice had increased resistance to L. monocytogenes, indicating that miR-146a deficiency guides the gut microbiota to alleviate infection. Together, these results suggest that miR-146a deficiency protects against L. monocytogenes infection by regulating the gut microbiota. Full article
(This article belongs to the Special Issue Host-Microbe Interaction 2018)
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14 pages, 15231 KiB  
Article
Co-Culture with Human Osteoblasts and Exposure to Extremely Low Frequency Pulsed Electromagnetic Fields Improve Osteogenic Differentiation of Human Adipose-Derived Mesenchymal Stem Cells
by Sabrina Ehnert, Martijn Van Griensven, Marina Unger, Hanna Scheffler, Karsten Falldorf, Anne-Kristin Fentz, Claudine Seeliger, Steffen Schröter, Andreas K. Nussler and Elizabeth R. Balmayor
Int. J. Mol. Sci. 2018, 19(4), 994; https://doi.org/10.3390/ijms19040994 - 27 Mar 2018
Cited by 39 | Viewed by 6585
Abstract
Human adipose-derived mesenchymal stem cells (Ad-MSCs) have been proposed as suitable option for cell-based therapies to support bone regeneration. In the bone environment, Ad-MSCs will receive stimuli from resident cells that may favor their osteogenic differentiation. There is recent evidence that this process [...] Read more.
Human adipose-derived mesenchymal stem cells (Ad-MSCs) have been proposed as suitable option for cell-based therapies to support bone regeneration. In the bone environment, Ad-MSCs will receive stimuli from resident cells that may favor their osteogenic differentiation. There is recent evidence that this process can be further improved by extremely low frequency pulsed electromagnetic fields (ELF-PEMFs). Thus, the project aimed at (i) investigating whether co-culture conditions of human osteoblasts (OBs) and Ad-MSCs have an impact on their proliferation and osteogenic differentiation; (ii) whether this effect can be further improved by repetitive exposure to two specific ELF-PEMFs (16 and 26 Hz); (iii) and the effect of these ELF-PEMFs on human osteoclasts (OCs). Osteogenic differentiation was improved by co-culturing OBs and Ad-MSCs when compared to the individual mono-cultures. An OB to Ad-MSC ratio of 3:1 had best effects on total protein content, alkaline phosphatase (AP) activity, and matrix mineralization. Osteogenic differentiation was further improved by both ELF-PEMFs investigated. Interestingly, only repetitive exposure to 26 Hz ELF-PEMF increased Trap5B activity in OCs. Considering this result, a treatment with gradually increasing frequency might be of interest, as the lower frequency (16 Hz) could enhance bone formation, while the higher frequency (26 Hz) could enhance bone remodeling. Full article
(This article belongs to the Special Issue Adipose Stem Cells)
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17 pages, 30939 KiB  
Article
Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses
by Jinxiang Xi, Qin Hu, Linlin Zhao and Xiuhua April Si
Int. J. Mol. Sci. 2018, 19(4), 997; https://doi.org/10.3390/ijms19040997 - 27 Mar 2018
Cited by 4 | Viewed by 4206
Abstract
Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed [...] Read more.
Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high-polarity chemicals such as acrolein. Full article
(This article belongs to the Special Issue Nanoparticle Deposition on Walls—Its Mechanism, Control, and Effect Evaluation)
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15 pages, 11556 KiB  
Article
ATP-Binding Cassette Transporter VcaM from Vibrio cholerae is Dependent on the Outer Membrane Factor Family for Its Function
by Wen-Jung Lu, Hsuan-Ju Lin, Thamarai K. Janganan, Cheng-Yi Li, Wei-Chiang Chin, Vassiliy N. Bavro and Hong-Ting Victor Lin
Int. J. Mol. Sci. 2018, 19(4), 1000; https://doi.org/10.3390/ijms19041000 - 27 Mar 2018
Cited by 19 | Viewed by 4484
Abstract
Vibrio cholerae ATP-binding cassette transporter VcaM (V. cholerae ABC multidrug resistance pump) has previously been shown to confer resistance to a variety of medically important drugs. In this study, we set to analyse its properties both in vitro in detergent-solubilised state and [...] Read more.
Vibrio cholerae ATP-binding cassette transporter VcaM (V. cholerae ABC multidrug resistance pump) has previously been shown to confer resistance to a variety of medically important drugs. In this study, we set to analyse its properties both in vitro in detergent-solubilised state and in vivo to differentiate its dependency on auxiliary proteins for its function. We report the first detailed kinetic parameters of purified VcaM and the rate of phosphate (Pi) production. To determine the possible functional dependencies of VcaM on the tripartite efflux pumps we then utilized different E. coli strains lacking the principal secondary transporter AcrB (Acriflavine resistance protein), as well as cells lacking the outer membrane factor (OMF) TolC (Tolerance to colicins). Consistent with the ATPase function of VcaM we found it to be susceptible to sodium orthovanadate (NaOV), however, we also found a clear dependency of VcaM function on TolC. Inhibitors targeting secondary active transporters had no effects on either VcaM-conferred resistance or Hoechst 33342 accumulation, suggesting that VcaM might be capable of engaging with the TolC-channel without periplasmic mediation by additional transporters. Our findings are indicative of VcaM being capable of a one-step substrate translocation from cytosol to extracellular space utilising the TolC-channel, making it the only multidrug ABC-transporter outside of the MacB-family with demonstrable TolC-dependency. Full article
(This article belongs to the Special Issue Proteins and Protein-Ligand Interactions)
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15 pages, 8414 KiB  
Article
Development and Characterisation of a Human Chronic Skin Wound Cell Line—Towards an Alternative for Animal Experimentation
by Matthew Caley, Ivan B. Wall, Matthew Peake, David Kipling, Peter Giles, David W. Thomas and Phil Stephens
Int. J. Mol. Sci. 2018, 19(4), 1001; https://doi.org/10.3390/ijms19041001 - 27 Mar 2018
Cited by 11 | Viewed by 4868
Abstract
Background: Chronic skin wounds are a growing financial burden for healthcare providers, causing discomfort/immobility to patients. Whilst animal chronic wound models have been developed to allow for mechanistic studies and to develop/test potential therapies, such systems are not good representations of the [...] Read more.
Background: Chronic skin wounds are a growing financial burden for healthcare providers, causing discomfort/immobility to patients. Whilst animal chronic wound models have been developed to allow for mechanistic studies and to develop/test potential therapies, such systems are not good representations of the human chronic wound state. As an alternative, human chronic wound fibroblasts (CWFs) have permitted an insight into the dysfunctional cellular mechanisms that are associated with these wounds. However, such cells strains have a limited replicative lifespan and therefore a limited reproducibility/usefulness. Objectives: To develop/characterise immortalised cell lines of CWF and patient-matched normal fibroblasts (NFs). Methods and Results: Immortalisation with human telomerase resulted in both CWF and NF proliferating well beyond their replicative senescence end-point (respective cell strains senesced as normal). Gene expression analysis demonstrated that, whilst proliferation-associated genes were up-regulated in the cell lines (as would be expected), the immortalisation process did not significantly affect the disease-specific genotype. Immortalised CWF (as compared to NF) also retained a distinct impairment in their wound repopulation potential (in line with CWF cell strains). Conclusions: These novel CWF cell lines are a credible animal alternative and could be a valuable research tool for understanding both the aetiology of chronic skin wounds and for therapeutic pre-screening. Full article
(This article belongs to the Special Issue New Innovations in Wound Healing and Repair)
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16 pages, 37600 KiB  
Article
Regulated Mesenchymal Stem Cells Mediated Colon Cancer Therapy Assessed by Reporter Gene Based Optical Imaging
by Senthilkumar Kalimuthu, Liya Zhu, Ji Min Oh, Ho Won Lee, Prakash Gangadaran, Ramya Lakshmi Rajendran, Se Hwan Baek, Yong Hyun Jeon, Shin Young Jeong, Sang-Woo Lee, Jaetae Lee and Byeong-Cheol Ahn
Int. J. Mol. Sci. 2018, 19(4), 1002; https://doi.org/10.3390/ijms19041002 - 27 Mar 2018
Cited by 14 | Viewed by 4861
Abstract
Colorectal cancer is the most common cancer in both men and women and the second most common cause of cancer-related deaths. Suicide gene-based therapy with suicide gene-transduced mesenchymal stem cells (MSCs) is a promising therapeutic strategy. A tetracycline-controlled Tet-On inducible system used to [...] Read more.
Colorectal cancer is the most common cancer in both men and women and the second most common cause of cancer-related deaths. Suicide gene-based therapy with suicide gene-transduced mesenchymal stem cells (MSCs) is a promising therapeutic strategy. A tetracycline-controlled Tet-On inducible system used to regulate gene expression may be a useful tool for gene-based therapies. The aim of this study was to develop therapeutic MSCs with a suicide gene that is induced by an artificial stimulus, to validate therapeutic gene expression, and to monitor the MSC therapy for colon cancer using optical molecular imaging. For our study, we designed the Tet-On system using a retroviral vector and developed a response plasmid RetroX-TRE (tetracycline response element) expressing a mutant form of herpes simplex virus thymidine kinase (HSV1-sr39TK) with dual reporters (eGFP-Fluc2). Bone marrow-derived MSCs were transduced using a RetroX-Tet3G (Clontech, CA, USA) regulatory plasmid and RetroX-TRE-HSV1-sr39TK-eGFP-IRES-Fluc2, for a system with a Tet-On (MSC-Tet-TK/Fluc2 or MSC-Tet-TK) or without a Tet-On (MSC-TK/Fluc2 or MSC-TK) function. Suicide gene engineered MSCs were co-cultured with colon cancer cells (CT26/Rluc) in the presence of the prodrug ganciclovir (GCV) after stimulation with or without doxycycline (DOX). Treatment efficiency was monitored by assessing Rluc (CT26/Rluc) and Fluc (MSC-Tet-TK and MSC-TK) activity using optical imaging. The bystander effect of therapeutic MSCs was confirmed in CT26/Rluc cells after GCV treatment. Rluc activity in CT26/Rluc cells decreased significantly with GCV treatment of DOX(+) cells (p < 0.05 and 0.01) whereas no significant changes were observed in DOX(−) cells. In addition, Fluc activity in also decreased significantly with DOX(+) MSC-Tet-TK cells, but no signal was observed in DOX(−) cells. In addition, an MSC-TK bystander effect was also confirmed. We assessed therapy with this system in a colon cancer xenograft model (CT26/Rluc). We successfully transduced cells and developed a Tet-On system with the suicide gene HSV1-sr39TK. Our results confirmed the therapeutic efficiency of a suicide gene with the Tet-On system for colon cancer. In addition, our results provide an innovative therapeutic approach using the Tet-On system to eradicate tumors by administration of MSC-Tet-TK cells with DOX and GCV. Full article
(This article belongs to the Section Biochemistry)
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14 pages, 43146 KiB  
Article
β4 and β6 Integrin Expression Is Associated with the Subclassification and Clinicopathological Features of Intrahepatic Cholangiocarcinoma
by Yurie Soejima, Miho Takeuchi, Takumi Akashi, Motoji Sawabe and Toshio Fukusato
Int. J. Mol. Sci. 2018, 19(4), 1004; https://doi.org/10.3390/ijms19041004 - 27 Mar 2018
Cited by 11 | Viewed by 4428
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a heterogeneous group of cancers of the intrahepatic biliary tract. However, few studies have evaluated integrin expression according to an ICC subgroup. We immunohistochemically investigated α6β4 (β4) and αvβ6 (β6) integrin expressions in 48 ICCs, and evaluated their relationship [...] Read more.
Intrahepatic cholangiocarcinoma (ICC) is a heterogeneous group of cancers of the intrahepatic biliary tract. However, few studies have evaluated integrin expression according to an ICC subgroup. We immunohistochemically investigated α6β4 (β4) and αvβ6 (β6) integrin expressions in 48 ICCs, and evaluated their relationship with clinical and pathological parameters and ligand expression, as well as transforming growth factor (TGF)-β1. β4 and β6 expressions were detected in 46 (96%) and 35 (73%) ICC cases, respectively. We classified ICC into negative, low (β4, 29 cases; β6, 36 cases), or high (β4, 19 cases; β6, 12 cases) integrin expression groups. β4 and β6 integrin levels were higher in the non-peripheral central localization type ICC than in the peripheral localization type; they were also higher in the periductal-infiltrating or intraductal-growth types than in the mass-forming type ICC; lastly, they were higher in the well-differentiated type than in the poorly-differentiated type ICC. High expression was related to bile duct invasion. In addition, β4 and β6 expressions were associated with mucin production and the expression of cytoplasmic epithelial membrane antigen, laminin-5, and tenascin-C. TGF-β1 was correlated with β6 expression and poor overall survival. These results suggest that integrin expression is associated with subclassification and clinicopathological features of ICC through the coincident expression of their ligands and TGF-β1. Full article
(This article belongs to the Special Issue Integrins and Human Pathologies)
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16 pages, 2947 KiB  
Article
PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality
by Yang Yang, Siddhaling Urolagin, Abhishek Niroula, Xuesong Ding, Bairong Shen and Mauno Vihinen
Int. J. Mol. Sci. 2018, 19(4), 1009; https://doi.org/10.3390/ijms19041009 - 28 Mar 2018
Cited by 44 | Viewed by 5849
Abstract
Several methods have been developed to predict effects of amino acid substitutions on protein stability. Benchmark datasets are essential for method training and testing and have numerous requirements including that the data is representative for the investigated phenomenon. Available machine learning algorithms for [...] Read more.
Several methods have been developed to predict effects of amino acid substitutions on protein stability. Benchmark datasets are essential for method training and testing and have numerous requirements including that the data is representative for the investigated phenomenon. Available machine learning algorithms for variant stability have all been trained with ProTherm data. We noticed a number of issues with the contents, quality and relevance of the database. There were errors, but also features that had not been clearly communicated. Consequently, all machine learning variant stability predictors have been trained on biased and incorrect data. We obtained a corrected dataset and trained a random forests-based tool, PON-tstab, applicable to variants in any organism. Our results highlight the importance of the benchmark quality, suitability and appropriateness. Predictions are provided for three categories: stability decreasing, increasing and those not affecting stability. Full article
(This article belongs to the Special Issue Biophysics of Human Genetic Diseases: Understanding Molecular Effects of Mutations)
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12 pages, 1746 KiB  
Article
Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enzyme Dimerization Surface and Characterization of Three New Patients
by Beatriz Puisac, Iñigo Marcos-Alcalde, María Hernández-Marcos, Pilar Tobajas Morlana, Alina Levtova, Bernd C. Schwahn, Corinne DeLaet, Baiba Lace, Paulino Gómez-Puertas and Juan Pié
Int. J. Mol. Sci. 2018, 19(4), 1010; https://doi.org/10.3390/ijms19041010 - 28 Mar 2018
Cited by 19 | Viewed by 5112
Abstract
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency (mitochondrial HMG-CoA synthase deficiency or mHS deficiency, OMIM #605911) is an inborn error of metabolism that affects ketone body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly, hypoglycemia and dicarboxylic aciduria. The diagnosis is difficult due to the relatively unspecific [...] Read more.
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency (mitochondrial HMG-CoA synthase deficiency or mHS deficiency, OMIM #605911) is an inborn error of metabolism that affects ketone body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly, hypoglycemia and dicarboxylic aciduria. The diagnosis is difficult due to the relatively unspecific clinical and biochemical presentation, and fewer than 30 patients have been described. This work describes three new patients with mHS deficiency and two missense mutations c.334C>T (p.R112W) and c.430G>T (p.V144L) previously not reported. We developed a new method to express and measure the activity of the enzyme and in this work the study is extended to ten new missense variants including those of our patients. Enzymatic assays showed that three of the mutant proteins retained some but seven completely lacked activity. The identification of a patient homozygous for a mutation that retains 70% of enzyme activity opens the door to a new interpretation of the disease by demonstrating that a modest impairment of enzyme function can actually produce symptoms. This is also the first study employing molecular dynamics modelling of the enzyme mutations. We show that the correct maintenance of the dimerization surface is crucial for retaining the structure of the active center and therefore the activity of the enzyme. Full article
(This article belongs to the Special Issue Rare Diseases: Molecular Mechanisms and Therapeutic Strategies)
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11 pages, 267 KiB  
Article
Opposite Genetic Effects of CMIP Polymorphisms on the Risk of Type 2 Diabetes and Obesity: A Family-Based Study in China
by Yaying Cao, Tao Wang, Yiqun Wu, Juan Juan, Xueying Qin, Xun Tang, Tao Wu and Yonghua Hu
Int. J. Mol. Sci. 2018, 19(4), 1011; https://doi.org/10.3390/ijms19041011 - 28 Mar 2018
Cited by 11 | Viewed by 3557
Abstract
C-Maf Inducing Protein (CMIP) gene polymorphisms were reported to be associated with type 2 diabetes mellitus (T2DM). Whether the association between CMIP and T2DM is mediated via obesity-related phenotypes is still unclear. We analyzed the association of CMIP rs2925979 with T2DM [...] Read more.
C-Maf Inducing Protein (CMIP) gene polymorphisms were reported to be associated with type 2 diabetes mellitus (T2DM). Whether the association between CMIP and T2DM is mediated via obesity-related phenotypes is still unclear. We analyzed the association of CMIP rs2925979 with T2DM and a comprehensive set of obesity-related phenotypes in 1576 families ascertained from a Chinese population. These families included a total of 3444 siblings (1582 with T2DM, 963 with prediabetes, and 899 with a normal glucose level). Using multi-level mixed effects regression models, we found that each copy of CMIP rs2925979_T allele was associated with a 29% higher risk of T2DM in females (p = 9.30 × 10−4), while it was not significantly associated with T2DM in males (p = 0.705). Meanwhile, rs2925979_T allele was associated with lower levels of body mass index (BMI), waist circumference (WC), hip circumference (HC), percentage of body fat (PBF), PBF of arms, PBF of legs, and PBF of trunk in nondiabetes females (all p < 0.05). The opposite associations of rs2925979_T allele with T2DM and obesity-related phenotypes suggest that CMIP may exert independent pleiotropic effects on T2DM and obesity-related phenotypes in females. Full article
(This article belongs to the Section Biochemistry)
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19 pages, 18381 KiB  
Article
Transcriptome Analysis Reveals Molecular Signatures of Luteoloside Accumulation in Senescing Leaves of Lonicera macranthoides
by Zexiong Chen, Guohua Liu, Ning Tang and Zhengguo Li
Int. J. Mol. Sci. 2018, 19(4), 1012; https://doi.org/10.3390/ijms19041012 - 28 Mar 2018
Cited by 19 | Viewed by 4339
Abstract
Lonicera macranthoides is an important medicinal plant widely used in traditional Chinese medicine. Luteoloside is a critical bioactive compound in L. macranthoides. To date, the molecular mechanisms underlying luteoloside biosynthesis are still largely unknown. In this work, high performance liquid chromatography (HPLC) [...] Read more.
Lonicera macranthoides is an important medicinal plant widely used in traditional Chinese medicine. Luteoloside is a critical bioactive compound in L. macranthoides. To date, the molecular mechanisms underlying luteoloside biosynthesis are still largely unknown. In this work, high performance liquid chromatography (HPLC) was employed to determine the luteoloside contents in leaves, stems, and flowers at different developmental stages. Results showed that senescing leaves can accumulate large amounts of luteoloside, extremely higher than that in young and semi-lignified leaves and other tissues. RNA-Seq analysis identified that twenty-four differentially expressed unigenes (DEGs) associated with luteoloside biosynthesis were significantly up-regulated in senescing leaves, which are positively correlated with luteoloside accumulation. These DEGs include phenylalanine ammonia lyase 2, cinnamate 4-hydroxylase 2, thirteen 4-coumarate-CoA ligases, chalcone synthase 2, six flavonoid 3′-monooxygenase (F3′H) and two flavone 7-O-β-glucosyltransferase (UFGT) genes. Further analysis demonstrated that two F3′Hs (CL11828.Contig1 and CL11828.Contig2) and two UFGTs (Unigene2918 and Unigene97915) might play vital roles in luteoloside generation. Furthermore, several transcription factors (TFs) related to flavonoid biosynthesis including MYB, bHLH and WD40, were differentially expressed during leaf senescence. Among these TFs, MYB12, MYB75, bHLH113 and TTG1 were considered to be key factors involved in the regulation of luteoloside biosynthesis. These findings provide insights for elucidating the molecular signatures of luteoloside accumulation in L. macranthoides. Full article
(This article belongs to the Section Biochemistry)
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19 pages, 58669 KiB  
Article
Silkworm Pupa Protein Hydrolysate Induces Mitochondria-Dependent Apoptosis and S Phase Cell Cycle Arrest in Human Gastric Cancer SGC-7901 Cells
by Xiaotong Li, Hongqing Xie, Yajie Chen, Mingzi Lang, Yuyin Chen and Liangen Shi
Int. J. Mol. Sci. 2018, 19(4), 1013; https://doi.org/10.3390/ijms19041013 - 28 Mar 2018
Cited by 32 | Viewed by 6799
Abstract
Silkworm pupae (Bombyx mori) are a high-protein nutrition source consumed in China since more than 2 thousand years ago. Recent studies revealed that silkworm pupae have therapeutic benefits to treat many diseases. However, the ability of the compounds of silkworm pupae [...] Read more.
Silkworm pupae (Bombyx mori) are a high-protein nutrition source consumed in China since more than 2 thousand years ago. Recent studies revealed that silkworm pupae have therapeutic benefits to treat many diseases. However, the ability of the compounds of silkworm pupae to inhibit tumourigenesis remains to be elucidated. Here, we separated the protein of silkworm pupae and performed alcalase hydrolysis. Silkworm pupa protein hydrolysate (SPPH) can specifically inhibit the proliferation and provoke abnormal morphologic features of human gastric cancer cells SGC-7901 in a dose- and time-dependent manner. Moreover, flow cytometry indicated that SPPH can induce apoptosis and arrest the cell-cycle in S phase. Furthermore, SPPH was shown to provoke accumulation of reactive oxygen species (ROS) and depolarization of mitochondrial membrane potential. Western blotting analysis indicated that SPPH inhibited Bcl-2 expression and promoted Bax expression, and subsequently induced apoptosis-inducing factor and cytochrome C release, which led to the activation of initiator caspase-9 and executioner caspase-3, cleavage of poly (ADP-ribose) polymerase (PARP), eventually caused cell apoptosis. Moreover, SPPH-induced S-phase arrest was mediated by up-regulating the expression of E2F1 and down-regulating those of cyclin E, CDK2 and cyclin A2. Transcriptome sequencing and gene set enrichment analysis (GSEA) also revealed that SPPH treatment could affect gene expression and pathway regulation related to tumourigenesis, apoptosis and cell cycle. In summary, our results suggest that SPPH could specifically suppress cell growth of SGC-7901 through an intrinsic apoptotic pathway, ROS accumulation and cell cycle arrest, and silkworm pupae have a potential to become a source of anticancer agents in the future. Full article
(This article belongs to the Section Biochemistry)
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14 pages, 25004 KiB  
Article
Probing Interactions between AuNPs/AgNPs and Giant Unilamellar Vesicles (GUVs) Using Hyperspectral Dark-field Microscopy
by Anupama Bhat, Kewei Huan, Tiana Cooks, Hacene Boukari and Qi Lu
Int. J. Mol. Sci. 2018, 19(4), 1014; https://doi.org/10.3390/ijms19041014 - 28 Mar 2018
Cited by 12 | Viewed by 5848
Abstract
Noble metallic nanoparticles (NPs) such as gold and silver nanoparticles (AuNPs and AgNPs) have been shown to exhibit anti-tumor effect in anti-angiogenesis, photothermal and radio therapeutics. On the other hand, cell membranes are critical locales for specific targeting of cancerous cells. Therefore, NP-membrane [...] Read more.
Noble metallic nanoparticles (NPs) such as gold and silver nanoparticles (AuNPs and AgNPs) have been shown to exhibit anti-tumor effect in anti-angiogenesis, photothermal and radio therapeutics. On the other hand, cell membranes are critical locales for specific targeting of cancerous cells. Therefore, NP-membrane interactions need be studied at molecular level to help better understand the underlying physicochemical mechanisms for future applications in cancer nanotechnology. Herein, we report our study on the interactions between citrate stabilized colloidal AuNPs/AgNPs (10 nm in size) and giant unilamellar vesicles (GUVs) using hyperspectral dark-field microscopy. GUVs are large model vesicle systems well established for the study of membrane dynamics. GUVs used in this study were prepared with dimyristoyl phosphatidylcholine (DMPC) and doped with cholesterol at various molar concentrations. Both imaging and spectral results support that AuNPs and AgNPs interact very differently with GUVs, i.e., AuNPs tend to integrate in between the lipid bilayer and form a uniform golden-brown crust on vesicles, whereas AgNPs are bejeweled on the vesicle surface as isolated particles or clusters with much varied configurations. The more disruptive capability of AuNPs is hypothesized to be responsible for the formation of golden brown crusts in AuNP-GUV interaction. GUVs of 20 mol% CHOL:DMPC were found to be a most economical concentration for GUVs to achieve the best integrity and the least permeability, consistent with the finding from other phase studies of lipid mixture that the liquid-ordered domains have the largest area fraction of the entire membrane at around 20 mol% of cholesterol. Full article
(This article belongs to the Special Issue Nanotechnology in Cancer Treatment)
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14 pages, 8645 KiB  
Article
Aged (Black) versus Raw Garlic against Ischemia/Reperfusion-Induced Cardiac Complications
by Attila Czompa, Kitti Szoke, Jozsef Prokisch, Alexandra Gyongyosi, Istvan Bak, Gyorgy Balla, Arpad Tosaki and Istvan Lekli
Int. J. Mol. Sci. 2018, 19(4), 1017; https://doi.org/10.3390/ijms19041017 - 28 Mar 2018
Cited by 20 | Viewed by 5437
Abstract
Recent evidence from studies suggests that aged black garlic also has an effect on health. The major aim of the present study is to compare the effect of raw and aged black garlic on postischemic cardiac recovery. Male Sprague Dawley rats were randomly [...] Read more.
Recent evidence from studies suggests that aged black garlic also has an effect on health. The major aim of the present study is to compare the effect of raw and aged black garlic on postischemic cardiac recovery. Male Sprague Dawley rats were randomly divided into three groups. Animals of the first group were fed with raw garlic, animals of the second group received aged black garlic, while the third group served as vehicle-treated controls. Upon conclusion of the treatment, isolated hearts were undertaken to ischemia/reperfusion. Heart function and infarct size were measured and the level of HO-1 and iNOS were studied. Superior postischemic cardiac function and reduced infarct size in both garlic treated groups compared to the drug-free control group, indicated cardioprotective effects. However, no significant differences between the garlic treated groups were observed. Western blot analysis revealed that raw garlic enhanced the level of HO-1 before ischemia, while in ischemic samples, we found elevated HO-1 expression in both garlic treated groups. The level of iNOS was the same before ischemia in all groups, however, a markedly reduced iNOS level in ischemic/reperfused hearts originating from control and raw garlic treated animals was observed. Samples from aged black garlic treated animals demonstrated that the level of iNOS was not significantly reduced after ischemia/reperfusion. Taken together these results indicate that not only raw but also aged black garlic possess a cardioprotective effect. Full article
(This article belongs to the Special Issue Plant Natural Products for Human Health)
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15 pages, 52582 KiB  
Article
Phasor-Based Endogenous NAD(P)H Fluorescence Lifetime Imaging Unravels Specific Enzymatic Activity of Neutrophil Granulocytes Preceding NETosis
by Ruth Leben, Lennard Ostendorf, Sofie Van Koppen, Asylkhan Rakhymzhan, Anja E. Hauser, Helena Radbruch and Raluca A. Niesner
Int. J. Mol. Sci. 2018, 19(4), 1018; https://doi.org/10.3390/ijms19041018 - 29 Mar 2018
Cited by 27 | Viewed by 7391
Abstract
Time-correlated single-photon counting combined with multi-photon laser scanning microscopy has proven to be a versatile tool to perform fluorescence lifetime imaging in biological samples and, thus, shed light on cellular functions, both in vitro and in vivo. Here, by means of phasor-analyzed endogenous [...] Read more.
Time-correlated single-photon counting combined with multi-photon laser scanning microscopy has proven to be a versatile tool to perform fluorescence lifetime imaging in biological samples and, thus, shed light on cellular functions, both in vitro and in vivo. Here, by means of phasor-analyzed endogenous NAD(P)H (nicotinamide adenine dinucleotide (phosphate)) fluorescence lifetime imaging, we visualize the shift in the cellular metabolism of healthy human neutrophil granulocytes during phagocytosis of Staphylococcus aureus pHrodo™ beads. We correlate this with the process of NETosis, i.e., trapping of pathogens by DNA networks. Hence, we are able to directly show the dynamics of NADPH oxidase activation and its requirement in triggering NETosis in contrast to other pathways of cell death and to decipher the dedicated spatio-temporal sequence between NADPH oxidase activation, nuclear membrane disintegration and DNA network formation. The endogenous FLIM approach presented here uniquely meets the increasing need in the field of immunology to monitor cellular metabolism as a basic mechanism of cellular and tissue functions. Full article
(This article belongs to the Special Issue Laser Application in Life Sciences 2018)
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19 pages, 62305 KiB  
Article
Distribution of Glutathione-Stabilized Gold Nanoparticles in Feline Fibrosarcomas and Their Role as a Drug Delivery System for Doxorubicin—Preclinical Studies in a Murine Model
by Katarzyna Zabielska-Koczywąs, Anna Wojtalewicz, Ewelina Użarowska, Agata Klejman, Agata Wojtkowska, Izabella Dolka, Marek Wojnicki, Katarzyna Sobczak, Michał Wójcik, Haifa Shen, Mauro Ferrari and Roman Lechowski
Int. J. Mol. Sci. 2018, 19(4), 1021; https://doi.org/10.3390/ijms19041021 - 29 Mar 2018
Cited by 14 | Viewed by 5593
Abstract
Feline injection site sarcomas (FISS) are malignant skin tumors with high recurrence rates despite the primary treatment of radical surgical resections. Adjunctive radiotherapy or chemotherapy with doxorubicin is mostly ineffective. Cellular and molecular causes of multidrug resistance, specific physio-chemical properties of solid tumors [...] Read more.
Feline injection site sarcomas (FISS) are malignant skin tumors with high recurrence rates despite the primary treatment of radical surgical resections. Adjunctive radiotherapy or chemotherapy with doxorubicin is mostly ineffective. Cellular and molecular causes of multidrug resistance, specific physio-chemical properties of solid tumors impairing drug transport, and the tumor microenvironment have been indicated for causing standard chemotherapy failure. Gold nanoparticles are promising imaging tools, nanotherapeutics, and drug delivery systems (DDS) for chemotherapeutics, improving drug transport within solid tumors. This study was conducted to assess the distribution of 4-nm glutathione-stabilized gold nanoparticles in FISS and their influence on kidney and liver parameters in nude mice. The role of gold nanoparticles as a doxorubicin DDS in FISS was examined to determine the potential reasons for failure to translate results from in vitro to in vivo studies. Grade III tumors characterized by a large area of necrosis at their core displayed positive immuneexpression of tumor-associated macrophages (TAM) at both the periphery and within the tumor core near the area of necrosis. Gold nanoparticles did not cause necrosis at the injection site and had no negative effect on liver and kidney parameters in nude mice. Gold nanoparticles accumulated in the tumor core and at the periphery and co-internalized with TAM—an important observation and potential therapeutic target warranting further investigation. The large area of necrosis and high immunoexpression of TAM, indicating “pro-tumor macrophages”, may be responsible for FISS tumor progression and therapeutic failure. However, further studies are required to test this hypothesis. Full article
(This article belongs to the Special Issue Translating Gold Nanoparticles to Diagnostics and Therapeutics)
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17 pages, 51034 KiB  
Article
Biofunctionalized Scaffold in Bone Tissue Repair
by Francesca Diomede, Marco D’Aurora, Agnese Gugliandolo, Ilaria Merciaro, Tiziana Orsini, Valentina Gatta, Adriano Piattelli, Oriana Trubiani and Emanuela Mazzon
Int. J. Mol. Sci. 2018, 19(4), 1022; https://doi.org/10.3390/ijms19041022 - 29 Mar 2018
Cited by 67 | Viewed by 6060
Abstract
Bone tissue engineering is based on bone grafting to repair bone defects. Bone graft substitutes can contribute to the addition of mesenchymal stem cells (MSCs) in order to enhance the rate and the quality of defect regeneration. The stem cell secretome contains many [...] Read more.
Bone tissue engineering is based on bone grafting to repair bone defects. Bone graft substitutes can contribute to the addition of mesenchymal stem cells (MSCs) in order to enhance the rate and the quality of defect regeneration. The stem cell secretome contains many growth factors and chemokines, which could affect cellular characteristics and behavior. Conditioned medium (CM) could be used in tissue regeneration avoiding several problems linked to the direct use of MSCs. In this study, we investigated the effect of human periodontal ligament stem cells (hPDLSCs) and their CM on bone regeneration using a commercially available membrane scaffold Evolution (EVO) implanted in rat calvarias. EVO alone or EVO + hPDLSCs with or without CM were implanted in Wistar male rats subjected to calvarial defects. The in vivo results revealed that EVO membrane enriched with hPDLSCs and CM showed a better osteogenic ability to repair the calvarial defect. These results were confirmed by acquired micro-computed tomography (CT) images and the increased osteopontin levels. Moreover, RT-PCR in vitro revealed the upregulation of three genes (Collagen (COL)5A1, COL16A1 and transforming growth factor (TGF)β1) and the down regulation of 26 genes involved in bone regeneration. These results suggest a promising potential application of CM from hPDLSCs and scaffolds for bone defect restoration and in particular for calvarial repair in case of trauma. Full article
(This article belongs to the Special Issue Cell-Biomaterial Interaction)
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13 pages, 15795 KiB  
Article
Preconditioning-Like Properties of Short-Term Hypothermia in Isolated Perfused Rat Liver (IPRL) System
by Norma Alva, Raquel G. Bardallo, David Basanta, Jesús Palomeque and Teresa Carbonell
Int. J. Mol. Sci. 2018, 19(4), 1023; https://doi.org/10.3390/ijms19041023 - 29 Mar 2018
Cited by 10 | Viewed by 3727
Abstract
Hypothermia may attenuate the progression of ischemia-induced damage in liver. Here, we determined the effects of a brief cycle of hypothermic preconditioning applied before an ischemic/reperfusion (I/R) episode in isolated perfused rat liver (IPRL) on tissue damage and oxidative stress. Rats (male, 200–250 [...] Read more.
Hypothermia may attenuate the progression of ischemia-induced damage in liver. Here, we determined the effects of a brief cycle of hypothermic preconditioning applied before an ischemic/reperfusion (I/R) episode in isolated perfused rat liver (IPRL) on tissue damage and oxidative stress. Rats (male, 200–250 g) were anaesthetised with sodium pentobarbital (60 mg·kg−1 i.p) and underwent laparatomy. The liver was removed and perfused in a temperature-regulated non-recirculating system. Livers were randomly divided into two groups (n = 6 each group). In the hypothermia-preconditioned group, livers were perfused with hypothermic buffer (cycle of 10 min at 22 °C plus 10 min at 37 °C) and the other group was perfused at 37 °C. Both groups were then submitted to 40 min of warm ischemia and 20 min of warm reperfusion. The level of tissue-damage indicators (alanine amino transferase, ALT; lactate dehydrogenase, LDH; and proteins), oxidative stress markers (thiobarbituric acid-reactive substances, TBARS; advanced oxidation protein products, AOPP; and glutathione, GSH) were measured in aliquots of perfusate sampled at different time intervals. Histological determinations and oxidative stress biomarkers in homogenized liver (AOPP; TBARS; nitric oxide derivatives, NOx; GSH and glutathione disulphide, GSSG) were also made in the tissue at the end. Results showed that both damage and oxidant indicators significantly decreased while antioxidant increased in hypothermic preconditioned livers. In addition, homogenized liver determinations and histological observations at the end of the protocol corroborate the results in the perfusate, confirming the utility of the perfusate as a non-invasive method. In conclusion, hypothermic preconditioning attenuates oxidative damage and appears to be a promising strategy to protect the liver against IR injury. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Pathophysiology of Ischemia-Reperfusion Injury)
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11 pages, 12827 KiB  
Article
Disruption of PTPS Gene Causing Pale Body Color and Lethal Phenotype in the Silkworm, Bombyx mori
by Xiaoling Tong, Pingfeng Liang, Songyuan Wu, Yuanhao Li, Liang Qiao, Hai Hu, Zhonghuai Xiang, Cheng Lu and Fangyin Dai
Int. J. Mol. Sci. 2018, 19(4), 1024; https://doi.org/10.3390/ijms19041024 - 29 Mar 2018
Cited by 10 | Viewed by 4045
Abstract
Phenylketonuria (PKU) is an inborn error of metabolism caused by mutations in the phenylalanine hydroxylase (PAH) gene or by defects in the tetrahydrobiopterin (BH4) synthesis pathway. Here, by positional cloning, we report that the 6-pyruvoyl-tetrahydropterin synthase (PTPS) gene, encoding [...] Read more.
Phenylketonuria (PKU) is an inborn error of metabolism caused by mutations in the phenylalanine hydroxylase (PAH) gene or by defects in the tetrahydrobiopterin (BH4) synthesis pathway. Here, by positional cloning, we report that the 6-pyruvoyl-tetrahydropterin synthase (PTPS) gene, encoding a key enzyme of BH4 biosynthesis, is responsible for the alc (albino C) mutation that displays pale body color, head shaking, and eventually lethality after the first molting in silkworm. Compared to wild type, the alc mutant produced more substrates (phenylalanine (Phe) and tyrosine (Tyr)) and generated less DOPA and dopamine. Application of 2,4-diamino-6-hydroxypyrimidine (DAHP) to block BH4 synthesis in the wild type effectively produced the alc-like phenotype, while BH4 supplementation rescued the defective body color and lethal phenotype in both alc and DAHP-treated individuals. The detection of gene expressions and metabolic substances after drugs treatments in alc and normal individuals imply that silkworms and humans have a high similarity in the drugs metabolic features and the gene pathway related to BH4 and the dopamine biosynthesis. We propose that the alc mutant could be used as an animal model for drug evaluation for BH4-deficient PKU. Full article
(This article belongs to the Section Biochemistry)
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9 pages, 21879 KiB  
Communication
Crystal Structure of CYP2B6 in Complex with an Efavirenz Analog
by Manish B. Shah, Qinghai Zhang and James R. Halpert
Int. J. Mol. Sci. 2018, 19(4), 1025; https://doi.org/10.3390/ijms19041025 - 29 Mar 2018
Cited by 6 | Viewed by 4794
Abstract
The over two dozen CYP2B structures of human, rabbit, and woodrat enzymes solved in the last decade have significantly enhanced our understanding of the structure-function relationships of drug metabolizing enzymes. More recently, an important role has emerged for halogen-π interactions in the CYP2B6 [...] Read more.
The over two dozen CYP2B structures of human, rabbit, and woodrat enzymes solved in the last decade have significantly enhanced our understanding of the structure-function relationships of drug metabolizing enzymes. More recently, an important role has emerged for halogen-π interactions in the CYP2B6 active site in substrate selectivity, explaining in part the preference for halogenated ligands as substrates. The mechanism by which such ligands interact with CYP2B enzymes involves conserved phenylalanine side chains, in particular F108, F115, or F297, in the active site, which form π bonds with halogens. To illustrate such halogen-π interactions using drugs that are major substrates of CYP2B6, we present here a crystal structure of CYP2B6 in complex with an analog of the widely used anti-HIV drug efavirenz, which contains a methyl group in place of the carbonyl oxygen. The chlorine of the efavirenz analog forms a π bond with the aromatic ring of F108, whereas the putative metabolism site on the distal end of the molecule is oriented towards the heme iron. The crystal structure showcases how CYP2B6 accommodates this important drug analog of considerable size in the active site by movement of various side chains without substantially increasing the active site volume. Furthermore, the CYP2B6-efavirenz analog complex provides a useful platform to investigate computationally as well as biophysically the effect of genetic polymorphisms on binding of the widely studied efavirenz. Full article
(This article belongs to the Special Issue Cytochromes P450: Drug Metabolism and Bioactivation)
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17 pages, 11822 KiB  
Article
Treatment of Arsenite Intoxication-Induced Peripheral Vasculopathy with Mesenchymal Stem Cells
by Yi-Hung Chiang, Chai-Chin Lin, Yen-Chung Chen and Oscar K. Lee
Int. J. Mol. Sci. 2018, 19(4), 1026; https://doi.org/10.3390/ijms19041026 - 29 Mar 2018
Cited by 6 | Viewed by 3947
Abstract
Arsenite (As), a notorious toxic metal, is ubiquitously distributed in the earth and poses a serious threat to human health. Histopathological lesions of As intoxication are known as thromboangiitis obliterans, which are resistant to current treatment and often lead to lower limb amputation. [...] Read more.
Arsenite (As), a notorious toxic metal, is ubiquitously distributed in the earth and poses a serious threat to human health. Histopathological lesions of As intoxication are known as thromboangiitis obliterans, which are resistant to current treatment and often lead to lower limb amputation. In this study, we attempt to find that treatment with mesenchymal stem cells (MSCs) may be effective for As-induced vasculopathy. We first conducted an in vitro study with a co-culture system containing human MSCs and human umbilical vein endothelial cells (HUVECs) and treated individual and co-cultured cells with various concentrations of arsenite. We also designed an in vivo study in which Sprague Dawley (SD) rats received periodic intraperitoneal (IP) injections of 16 ppm arsenite for 12 weeks. MSCs were harvested from BALB/c mice that were transplanted via tail vein injection. We found that there was significantly higher cellular viability in human mesenchymal stem cells (hMSCs) than in HUVECs under concentrations of arsenite between 15 and 25 μM. The Annexin V apoptosis assay further confirmed this finding. Cytokine array assay for As-conditioned media revealed an elevated vascular endothelial growth factor (VEGF) level secreted by MSCs, which is crucial for HUVEC survival and was evaluated by an siRNA VEGF knockdown test. In the in vivo study, we demonstrated early apoptotic changes in the anterior tibial vessels of As-injected SD rats with a Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, but these apoptotic changes were less frequently observed upon MSCs transplantation, indicating that the cytoprotective effect of MSCs successfully protected against As-induced peripheral vasculopathy. The feasibility of MSCs to treat and /or prevent the progression of As-induced vasculopathy is justified. Further clinical studies are required to demonstrate the therapeutic efficacy of MSCs in patients suffering from As intoxication with vasculopathy. Full article
(This article belongs to the Section Molecular Toxicology)
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16 pages, 12416 KiB  
Article
New Gene Markers for Metabolic Processes and Homeostasis in Porcine Buccal Pouch Mucosa during Cells Long Term-Cultivation—A Primary Culture Approach
by Marta Dyszkiewicz-Konwińska, Mariusz J. Nawrocki, Yan Huang, Artur Bryja, Piotr Celichowski, Maurycy Jankowski, Katarzyna Błochowiak, Katarzyna Mehr, Małgorzata Bruska, Michał Nowicki, Maciej Zabel and Bartosz Kempisty
Int. J. Mol. Sci. 2018, 19(4), 1027; https://doi.org/10.3390/ijms19041027 - 29 Mar 2018
Cited by 6 | Viewed by 3446
Abstract
The oral mucosal tissue is a compound structure composed of morphologically and physiologically different cell types. The morphological modification involves genetically determined lifespan, which may be recognized as the balance between cell survival and apoptosis. Although the biochemical processes and pathways in oral [...] Read more.
The oral mucosal tissue is a compound structure composed of morphologically and physiologically different cell types. The morphological modification involves genetically determined lifespan, which may be recognized as the balance between cell survival and apoptosis. Although the biochemical processes and pathways in oral mucosa, with special regards to drug transport, delivery, and metabolism, are well known, the cellular physiological homeostasis in this tissue requires further investigation. The porcine buccal pouch mucosal cells (BPMCs) collected from 20 pubertal crossbred Landrace gilts, were used in this study. Immediately after recovery, the oral mucosa was separated micro-surgically, and treated enzymatically. The dispersed cells were transferred into primary in vitro culture systems for a long-term cultivation of 30 days. After each step of in vitro culture (IVC), the cells were collected for isolation of total RNA at 24 h, 7, 15, and 30 days of IVC. While the expression was analyzed for days 7, 15, and 30, the 24th hour was used as a reference for outcome calibration. The gene expression profile was determined using Affymetrix microarray assays and necessary procedures. In results, we observed significant up-regulation of SCARB1, PTGS2, DUSP5, ITGB3, PLK2, CCL2, TGFB1, CCL8, RFC4, LYN, ETS1, REL, LIF, SPP1, and FGER1G genes, belonging to two ontological groups, namely “positive regulation of metabolic process”, and “regulation of homeostatic process” at 7 day of IVC as compared to down-regulation at days 15 and 30. These findings suggest that the metabolic processes and homeostatic regulations are much more intense in porcine mucosal cells at day 7 of IVC. Moreover, the increased expression of marker genes, for both of these ontological groups, may suggest the existence of not only “morphological lifespan” during tissue keratinization, but also “physiological checkpoint” dedicated to metabolic processes in oral mucosa. This knowledge may be useful for preclinical experiments with drugs delivery and metabolism in both animals and humans. Full article
(This article belongs to the Section Biochemistry)
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20 pages, 47623 KiB  
Article
Genome-Wide Analyses of the NAC Transcription Factor Gene Family in Pepper (Capsicum annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements in the Promoter, and Interaction Network
by Weiping Diao, John C. Snyder, Shubin Wang, Jinbing Liu, Baogui Pan, Guangjun Guo, Wei Ge and Mohammad Hasan Salman Ali Dawood
Int. J. Mol. Sci. 2018, 19(4), 1028; https://doi.org/10.3390/ijms19041028 - 29 Mar 2018
Cited by 66 | Viewed by 8768
Abstract
The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, [...] Read more.
The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, gene phylogeny, conserved motifs, or gene expression of NAC in pepper (Capsicum annuum L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of Capsicum annuum L. NAC (CaNAC) proteins. In the present study, a comprehensive analysis of the CaNAC gene family in pepper was performed, and a total of 104 CaNAC genes were identified. Genome mapping analysis revealed that CaNAC genes were enriched on four chromosomes (chromosomes 1, 2, 3, and 6). In addition, phylogenetic analysis of the NAC domains from pepper, potato, Arabidopsis, and rice showed that CaNAC genes could be clustered into three groups (I, II, and III). Group III, which contained 24 CaNAC genes, was exclusive to the Solanaceae plant family. Gene structure and protein motif analyses showed that these genes were relatively conserved within each subgroup. The number of introns in CaNAC genes varied from 0 to 8, with 83 (78.9%) of CaNAC genes containing two or less introns. Promoter analysis confirmed that CaNAC genes are involved in pepper growth, development, and biotic or abiotic stress responses. Further, the expression of 22 selected CaNAC genes in response to seven different biotic and abiotic stresses [salt, heat shock, drought, Phytophthora capsici, abscisic acid, salicylic acid (SA), and methyl jasmonate (MeJA)] was evaluated by quantitative RT-PCR to determine their stress-related expression patterns. Several putative stress-responsive CaNAC genes, including CaNAC72 and CaNAC27, which are orthologs of the known stress-responsive Arabidopsis gene ANAC055 and potato gene StNAC30, respectively, were highly regulated by treatment with different types of stress. Our results also showed that CaNAC36 plays an important role in the interaction network, interacting with 48 genes. Most of these genes are in the mitogen-activated protein kinase (MAPK) family. Taken together, our results provide a platform for further studies to identify the biological functions of CaNAC genes. Full article
(This article belongs to the Section Molecular Plant Sciences)
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13 pages, 2668 KiB  
Article
PCLPred: A Bioinformatics Method for Predicting Protein–Protein Interactions by Combining Relevance Vector Machine Model with Low-Rank Matrix Approximation
by Li-Ping Li, Yan-Bin Wang, Zhu-Hong You, Yang Li and Ji-Yong An
Int. J. Mol. Sci. 2018, 19(4), 1029; https://doi.org/10.3390/ijms19041029 - 29 Mar 2018
Cited by 27 | Viewed by 4936
Abstract
Protein–protein interactions (PPI) are key to protein functions and regulations within the cell cycle, DNA replication, and cellular signaling. Therefore, detecting whether a pair of proteins interact is of great importance for the study of molecular biology. As researchers have become aware of [...] Read more.
Protein–protein interactions (PPI) are key to protein functions and regulations within the cell cycle, DNA replication, and cellular signaling. Therefore, detecting whether a pair of proteins interact is of great importance for the study of molecular biology. As researchers have become aware of the importance of computational methods in predicting PPIs, many techniques have been developed for performing this task computationally. However, there are few technologies that really meet the needs of their users. In this paper, we develop a novel and efficient sequence-based method for predicting PPIs. The evolutionary features are extracted from the position-specific scoring matrix (PSSM) of protein. The features are then fed into a robust relevance vector machine (RVM) classifier to distinguish between the interacting and non-interacting protein pairs. In order to verify the performance of our method, five-fold cross-validation tests are performed on the Saccharomyces cerevisiae dataset. A high accuracy of 94.56%, with 94.79% sensitivity at 94.36% precision, was obtained. The experimental results illustrated that the proposed approach can extract the most significant features from each protein sequence and can be a bright and meaningful tool for the research of proteomics. Full article
(This article belongs to the Special Issue Special Protein or RNA Molecules Computational Identification 2018)
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15 pages, 4422 KiB  
Article
Resveratrol Suppresses the Growth and Enhances Retinoic Acid Sensitivity of Anaplastic Thyroid Cancer Cells
by Yi-Tian Li, Xiao-Ting Tian, Mo-Li Wu, Xu Zheng, Qing-You Kong, Xiao-Xin Cheng, Guang-Wen Zhu, Jia Liu and Hong Li
Int. J. Mol. Sci. 2018, 19(4), 1030; https://doi.org/10.3390/ijms19041030 - 29 Mar 2018
Cited by 35 | Viewed by 5239
Abstract
Anaplastic thyroid cancer (ATC) is a highly lethal undifferentiated malignancy without reliable therapies. Retinoic acid (RA) has been employed to promote redifferentiation of thyroid cancers by increasing their I131 uptake and radio-sensitivity, but its effect(s) on ATCs has not yet been ascertained. [...] Read more.
Anaplastic thyroid cancer (ATC) is a highly lethal undifferentiated malignancy without reliable therapies. Retinoic acid (RA) has been employed to promote redifferentiation of thyroid cancers by increasing their I131 uptake and radio-sensitivity, but its effect(s) on ATCs has not yet been ascertained. Likewise, resveratrol induces cancer redifferentiation but, also in this case, its effects on ATCs remain unknown. These issues have been addresses in the current study using three human ATC cell lines (THJ-11T, THJ-16T, and THJ-21T) through multiple experimental approaches. The results reveal that RA exerts a small inhibitory effect on these cell lines. In comparison with normally cultured cells, the total cell number in resveratrol-treated THJ-16T and THJ-21T cultures significantly decreased (p < 0.05), and this effect was accompanied by reduced Cyclin D1 immuno-labeling, increased apoptotic fractions, and distinct caspase-3 activation. Resveratrol failed to inhibit growth but enhanced RA sensitivity of THJ-11T cells, suppressed peroxisome proliferator-activated receptor-β/δ (PPAR-β/δ), and upregulated cellular retinoic acid-binding protein 2 (CRABP2) and retinoic acid receptor beta (RAR-β) expression. Increased thyroglobulin (Tg) and E-cadherin levels and appearance of membranous E-cadherin were evidenced in resveratrol-treated THJ-11T cells. Our results demonstrate for the first time: (1) the therapeutic value of resveratrol by itself or in combination with RA in the management of ATCs, (2) the capacity of resveratrol to overcome RA resistance in ATC cells by reprogramming CRABP2/RAR- and fatty acid-binding protein 5 (FABP5)/PPAR-β/δ-mediated RA signaling, and (3) the redifferentiating potential of resveratrol in ATC cells. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology)
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15 pages, 29028 KiB  
Article
Mesenchymal Cells Affect Salivary Epithelial Cell Morphology on PGS/PLGA Core/Shell Nanofibers
by Lauren Sfakis, Tim Kamaldinov, Alexander Khmaladze, Zeinab F. Hosseini, Deirdre A. Nelson, Melinda Larsen and James Castracane
Int. J. Mol. Sci. 2018, 19(4), 1031; https://doi.org/10.3390/ijms19041031 - 29 Mar 2018
Cited by 17 | Viewed by 3996
Abstract
Engineering salivary glands is of interest due to the damaging effects of radiation therapy and the autoimmune disease Sjögren’s syndrome on salivary gland function. One of the current problems in tissue engineering is that in vitro studies often fail to predict in vivo [...] Read more.
Engineering salivary glands is of interest due to the damaging effects of radiation therapy and the autoimmune disease Sjögren’s syndrome on salivary gland function. One of the current problems in tissue engineering is that in vitro studies often fail to predict in vivo regeneration due to failure of cells to interact with scaffolds and of the single cell types that are typically used for these studies. Although poly (lactic co glycolic acid) (PLGA) nanofiber scaffolds have been used for in vitro growth of epithelial cells, PLGA has low compliance and cells do not penetrate the scaffolds. Using a core-shell electrospinning technique, we incorporated poly (glycerol sebacate) (PGS) into PLGA scaffolds to increase the compliance and decrease hydrophobicity. PGS/PLGA scaffolds promoted epithelial cell penetration into the scaffold and apical localization of tight junction proteins, which is necessary for epithelial cell function. Additionally, co-culture of the salivary epithelial cells with NIH3T3 mesenchymal cells on PGS/PLGA scaffolds facilitated epithelial tissue reorganization and apical localization of tight junction proteins significantly more than in the absence of the mesenchyme. These data demonstrate the applicability of PGS/PLGA nanofibers for epithelial cell self-organization and facilitation of co-culture cell interactions that promote tissue self-organization in vitro. Full article
(This article belongs to the Section Biochemistry)
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20 pages, 19826 KiB  
Article
Towards a Novel Patch Material for Cardiac Applications: Tissue-Specific Extracellular Matrix Introduces Essential Key Features to Decellularized Amniotic Membrane
by Matthias Becker, Janita A. Maring, Maria Schneider, Aarón X. Herrera Martin, Martina Seifert, Oliver Klein, Thorsten Braun, Volkmar Falk and Christof Stamm
Int. J. Mol. Sci. 2018, 19(4), 1032; https://doi.org/10.3390/ijms19041032 - 29 Mar 2018
Cited by 34 | Viewed by 6553
Abstract
There is a growing need for scaffold material with tissue-specific bioactivity for use in regenerative medicine, tissue engineering, and for surgical repair of structural defects. We developed a novel composite biomaterial by processing human cardiac extracellular matrix (ECM) into a hydrogel and combining [...] Read more.
There is a growing need for scaffold material with tissue-specific bioactivity for use in regenerative medicine, tissue engineering, and for surgical repair of structural defects. We developed a novel composite biomaterial by processing human cardiac extracellular matrix (ECM) into a hydrogel and combining it with cell-free amniotic membrane via a dry-coating procedure. Cardiac biocompatibility and immunogenicity were tested in vitro using human cardiac fibroblasts, epicardial progenitor cells, murine HL-1 cells, and human immune cells derived from buffy coat. Processing of the ECM preserved important matrix proteins as demonstrated by mass spectrometry. ECM coating did not alter the mechanical characteristics of decellularized amniotic membrane but did cause a clear increase in adhesion capacity, cell proliferation and viability. Activated monocytes secreted less pro-inflammatory cytokines, and both macrophage polarization towards the pro-inflammatory M1 type and T cell proliferation were prevented. We conclude that the incorporation of human cardiac ECM hydrogel shifts and enhances the bioactivity of decellularized amniotic membrane, facilitating its use in future cardiac applications. Full article
(This article belongs to the Special Issue Cell Colonization in Scaffolds)
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17 pages, 10527 KiB  
Article
TASK-3 Downregulation Triggers Cellular Senescence and Growth Inhibition in Breast Cancer Cell Lines
by Rafael Zúñiga, Claudio Valenzuela, Guierdy Concha, Nelson Brown and Leandro Zúñiga
Int. J. Mol. Sci. 2018, 19(4), 1033; https://doi.org/10.3390/ijms19041033 - 29 Mar 2018
Cited by 19 | Viewed by 4560
Abstract
TASK-3 potassium channels are believed to promote proliferation and survival of cancer cells, in part, by augmenting their resistance to both hypoxia and serum deprivation. While overexpression of TASK-3 is frequently observed in cancers, the understanding of its role and regulation during tumorigenesis [...] Read more.
TASK-3 potassium channels are believed to promote proliferation and survival of cancer cells, in part, by augmenting their resistance to both hypoxia and serum deprivation. While overexpression of TASK-3 is frequently observed in cancers, the understanding of its role and regulation during tumorigenesis remains incomplete. Here, we evaluated the effect of reducing the expression of TASK-3 in MDA-MB-231 and MCF-10F human mammary epithelial cell lines through small hairpin RNA (shRNA)-mediated knockdown. Our results show that knocking down TASK-3 in fully transformed MDA-MB-231 cells reduces proliferation, which was accompanied by an induction of cellular senescence and cell cycle arrest, with an upregulation of cyclin-dependent kinase (CDK) inhibitors p21 and p27. In non-tumorigenic MCF-10F cells, however, TASK-3 downregulation did not lead to senescence induction, although cell proliferation was impaired and an upregulation of CDK inhibitors was also evident. Our observations implicate TASK-3 as a critical factor in cell cycle progression and corroborate its potential as a therapeutic target in breast cancer treatment. Full article
(This article belongs to the Section Biochemistry)
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20 pages, 45109 KiB  
Article
The Role of Serotonin during Skin Healing in Post-Thermal Injury
by Alia Sadiq, Ahmed Shah, Marc G. Jeschke, Cassandra Belo, Muhammad Qasim Hayat, Sheeba Murad and Saeid Amini-Nik
Int. J. Mol. Sci. 2018, 19(4), 1034; https://doi.org/10.3390/ijms19041034 - 29 Mar 2018
Cited by 44 | Viewed by 9047
Abstract
Post-burn trauma significantly raises tissue serotonin concentration at the initial stages of injury, which leads us to investigate its possible role in post burn wound healing. Therefore, we planned this study to examine the role of serotonin in wound healing through in vitro [...] Read more.
Post-burn trauma significantly raises tissue serotonin concentration at the initial stages of injury, which leads us to investigate its possible role in post burn wound healing. Therefore, we planned this study to examine the role of serotonin in wound healing through in vitro and in vivo models of burn injuries. Results from in vitro analysis revealed that serotonin decreased apoptosis and increased cell survival significantly in human fibroblasts and neonatal keratinocytes. Cellular proliferation also increased significantly in both cell types. Moreover, serotonin stimulation significantly accelerated the cell migration, resulting in narrowing of the scratch zone in human neonatal keratinocytes and fibroblasts cultures. Whereas, fluoxetine (a selective serotonin reuptake inhibitor) and ketanserin (serotonin receptor 2A inhibitor) reversed these effects. Scald burn mice model (20% total body surface area) showed that endogenous serotonin improved wound healing process in control group, whereas fluoxetine and ketanserin treatments (disruptors of endogenous serotonin stimulation), resulted in poor reepithelization, bigger wound size and high alpha smooth muscle actin (α-SMA) count. All of these signs refer a prolonged differentiation state, which ultimately exhibits poor wound healing outcomes. Collectively, data showed that the endogenous serotonin pathway contributes to regulating the skin wound healing process. Hence, the results of this study signify the importance of serotonin as a potential therapeutic candidate for enhancing skin healing in burn patients. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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14 pages, 47188 KiB  
Article
Genetic Variants in STAT3 Promoter Regions and Their Application in Molecular Breeding for Body Size Traits in Qinchuan Cattle
by Sen Wu, Yaning Wang, Yue Ning, Hongfang Guo, Xiaoyu Wang, Le Zhang, Rajwali Khan, Gong Cheng, Hongbao Wang and Linsen Zan
Int. J. Mol. Sci. 2018, 19(4), 1035; https://doi.org/10.3390/ijms19041035 - 29 Mar 2018
Cited by 32 | Viewed by 5164
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation [...] Read more.
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation in STAT3, followed by measurements of its mRNA expression during fetal and adult stages of Qinchuan cattle. We then sequenced the STAT3 promoter region to determine genetic variants and evaluate their association with body size traits. From fetus to adult, STAT3 expression increased significantly in muscle, fat, heart, liver, and spleen tissues (p < 0.01), but decreased in the intestine, lung, and rumen (p < 0.01). We identified and named five single nucleotide polymorphisms (SNPs): SNP1-304A>C, SNP2-285G>A, SNP3-209A>C, SNP4-203A>G, and SNP5-188T>C. These five mutations fell significantly outside the Hardy–Weinberg equilibrium (HWE) (Chi-squared test, p < 0.05) and significantly associated with body size traits (p < 0.05). Individuals with haplotype H3H3 (CC-GG-CC-GG-CC) were larger in body size than other haplotypes. Therefore, variations in the STAT3 gene promoter regions, most notably haplotype H3H3, may benefit marker-assisted breeding of Qinchuan cattle. Full article
(This article belongs to the Special Issue Advances in Biological Functions of STAT3)
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12 pages, 14467 KiB  
Article
LGR5 and BMI1 Increase Pig Intestinal Epithelial Cell Proliferation by Stimulating WNT/β-Catenin Signaling
by Xiang-Guang Li, Zhe Wang, Rong-Qiang Chen, Hou-Long Fu, Chun-Qi Gao, Hui-Chao Yan, Guang-Xu Xing and Xiu-Qi Wang
Int. J. Mol. Sci. 2018, 19(4), 1036; https://doi.org/10.3390/ijms19041036 - 30 Mar 2018
Cited by 35 | Viewed by 4939
Abstract
Leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5) and B-cell-specific Moloney murine leukemia virus insertion site 1 (BMI1) are markers of fast-cycling and quiescent intestinal stem cells, respectively. To determine the functions of these proteins in large animals, we investigated their effects on the [...] Read more.
Leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5) and B-cell-specific Moloney murine leukemia virus insertion site 1 (BMI1) are markers of fast-cycling and quiescent intestinal stem cells, respectively. To determine the functions of these proteins in large animals, we investigated their effects on the proliferation of intestinal epithelial cells from pigs. Our results indicated that LGR5 and BMI1 are highly conserved proteins and that the pig proteins have greater homology with the human proteins than do mouse proteins. Overexpression of either LGR5 or BMI1 promoted cell proliferation and WNT/β-catenin signaling in pig intestinal epithelial cells (IPEC-J2). Moreover, the activation of WNT/β-catenin signaling by recombinant human WNT3A protein increased cell proliferation and LGR5 and BMI1 protein levels. Conversely, inhibition of WNT/β-catenin signaling using XAV939 reduced cell proliferation and LGR5 and BMI1 protein levels. This is the first report that LGR5 and BMI1 can increase proliferation of pig intestinal epithelial cells by activating WNT/β-catenin signaling. Full article
(This article belongs to the Section Biochemistry)
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16 pages, 4201 KiB  
Article
Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver
by Wencai Wang, Siyun Chen and Xianzhi Zhang
Int. J. Mol. Sci. 2018, 19(4), 1037; https://doi.org/10.3390/ijms19041037 - 30 Mar 2018
Cited by 29 | Viewed by 5062
Abstract
Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to [...] Read more.
Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future. Full article
(This article belongs to the Special Issue Chloroplast)
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16 pages, 31111 KiB  
Article
Genome-Wide Analysis of DCL, AGO, and RDR Gene Families in Pepper (Capsicum Annuum L.)
by Lei Qin, Ning Mo, Tayeb Muhammad and Yan Liang
Int. J. Mol. Sci. 2018, 19(4), 1038; https://doi.org/10.3390/ijms19041038 - 30 Mar 2018
Cited by 55 | Viewed by 7813
Abstract
RNA silencing is an evolutionarily conserved mechanism that regulates variety of cellular processes in plants. Argonaute protein (AGO), Dicer-like protein (DCL) and RNA-dependent RNA polymerase (RDR) are critical components of RNA silencing. These efficient and indispensable components of the RNAi pathway have not [...] Read more.
RNA silencing is an evolutionarily conserved mechanism that regulates variety of cellular processes in plants. Argonaute protein (AGO), Dicer-like protein (DCL) and RNA-dependent RNA polymerase (RDR) are critical components of RNA silencing. These efficient and indispensable components of the RNAi pathway have not been identified and characterized in pepper. In this study, we identified 12 CaAGO, 4 CaDCL and 6 CaRDR genes in pepper and compared them with those of Arabidopsis, tobacco, potato and tomato. Detailed phylogenetic analyses revealed that each CaAGO, CaDCL and CaRDR protein family were classified into four clades. The tissue specific expression and respond to abiotic or biotic stress were studied. The real-time quantitative polymerase chain reaction (PCR) results demonstrated that CaAGO2, CaAGO10b, CaDCL2 and CaDCL4 were upregulated with cucumber mosaic virus (CMV), potato virus Y (PVY) and tobacco mosaic virus (TMV) infections, whereas they showed difference expression patterns in response to abiotic stress. In addition, we found that many of the candidate genes were induced by phytohormones and H2O2 treatment. Our results provide useful information for further elucidation of gene silencing pathways and RNAi-mediated host immunity in pepper. Full article
(This article belongs to the Special Issue Plant Defense Genes Against Biotic Stresses)
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16 pages, 13682 KiB  
Article
MetStabOn—Online Platform for Metabolic Stability Predictions
by Sabina Podlewska and Rafał Kafel
Int. J. Mol. Sci. 2018, 19(4), 1040; https://doi.org/10.3390/ijms19041040 - 30 Mar 2018
Cited by 31 | Viewed by 6329
Abstract
Metabolic stability is an important parameter to be optimized during the complex process of designing new active compounds. Tuning this parameter with the simultaneous maintenance of a desired compound’s activity is not an easy task due to the extreme complexity of metabolic pathways [...] Read more.
Metabolic stability is an important parameter to be optimized during the complex process of designing new active compounds. Tuning this parameter with the simultaneous maintenance of a desired compound’s activity is not an easy task due to the extreme complexity of metabolic pathways in living organisms. In this study, the platform for in silico qualitative evaluation of metabolic stability, expressed as half-lifetime and clearance was developed. The platform is based on the application of machine learning methods and separate models for human, rat and mouse data were constructed. The compounds’ evaluation is qualitative and two types of experiments can be performed—regression, which is when the compound is assigned to one of the metabolic stability classes (low, medium, high) on the basis of numerical value of the predicted half-lifetime, and classification, in which the molecule is directly assessed as low, medium or high stability. The results show that the models have good predictive power, with accuracy values over 0.7 for all cases, for Sequential Minimal Optimization (SMO), k-nearest neighbor (IBk) and Random Forest algorithms. Additionally, for each of the analyzed compounds, 10 of the most similar structures from the training set (in terms of Tanimoto metric similarity) are identified and made available for download as separate files for more detailed manual inspection. The predictive power of the models was confronted with the external dataset, containing metabolic stability assessment via the GUSAR software, leading to good consistency of results for SMOreg and Naïve Bayes (~0.8 on average). The tool is available online. Full article
(This article belongs to the Section Biochemistry)
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15 pages, 22427 KiB  
Article
Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species
by Kangquan Yin, Yue Zhang, Yuejuan Li and Fang K. Du
Int. J. Mol. Sci. 2018, 19(4), 1042; https://doi.org/10.3390/ijms19041042 - 30 Mar 2018
Cited by 40 | Viewed by 5621
Abstract
Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species [...] Read more.
Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of Q. aquifolioides with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four Quercus cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the Q. aquifolioides repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the atpF gene of Q. aquifolioides compared to two deciduous oak species, and that there had been significant purifying selection on the atpF gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined Q. aquifolioides as belonging to sect. Heterobalanus and being closely related to Q. rubra and Q. aliena. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus Quercus. Full article
(This article belongs to the Special Issue Chloroplast)
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17 pages, 3748 KiB  
Article
Feature Tracking for High Speed AFM Imaging of Biopolymers
by Brett Hartman and Sean B. Andersson
Int. J. Mol. Sci. 2018, 19(4), 1044; https://doi.org/10.3390/ijms19041044 - 31 Mar 2018
Cited by 12 | Viewed by 3597
Abstract
The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates [...] Read more.
The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates are needed with scan ranges larger than are currently achievable. Moreover, there is a significant installed base of slower instruments that would benefit from algorithmic approaches to increasing their frame rate without requiring significant hardware modifications. In this paper, we present an experimental demonstration of high speed scanning on an existing, non-high speed instrument, through the use of a feedback-based, feature-tracking algorithm that reduces imaging time by focusing on features of interest to reduce the total imaging area. Experiments on both circular and square gratings, as well as silicon steps and DNA strands show a reduction in imaging time by a factor of 3–12 over raster scanning, depending on the parameters chosen. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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16 pages, 58680 KiB  
Article
Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes
by Yaogeng Lei, Abdelali Hannoufa, David Christensen, Haitao Shi, Luciana L. Prates and Peiqiang Yu
Int. J. Mol. Sci. 2018, 19(4), 1046; https://doi.org/10.3390/ijms19041046 - 31 Mar 2018
Cited by 20 | Viewed by 4902
Abstract
This study investigated the spectral changes in alfalfa molecular structures induced by silencing of Transparent Testa 8 (TT8) and Homeobox 12 (HB12) genes with univariate and multivariate analyses. TT8-silenced (TT8i), HB12-silenced (HB12i) and wild type (WT) alfalfa [...] Read more.
This study investigated the spectral changes in alfalfa molecular structures induced by silencing of Transparent Testa 8 (TT8) and Homeobox 12 (HB12) genes with univariate and multivariate analyses. TT8-silenced (TT8i), HB12-silenced (HB12i) and wild type (WT) alfalfa were grown in a greenhouse under normal conditions and were harvested at early-to-mid vegetative stage. Samples were free-dried and grounded through 0.02 mm sieve for spectra collections with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Afterwards, both univariate and multivariate analyses were conducted on amide, carbohydrate and lipid regions. Univariate results showed that silencing of TT8 and HB12 genes affected peak heights of most total carbohydrate (TC) and structural carbohydrate (STC), and structural carbohydrate area (STCA) in carbohydrate regions; and β-sheet height, amide areas, and ratios of amide I/II and α-helix/β-sheet in amide region; and symmetric CH2 (SyCH2), asymmetric CH2 (AsCH2) and (a)symmetric CH2 and CH3 area (ASCCA) in the lipid region. Multivariate analysis showed that both hierarchy cluster analysis (HCA) and principal component analysis (PCA) clearly separated WT from transgenic plants in all carbohydrate regions and (a)symmetric CH2 and CH3 (ASCC) lipid region. In the amide region, PCA separated WT, TT8i and HB12i into different groups, while HCA clustered WT into a separate group. In conclusion, silencing of TT8 and HB12 affected intrinsic molecular structures of both amide and carbohydrate profiles in alfalfa, and multivariate analyses successfully distinguished gene-silenced alfalfa from its parental WT control. Full article
(This article belongs to the Section Molecular Biophysics)
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14 pages, 12654 KiB  
Article
Mixture Concentration-Response Modeling Reveals Antagonistic Effects of Estradiol and Genistein in Combination on Brain Aromatase Gene (cyp19a1b) in Zebrafish
by Nathalie Hinfray, Cleo Tebby, Benjamin Piccini, Gaelle Bourgine, Sélim Aït-Aïssa, Jean-Marc Porcher, Farzad Pakdel and François Brion
Int. J. Mol. Sci. 2018, 19(4), 1047; https://doi.org/10.3390/ijms19041047 - 1 Apr 2018
Cited by 15 | Viewed by 4296
Abstract
Comprehension of compound interactions in mixtures is of increasing interest to scientists, especially from a perspective of mixture risk assessment. However, most of conducted studies have been dedicated to the effects on gonads, while only few of them were. interested in the effects [...] Read more.
Comprehension of compound interactions in mixtures is of increasing interest to scientists, especially from a perspective of mixture risk assessment. However, most of conducted studies have been dedicated to the effects on gonads, while only few of them were. interested in the effects on the central nervous system which is a known target for estrogenic compounds. In the present study, the effects of estradiol (E2), a natural estrogen, and genistein (GEN), a phyto-estrogen, on the brain ER-regulated cyp19a1b gene in radial glial cells were investigated alone and in mixtures. For that, zebrafish-specific in vitro and in vivo bioassays were used. In U251-MG transactivation assays, E2 and GEN produced antagonistic effects at low mixture concentrations. In the cyp19a1b-GFP transgenic zebrafish, this antagonism was observed at all ratios and all concentrations of mixtures, confirming the in vitro effects. In the present study, we confirm (i) that our in vitro and in vivo biological models are valuable complementary tools to assess the estrogenic potency of chemicals both alone and in mixtures; (ii) the usefulness of the ray design approach combined with the concentration-addition modeling to highlight interactions between mixture components. Full article
(This article belongs to the Special Issue Molecular Pathways of Estrogen Receptor Action)
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23 pages, 2626 KiB  
Article
Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris
by Martina Lardi, Yilei Liu, Gaetano Giudice, Christian H. Ahrens, Nicola Zamboni and Gabriella Pessi
Int. J. Mol. Sci. 2018, 19(4), 1049; https://doi.org/10.3390/ijms19041049 - 1 Apr 2018
Cited by 12 | Viewed by 5948
Abstract
RpoN (or σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815T [...] Read more.
RpoN (or σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815T formed root nodules on Phaseolus vulgaris cv. Negro jamapa, which were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by a P. phymatum rpoN Fix− mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix− and Fix+ nodules—combined with a search for RpoN binding sequences in promoter regions of regulated genes—confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also allowed us to identify additional target genes, whose differential expression was able to explain the observed metabolite changes in numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant, and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype, as fewer but heavier nodules were formed on P. vulgaris roots. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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16 pages, 6591 KiB  
Article
Comparative Plastid Genomes of Primula Species: Sequence Divergence and Phylogenetic Relationships
by Ting Ren, Yanci Yang, Tao Zhou and Zhan-Lin Liu
Int. J. Mol. Sci. 2018, 19(4), 1050; https://doi.org/10.3390/ijms19041050 - 1 Apr 2018
Cited by 46 | Viewed by 5580
Abstract
Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. Primula is the largest genus in the family Primulaceae, with members distributed mainly throughout temperate and arctic areas of the Northern Hemisphere. The phylogenetic relationships among [...] Read more.
Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. Primula is the largest genus in the family Primulaceae, with members distributed mainly throughout temperate and arctic areas of the Northern Hemisphere. The phylogenetic relationships among Primula taxa still maintain unresolved, mainly due to intra- and interspecific morphological variation, which was caused by frequent hybridization and introgression. In this study, we sequenced and assembled four complete plastid genomes (Primula handeliana, Primula woodwardii, Primula knuthiana, and Androsace laxa) by Illumina paired-end sequencing. A total of 10 Primula species (including 7 published plastid genomes) were analyzed to investigate the plastid genome sequence divergence and their inferences for the phylogeny of Primula. The 10 Primula plastid genomes were similar in terms of their gene content and order, GC content, and codon usage, but slightly different in the number of the repeat. Moderate sequence divergence was observed among Primula plastid genomes. Phylogenetic analysis strongly supported that Primula was monophyletic and more closely related to Androsace in the Primulaceae family. The phylogenetic relationships among the 10 Primula species showed that the placement of P. knuthiana–P. veris clade was uncertain in the phylogenetic tree. This study indicated that plastid genome data were highly effective to investigate the phylogeny. Full article
(This article belongs to the Special Issue Chloroplast)
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18 pages, 7072 KiB  
Article
Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds
by Chunli Mao, Yanqiao Zhu, Hang Cheng, Huifang Yan, Liyuan Zhao, Jia Tang, Xiqing Ma and Peisheng Mao
Int. J. Mol. Sci. 2018, 19(4), 1052; https://doi.org/10.3390/ijms19041052 - 2 Apr 2018
Cited by 46 | Viewed by 5186
Abstract
Mitochondria are the source of reactive oxygen species (ROS) in plant cells and play a central role in the mitochondrial electron transport chain (ETC) and tricarboxylic acid cycle (TCA) cycles; however, ROS production and regulation for seed germination, seedling growth, as well as [...] Read more.
Mitochondria are the source of reactive oxygen species (ROS) in plant cells and play a central role in the mitochondrial electron transport chain (ETC) and tricarboxylic acid cycle (TCA) cycles; however, ROS production and regulation for seed germination, seedling growth, as well as mitochondrial responses to abiotic stress, are not clear. This study was conducted to obtain basic information on seed germination, embryo mitochondrial antioxidant responses, and protein profile changes in artificial aging in oat seeds (Avena sativa L.) exposed to exogenous nitric oxide (NO) treatment. The results showed that the accumulation of H2O2 in mitochondria increased significantly in aged seeds. Artificial aging can lead to a loss of seed vigor, which was shown by a decline in seed germination and the extension of mean germination time (MGT). Seedling growth was also inhibited. Some enzymes, including catalase (CAT), glutathione reductase (GR), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR), maintained a lower level in the ascorbate-glutathione (AsA-GSH) scavenging system. Proteomic analysis revealed that the expression of some proteins related to the TCA cycle were down-regulated and several enzymes related to mitochondrial ETC were up-regulated. With the application of 0.05 mM NO in aged oat seeds, a protective effect was observed, demonstrated by an improvement in seed vigor and increased H2O2 scavenging ability in mitochondria. There were also higher activities of CAT, GR, MDHAR, and DHAR in the AsA-GSH scavenging system, enhanced TCA cycle-related enzymes (malate dehydrogenase, succinate-CoA ligase, fumarate hydratase), and activated alternative pathways, as the cytochrome pathway was inhibited. Therefore, our results indicated that seedling growth and seed germinability could retain a certain level in aged oat seeds, predominantly depending on the lower NO regulation of the TCA cycle and AsA-GSH. Thus, it could be concluded that the application of 0.05 mM NO in aged oat seeds improved seed vigor by enhancing the mitochondrial TCA cycle and activating alternative pathways for improvement. Full article
(This article belongs to the Special Issue Plant Mitochondria)
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12 pages, 30162 KiB  
Article
20(S)-Protopanaxadiol-Induced Apoptosis in MCF-7 Breast Cancer Cell Line through the Inhibition of PI3K/AKT/mTOR Signaling Pathway
by Hong Zhang, Hua-Li Xu, Yu-Chen Wang, Ze-Yuan Lu, Xiao-Feng Yu and Da-Yun Sui
Int. J. Mol. Sci. 2018, 19(4), 1053; https://doi.org/10.3390/ijms19041053 - 2 Apr 2018
Cited by 36 | Viewed by 5289
Abstract
20(S)-Protopanaxadiol (PPD) is one of the major active metabolites of ginseng. It has been reported that 20(S)-PPD shows a broad spectrum of antitumor effects. Our research study aims were to investigate whether apoptosis of human breast cancer MCF-7 cells could be induced by [...] Read more.
20(S)-Protopanaxadiol (PPD) is one of the major active metabolites of ginseng. It has been reported that 20(S)-PPD shows a broad spectrum of antitumor effects. Our research study aims were to investigate whether apoptosis of human breast cancer MCF-7 cells could be induced by 20(S)-PPD by targeting the Phosphatidylinositol 3-kinase/Protein kinase B/Mammalian target of rapamycin (PI3K/AKT/mTOR) signal pathway in vitro and in vivo. Cell cycle analysis was performed by Propidium Iodide (PI) staining. To overexpress and knock down the expression of mTOR, pcDNA3.1-mTOR and mTOR small interfering RNA (siRNA) transient transfection assays were used, respectively. Cell viability and apoptosis were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)-test and Annexin V /PI double-staining after transfection. The antitumor effect in vivo was determined by the nude mice xenograft assay. After 24 h of incubation, treatment with 20(S)-PPD could upregulate phosphorylated-Phosphatase and tensin homologue deleted on chromosome 10 (p-PTEN) expression and downregulate PI3K/AKT/mTOR-pathway protein expression. Moreover, G0/G1 cell cycle arrest in MCF-7 cells could be induced by 20(S)-PPD treatment at high concentrations. Furthermore, overexpression or knockdown of mTOR could inhibit or promote the apoptotic effects of 20(S)-PPD. In addition, tumor volumes were partially reduced by 20(S)-PPD at 100 mg/kg in a MCF-7 xenograft model. Immunohistochemical staining indicated a close relationship between the inhibition of tumor growth and the PI3K/AKT/mTOR signal pathway. PI3K/AKT/mTOR pathway-mediated apoptosis may be one of the potential mechanisms of 20(S)-PPD treatment. Full article
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20 pages, 9660 KiB  
Article
Targeted Metabolomic and Transcriptomic Analyses of “Red Russian” Kale (Brassicae napus var. pabularia) Following Methyl Jasmonate Treatment and Larval Infestation by the Cabbage Looper (Trichoplusia ni Hübner)
by Yu-Chun Chiu, John A. Juvik and Kang-Mo Ku
Int. J. Mol. Sci. 2018, 19(4), 1058; https://doi.org/10.3390/ijms19041058 - 2 Apr 2018
Cited by 14 | Viewed by 4645
Abstract
Methyl jasmonate (MeJA), synthesized in the jasmonic acid (JA) pathway, has been found to upregulate glucosinolate (GS) biosynthesis in plant species of the Brassicaceae family. Exogenous application of MeJA has shown to increase tissue GS concentrations and the formation of myrosinase-mediated GS hydrolysis [...] Read more.
Methyl jasmonate (MeJA), synthesized in the jasmonic acid (JA) pathway, has been found to upregulate glucosinolate (GS) biosynthesis in plant species of the Brassicaceae family. Exogenous application of MeJA has shown to increase tissue GS concentrations and the formation of myrosinase-mediated GS hydrolysis products (GSHPs). In vitro and in vivo assays have demonstrated the potential health-promoting effects of certain GSHPs. MeJA is also known to elicit and induce genes associated with defense mechanisms to insect herbivory in Brassica species. To investigate the relationship between MeJA-induced GS biosynthesis and insect defense, three treatments were applied to “Red Russian” kale (Brassicae napus var. pabularia) seedlings: (1) a 250 µM MeJA leaf spray treatment; (2) leaf infestation with larvae of the cabbage looper (Trichoplusia ni (Hübner)); (3) control treatment (neither larval infestation nor MeJA application). Samples of leaf tissue from the three treatments were then assayed for changes in GS and GSHP concentrations, GS gene biosynthesis expression, and myrosinase activity. Major differences were observed between the three treatments in the levels of GS accumulation and GS gene expression. The insect-damaged samples showed significantly lower aliphatic GS accumulation, while both MeJA and T. ni infestation treatments induced greater accumulation of indolyl GS. The gene expression levels of CYP81F4, MYB34, and MYB122 were significantly upregulated in samples treated with MeJA and insects compared to the control group, which explained the increased indolyl GS concentration. The results suggest that the metabolic changes promoted by MeJA application and the insect herbivory response share common mechanisms of induction. This work provides potentially useful information for kale pest control and nutritional quality. Full article
(This article belongs to the Section Molecular Plant Sciences)
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20 pages, 32860 KiB  
Article
Ixeris dentata Extract Increases Salivary Secretion through the Regulation of Endoplasmic Reticulum Stress in a Diabetes-Induced Xerostomia Rat Model
by Kashi Raj Bhattarai, Hwa-Young Lee, Seung-Hyun Kim, Hyung-Ryong Kim and Han-Jung Chae
Int. J. Mol. Sci. 2018, 19(4), 1059; https://doi.org/10.3390/ijms19041059 - 2 Apr 2018
Cited by 20 | Viewed by 6974
Abstract
This study aimed to investigate the molecular mechanism of diabetes mellitus (DM)-induced dry mouth and an application of natural products from Ixeris dentata (IXD), a recently suggested regulator of amylase secretion in salivary cells. Vehicle-treated or diabetic rats were orally treated with either [...] Read more.
This study aimed to investigate the molecular mechanism of diabetes mellitus (DM)-induced dry mouth and an application of natural products from Ixeris dentata (IXD), a recently suggested regulator of amylase secretion in salivary cells. Vehicle-treated or diabetic rats were orally treated with either water or an IXD extract for 10 days to observe the effect on salivary flow. We found that the IXD extract increased aquaporin 5 (AQP5) and alpha-amylase protein expression in the submandibular gland along with salivary flow rate. Similarly, the IXD extract and its purified compound increased amylase secretion in high glucose-exposed human salivary gland cells. Furthermore, increased endoplasmic reticulum stress response in the submandibular gland of diabetic rats was inhibited by treatment with the IXD extract, suggesting that IXD extract treatment improves the ER environment by increasing the protein folding capacity. Thus, pharmacological treatment with the IXD extract is suggested to relieve DM-induced dry mouth symptoms. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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13 pages, 20456 KiB  
Article
Rhein Induces Cell Death in HepaRG Cells through Cell Cycle Arrest and Apoptotic Pathway
by Longtai You, Xiaoxv Dong, Xingbin Yin, Chunjing Yang, Xin Leng, Wenping Wang and Jian Ni
Int. J. Mol. Sci. 2018, 19(4), 1060; https://doi.org/10.3390/ijms19041060 - 2 Apr 2018
Cited by 30 | Viewed by 4808
Abstract
Rhein, a naturally occurring active anthraquinone found abundantly in various medicinal and nutritional herbs, possesses a wide spectrum of pharmacological effects. Furthermore, previous studies have reported that rhein could induce hepatotoxicity in rats. However, its cytotoxicity and potential molecular mechanisms remain unclear. Therefore, [...] Read more.
Rhein, a naturally occurring active anthraquinone found abundantly in various medicinal and nutritional herbs, possesses a wide spectrum of pharmacological effects. Furthermore, previous studies have reported that rhein could induce hepatotoxicity in rats. However, its cytotoxicity and potential molecular mechanisms remain unclear. Therefore, the present study aimed to investigate the cytotoxicity of rhein on HepaRG cells and the underlying mechanisms of its cytotoxicity. Our results demonstrate, by 3-(4,5-dimethyl thiazol-2-yl-)-2,5-diphenyl tetrazolium bromide (MTT) and Annexin V-fluoresce isothiocyanate (FITC)/propidium iodide (PI) double-staining assays, that rhein significantly inhibited cell viability and induced apoptosis in HepaRG cells. Moreover, rhein treatment resulted in the generation of reactive oxygen species (ROS), loss of mitochondrial membrane potential (MMP), and S phase cell cycle arrest. The results of Western blotting showed that rhein treatment resulted in a significant increase in the protein levels of Fas, p53, p21, Bax, cleaved caspases-3, -8, -9, and poly(ADP-ribose)polymerase (PARP). The protein expression of Bcl-2, cyclin A, and cyclin-dependent kinase 2 (CDK 2) was decreased. In conclusion, these results suggest that rhein treatment could inhibit cell viability of HepaRG cells and induce cell death through cell cycle arrest in the S phase and activation of Fas- and mitochondrial-mediated pathways of apoptosis. These findings emphasize the need to assess the risk of exposure for humans to rhein. Full article
(This article belongs to the Special Issue Frontiers in Drug Toxicity Prediction)
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17 pages, 23846 KiB  
Article
Kv3.1 and Kv3.4, Are Involved in Cancer Cell Migration and Invasion
by Min Seok Song, Su Min Park, Jeong Seok Park, Jin Ho Byun, Hee Jung Jin, Seung Hyun Seo, Pan Dong Ryu and So Yeong Lee
Int. J. Mol. Sci. 2018, 19(4), 1061; https://doi.org/10.3390/ijms19041061 - 2 Apr 2018
Cited by 30 | Viewed by 5654
Abstract
Voltage-gated potassium (Kv) channels, including Kv3.1 and Kv3.4, are known as oxygen sensors, and their function in hypoxia has been well investigated. However, the relationship between Kv channels and tumor hypoxia has yet to be investigated. This study demonstrates that Kv3.1 and Kv3.4 [...] Read more.
Voltage-gated potassium (Kv) channels, including Kv3.1 and Kv3.4, are known as oxygen sensors, and their function in hypoxia has been well investigated. However, the relationship between Kv channels and tumor hypoxia has yet to be investigated. This study demonstrates that Kv3.1 and Kv3.4 are tumor hypoxia-related Kv channels involved in cancer cell migration and invasion. Kv3.1 and Kv3.4 protein expression in A549 and MDA-MB-231 cells increased in a cell density-dependent manner, and the pattern was similar to the expression patterns of hypoxia-inducible factor-1α (HIF-1α) and reactive oxygen species (ROS) according to cell density, whereas Kv3.3 protein expression did not change in A549 cells with an increase in cell density. The Kv3.1 and Kv3.4 blocker blood depressing substance (BDS) did not affect cell proliferation; instead, BDS inhibited cell migration and invasion. We found that BDS inhibited intracellular pH regulation and extracellular signal-regulated kinase (ERK) activation in A549 cells cultured at a high density, potentially resulting in BDS-induced inhibition of cell migration and invasion. Our data suggest that Kv3.1 and Kv3.4 might be new therapeutic targets for cancer metastasis. Full article
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19 pages, 14471 KiB  
Article
CRISPR/Cas9-Mediated Mutagenesis of Carotenoid Cleavage Dioxygenase 8 (CCD8) in Tobacco Affects Shoot and Root Architecture
by Junping Gao, Tong Zhang, Bingxin Xu, Ling Jia, Bingguang Xiao, He Liu, Lijing Liu, Hao Yan and Qingyou Xia
Int. J. Mol. Sci. 2018, 19(4), 1062; https://doi.org/10.3390/ijms19041062 - 2 Apr 2018
Cited by 45 | Viewed by 6883
Abstract
Strigolactones (SLs) are a class of phytohormones that regulate plant architecture. Carotenoid cleavage dioxygenase (CCD) genes are involved in the biosynthesis of SLs and are identified and characterized in many plants. However, the function of CCD genes in tobacco remains poorly [...] Read more.
Strigolactones (SLs) are a class of phytohormones that regulate plant architecture. Carotenoid cleavage dioxygenase (CCD) genes are involved in the biosynthesis of SLs and are identified and characterized in many plants. However, the function of CCD genes in tobacco remains poorly understood. In this study, two closely related genes NtCCD8A and NtCCD8B were cloned from tobacco (Nicotiana tabacum L.). The two NtCCD8 genes are orthologues of the tomato (Solanum lycopersicum) carotenoid cleavage dioxygenase 8 (SlCCD8) gene. NtCCD8A and NtCCD8B were primarily expressed in tobacco roots, but low expression levels of these genes were detected in all plant tissues, and their transcript levels significantly increased in response to phosphate limitation. NtCCD8A and NtCCD8B mutations were introduced into tobacco using the CRISPR/Cas9 system and transgenic tobacco lines for both ntccd8 mutant alleles were identified. The ntccd8a and ntccd8b mutant alleles were inactivated by a deletion of three nucleotides and insertion of one nucleotide, respectively, both of which led to the production of premature stop codons. The ntccd8 mutants had increased shoot branching, reduced plant height, increased number of leaves and nodes, and reduced total plant biomass compared to wild-type plants; however, the root-to-shoot ratio was unchanged. In addition, mutant lines had shorter primary roots and more of lateral roots than wild type. These results suggest that NtCCD8 genes are important for changes in tobacco plant architecture. Full article
(This article belongs to the Special Issue Phytohormones and Their Crosstalk during Plant Growth, Development and Environmental Stress Adaptation)
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13 pages, 2640 KiB  
Article
Expression, Tissue Localization and Serodiagnostic Potential of Echinococcus granulosus Leucine Aminopeptidase
by Maodi Wu, Min Yan, Jing Xu, Yuqing Liang, Xiaobin Gu, Yue Xie, Bo Jing, Weimin Lai, Xuerong Peng and Guangyou Yang
Int. J. Mol. Sci. 2018, 19(4), 1063; https://doi.org/10.3390/ijms19041063 - 3 Apr 2018
Cited by 11 | Viewed by 5058
Abstract
Echinococcus granulosus is the causative agent of cystic echinococcosis (CE), a widespread parasitic zoonosis. Leucine aminopeptidases (LAPs) of the M17 peptidase family have important functions in regulating the balance of catabolism and anabolism, cell maintenance, growth and defense. In this study, we presented [...] Read more.
Echinococcus granulosus is the causative agent of cystic echinococcosis (CE), a widespread parasitic zoonosis. Leucine aminopeptidases (LAPs) of the M17 peptidase family have important functions in regulating the balance of catabolism and anabolism, cell maintenance, growth and defense. In this study, we presented a bioinformatic characterization and experimentally determined the tissue distribution characteristics of E. granulosus LAP (Eg-LAP), and explored its potential value for diagnosis of CE in sheep based on indirect ELISA. Through fluorescence immunohistochemistry, we found that Eg-LAP was present in the tegument and hooks of PSCs, the whole germinal layer and adult worm parenchymatous tissue. Western blotting results revealed that the recombinant protein could be identified using E. granulosus-infected sheep serum. The diagnostic value of this recombinant protein was assessed by indirect ELISA, and compared with indirect ELISA based on hydatid fluid antigen. The sensitivity and specificity rEgLAP-ELISA were 95.8% (23/24) and 79.09% (87/110), respectively, while using hydatid fluid as antigen showed the values 41.7% (10/24) and 65.45% (72/110). This is the first report concerning leucine aminopeptidase from E. granulosus, and the results showed that Eg-LAP belong to M17 peptidase families, and that it is involved in important biological function of E. granulosus. Furthermore, rEg-LAP is appropriate for diagnosing and monitoring CE in sheep in field. Development of a rapid test using rEg-LAP to diagnose sheep CE deserves further study. Full article
(This article belongs to the Section Biochemistry)
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23 pages, 2444 KiB  
Article
In Vitro Influence of Extracts from Snail Helix aspersa Müller on the Colon Cancer Cell Line Caco-2
by Magdalena Matusiewicz, Iwona Kosieradzka, Tomasz Niemiec, Marta Grodzik, Hanna Antushevich, Barbara Strojny and Małgorzata Gołębiewska
Int. J. Mol. Sci. 2018, 19(4), 1064; https://doi.org/10.3390/ijms19041064 - 3 Apr 2018
Cited by 26 | Viewed by 7662
Abstract
Colorectal cancer is the third most widely diagnosed cancer. Extracts from snails may modulate growth and development of colorectal cancer cells. The objective of this study was to determine the chemical composition of tissues derived from Helix aspersa Müller and red-ox properties of [...] Read more.
Colorectal cancer is the third most widely diagnosed cancer. Extracts from snails may modulate growth and development of colorectal cancer cells. The objective of this study was to determine the chemical composition of tissues derived from Helix aspersa Müller and red-ox properties of tissue extracts. Then, the influence of extracts and their fractions of different molecular weights on viability of Caco-2 cells was examined. Tissue lyophilisates contained antioxidants that could be important in the prevention of colorectal cancer. Moreover, we confirmed the presence of a wide array of compounds that might be used in treatment of this disease. The decrease of cell viability after the application of extracts from lyophilized mucus and foot tissues was affirmed. The effect of extract from mucus could be related to the content of some proteins and peptides, proper essential amino acids (EAA)/non-essential amino acids (NEAA) ratio, Met restriction and the presence of Cu, Ca, Zn, Se. The influence of the extract from foot tissues could be assigned additionally to the presence of eicosapentaenoic, α-linolenic, linoleic and γ-linolenic acids. The opposite effect was demonstrated by extract from lyophilized shells which increased cell viability. Further studies are needed to know whether dietary supplying of H. aspersa Müller tissues can be used as an approach in colorectal cancer management. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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24 pages, 9492 KiB  
Article
Non-Metastatic Cutaneous Melanoma Induces Chronodisruption in Central and Peripheral Circadian Clocks
by Leonardo Vinícius Monteiro De Assis, Maria Nathália Moraes, Keila Karoline Magalhães-Marques, Gabriela Sarti Kinker, Sanseray Da Silveira Cruz-Machado and Ana Maria De Lauro Castrucci
Int. J. Mol. Sci. 2018, 19(4), 1065; https://doi.org/10.3390/ijms19041065 - 3 Apr 2018
Cited by 34 | Viewed by 6007
Abstract
The biological clock has received increasing interest due to its key role in regulating body homeostasis in a time-dependent manner. Cancer development and progression has been linked to a disrupted molecular clock; however, in melanoma, the role of the biological clock is largely [...] Read more.
The biological clock has received increasing interest due to its key role in regulating body homeostasis in a time-dependent manner. Cancer development and progression has been linked to a disrupted molecular clock; however, in melanoma, the role of the biological clock is largely unknown. We investigated the effects of the tumor on its micro- (TME) and macro-environments (TMaE) in a non-metastatic melanoma model. C57BL/6J mice were inoculated with murine B16-F10 melanoma cells and 2 weeks later the animals were euthanized every 6 h during 24 h. The presence of a localized tumor significantly impaired the biological clock of tumor-adjacent skin and affected the oscillatory expression of genes involved in light- and thermo-reception, proliferation, melanogenesis, and DNA repair. The expression of tumor molecular clock was significantly reduced compared to healthy skin but still displayed an oscillatory profile. We were able to cluster the affected genes using a human database and distinguish between primary melanoma and healthy skin. The molecular clocks of lungs and liver (common sites of metastasis), and the suprachiasmatic nucleus (SCN) were significantly affected by tumor presence, leading to chronodisruption in each organ. Taken altogether, the presence of non-metastatic melanoma significantly impairs the organism’s biological clocks. We suggest that the clock alterations found in TME and TMaE could impact development, progression, and metastasis of melanoma; thus, making the molecular clock an interesting pharmacological target. Full article
(This article belongs to the Special Issue Animal Models of Melanoma)
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13 pages, 7119 KiB  
Article
Prenatal Metformin Therapy Attenuates Hypertension of Developmental Origin in Male Adult Offspring Exposed to Maternal High-Fructose and Post-Weaning High-Fat Diets
by You-Lin Tain, Kay L. H. Wu, Wei-Chia Lee, Steve Leu and Julie Y. H. Chan
Int. J. Mol. Sci. 2018, 19(4), 1066; https://doi.org/10.3390/ijms19041066 - 3 Apr 2018
Cited by 21 | Viewed by 4448
Abstract
Widespread consumption of a Western diet, comprised of highly refined carbohydrates and fat, may play a role in the epidemic of hypertension. Hypertension can take origin from early life. Metformin is the preferred treatment for type 2 diabetes. We examined whether prenatal metformin [...] Read more.
Widespread consumption of a Western diet, comprised of highly refined carbohydrates and fat, may play a role in the epidemic of hypertension. Hypertension can take origin from early life. Metformin is the preferred treatment for type 2 diabetes. We examined whether prenatal metformin therapy can prevent maternal high-fructose plus post-weaning high-fat diets-induced hypertension of developmental origins via regulation of nutrient sensing signals, uric acid, oxidative stress, and the nitric oxide (NO) pathway. Gestating Sprague–Dawley rats received regular chow (ND) or chow supplemented with 60% fructose diet (HFR) throughout pregnancy and lactation. Male offspring were onto either the ND or high-fat diet (HFA) from weaning to 12 weeks of age. A total of 40 male offspring were assigned to five groups (n = 8/group): ND/ND, HFR/ND, ND/HFA, HFR/HFA, and HFR/HFA+metformin. Metformin (500 mg/kg/day) was administered via gastric gavage for three weeks during the pregnancy period. Combined maternal HFR plus post-weaning HFA induced hypertension in male adult offspring, which prenatal metformin therapy prevented. The protective effects of prenatal metformin therapy on HFR/HFA-induced hypertension, including downregulation of the renin-angiotensin system, decrease in uric acid level, and reduction of oxidative stress. Our results highlighted that the programming effects of metformin administered prenatally might be different from those reported in adults, and that deserves further elucidation. Full article
(This article belongs to the Special Issue Metformin: Mechanism and Application)
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12 pages, 8877 KiB  
Article
Novel (1E,3E,5E)-1,6-bis(Substituted phenyl)hexa-1,3,5-triene Analogs Inhibit Melanogenesis in B16F10 Cells and Zebrafish
by Jisun Oh, Jungeun Kim, Jin Ho Jang, Sangwoo Lee, Chul Min Park, Woo-Keun Kim and Jong-Sang Kim
Int. J. Mol. Sci. 2018, 19(4), 1067; https://doi.org/10.3390/ijms19041067 - 3 Apr 2018
Cited by 10 | Viewed by 4867
Abstract
The present study aimed to evaluate the anti-melanogenic activity of 1,6-diphenyl-1,3,5-hexatriene and its derivatives in B16F10 murine melanoma cells and zebrafish embryos. Twenty five (1E,3E,5E)-1,6-bis(substituted phenyl)hexa-1,3,5-triene analogs were synthesized and their non-cytotoxic effects were predictively [...] Read more.
The present study aimed to evaluate the anti-melanogenic activity of 1,6-diphenyl-1,3,5-hexatriene and its derivatives in B16F10 murine melanoma cells and zebrafish embryos. Twenty five (1E,3E,5E)-1,6-bis(substituted phenyl)hexa-1,3,5-triene analogs were synthesized and their non-cytotoxic effects were predictively analyzed using three-dimensional quantitative structure-activity relationship approach. Inhibitory activities of these synthetic compounds against melanin synthesis were determined by evaluating melanin content and melanogenic regulatory enzyme expression in B16F10 cells. The anti-melanogenic activity was verified by observing body pigmentation in zebrafishes treated with these compounds. Compound #2, #4, and #6 effectively decreased melanogenesis induced by α-melanocyte-stimulating hormone. In particular, compound #2 remarkably lowered the mRNA and protein expression levels of microphthalmia-associated transcription factor (MITF), tyrosinase (TYR), tyrosinase-related protein 1 (TYRP1), and TYRP2 in B16F10 cells and substantially reduced skin pigmentation in the developed larvae of zebrafish. These findings suggest that compound #2 may be used as an anti-melanogenic agent for cosmetic purpose. Full article
(This article belongs to the Special Issue Melanins and Melanogenesis: From Nature to Applications)
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17 pages, 2730 KiB  
Article
Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
by Hui Tian, Bailiang Li, Smith Etareri Evivie, Shuvan Kumar Sarker, Sathi Chowdhury, Jingjing Lu, Xiuyun Ding and Guicheng Huo
Int. J. Mol. Sci. 2018, 19(4), 1068; https://doi.org/10.3390/ijms19041068 - 3 Apr 2018
Cited by 22 | Viewed by 4488
Abstract
The cell-envelope protease PrtS was proved to be efficient in optimal bacterial growth and fast acidification in pure culture, while its positive effect on the performance of mixed-cultures in milk fermentation was not defined. The aim was to analyze effects of the PrtS [...] Read more.
The cell-envelope protease PrtS was proved to be efficient in optimal bacterial growth and fast acidification in pure culture, while its positive effect on the performance of mixed-cultures in milk fermentation was not defined. The aim was to analyze effects of the PrtS on the symbiosis between strains during yoghurt production and cold storage. Two Streptococcus thermophilus strains, KLDS3.1012 and KLDS SM, and two different proteolytic strains of Lactobacillus delbrueckii subsp. Bulgaricus, L7 and L12, were used. Technological properties (viability, acid production, and proteolysis) were determined. Comparative genomics was used to analyze the proteolytic system (cell-envelope protease, transport system, intracellular peptidase) of Streptococcus thermophilus strains. S. thermophilus KLDS SM possesses an intact gene encoding PrtS (A9497_00420), which was not found in the genome of S. thermophilus KLDS3.1012. This gene is the main difference in the proteolytic system between the two genomes. PrtS endowed KLDS SM high levels of viability during fermentation and cold storage. When combined with a weaker lactobacillus strain during fermentation, the acceleration of acid production of mixed-culture by KLDS SM would start at an earlier time. KLDS SM increased the post-acidification of yoghurts during cold storage, but the pH was steadily maintained during 14–28 days. Results suggest that strains of Streptococcus thermophilus with strong proteolytic ability could be used in a wide range of dairy production. The present study provided data for yoghurt starter development from the point of view of proteolysis. Full article
(This article belongs to the Section Biochemistry)
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17 pages, 26585 KiB  
Article
Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes
by Benedetta Izzi, Fabrizia Noro, Katrien Cludts, Kathleen Freson and Marc F. Hoylaerts
Int. J. Mol. Sci. 2018, 19(4), 1069; https://doi.org/10.3390/ijms19041069 - 3 Apr 2018
Cited by 10 | Viewed by 4483
Abstract
Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled [...] Read more.
Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled by DNA methylation at its first CpG island. We identified a PEAR1 cell-specific methylation sensitive region in endothelial cells and megakaryocytes that showed strong chromosomal interactions with ISGL20L2, RRNAD1, MRLP24, HDGF and PRCC, using available promoter capture Hi-C datasets. These genes are involved in ribosome processing, protein synthesis, cell cycle and cell proliferation. We next studied the methylation and expression profile of these five genes in Human Umbilical Vein Endothelial Cells (HUVECs) and megakaryocyte precursors. While cell-specific PEAR1 methylation corresponded to variability in expression for four out of five genes, no methylation change was observed in their promoter regions across cell types. Our data suggest that PEAR1 cell-type specific methylation changes may control long distance interactions with other genes. Further studies are needed to show whether such interaction data might be relevant for the genome-wide association data that showed a role for non-coding PEAR1 variants in the same region and platelet function, platelet count and cardiovascular risk. Full article
(This article belongs to the Special Issue DNA Methylation)
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13 pages, 4281 KiB  
Article
Impact of Mutagens on DNA Replication in Barley Chromosomes
by Jolanta Kwasniewska, Karolina Zubrzycka and Arita Kus
Int. J. Mol. Sci. 2018, 19(4), 1070; https://doi.org/10.3390/ijms19041070 - 3 Apr 2018
Cited by 5 | Viewed by 4390
Abstract
Replication errors that are caused by mutagens are critical for living cells. The aim of the study was to analyze the distribution of a DNA replication pattern on chromosomes of the H. vulgare ‘Start’ variety using pulse 5-ethynyl-2′-deoxyuridine (EdU) labeling, as well as [...] Read more.
Replication errors that are caused by mutagens are critical for living cells. The aim of the study was to analyze the distribution of a DNA replication pattern on chromosomes of the H. vulgare ‘Start’ variety using pulse 5-ethynyl-2′-deoxyuridine (EdU) labeling, as well as its relationship to the DNA damage that is induced by mutagenic treatment with maleic hydrazide (MH) and γ ray. To the best of our knowledge, this is the first example of a study of the effects of mutagens on the DNA replication pattern in chromosomes, as well as the first to use EdU labeling for these purposes. The duration of the cell cycle of the Hordeum vulgare ‘Start’ variety was estimated for the first time, as well as the influence of MH and γ ray on it. The distribution of the signals of DNA replication along the chromosomes revealed relationships between DNA replication, the chromatin structure, and DNA damage. MH has a stronger impact on replication than γ ray. Application of EdU seems to be promising for precise analyses of cell cycle disturbances in the future, especially in plant species with small genomes. Full article
(This article belongs to the Special Issue DNA Replication Stress)
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12 pages, 3835 KiB  
Article
Binding Interactions of Zinc Cationic Porphyrin with Duplex DNA: From B-DNA to Z-DNA
by Tingxiao Qin, Kunhui Liu, Di Song, Chunfan Yang, Hongmei Zhao and Hongmei Su
Int. J. Mol. Sci. 2018, 19(4), 1071; https://doi.org/10.3390/ijms19041071 - 4 Apr 2018
Cited by 10 | Viewed by 5365
Abstract
Recognition of unusual left-handed Z-DNA by specific binding of small molecules is crucial for understanding biological functions in which this particular structure participates. Recent investigations indicate that zinc cationic porphyrin (ZnTMPyP4) is promising as a probe for recognizing Z-DNA due to its characteristic [...] Read more.
Recognition of unusual left-handed Z-DNA by specific binding of small molecules is crucial for understanding biological functions in which this particular structure participates. Recent investigations indicate that zinc cationic porphyrin (ZnTMPyP4) is promising as a probe for recognizing Z-DNA due to its characteristic chiroptical properties upon binding with Z-DNA. However, binding mechanisms of the ZnTMPyP4/Z-DNA complex remain unclear. By employing time-resolved UV-visible absorption spectroscopy in conjunction with induced circular dichroism (ICD), UV-vis, and fluorescence measurements, we examined the binding interactions of ZnTMPyP4 towards B-DNA and Z-DNA. For the ZnTMPyP4/Z-DNA complex, two coexisting binding modes were identified as the electrostatic interaction between pyridyl groups and phosphate backbones, and the major groove binding by zinc(II) coordinating with the exposed guanine N7. The respective contribution of each mode is assessed, allowing a complete scenario of binding modes revealed for the ZnTMPyP4/Z-DNA. These interaction modes are quite different from those (intercalation and partial intercalation modes) for the ZnTMPyP4/B-DNA complex, thereby resulting in explicit differentiation between B-DNA and Z-DNA. Additionally, the binding interactions of planar TMPyP4 to DNA were also investigated as a comparison. It is shown that without available virtual orbitals to coordinate, TMPyP4 binds with Z-DNA solely in the intercalation mode, as with B-DNA, and the intercalation results in a structural transition from Z-DNA to B-ZNA. These results provide mechanistic insights for understanding ZnTMPyP4 as a probe of recognizing Z-DNA and afford a possible strategy for designing new porphyrin derivatives with available virtual orbitals for the discrimination of B-DNA and Z-DNA. Full article
(This article belongs to the Special Issue A Commemorative Issue in Honor of Professor Nick Hadjiliadis: Metal Complex Interactions with Nucleic Acids and/or DNA)
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14 pages, 1293 KiB  
Article
Regulation of Bicarbonate Secretion in Marine Fish Intestine by the Calcium-Sensing Receptor
by Sílvia F. Gregório and Juan Fuentes
Int. J. Mol. Sci. 2018, 19(4), 1072; https://doi.org/10.3390/ijms19041072 - 4 Apr 2018
Cited by 12 | Viewed by 4009
Abstract
In marine fish, high epithelial intestinal HCO3− secretion generates luminal carbonate precipitates of divalent cations that play a key role in water and ion homeostasis. The present study was designed to expose the putative role for calcium and the calcium-sensing receptor [...] Read more.
In marine fish, high epithelial intestinal HCO3− secretion generates luminal carbonate precipitates of divalent cations that play a key role in water and ion homeostasis. The present study was designed to expose the putative role for calcium and the calcium-sensing receptor (CaSR) in the regulation of HCO3− secretion in the intestine of the sea bream (Sparus aurata L.). Effects on the expression of the CaSR in the intestine were evaluated by qPCR and an increase was observed in the anterior intestine in fed fish compared with unfed fish and with different regions of intestine. CaSR expression reflected intestinal fluid calcium concentration. In addition, anterior intestine tissue was mounted in Ussing chambers to test the putative regulation of HCO3− secretion in vitro using the anterior intestine. HCO3− secretion was sensitive to varying calcium levels in luminal saline and to calcimimetic compounds known to activate/block the CaSR i.e., R 568 and NPS-2143. Subsequent experiments were performed in intestinal sacs to measure water absorption and the sensitivity of water absorption to varying luminal levels of calcium and calcimimetics were exposed as well. It appears, that CaSR mediates HCO3− secretion and water absorption in marine fish as shown by responsiveness to calcium levels and calcimimetic compounds. Full article
(This article belongs to the Special Issue Ion Transporters and Channels in Physiology and Pathophysiology)
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15 pages, 2888 KiB  
Article
A Developed NK-92MI Cell Line with Siglec-7neg Phenotype Exhibits High and Sustainable Cytotoxicity against Leukemia Cells
by Chin-Han Huang, Yi-Jen Liao, Ting-Hsi Fan, Tzeon-Jye Chiou, Yen-Hsi Lin and Yuh-Ching Twu
Int. J. Mol. Sci. 2018, 19(4), 1073; https://doi.org/10.3390/ijms19041073 - 4 Apr 2018
Cited by 17 | Viewed by 5662
Abstract
Altered sialic acid processing that leads to upregulation of cell surface sialylation is recognized as a key change in malignant tissue glycosylation. This cancer-associated hypersialylation directly impacts the signaling interactions between tumor cells and their surrounding microenvironment, especially the interactions mediated by immune [...] Read more.
Altered sialic acid processing that leads to upregulation of cell surface sialylation is recognized as a key change in malignant tissue glycosylation. This cancer-associated hypersialylation directly impacts the signaling interactions between tumor cells and their surrounding microenvironment, especially the interactions mediated by immune cell surface sialic acid-binding immunoglobulin-like lectins (Siglecs) to relay inhibitory signals for cytotoxicity. First, we obtained a Siglec-7neg NK-92MI cell line, NK-92MI-S7N, by separating a group of Siglec-7neg cell population from an eight-month-long-term NK-92MI in vitro culture by fluorescence-activated cell sorting (FACS). The effect of Siglec-7 loss on NK-92MI-S7N cells was characterized by the cell morphology, proliferation, and cytotoxic activity via FACS, MTS assay, cytotoxic assay, and natural killer (NK) degranulation assay. We found the expression levels of Siglec-7 in NK-92MI were negatively correlated with NK cytotoxicity against leukemia cells. This NK-92MI-S7N cell not only shared very similar phenotypes with its parental cells but also possessed a high and sustainable killing activity. Furthermore, this Siglec-7neg NK line was unexpectedly capable of eliminating a NK-92MI-resistant leukemia cell, THP-1, through enhancing the effector-target interaction. In this study, a NK cell line with high and sustainable cytotoxicity was established and this cell may provide a potential application in NK-based treatment for leukemia patients. Full article
(This article belongs to the Section Molecular Toxicology)
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15 pages, 31594 KiB  
Article
Macrophage Populations in Visceral Adipose Tissue from Pregnant Women: Potential Role of Obesity in Maternal Inflammation
by Eyerahi Bravo-Flores, Ismael Mancilla-Herrera, Salvador Espino y Sosa, Marco Ortiz-Ramirez, Verónica Flores-Rueda, Francisco Ibargüengoitia-Ochoa, Carlos A. Ibañez, Elena Zambrano, Mario Solis-Paredes, Otilia Perichart-Perera, Maribel Sanchez-Martinez, Diana Medina-Bastidas, Enrique Reyes-Muñoz and Guadalupe Estrada-Gutierrez
Int. J. Mol. Sci. 2018, 19(4), 1074; https://doi.org/10.3390/ijms19041074 - 4 Apr 2018
Cited by 15 | Viewed by 5865
Abstract
Obesity is associated with inflammatory changes and accumulation and phenotype polarization of adipose tissue macrophages (ATMs). Obese pregnant women have alterations in adipose tissue composition, but a detailed description of macrophage population is not available. In this study, we characterized macrophage populations in [...] Read more.
Obesity is associated with inflammatory changes and accumulation and phenotype polarization of adipose tissue macrophages (ATMs). Obese pregnant women have alterations in adipose tissue composition, but a detailed description of macrophage population is not available. In this study, we characterized macrophage populations in visceral adipose tissue (VAT) from pregnant women with normal, overweight, and obese pregestational weight. Immunophenotyping of macrophages from VAT biopsies was performed by flow cytometry using CD45 and CD14 as markers of hematopoietic and monocyte linage, respectively, while HLA-DR, CD11c, CD163, and CD206 were used as pro- and anti-inflammatory markers. Adipocyte number and size were evaluated by light microscopy. The results show that pregnant women that were overweight and obese during the pregestational period had adipocyte hypertrophy. Two different macrophage populations in VAT were identified: recruited macrophages (CD45+CD14+), and a novel population lacking CD45, which was considered to be a resident macrophages subset (CD45−CD14+). The number of resident HLA−DRlow/− macrophages showed a negative correlation with body mass index (BMI). Both resident and recruited macrophages from obese women expressed higher CD206 levels. CD11c expression was higher in resident HLA-DR+ macrophages from obese women. A strong correlation between CD206 and CD11c markers and BMI was observed. Our findings show that being overweight and obese in the pregestational period is associated with adipocyte hypertrophy and specific ATMs populations in VAT. Full article
(This article belongs to the Special Issue Macrophages in Inflammation)
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15 pages, 3905 KiB  
Article
The Combinational Use of CRISPR/Cas9 and Targeted Toxin Technology Enables Efficient Isolation of Bi-Allelic Knockout Non-Human Mammalian Clones
by Satoshi Watanabe, Takayuki Sakurai, Shingo Nakamura, Kazuchika Miyoshi and Masahiro Sato
Int. J. Mol. Sci. 2018, 19(4), 1075; https://doi.org/10.3390/ijms19041075 - 4 Apr 2018
Cited by 9 | Viewed by 5199
Abstract
Recent advances in genome editing systems such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease (CRISPR/Cas9) have facilitated genomic modification in mammalian cells. However, most systems employ transient treatment with selective drugs such as puromycin to obtain the desired genome-edited cells, which [...] Read more.
Recent advances in genome editing systems such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease (CRISPR/Cas9) have facilitated genomic modification in mammalian cells. However, most systems employ transient treatment with selective drugs such as puromycin to obtain the desired genome-edited cells, which often allows some untransfected cells to survive and decreases the efficiency of generating genome-edited cells. Here, we developed a novel targeted toxin-based drug-free selection system for the enrichment of genome-edited cells. Cells were transfected with three expression vectors, each of which carries a guide RNA (gRNA), humanized Cas9 (hCas9) gene, or Clostridium perfringens-derived endo-β-galactosidase C (EndoGalC) gene. Once EndoGalC is expressed in a cell, it digests the cell-surface α-Gal epitope, which is specifically recognized by BS-I-B4 lectin (IB4). Three days after transfection, these cells were treated with cytotoxin saporin-conjugated IB4 (IB4SAP) for 30 min at 37 °C prior to cultivation in a normal medium. Untransfected cells and those weakly expressing EndoGalC will die due to the internalization of saporin. Cells transiently expressing EndoGalC strongly survive, and some of these surviving clones are expected to be genome-edited bi-allelic knockout (KO) clones due to their strong co-expression of gRNA and hCas9. When porcine α-1,3-galactosyltransferase gene, which can synthesize the α-Gal epitope, was attempted to be knocked out, 16.7% and 36.7% of the surviving clones were bi-allelic and mono-allelic knockout (KO) cells, respectively, which was in contrast to the isolation of clones in the absence of IB4SAP treatment. Namely, 0% and 13.3% of the resulting clones were bi-allelic and mono-allelic KO cells, respectively. A similar tendency was seen when other target genes such as DiGeorge syndrome critical region gene 2 and transforming growth factor-β receptor type 1 gene were targeted to be knocked out. Our results indicate that a combination of the CRISPR/Cas9 system and targeted toxin technology using IB4SAP allows efficient enrichment of genome-edited clones, particularly bi-allelic KO clones. Full article
(This article belongs to the Special Issue Genome Editing 2018)
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20 pages, 10767 KiB  
Article
Lectin-Binding Specificity of the Fertilization-Relevant Protein PDC-109 by Means of Surface Plasmon Resonance and Carbohydrate REcognition Domain EXcision-Mass Spectrometry
by Sira Defaus, Manuel Avilés, David Andreu and Ricardo Gutiérrez-Gallego
Int. J. Mol. Sci. 2018, 19(4), 1076; https://doi.org/10.3390/ijms19041076 - 4 Apr 2018
Cited by 6 | Viewed by 3905
Abstract
Seminal plasma proteins are relevant for sperm functionality and some appear responsible for establishing sperm interactions with the various environments along the female genital tract towards the oocyte. In recent years, research has focused on characterizing the role of these proteins in the [...] Read more.
Seminal plasma proteins are relevant for sperm functionality and some appear responsible for establishing sperm interactions with the various environments along the female genital tract towards the oocyte. In recent years, research has focused on characterizing the role of these proteins in the context of reproductive biology, fertility diagnostics and treatment of related problems. Herein, we focus on the main protein of bovine seminal plasma, PDC-109 (BSP-A1/-A2), which by virtue of its lectin properties is involved in fertilization. By means of surface plasmon resonance, the interaction of PDC-109 with a panel of the most relevant glycosidic epitopes of mammals has been qualitatively and quantitatively characterized, and a higher affinity for carbohydrates containing fucose has been observed, in line with previous studies. Additionally, using the orthogonal technique of Carbohydrate REcognition Domain EXcision-Mass Spectrometry (CREDEX-MS), the recognition domain of the interaction complexes between PDC-109 and all fucosylated disaccharides [(Fuc-α1,(3,4,6)-GlcNAc)] has been defined, revealing the specific glycotope and the peptide domain likely to act as the PDC-109 carbohydrate binding site. Full article
(This article belongs to the Special Issue Molecular Recognition of Carbohydrates)
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13 pages, 1962 KiB  
Article
A Comparison of the Effects of FATTY ACID DESATURASE 7 and HYDROPEROXIDE LYASE on Plant–Aphid Interactions
by Jiamei Li, Carlos A. Avila, Denise M. Tieman, Harry J. Klee and Fiona L. Goggin
Int. J. Mol. Sci. 2018, 19(4), 1077; https://doi.org/10.3390/ijms19041077 - 4 Apr 2018
Cited by 6 | Viewed by 4140
Abstract
The spr2 mutation in tomato (Solanum lycopersicum), which disrupts function of FATTY ACID DESATURASE 7 (FAD7), confers resistance to the potato aphid (Macrosiphum euphorbiae) and modifies the plant’s C6 volatile profiles. To investigate whether C6 volatiles play a role [...] Read more.
The spr2 mutation in tomato (Solanum lycopersicum), which disrupts function of FATTY ACID DESATURASE 7 (FAD7), confers resistance to the potato aphid (Macrosiphum euphorbiae) and modifies the plant’s C6 volatile profiles. To investigate whether C6 volatiles play a role in resistance, HYDROPEROXIDE LYASE (HPL), which encodes a critical enzyme in C6 volatile synthesis, was silenced in wild-type tomato plants and spr2 mutants. Silencing HPL in wild-type tomato increased potato aphid host preference and reproduction on 5-week old plants but had no influence on 3-week old plants. The spr2 mutation, in contrast, conferred strong aphid resistance at both 3 and 5 weeks, and silencing HPL in spr2 did not compromise this aphid resistance. Moreover, a mutation in the FAD7 gene in Arabidopsis thaliana also conferred resistance to the green peach aphid (Myzus persicae) in a genetic background that carries a null mutation in HPL. These results indicate that HPL contributes to certain forms of aphid resistance in tomato, but that the effects of FAD7 on aphids in tomato and Arabidopsis are distinct from and independent of HPL. Full article
(This article belongs to the Special Issue Plant Innate Immunity 2.0)
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18 pages, 10098 KiB  
Article
A Systematic Study of RNAi Effects and dsRNA Stability in Tribolium castaneum and Acyrthosiphon pisum, Following Injection and Ingestion of Analogous dsRNAs
by Min Cao, John A. Gatehouse and Elaine C. Fitches
Int. J. Mol. Sci. 2018, 19(4), 1079; https://doi.org/10.3390/ijms19041079 - 4 Apr 2018
Cited by 73 | Viewed by 7432
Abstract
RNA interference (RNAi) effects in insects are highly variable and may be largely dependent upon the stability of introduced double-stranded RNAs to digestion by nucleases. Here, we report a systematic comparison of RNAi effects in susceptible red flour beetle (Tribolium castaneum) [...] Read more.
RNA interference (RNAi) effects in insects are highly variable and may be largely dependent upon the stability of introduced double-stranded RNAs to digestion by nucleases. Here, we report a systematic comparison of RNAi effects in susceptible red flour beetle (Tribolium castaneum) and recalcitrant pea aphid (Acyrthosiphon pisum) following delivery of dsRNAs of identical length targeting expression of V-type ATPase subunit E (VTE) and inhibitor of apoptosis (IAP) genes. Injection and ingestion of VTE and IAP dsRNAs resulted in up to 100% mortality of T. castaneum larvae and sustained suppression (>80%) of transcript levels. In A. pisum, injection of VTE but not IAP dsRNA resulted in up to 65% mortality and transient suppression (ca. 40%) of VTE transcript levels. Feeding aphids on VTE dsRNA reduced growth and fecundity although no evidence for gene suppression was obtained. Rapid degradation of dsRNAs by aphid salivary, haemolymph and gut nucleases contrasted with stability in T. castaneum larvae where it appears that exo-nuclease activity is responsible for relatively slow digestion of dsRNAs. This is the first study to directly compare RNAi effects and dsRNA stability in receptive and refractory insect species and provides further evidence that dsRNA susceptibility to nucleases is a key factor in determining RNAi efficiency. Full article
(This article belongs to the Special Issue Molecular Entomology of Insects of Economic Importance)
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14 pages, 4248 KiB  
Article
Effective Delivery of Arsenic Trioxide to HPV-Positive Cervical Cancer Cells Using Optimised Liposomes: A Size and Charge Study
by Anam Akhtar, Scarlet Xiaoyan Wang, Lucy Ghali, Celia Bell and Xuesong Wen
Int. J. Mol. Sci. 2018, 19(4), 1081; https://doi.org/10.3390/ijms19041081 - 4 Apr 2018
Cited by 23 | Viewed by 4220
Abstract
Despite the success of arsenic trioxide (ATO) in treating haematological malignancies, its potential to treat solid tumours has not been fully exploited, owing to its dose-limiting toxicity and poor pharmacokinetics. In order to overcome this hurdle, liposomal encapsulation of the drug with different [...] Read more.
Despite the success of arsenic trioxide (ATO) in treating haematological malignancies, its potential to treat solid tumours has not been fully exploited, owing to its dose-limiting toxicity and poor pharmacokinetics. In order to overcome this hurdle, liposomal encapsulation of the drug with different surface charges (neutral, negative, and positive) and sizes (100, 200 and 400 nm) were synthesised and tested on human papilloma virus (HPV)-positive HeLa and HPV-negative HT-3 cervical cancer cell lines. Two epithelial cell lines—human keratinocytes (HK) and human colon cells (CRL-1790)—were used as controls. The synthesised liposomes were tested for their physico-chemical characteristics, drug loading efficiency, and toxicity on the studied cell lines. Neutral liposomes of 100 nm in size were the chosen formulation for delivering ATO into the studied cells, as they showed the least intrinsic cytotoxicity and the highest loading efficiency. The findings demonstrated that the optimised formulation of liposomes was an effective drug delivery method for HPV-infected cervical cancer cells. Furthermore, the toxicity vs. uptake ratio was highest for HeLa cells, while a reduced or minimal toxic effect was observed for non-HPV-infected cervical cancer cells and control cells. These findings may provide a promising therapeutic strategy for effectively managing cervical cancers. Full article
(This article belongs to the Special Issue Nanotechnology in Drug Delivery)
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15 pages, 17175 KiB  
Article
Loss of ISWI Function in Drosophila Nuclear Bodies Drives Cytoplasmic Redistribution of Drosophila TDP-43
by Luca Lo Piccolo, Rosa Bonaccorso, Andrea Attardi, Lorenzo Li Greci, Giulia Romano, Martina Sollazzo, Giorgio Giurato, Antonia Maria Rita Ingrassia, Fabian Feiguin, Davide F. V. Corona and Maria Cristina Onorati
Int. J. Mol. Sci. 2018, 19(4), 1082; https://doi.org/10.3390/ijms19041082 - 4 Apr 2018
Cited by 13 | Viewed by 5447
Abstract
Over the past decade, evidence has identified a link between protein aggregation, RNA biology, and a subset of degenerative diseases. An important feature of these disorders is the cytoplasmic or nuclear aggregation of RNA-binding proteins (RBPs). Redistribution of RBPs, such as the human [...] Read more.
Over the past decade, evidence has identified a link between protein aggregation, RNA biology, and a subset of degenerative diseases. An important feature of these disorders is the cytoplasmic or nuclear aggregation of RNA-binding proteins (RBPs). Redistribution of RBPs, such as the human TAR DNA-binding 43 protein (TDP-43) from the nucleus to cytoplasmic inclusions is a pathological feature of several diseases. Indeed, sporadic and familial forms of amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration share as hallmarks ubiquitin-positive inclusions. Recently, the wide spectrum of neurodegenerative diseases characterized by RBPs functions’ alteration and loss was collectively named proteinopathies. Here, we show that TBPH (TAR DNA-binding protein-43 homolog), the Drosophila ortholog of human TDP-43 TAR DNA-binding protein-43, interacts with the arcRNA hsrω and with hsrω-associated hnRNPs. Additionally, we found that the loss of the omega speckles remodeler ISWI (Imitation SWI) changes the TBPH sub-cellular localization to drive a TBPH cytoplasmic accumulation. Our results, hence, identify TBPH as a new component of omega speckles and highlight a role of chromatin remodelers in hnRNPs nuclear compartmentalization. Full article
(This article belongs to the Special Issue Drosophila Model and Human Disease)
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15 pages, 7117 KiB  
Article
Radiation-Induced Gene Expression Changes in High and Low Grade Breast Cancer Cell Types
by Valentina Bravatà, Claudia Cava, Luigi Minafra, Francesco Paolo Cammarata, Giorgio Russo, Maria Carla Gilardi, Isabella Castiglioni and Giusi Irma Forte
Int. J. Mol. Sci. 2018, 19(4), 1084; https://doi.org/10.3390/ijms19041084 - 4 Apr 2018
Cited by 27 | Viewed by 5135
Abstract
Background: There is extensive scientific evidence that radiation therapy (RT) is a crucial treatment, either alone or in combination with other treatment modalities, for many types of cancer, including breast cancer (BC). BC is a heterogeneous disease at both clinical and molecular levels, [...] Read more.
Background: There is extensive scientific evidence that radiation therapy (RT) is a crucial treatment, either alone or in combination with other treatment modalities, for many types of cancer, including breast cancer (BC). BC is a heterogeneous disease at both clinical and molecular levels, presenting distinct subtypes linked to the hormone receptor (HR) status and associated with different clinical outcomes. The aim of this study was to assess the molecular changes induced by high doses of ionizing radiation (IR) on immortalized and primary BC cell lines grouped according to Human epidermal growth factor receptor (HER2), estrogen, and progesterone receptors, to study how HR status influences the radiation response. Our genomic approach using in vitro and ex-vivo models (e.g., primary cells) is a necessary first step for a translational study to describe the common driven radio-resistance features associated with HR status. This information will eventually allow clinicians to prescribe more personalized total doses or associated targeted therapies for specific tumor subtypes, thus enhancing cancer radio-sensitivity. Methods: Nontumorigenic (MCF10A) and BC (MCF7 and MDA-MB-231) immortalized cell lines, as well as healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures, were divided into low grade, high grade, and healthy groups according to their HR status. At 24 h post-treatment, the gene expression profiles induced by two doses of IR treatment with 9 and 23 Gy were analyzed by cDNA microarray technology to select and compare the differential gene and pathway expressions among the experimental groups. Results: We present a descriptive report of the substantial alterations in gene expression levels and pathways after IR treatment in both immortalized and primary cell cultures. Overall, the IR-induced gene expression profiles and pathways appear to be cell-line dependent. The data suggest that some specific gene and pathway signatures seem to be linked to HR status. Conclusions: Genomic biomarkers and gene-signatures of specific tumor subtypes, selected according to their HR status and molecular features, could facilitate personalized biological-driven RT treatment planning alone and in combination with targeted therapies. Full article
(This article belongs to the Special Issue Advances and Challenges in Biomolecular Radiation Research)
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15 pages, 10091 KiB  
Article
Taurine Administration Recovers Motor and Learning Deficits in an Angelman Syndrome Mouse Model
by Sara Guzzetti, Luciano Calzari, Lucia Buccarello, Valentina Cesari, Ivan Toschi, Stefania Cattaldo, Alessandro Mauro, Francesca Pregnolato, Silvia Michela Mazzola and Silvia Russo
Int. J. Mol. Sci. 2018, 19(4), 1088; https://doi.org/10.3390/ijms19041088 - 5 Apr 2018
Cited by 15 | Viewed by 8460
Abstract
Angelman syndrome (AS, MIM 105830) is a rare neurodevelopmental disorder affecting 1:10–20,000 children. Patients show moderate to severe intellectual disability, ataxia and absence of speech. Studies on both post-mortem AS human brains and mouse models revealed dysfunctions in the extra synaptic gamma-aminobutyric acid [...] Read more.
Angelman syndrome (AS, MIM 105830) is a rare neurodevelopmental disorder affecting 1:10–20,000 children. Patients show moderate to severe intellectual disability, ataxia and absence of speech. Studies on both post-mortem AS human brains and mouse models revealed dysfunctions in the extra synaptic gamma-aminobutyric acid (GABA) receptors implicated in the pathogenesis. Taurine is a free intracellular sulfur-containing amino acid, abundant in brain, considered an inhibiting neurotransmitter with neuroprotective properties. As taurine acts as an agonist of GABA-A receptors, we aimed at investigating whether it might ameliorate AS symptoms. Since mice weaning, we orally administered 1 g/kg/day taurine in water to Ube3a-deficient mice. To test the improvement of motor and cognitive skills, Rotarod, Novel Object Recognition and Open Field tests were assayed at 7, 14, 21 and 30 weeks, while biochemical tests and amino acid dosages were carried out, respectively, by Western-blot and high-performance liquid chromatography (HPLC) on frozen whole brains. Treatment of Ube3am−/p+ mice with taurine significantly improved motor and learning skills and restored the levels of the post-synaptic PSD-95 and pERK1/2-ERK1/2 ratio to wild type values. No side effects of taurine were observed. Our study indicates taurine administration as a potential therapy to ameliorate motor deficits and learning difficulties in AS. Full article
(This article belongs to the Special Issue Rare Diseases: Molecular Mechanisms and Therapeutic Strategies)
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13 pages, 7727 KiB  
Article
The Flavonoid Isoquercitrin Precludes Initiation of Zika Virus Infection in Human Cells
by Arnaud Gaudry, Sandra Bos, Wildriss Viranaicken, Marjolaine Roche, Pascale Krejbich-Trotot, Gilles Gadea, Philippe Desprès and Chaker El-Kalamouni
Int. J. Mol. Sci. 2018, 19(4), 1093; https://doi.org/10.3390/ijms19041093 - 5 Apr 2018
Cited by 66 | Viewed by 6397
Abstract
The medical importance of Zika virus (ZIKV) was fully highlighted during the recent epidemics in South Pacific islands and Americas due to ZIKV association with severe damage to fetal brain development and neurological complications in adult patients. A worldwide research effort has been [...] Read more.
The medical importance of Zika virus (ZIKV) was fully highlighted during the recent epidemics in South Pacific islands and Americas due to ZIKV association with severe damage to fetal brain development and neurological complications in adult patients. A worldwide research effort has been undertaken to identify effective compounds to prevent or treat ZIKV infection. Fruits and vegetables may be sources of compounds with medicinal properties. Flavonoids are one class of plant compounds that emerge as promising antiviral molecules against ZIKV. In the present study, we demonstrated that flavonoid isoquercitrin exerts antiviral activity against African historical and Asian epidemic strains of ZIKV in human hepatoma, epithelial, and neuroblastoma cell lines. Time-of-drug addition assays showed that isoquercitrin acts on ZIKV entry by preventing the internalisation of virus particles into the host cell. Our data also suggest that the glycosylated moiety of isoquercitrin might play a role in the antiviral effect of the flavonoid against ZIKV. Our results highlight the importance of isoquercitrin as a promising natural antiviral compound to prevent ZIKV infection. Full article
(This article belongs to the Special Issue Bioactive Phenolics and Polyphenols 2018)
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13 pages, 9715 KiB  
Article
Remote Ischemic Preconditioning Does Not Affect the Release of Humoral Factors in Propofol-Anesthetized Cardiac Surgery Patients: A Secondary Analysis of the RIPHeart Study
by Julia Ney, Katleen Hoffmann, Patrick Meybohm, Andreas Goetzenich, Sandra Kraemer, Carina Benstöm, Nina C. Weber, Johannes Bickenbach, Rolf Rossaint, Gernot Marx, Kai Zacharowski, Jürgen Bernhagen and Christian Stoppe
Int. J. Mol. Sci. 2018, 19(4), 1094; https://doi.org/10.3390/ijms19041094 - 5 Apr 2018
Cited by 19 | Viewed by 5175
Abstract
In contrast to several smaller studies, which demonstrate that remote ischemic preconditioning (RIPC) reduces myocardial injury in patients that undergo cardiovascular surgery, the RIPHeart study failed to demonstrate beneficial effects of troponin release and clinical outcome in propofol-anesthetized cardiac surgery patients. Therefore, we [...] Read more.
In contrast to several smaller studies, which demonstrate that remote ischemic preconditioning (RIPC) reduces myocardial injury in patients that undergo cardiovascular surgery, the RIPHeart study failed to demonstrate beneficial effects of troponin release and clinical outcome in propofol-anesthetized cardiac surgery patients. Therefore, we addressed the potential biochemical mechanisms triggered by RIPC. This is a predefined prospective sub-analysis of the randomized and controlled RIPHeart study in cardiac surgery patients (n = 40) that was recently published. Blood samples were drawn from patients prior to surgery, after RIPC of four cycles of 5 min arm ischemia/5 min reperfusion (n = 19) and the sham (n = 21) procedure, after connection to cardiopulmonary bypass (CPB), at the end of surgery, 24 h postoperatively, and 48 h postoperatively for the measurement of troponin T, macrophage migration inhibitory factor (MIF), stromal cell-derived factor 1 (CXCL12), IL-6, CXCL8, and IL-10. After RIPC, right atrial tissue samples were taken for the measurement of extracellular-signal regulated kinase (ERK1/2), protein kinase B (AKT), Glycogen synthase kinase 3 (GSK-3β), protein kinase C (PKCε), and MIF content. RIPC did not significantly reduce the troponin release when compared with the sham procedure. MIF serum levels intraoperatively increased, peaking at intensive care unit (ICU) admission (with an increase of 48.04%, p = 0.164 in RIPC; and 69.64%, p = 0.023 over the baseline in the sham procedure), and decreased back to the baseline 24 h after surgery, with no differences between the groups. In the right atrial tissue, MIF content decreased after RIPC (1.040 ± 1.032 Arbitrary units [au] in RIPC vs. 2.028 ± 1.631 [au] in the sham procedure, p < 0.05). CXCL12 serum levels increased significantly over the baseline at the end of surgery, with no differences between the groups. ERK1/2, AKT, GSK-3β, and PKCɛ phosphorylation in the right atrial samples were no different between the groups. No difference was found in IL-6, CXCL8, and IL10 serum levels between the groups. In this cohort of cardiac surgery patients that received propofol anesthesia, we could not show a release of potential mediators of signaling, nor an effect on the inflammatory response, nor an activation of well-established protein kinases after RIPC. Based on these data, we cannot exclude that confounding factors, such as propofol, may have interfered with RIPC. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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20 pages, 15526 KiB  
Article
Global Transcriptome Analysis of Brown Adipose Tissue of Diet-Induced Obese Mice
by Jingyi Cao, Qi Zhu, Lin Liu, Bradley J. Glazier, Benjamin C. Hinkel, Chun Liang and Haifei Shi
Int. J. Mol. Sci. 2018, 19(4), 1095; https://doi.org/10.3390/ijms19041095 - 6 Apr 2018
Cited by 18 | Viewed by 7262
Abstract
Consumption of a high-fat diet (HFD) promotes the development of obesity, a disease resulting from an imbalance between energy intake and energy expenditure. Brown adipose tissue (BAT) has thermogenic capacity that burns calories to produce heat, and it is a potential target for [...] Read more.
Consumption of a high-fat diet (HFD) promotes the development of obesity, a disease resulting from an imbalance between energy intake and energy expenditure. Brown adipose tissue (BAT) has thermogenic capacity that burns calories to produce heat, and it is a potential target for the treatment and prevention of obesity. There is limited information regarding the impact of HFD on the BAT transcriptome. We hypothesized that HFD-induced obesity would lead to transcriptional regulation of BAT genes. RNA sequencing was used to generate global transcriptome profiles from BAT of lean mice fed with a low-fat diet (LFD) and obese mice fed with a HFD. Gene Ontology (GO) analysis identified increased expression of genes involved in biological processes (BP) related to immune responses, which enhanced molecular function (MF) in chemokine activity; decreased expression of genes involved in BP related to ion transport and muscle structure development, which reduced MF in channel and transporter activity and structural binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathway analysis indicated that pathways associated with innate immunity were enhanced by HFD, while pathways associated with muscle contraction and calcium signaling were suppressed by HFD. Collectively, these results suggest that diet-induced obesity changes transcriptomic signatures of BAT, leading to dysfunction involving inflammation, calcium signaling, ion transport, and cell structural development. Full article
(This article belongs to the Special Issue Nutrition, Brown and White Adipose Tissue)
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10 pages, 11655 KiB  
Article
Molecular Characterization of Gastric Epithelial Cells Using Flow Cytometry
by Kevin A. Bockerstett, Chun Fung Wong, Sherri Koehm, Eric L. Ford and Richard J. DiPaolo
Int. J. Mol. Sci. 2018, 19(4), 1096; https://doi.org/10.3390/ijms19041096 - 6 Apr 2018
Cited by 7 | Viewed by 5857
Abstract
The ability to analyze individual epithelial cells in the gastric mucosa would provide important insight into gastric disease, including chronic gastritis and progression to gastric cancer. However, the successful isolation of viable gastric epithelial cells (parietal cells, neck cells, chief cells, and foveolar [...] Read more.
The ability to analyze individual epithelial cells in the gastric mucosa would provide important insight into gastric disease, including chronic gastritis and progression to gastric cancer. However, the successful isolation of viable gastric epithelial cells (parietal cells, neck cells, chief cells, and foveolar cells) from gastric glands has been limited due to difficulties in tissue processing. Furthermore, analysis and interpretation of gastric epithelial cell flow cytometry data has been difficult due to the varying sizes and light scatter properties of the different epithelial cells, high levels of autofluorescence, and poor cell viability. These studies were designed to develop a reliable method for isolating viable single cells from the corpus of stomachs and to optimize analyses examining epithelial cells from healthy and diseased stomach tissue by flow cytometry. We performed a two stage enzymatic digestion in which collagenase released individual gastric glands from the stromal tissue of the corpus, followed by a Dispase II digestion that dispersed these glands into greater than 1 × 106 viable single cells per gastric corpus. Single cell suspensions were comprised of all major cell lineages found in the normal gastric glands. A method describing light scatter, size exclusion, doublet discrimination, viability staining, and fluorescently-conjugated antibodies and lectins was used to analyze individual epithelial cells and immune cells. This technique was capable of identifying parietal cells and revealed that gastric epithelial cells in the chronically inflamed mucosa significantly upregulated major histocompatibility complexes (MHC) I and II but not CD80 or CD86, which are costimulatory molecules involved in T cell activation. These studies describe a method for isolating viable single cells and a detailed description of flow cytometric analysis of cells from healthy and diseased stomachs. These studies begin to identify effects of chronic inflammation on individual gastric epithelial cells, a critical consideration for the study of gastric cancer. Full article
(This article belongs to the Special Issue Molecular Features Distinguishing Gastric Cancer Subtypes)
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12 pages, 2138 KiB  
Article
MicroRNAs as Potential Mediators for Cigarette Smoking Induced Atherosclerosis
by Yuka Yokoyama, Nathan Mise, Yuka Suzuki, Saeko Tada-Oikawa, Kiyora Izuoka, Lingyi Zhang, Cai Zong, Akira Takai, Yoshiji Yamada and Sahoko Ichihara
Int. J. Mol. Sci. 2018, 19(4), 1097; https://doi.org/10.3390/ijms19041097 - 6 Apr 2018
Cited by 24 | Viewed by 5058
Abstract
Smoking increases the risk of atherosclerosis-related events, such as myocardial infarction and ischemic stroke. Recent studies have examined the expression levels of altered microRNAs (miRNAs) in various diseases. The profiles of tissue miRNAs can be potentially used in diagnosis or prognosis. However, there [...] Read more.
Smoking increases the risk of atherosclerosis-related events, such as myocardial infarction and ischemic stroke. Recent studies have examined the expression levels of altered microRNAs (miRNAs) in various diseases. The profiles of tissue miRNAs can be potentially used in diagnosis or prognosis. However, there are limited studies on miRNAs following exposure to cigarette smoke (CS). The present study was designed to dissect the effects and cellular/molecular mechanisms of CS-induced atherosclerogenesis. Apolipoprotein E knockout (ApoE KO) mice were exposed to CS for five days a week for two months at low (two puffs/min for 40 min/day) or high dose (two puffs/min for 120 min/day). We measured the area of atherosclerotic plaques in the aorta, representing the expression of miRNAs after the exposure period. Two-month exposure to the high dose of CS significantly increased the plaque area in aortic arch, and significantly upregulated the expression of atherosclerotic markers (VCAM-1, ICAM-1, MCP1, p22phox, and gp91phox). Exposure to the high dose of CS also significantly upregulated the miRNA-155 level in the aortic tissues of ApoE KO mice. Moreover, the expression level of miR-126 tended to be downregulated and that of miR-21 tended to be upregulated in ApoE KO mice exposed to the high dose of CS, albeit statistically insignificant. The results suggest that CS induces atherosclerosis through increased vascular inflammation and NADPH oxidase expression and also emphasize the importance of miRNAs in the pathogenesis of CS-induced atherosclerosis. Our findings provide evidence for miRNAs as potential mediators of inflammation and atherosclerosis induced by CS. Full article
(This article belongs to the Special Issue The Role of MicroRNAs in Human Diseases)
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12 pages, 8225 KiB  
Article
Hedgehog Signals Mediate Anti-Cancer Drug Resistance in Three-Dimensional Primary Colorectal Cancer Organoid Culture
by Tatsuya Usui, Masashi Sakurai, Koji Umata, Mohamed Elbadawy, Takashi Ohama, Hideyuki Yamawaki, Shoichi Hazama, Hiroko Takenouchi, Masao Nakajima, Ryouichi Tsunedomi, Nobuaki Suzuki, Hiroaki Nagano, Koichi Sato, Masahiro Kaneda and Kazuaki Sasaki
Int. J. Mol. Sci. 2018, 19(4), 1098; https://doi.org/10.3390/ijms19041098 - 6 Apr 2018
Cited by 74 | Viewed by 9091
Abstract
Colorectal cancer is one of the most common causes of cancer death worldwide. In patients with metastatic colorectal cancer, combination treatment with several anti-cancer drugs is employed and improves overall survival in some patients. Nevertheless, most patients with metastatic disease are not cured [...] Read more.
Colorectal cancer is one of the most common causes of cancer death worldwide. In patients with metastatic colorectal cancer, combination treatment with several anti-cancer drugs is employed and improves overall survival in some patients. Nevertheless, most patients with metastatic disease are not cured owing to the drug resistance. Cancer stem cells are known to regulate resistance to chemotherapy. In the previous study, we established a novel three-dimensional organoid culture model from tumor colorectal tissues of human patients using an air–liquid interface (ALI) method, which contained numerous cancer stem cells and showed resistance to 5-fluorouracil (5-FU) and Irinotecan. Here, we investigate which inhibitor for stem cell-related signal improves the sensitivity for anti-cancer drug treatment in tumor ALI organoids. Treatment with Hedgehog signal inhibitors (AY9944, GANT61) decreases the cell viability of organoids compared with Notch (YO-01027, DAPT) and Wnt (WAV939, Wnt-C59) signal inhibitors. Combination treatment of AY9944 or GANT61 with 5-FU, Irinotecan or Oxaliplatin decreases the cell viability of tumor organoids compared with each anti-cancer drug alone treatment. Treatment with AY9944 or GANT61 inhibits expression of stem cell markers c-Myc, CD44 and Nanog, likely through the decrease of their transcription factor, GLI-1 expression. Combination treatment of AY9944 or GANT61 with 5-FU or Irinotecan also prevents colony formation of colorectal cancer cell lines HCT116 and SW480. These findings suggest that Hedgehog signals mediate anti-cancer drug resistance in colorectal tumor patient-derived ALI organoids and that the inhibitors are useful as a combinational therapeutic strategy against colorectal cancer. Full article
(This article belongs to the Special Issue Tumor Microenvironment)
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18 pages, 47336 KiB  
Article
Oligodendroglioma Cells Lack Glutamine Synthetase and Are Auxotrophic for Glutamine, but Do not Depend on Glutamine Anaplerosis for Growth
by Martina Chiu, Giuseppe Taurino, Massimiliano G. Bianchi, Laura Ottaviani, Roberta Andreoli, Tecla Ciociola, Costanza A. M. Lagrasta, Saverio Tardito and Ovidio Bussolati
Int. J. Mol. Sci. 2018, 19(4), 1099; https://doi.org/10.3390/ijms19041099 - 6 Apr 2018
Cited by 20 | Viewed by 4956
Abstract
In cells derived from several types of cancer, a transcriptional program drives high consumption of glutamine (Gln), which is used for anaplerosis, leading to a metabolic addiction for the amino acid. Low or absent expression of Glutamine Synthetase (GS), the only enzyme that [...] Read more.
In cells derived from several types of cancer, a transcriptional program drives high consumption of glutamine (Gln), which is used for anaplerosis, leading to a metabolic addiction for the amino acid. Low or absent expression of Glutamine Synthetase (GS), the only enzyme that catalyzes de novo Gln synthesis, has been considered a marker of Gln-addicted cancers. In this study, two human cell lines derived from brain tumors with oligodendroglioma features, HOG and Hs683, have been shown to be GS-negative. Viability of both lines depends from extracellular Gln with EC50 of 0.175 ± 0.056 mM (Hs683) and 0.086 ± 0.043 mM (HOG), thus suggesting that small amounts of extracellular Gln are sufficient for OD cell growth. Gln starvation does not significantly affect the cell content of anaplerotic substrates, which, consistently, are not able to rescue cell growth, but causes hindrance of the Wnt/β-catenin pathway and protein synthesis attenuation, which is mitigated by transient GS expression. Gln transport inhibitors cause partial depletion of intracellular Gln and cell growth inhibition, but do not lower cell viability. Therefore, GS-negative human oligodendroglioma cells are Gln-auxotrophic but do not use the amino acid for anaplerosis and, hence, are not Gln addicted, exhibiting only limited Gln requirements for survival and growth. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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14 pages, 3373 KiB  
Article
Neuroprotective Effects of Platonin, a Therapeutic Immunomodulating Medicine, on Traumatic Brain Injury in Mice after Controlled Cortical Impact
by Ting-Lin Yen, Chao-Chien Chang, Chi-Li Chung, Wen-Chin Ko, Chih-Hao Yang and Cheng-Ying Hsieh
Int. J. Mol. Sci. 2018, 19(4), 1100; https://doi.org/10.3390/ijms19041100 - 6 Apr 2018
Cited by 15 | Viewed by 4912
Abstract
Traumatic brain injury (TBI) is one of the leading causes of mortality worldwide and leads to persistent cognitive, sensory, motor dysfunction, and emotional disorders. TBI-caused primary injury results in structural damage to brain tissues. Following the primary injury, secondary injuries which are accompanied [...] Read more.
Traumatic brain injury (TBI) is one of the leading causes of mortality worldwide and leads to persistent cognitive, sensory, motor dysfunction, and emotional disorders. TBI-caused primary injury results in structural damage to brain tissues. Following the primary injury, secondary injuries which are accompanied by neuroinflammation, microglial activation, and additional cell death subsequently occur. Platonin, a cyanine photosensitizing dye, has been used to treat trauma, ulcers, and some types of acute inflammation. In the present study, the neuroprotective effects of platonin against TBI were explored in a controlled cortical impact (CCI) injury model in mice. Treatment with platonin (200 µg/kg) significantly reduced the neurological severity score, general locomotor activity, and anxiety-related behavior, and improved the rotarod performance of CCI-injured mice. In addition, platonin reduced lesion volumes, the expression of cleaved caspase-3, and microglial activation in TBI-insulted brains. Platonin also suppressed messenger (m)RNA levels of caspase-3, caspase-1, cyclooxygenase-2, tumor necrosis factor-α, interleukin-6, and interleukin-1β. On the other hand, free radical production after TBI was obviously attenuated in platonin-treated mice. Treatment with platonin exhibited prominent neuroprotective properties against TBI in a CCI mouse model through its anti-inflammatory, anti-apoptotic, and anti-free radical capabilities. This evidence collectively indicates that platonin may be a potential therapeutic medicine for use with TBIs. Full article
(This article belongs to the Special Issue Molecular Pharmacology and Pathology of Strokes)
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18 pages, 14276 KiB  
Article
Novel Nanoparticulate and Ionic Titanium Antigens for Hypersensitivity Testing
by Paul Johan Høl, Einar K. Kristoffersen, Nils Roar Gjerdet and Amanda S. Pellowe
Int. J. Mol. Sci. 2018, 19(4), 1101; https://doi.org/10.3390/ijms19041101 - 6 Apr 2018
Cited by 10 | Viewed by 4717
Abstract
Titanium is used in a wide variety of materials ranging from medical devices to materials used in everyday life. Adverse biological reactions that could occur in patients, consumers, and workers should be monitored and prevented. There is a lack of available agents to [...] Read more.
Titanium is used in a wide variety of materials ranging from medical devices to materials used in everyday life. Adverse biological reactions that could occur in patients, consumers, and workers should be monitored and prevented. There is a lack of available agents to test and predict titanium-related hypersensitivity. The aim of this study was to develop two bioavailable titanium substances in ionic and nanoparticulate form to serve as antigens for hypersensitivity testing in vitro. Peripheral blood mononuclear cells from 20 test subjects were stimulated with the antigens and secretion of monocytic and lymphatic cytokines and chemokines were measured by a multiplex bead assay. Lymphocyte stimulation indices were also determined in a subset of test subjects by measuring CD69 and HLA-DR expression by flow cytometry. Cytokine profiling revealed that both antigens increased production of typical monocyte and macrophage secreted cytokines after 24 h, with significant increases in IL-1β, IL-7, IL-10, IL-12, IL-2R, IL-6, GM-CSF, TNF-α, IL-1RA, MIP-1α, MIP-1β, IFN-α, and IL-15. Lymphatic cytokines and chemokines were not significantly induced by activation. After seven days of stimulation, ionic-Ti (2.5 μg/mL) caused proliferation (stimulation index > 2) of CD4+ cells and CD8+ cells in all persons tested (N = 6), while titanium dioxide nanoparticles (50 μg/mL) only caused significant proliferation of CD4+ cells. Our preliminary results show that the experimental titanium antigens, especially the ionic form, induce a general inflammatory response in vitro. A relevant cohort of test subjects is required to further elucidate their potential for predictive hypersensitivity testing. Full article
(This article belongs to the Special Issue Nanotoxicology and Nanosafety)
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17 pages, 13858 KiB  
Article
Rothmund-Thomson Syndrome: Insights from New Patients on the Genetic Variability Underpinning Clinical Presentation and Cancer Outcome
by Elisa A. Colombo, Andrea Locatelli, Laura Cubells Sánchez, Sara Romeo, Nursel H. Elcioglu, Isabelle Maystadt, Altea Esteve Martínez, Alessandra Sironi, Laura Fontana, Palma Finelli, Cristina Gervasini, Vanna Pecile and Lidia Larizza
Int. J. Mol. Sci. 2018, 19(4), 1103; https://doi.org/10.3390/ijms19041103 - 6 Apr 2018
Cited by 19 | Viewed by 6183
Abstract
Biallelic mutations in RECQL4 gene, a caretaker of the genome, cause Rothmund-Thomson type-II syndrome (RTS-II) and confer increased cancer risk if they damage the helicase domain. We describe five families exemplifying clinical and allelic heterogeneity of RTS-II, and report the effect of pathogenic [...] Read more.
Biallelic mutations in RECQL4 gene, a caretaker of the genome, cause Rothmund-Thomson type-II syndrome (RTS-II) and confer increased cancer risk if they damage the helicase domain. We describe five families exemplifying clinical and allelic heterogeneity of RTS-II, and report the effect of pathogenic RECQL4 variants by in silico predictions and transcripts analyses. Complete phenotype of patients #39 and #42 whose affected siblings developed osteosarcoma correlates with their c.[1048_1049del], c.[1878+32_1878+55del] and c.[1568G>C;1573delT], c.[3021_3022del] variants which damage the helicase domain. Literature survey highlights enrichment of these variants affecting the helicase domain in patients with cancer outcome raising the issue of strict oncological surveillance. Conversely, patients #29 and #19 have a mild phenotype and carry, respectively, the unreported homozygous c.3265G>T and c.3054A>G variants, both sparing the helicase domain. Finally, despite matching several criteria for RTS clinical diagnosis, patient #38 is heterozygous for c.2412_2414del; no pathogenic CNVs out of those evidenced by high-resolution CGH-array, emerged as contributors to her phenotype. Full article
(This article belongs to the Special Issue Rare Diseases: Molecular Mechanisms and Therapeutic Strategies)
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20 pages, 8641 KiB  
Article
The Recombinant Inhibitor of DNA Binding Id2 Forms Multimeric Structures via the Helix-Loop-Helix Domain and the Nuclear Export Signal
by Cornelia Roschger, Mario Schubert, Christof Regl, Ancuela Andosch, Augusto Marquez, Thomas Berger, Christian G. Huber, Ursula Lütz-Meindl and Chiara Cabrele
Int. J. Mol. Sci. 2018, 19(4), 1105; https://doi.org/10.3390/ijms19041105 - 7 Apr 2018
Cited by 2 | Viewed by 4510
Abstract
The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic [...] Read more.
The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic or recombinant fragments reproducing single domains (N-terminus, HLH, C-terminus): the HLH domain tends to dimerize into a four-helix bundle, whereas the flanking regions are flexible. In this work, the intact protein was expressed in E. coli, solubilized from inclusion bodies with urea, purified and dissolved in water at pH~4. Under these conditions, Id2 was obtained with both cysteine residues disulfide-bonded to β-mercaptoethanol that was present during the solubilization process. Moreover, it existed in a self-assembled state, in which the N-terminus remained highly flexible, while the HLH domain and, surprisingly, part of the C-terminus, which corresponds to the nuclear export signal (NES), both were involved in slowly tumbling, rigid structures. The protein oligomers also formed twisted fibrils that were several micrometers long and up to 80 nm thick. These results show that self-assembly decreases the backbone flexibility of those two protein regions (HLH and NES) that are important for interaction with basic-HLH transcription factors or for nucleocytoplasmic shuttling. Full article
(This article belongs to the Section Molecular Biophysics)
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17 pages, 31926 KiB  
Article
A Single Dose of Atorvastatin Applied Acutely after Spinal Cord Injury Suppresses Inflammation, Apoptosis, and Promotes Axon Outgrowth, Which Might Be Essential for Favorable Functional Outcome
by Katarina Bimbova, Maria Bacova, Alexandra Kisucka, Jaroslav Pavel, Jan Galik, Peter Zavacky, Martin Marsala, Andrea Stropkovska, Jana Fedorova, Stefania Papcunova, Jana Jachova and Nadezda Lukacova
Int. J. Mol. Sci. 2018, 19(4), 1106; https://doi.org/10.3390/ijms19041106 - 7 Apr 2018
Cited by 22 | Viewed by 4205
Abstract
The aim of our study was to limit the inflammatory response after a spinal cord injury (SCI) using Atorvastatin (ATR), a potent inhibitor of cholesterol biosynthesis. Adult Wistar rats were divided into five experimental groups: one control group, two Th9 compression (40 g/15 [...] Read more.
The aim of our study was to limit the inflammatory response after a spinal cord injury (SCI) using Atorvastatin (ATR), a potent inhibitor of cholesterol biosynthesis. Adult Wistar rats were divided into five experimental groups: one control group, two Th9 compression (40 g/15 min) groups, and two Th9 compression + ATR (5 mg/kg, i.p.) groups. The animals survived one day and six weeks. ATR applied in a single dose immediately post-SCI strongly reduced IL-1β release at 4 and 24 h and considerably reduced the activation of resident cells at one day post-injury. Acute ATR treatment effectively prevented the excessive infiltration of destructive M1 macrophages cranially, at the lesion site, and caudally (by 66%, 62%, and 52%, respectively) one day post-injury, whereas the infiltration of beneficial M2 macrophages was less affected (by 27%, 41%, and 16%). In addition, at the same time point, ATR visibly decreased caspase-3 cleavage in neurons, astrocytes, and oligodendrocytes. Six weeks post-SCI, ATR increased the expression of neurofilaments in the dorsolateral columns and Gap43-positive fibers in the lateral columns around the epicenter, and from day 30 to 42, significantly improved the motor activity of the hindlimbs. We suggest that early modulation of the inflammatory response via effects on the M1/M2 macrophages and the inhibition of caspase-3 expression could be crucial for the functional outcome. Full article
(This article belongs to the Special Issue Therapeutic Strategies to Spinal Cord Injury)
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17 pages, 18756 KiB  
Article
Photodynamic Effect of Methylene Blue and Low Level Laser Radiation in Head and Neck Squamous Cell Carcinoma Cell Lines
by Barbara Kofler, Angela Romani, Christian Pritz, Teresa Bernadette Steinbichler, Volker Hans Schartinger, Herbert Riechelmann and Jozsef Dudas
Int. J. Mol. Sci. 2018, 19(4), 1107; https://doi.org/10.3390/ijms19041107 - 7 Apr 2018
Cited by 56 | Viewed by 7283
Abstract
Photodynamic therapy (PDT) is suggested to have an impact on the treatment of early stage head and neck cancers (HNSCC). We investigated the effect of PDT with methylene blue (MB) and a diode laser (660 nm) as the laser source on HNSCC cell [...] Read more.
Photodynamic therapy (PDT) is suggested to have an impact on the treatment of early stage head and neck cancers (HNSCC). We investigated the effect of PDT with methylene blue (MB) and a diode laser (660 nm) as the laser source on HNSCC cell lines as an in vitro model of surface oral squamous cell carcinoma. Cell-cultures were exposed to 160 µM MB for 4 min and to laser light for 8 min. Viability was proven via cell viability assay and clonogenic survival via clone counting assay. The combination of MB and diode laser evidenced high efficient loss of cell viability by 5% of the control, while treatment with the same concentration of MB for 4 min alone showed a viability of 46% of the control. In both SCC-25 and Detroit 562 HNSCC cells, MB combined with the laser allowed a significant abrogation of clonogenic growth (p < 0.01), especially in the case of Detroit 562 cells less than 1% of the suspension plated cells were able to grow tumor cell nests. Multiresistant (Detroit 562) HNSCC cells expressing cancer stem cell markers are sensitive to MB/red laser combined PDT. Full article
(This article belongs to the Special Issue Oral Cancer—Diagnosis and Therapeutics)
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14 pages, 14760 KiB  
Article
Sesamol Inhibited Melanogenesis by Regulating Melanin-Related Signal Transduction in B16F10 Cells
by Po-Yuan Wu, Ya-Jhen You, Yi-Jung Liu, Chien-Wei Hou, Chin-Sheng Wu, Kuo-Ching Wen, Chien-Yih Lin and Hsiu-Mei Chiang
Int. J. Mol. Sci. 2018, 19(4), 1108; https://doi.org/10.3390/ijms19041108 - 7 Apr 2018
Cited by 45 | Viewed by 9451
Abstract
Melanin is synthesized through a series of interactions catalyzed by melanogenic enzymes such as tyrosinase, dopachrome tautomerase (tyrosinase-related protein-2; TRP-2), and tyrosinase-related protein-1 (TRP-1). Tyrosinase plays a key role in catalysing the initial and limiting steps of melanogenesis. The melanin that results from [...] Read more.
Melanin is synthesized through a series of interactions catalyzed by melanogenic enzymes such as tyrosinase, dopachrome tautomerase (tyrosinase-related protein-2; TRP-2), and tyrosinase-related protein-1 (TRP-1). Tyrosinase plays a key role in catalysing the initial and limiting steps of melanogenesis. The melanin that results from melanogenesis has the protective effect of absorbing ultraviolet radiation. However, overproduction of melanin, in addition to altering the appearance of skin, may lead to skin disorders such as melasma, solar lentigo, and postinflammatory hyperpigmentation. Previous studies have revealed that sesamol is a strong antioxidant and a free radical scavenger. In this study, we investigated the effects of sesamol on the regulation of melanogenesis and related mechanisms in B16F10 cells. The results indicated that sesamol inhibited tyrosinase activity and melanogenesis induced by α-melanocyte-stimulating hormone (α-MSH) in B16F10 melanoma cells. Sesamol decreased the protein level of melanocortin 1 receptor (MC1R), microphthalmia-associated transcription factor (MITF), tyrosinase, and TRP-1 by downregulating cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathways that had been activated by α-MSH. Sesamol increased glycogen synthase kinase 3 beta (GSK3β), protein kinase B (AKT), and extracellular signal-related kinase (ERK) phosphorylation, thus inhibiting the transcription of MITF. Sesamol also inhibited melanin synthesis and tyrosinase expression by modulating ERK, phosphoinositide 3-kinase (PI3K)/AKT, p38, and c-Jun amino-terminal kinase (JNK) signalling pathways. These results indicate that sesamol acted as a potent depigmenting agent. Full article
(This article belongs to the Special Issue Melanins and Melanogenesis: From Nature to Applications)
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12 pages, 1203 KiB  
Article
d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere
by Claudia Hener, Sabine Hummel, Juan Suarez, Mark Stahl and Üner Kolukisaoglu
Int. J. Mol. Sci. 2018, 19(4), 1109; https://doi.org/10.3390/ijms19041109 - 7 Apr 2018
Cited by 12 | Viewed by 5082
Abstract
Proteinogenic l-amino acids (l-AAs) are essential in all kingdoms as building blocks of proteins. Their d-enantiomers are also known to fulfill important functions in microbes, fungi, and animals, but information about these molecules in plants is still sparse. Previously, [...] Read more.
Proteinogenic l-amino acids (l-AAs) are essential in all kingdoms as building blocks of proteins. Their d-enantiomers are also known to fulfill important functions in microbes, fungi, and animals, but information about these molecules in plants is still sparse. Previously, it was shown that d-amino acids (d-AAs) are taken up and utilized by plants, but their ways to reduce excessive amounts of them still remained unclear. Analyses of plant d-AA content after d-Ala and d-Glu feeding opened the question if exudation of d-AAs into the rhizosphere takes place and plays a role in the reduction of d-AA content in plants. The exudation of d-Ala and d-Glu could be confirmed by amino acid analyses of growth media from plants treated with these d-AAs. Further tests revealed that other d-AAs were also secreted. Nevertheless, treatments with d-Ala and d-Glu showed that plants are still able to reduce their contents within the plant without exudation. Further exudation experiments with transport inhibitors revealed that d-AA root exudation is rather passive and comparable to the secretion of l-AAs. Altogether, these observations argued against a dominant role of exudation in the regulation of plant d-AA content, but may influence the composition of the rhizosphere. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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14 pages, 7419 KiB  
Article
Global and Complement Gene-Specific DNA Methylation in Grass Carp after Grass Carp Reovirus (GCRV) Infection
by Lv Xiong, Libo He, Lifei Luo, Yongming Li, Lanjie Liao, Rong Huang, Zuoyan Zhu and Yaping Wang
Int. J. Mol. Sci. 2018, 19(4), 1110; https://doi.org/10.3390/ijms19041110 - 7 Apr 2018
Cited by 13 | Viewed by 4026
Abstract
Grass carp reovirus (GCRV) causes huge economic loss to the grass carp cultivation industry but the mechanism remains largely unknown. In this study, we investigated the global and complement gene-specific DNA methylation in grass carp after GCRV infection aimed to uncover the mechanism [...] Read more.
Grass carp reovirus (GCRV) causes huge economic loss to the grass carp cultivation industry but the mechanism remains largely unknown. In this study, we investigated the global and complement gene-specific DNA methylation in grass carp after GCRV infection aimed to uncover the mechanism underlying GCRV infection. The global DNA methylation level was increased after GCRV infection. Expression levels of enzymes involved in DNA methylation including DNA methyltransferase (DNMT), ten-eleven translocation proteins (TETs), and glycine N-methyltransferase (GNMT) were significantly altered after GCRV infection. In order to investigate the relationship between the gene expression level and DNA methylation level, two representative complement genes, complement component 3 (C3) and kininogen-1 (KNG1), were selected for further analysis. mRNA expression levels of the two genes were significantly increased at 5 and 7 days after GCRV infection, whereas the DNA methylation level at the 5′ flanking regions of the two genes were down-regulated at the same time-points. Moreover, a negative correlation was detected between gene expression levels and DNA methylation levels of the two genes. Therefore, the current data revealed a global and complement gene-specific DNA methylation profile after GCRV infection. Our study would provide new insights into understanding the mechanism underlying GCRV infection. Full article
(This article belongs to the Section Biochemistry)
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17 pages, 32507 KiB  
Article
Transcriptome Profile in Unilateral Adrenalectomy-Induced Compensatory Adrenal Growth in the Rat
by Karol Jopek, Marianna Tyczewska, Piotr Celichowski, Ludwik K. Malendowicz and Marcin Rucinski
Int. J. Mol. Sci. 2018, 19(4), 1111; https://doi.org/10.3390/ijms19041111 - 7 Apr 2018
Cited by 13 | Viewed by 4268
Abstract
Compensatory adrenal growth evoked by unilateral adrenalectomy (hemiadrenalectomy) constitutes one of the most frequently studied in vivo models of adrenocortical enlargement. This type of growth has been quite well characterized for its morphological, biochemical, and morphometric parameters. However, the molecular basis of compensatory [...] Read more.
Compensatory adrenal growth evoked by unilateral adrenalectomy (hemiadrenalectomy) constitutes one of the most frequently studied in vivo models of adrenocortical enlargement. This type of growth has been quite well characterized for its morphological, biochemical, and morphometric parameters. However, the molecular basis of compensatory adrenal growth is poorly understood. Therefore, the aim of this study was to investigate the rat adrenal transcriptome profile during the time of two previously described adrenocortical proliferation waves at 24 and 72 h after unilateral adrenalectomy. Surgical removal of the left adrenal or a sham operation was accomplished via the classic dorsal approach. As expected, the weight of the remaining right adrenal glands collected at 24 and 72 h after hemiadrenalectomy increased significantly. The transcriptome profile was identified by means of Affymetrix® Rat Gene 2.1 ST Array. The general profiles of differentially expressed genes were visualized as volcano plots and heatmaps. Detailed analyzes consisted of identifying significantly enriched gene ontological groups relevant to adrenal physiology, by means of DAVID and GOplot bioinformatics tools. The results of our studies showed that compensatory adrenal growth induced by unilateral adrenalectomy exerts a limited influence on the global transcriptome profile of the rat adrenal gland; nevertheless, it leads to significant changes in the expression of key genes regulating the circadian rhythm. Our results confirm also that regulation of compensatory adrenal growth is under complex and multifactorial control with a pivotal role of neural regulatory mechanisms and a supportive role of other components. Full article
(This article belongs to the Section Biochemistry)
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17 pages, 4577 KiB  
Article
Dandelion Root Extract Induces Intracellular Ca2+ Increases in HEK293 Cells
by Andrea Gerbino, Daniela Russo, Matilde Colella, Giuseppe Procino, Maria Svelto, Luigi Milella and Monica Carmosino
Int. J. Mol. Sci. 2018, 19(4), 1112; https://doi.org/10.3390/ijms19041112 - 7 Apr 2018
Cited by 15 | Viewed by 7222
Abstract
Dandelion (Taraxacum officinale Weber ex F.H.Wigg.) has been used for centuries as an ethnomedical remedy. Nonetheless, the extensive use of different kinds of dandelion extracts and preparations is based on empirical findings. Some of the tissue-specific effects reported for diverse dandelion extracts may [...] Read more.
Dandelion (Taraxacum officinale Weber ex F.H.Wigg.) has been used for centuries as an ethnomedical remedy. Nonetheless, the extensive use of different kinds of dandelion extracts and preparations is based on empirical findings. Some of the tissue-specific effects reported for diverse dandelion extracts may result from their action on intracellular signaling cascades. Therefore, the aim of this study was to evaluate the effects of an ethanolic dandelion root extract (DRE) on Ca2+ signaling in human embryonic kidney (HEK) 293 cells. The cytotoxicity of increasing doses of crude DRE was determined by the Calcein viability assay. Fura-2 and the fluorescence resonance energy transfer (FRET)-based probe ERD1 were used to measure cytoplasmic and intraluminal endoplasmic reticulum (ER) Ca2+ levels, respectively. Furthermore, a green fluorescent protein (GFP)-based probe was used to monitor phospholipase C (PLC) activation (pleckstrin homology [PH]–PLCδ–GFP). DRE (10–400 µg/mL) exposure, in the presence of external Ca2+, dose-dependently increased intracellular Ca2+ levels. The DRE-induced Ca2+ increase was significantly reduced in the absence of extracellular Ca2+. In addition, DRE caused a significant Ca2+ release from the ER of intact cells and a concomitant translocation of PH–PLCδ–GFP. In conclusion, DRE directly activates both the release of Ca2+ from internal stores and a significant Ca2+ influx at the plasma membrane. The resulting high Ca2+ levels within the cell seem to directly stimulate PLC activity. Full article
(This article belongs to the Special Issue Calcium Signaling in Human Health and Diseases)
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15 pages, 12579 KiB  
Article
Differential Expression and Clinical Significance of Transforming Growth Factor-Beta Isoforms in GBM Tumors
by Laurent-Olivier Roy, Marie-Belle Poirier and David Fortin
Int. J. Mol. Sci. 2018, 19(4), 1113; https://doi.org/10.3390/ijms19041113 - 8 Apr 2018
Cited by 36 | Viewed by 4380
Abstract
Glioblastoma (GBM) represents the most common and aggressive malignant primary brain tumors in adults. Response to standard treatment is transitory and the survival of clinical trial cohorts are little more than 14 months. GBM are characterized by excessive proliferation, invasiveness, and radio-/chemoresistance features; [...] Read more.
Glioblastoma (GBM) represents the most common and aggressive malignant primary brain tumors in adults. Response to standard treatment is transitory and the survival of clinical trial cohorts are little more than 14 months. GBM are characterized by excessive proliferation, invasiveness, and radio-/chemoresistance features; which are strongly upregulated by transforming growth factor-beta (TGF-β). We hypothesized that TGF-β gene expression could correlate with overall survival (OS) and serve as a prognostic biomarker. TGF-β1 and -β2 expression were analyzed by qPCR in 159 GBM tumor specimens. Kaplan–Meier and multivariate analyses were used to correlate expression with OS and progression-free survival (PFS). In GBM, TGF-β1 and -β2 levels were 33- and 11-fold higher respectively than in non-tumoral samples. Kaplan–Meier and multivariate analyses revealed that high to moderate expressions of TGF-β1 significantly conferred a strikingly poorer OS and PFS in newly diagnosed patients. Interestingly, at relapse, neither isoforms had meaningful impact on clinical evolution. We demonstrate that TGF-β1 is the dominant isoform in newly diagnosed GBM rather than the previously acknowledged TGF-β2. We believe our study is the first to unveil a significant relationship between TGF-β1 expression and OS or PFS in newly diagnosed GBM. TGF-β1 could serve as a prognostic biomarker or target affecting treatment planning and patient follow-up. Full article
(This article belongs to the Section Biochemistry)
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12 pages, 30819 KiB  
Article
BMP9 Promotes the Proliferation and Migration of Bladder Cancer Cells through Up-Regulating lncRNA UCA1
by Liyao Gou, Mengyao Liu, Jing Xia, Qun Wan, Yayun Jiang, Shilei Sun, Min Tang, Lan Zhou, Tongchuan He and Yan Zhang
Int. J. Mol. Sci. 2018, 19(4), 1116; https://doi.org/10.3390/ijms19041116 - 8 Apr 2018
Cited by 33 | Viewed by 3753
Abstract
As the most common malignant tumor of the urinary system worldwide, the bladder tumor has a high mortality rate, which is mainly due to its onset of concealment. Therefore, research into novel diagnostic markers and treatment of bladder cancer is urgently needed. BMP9 [...] Read more.
As the most common malignant tumor of the urinary system worldwide, the bladder tumor has a high mortality rate, which is mainly due to its onset of concealment. Therefore, research into novel diagnostic markers and treatment of bladder cancer is urgently needed. BMP9 (Bone morphogenetic protein 9) is a member of BMP, which belongs to the TGF-β (transforming growth factor-β) superfamily. It has been associated with multiple tumors. We found that BMP9 is highly expressed in bladder cancer cells and it could significantly promote the proliferation and migration of bladder cancer cells. In the study of the mechanism of this effect, we found that BMP9 can increase the expression of lncRNA UCA1 (Urothelial cancer associated 1) through phosphorylated AKT. The promoting effect of BMP9 on bladder cancer cells was rescued after interfering with UCA1 in BMP9 overexpressed bladder cancer cells both in vitro and in vivo. Our research confirms that BMP9 promotes the proliferation and migration of bladder cancer cells through up-regulated lncRNA UCA1. It also shows that BMP9 is a novel diagnostic marker and a potential therapeutic target in bladder cancer. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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9 pages, 5100 KiB  
Communication
Beneficial Effects of Bioactive Compounds in Mulberry Fruits against Cisplatin-Induced Nephrotoxicity
by Dahae Lee, Jae Sik Yu, Seoung Rak Lee, Gwi Seo Hwang, Ki Sung Kang, Jae Gyu Park, Hyun Young Kim, Ki Hyun Kim and Noriko Yamabe
Int. J. Mol. Sci. 2018, 19(4), 1117; https://doi.org/10.3390/ijms19041117 - 9 Apr 2018
Cited by 27 | Viewed by 7663
Abstract
Mulberry, the fruit of white mulberry tree (Morus alba L., Moraceae), is commonly used in traditional Chinese medicines as a sedative, tonic, laxative, and emetic. In our continuing research of the bioactive metabolites from mulberry, chemical analysis of the fruits led to [...] Read more.
Mulberry, the fruit of white mulberry tree (Morus alba L., Moraceae), is commonly used in traditional Chinese medicines as a sedative, tonic, laxative, and emetic. In our continuing research of the bioactive metabolites from mulberry, chemical analysis of the fruits led to the isolation of five compounds, 1–5. The compounds were identified as butyl pyroglutamate (1), quercetin 3-O-β-d-glucoside (2), kaempferol 3-O-β-d-rutinoside (3), rutin (4), and 2-phenylethyl d-rutinoside (5) by spectroscopic data analysis, comparing their nuclear magnetic resonance (NMR) data with those in published literature, and liquid chromatography–mass spectrometry analysis. The isolated compounds 1–5 were evaluated for their effects on anticancer drug-induced side effects by cell-based assays. Compound 1 exerted the highest protective effect against cisplatin-induced kidney cell damage. This effect was found to be mediated through the attenuation of phosphorylation of c-Jun N-terminal kinase, extracellular signal-regulated kinase, p38, mitogen-activated protein kinase, and caspase-3 in cisplatin-induced kidney cell damage. Full article
(This article belongs to the Section Molecular Toxicology)
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13 pages, 4851 KiB  
Article
Melatonin Protects against Lung Fibrosis by Regulating the Hippo/YAP Pathway
by Xiaoguang Zhao, Jian Sun, Wei Su, Huitong Shan, Bowen Zhang, Yining Wang, Azaliia Shabanova, Hongli Shan and Haihai Liang
Int. J. Mol. Sci. 2018, 19(4), 1118; https://doi.org/10.3390/ijms19041118 - 9 Apr 2018
Cited by 51 | Viewed by 9989
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, fibrotic interstitial pneumonia with high mortality. Melatonin, a hormone predominantly secreted by the pineal gland, has been reported to participate in the process of IPF. However, the mechanisms underlying the effect of melatonin in pulmonary fibrosis [...] Read more.
Idiopathic pulmonary fibrosis (IPF) is a progressive, fibrotic interstitial pneumonia with high mortality. Melatonin, a hormone predominantly secreted by the pineal gland, has been reported to participate in the process of IPF. However, the mechanisms underlying the effect of melatonin in pulmonary fibrosis have not been elucidated to date. This study was designed to evaluate the anti-fibrotic role of melatonin in pulmonary fibrosis and to elucidate the potential mechanisms. We observed that melatonin markedly attenuated bleomycin (BLM)-induced experimental lung fibrosis in mice and inhibited TGF-β1-induced fibrogenesis in lung fibroblasts. Additionally, we determined that luzindole, a melatonin receptor inhibitor, reduced the anti-fibrotic effect of melatonin. Further studies showed that melatonin alleviated the translocation of YAP1 from cytoplasm to nucleus, a key downstream effector of the Hippo pathway, in vivo and in vitro by interacting with its receptor. Taken together, our results suggest that melatonin prevents lung fibrosis by inhibiting YAP1 and indicate that melatonin replacement could be a novel strategy for the treatment of lung fibrosis. Full article
(This article belongs to the Special Issue TGF-Beta Super Family Signaling)
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13 pages, 5820 KiB  
Article
Cytochrome P450 CYP6EV11 in Chironomus kiiensis Larvae Involved in Phenol Stress
by Qihui Zhang, Dong Chu, Lili Sun and Chuanwang Cao
Int. J. Mol. Sci. 2018, 19(4), 1119; https://doi.org/10.3390/ijms19041119 - 9 Apr 2018
Cited by 5 | Viewed by 3356
Abstract
Phenol is one of the organic pollutants which can cause water environment pollution. It is not only enriched in aquatic organisms but is also a serious threat to human health. Chironomus kiiensis is very sensitive to the contaminants in water and its cytochrome [...] Read more.
Phenol is one of the organic pollutants which can cause water environment pollution. It is not only enriched in aquatic organisms but is also a serious threat to human health. Chironomus kiiensis is very sensitive to the contaminants in water and its cytochrome P450s are usually chosen as biomarkers for water pollution. To examine whether CYP6EV11 plays a role in the oxidative metabolism of phenol, we measured the silencing efficiency of CYP6EV11 and evaluated larval susceptibility to sublethal phenol levels by RNA interference (RNAi) technology. The results showed that the transcription of CYP6EV11 was found significantly up-regulated when the 4th instar C. kiiensis larvae were exposed to three doses of phenol. However, the transcriptional levels of CYP6EV11 were significantly suppressed by 92.7% in the 4th instar C. kiiensis larvae soaked in dsCYP6EV11 compared with those soaked in dsGFP for 6 h. The CYP6EV11 expression and mortality of the 4th instar C. kiiensis larvae with CYP6EV11 silencing were mostly decreased under phenol stress. Therefore, the CYP6EV11 gene may be used as a molecular biomarker for earlier warning and monitoring for water pollution. Full article
(This article belongs to the Special Issue Cytochromes P450: Drug Metabolism and Bioactivation)
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17 pages, 2563 KiB  
Article
Ursodeoxycholate Restores Biliary Excretion of Methotrexate in Rats with Ethinyl Estradiol Induced-Cholestasis by Restoring Canalicular Mrp2 Expression
by Min Ju Kim, Yun Ju Kang, Mihwa Kwon, Young A. Choi, Min-Koo Choi, Hye-Young Chi, Hye Hyun Yoo, Chang-Koo Shim and Im-Sook Song
Int. J. Mol. Sci. 2018, 19(4), 1120; https://doi.org/10.3390/ijms19041120 - 9 Apr 2018
Cited by 12 | Viewed by 4169
Abstract
The in vivo relevance of ursodeoxycholate (UDCA) treatment (100 mg/kg/day, per oral tid for 5 days before cholestasis induction followed by the same dosing for 5 days) on hepatic function was investigated in rats with 17α-ethinylestradiol (EE, 10 mg/kg, subcutaneous for 5 days)-induced [...] Read more.
The in vivo relevance of ursodeoxycholate (UDCA) treatment (100 mg/kg/day, per oral tid for 5 days before cholestasis induction followed by the same dosing for 5 days) on hepatic function was investigated in rats with 17α-ethinylestradiol (EE, 10 mg/kg, subcutaneous for 5 days)-induced experimental cholestasis. The bile flow rate and the expression level of hepatic multidrug resistance-associated protein 2 (Mrp 2) that were decreased in cholestasis were restored after UDCA treatment. Consistent with this, the biliary excretion clearance (CLexc,bile) of a representative Mrp2 substrate—methotrexate (MTX)—was decreased in cholestatic rats but was restored after UDCA treatment. Consequently, the plasma concentrations of MTX, which were increased by cholestasis, were decreased to control levels by UDCA treatment. Thus, the restoration of CLexc,bile appears to be associated with the increase in Mrp2 expression on the canalicular membrane by UDCA treatment followed by Mrp2-mediated biliary excretion of MTX. On the other hand, the hepatic uptake clearance (CLup,liver) of MTX was unchanged by cholestasis or UDCA treatment, suggestive of the absence of any association between the uptake process and the overall biliary excretion of MTX. Since UDCA has been known to induce the expression of canalicular MRP2 in humans, UDCA treatment might be effective in humans to maintain or accelerate the hepatobiliary elimination of xenobiotics or metabolic conjugates that are MRP2 substrates. Full article
(This article belongs to the Section Biochemistry)
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11 pages, 9302 KiB  
Article
Instillation of Sericin Enhances Corneal Wound Healing through the ERK Pathway in Rat Debrided Corneal Epithelium
by Noriaki Nagai, Yuya Fukuoka, Miyu Ishii, Hiroko Otake, Tetsushi Yamamoto, Atsushi Taga, Norio Okamoto and Yoshikazu Shimomura
Int. J. Mol. Sci. 2018, 19(4), 1123; https://doi.org/10.3390/ijms19041123 - 9 Apr 2018
Cited by 23 | Viewed by 6381
Abstract
Sericin is a major constituent of silk produced by silkworms. We previously found that the instillation of sericin enhanced the proliferation of corneal epithelial cells, and acted to promote corneal wound healing in both normal and diabetic model rats. However, the mechanisms by [...] Read more.
Sericin is a major constituent of silk produced by silkworms. We previously found that the instillation of sericin enhanced the proliferation of corneal epithelial cells, and acted to promote corneal wound healing in both normal and diabetic model rats. However, the mechanisms by which sericin promotes the proliferation of corneal cells have not been established. In this study, we investigated the effects of sericin on Akt and ERK activation in a human corneal epithelial cell line (HCE-T cells) and rat debrided corneal epithelium. Although Akt phosphorylation was not detected following the treatment of HCE-T cells with sericin, ERK1/2 phosphorylation was enhanced. The growth of HCE-T cells treated with sericin was significantly increased, with the cell growth of sericin-treated HCE-T cells being 1.7-fold higher in comparison with vehicle-treated HCE-T cells. On the other hand, both of an ERK inhibitor U0126 (non-specific specific inhibitor) and SCH772984 (specific inhibitor) attenuated the enhanced cell growth by sericin, and the growth level in the case of co-treatment with sericin and ERK1/2 inhibitor was similar to that of cells treated with ERK1/2 inhibitor alone. In an in vivo study using rat debrided corneal epithelium, the corneal wound healing rate was enhanced by the instillation of sericin, and this enhancement was also attenuated by the instillation of U0126. In addition, the corneal wound healing rate in rats co-instilled with sericin and U0126 was similar to that following the instillation of U0126 alone. In conclusion, we found that the instillation of sericin enhanced cell proliferation via the activation of the MAPK/ERK pathway, resulting in the promotion of corneal wound healing in rat eyes. These findings provide significant information for designing further studies to develop potent corneal wound-healing drugs. Full article
(This article belongs to the Special Issue New Innovations in Wound Healing and Repair)
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14 pages, 3210 KiB  
Article
Healing of Osteochondral Defects Implanted with Biomimetic Scaffolds of Poly(ε-Caprolactone)/Hydroxyapatite and Glycidyl-Methacrylate-Modified Hyaluronic Acid in a Minipig
by Yi-Ho Hsieh, Bo-Yuan Shen, Yao-Horng Wang, Bojain Lin, Hung-Maan Lee and Ming-Fa Hsieh
Int. J. Mol. Sci. 2018, 19(4), 1125; https://doi.org/10.3390/ijms19041125 - 9 Apr 2018
Cited by 46 | Viewed by 5894
Abstract
Articular cartilage is a structure lack of vascular distribution. Once the cartilage is injured or diseased, it is unable to regenerate by itself. Surgical treatments do not effectively heal defects in articular cartilage. Tissue engineering is the most potential solution to this problem. [...] Read more.
Articular cartilage is a structure lack of vascular distribution. Once the cartilage is injured or diseased, it is unable to regenerate by itself. Surgical treatments do not effectively heal defects in articular cartilage. Tissue engineering is the most potential solution to this problem. In this study, methoxy poly(ethylene glycol)-block-poly(ε-caprolactone) (mPEG-PCL) and hydroxyapatite at a weight ratio of 2:1 were mixed via fused deposition modeling (FDM) layer by layer to form a solid scaffold. The scaffolds were further infiltrated with glycidyl methacrylate hyaluronic acid loading with 10 ng/mL of Transforming Growth Factor-β1 and photo cross-linked on top of the scaffolds. An in vivo test was performed on the knees of Lanyu miniature pigs for a period of 12 months. The healing process of the osteochondral defects was followed by computer tomography (CT). The defect was fully covered with regenerated tissues in the control pig, while different tissues were grown in the defect of knee of the experimental pig. In the gross anatomy of the cross section, the scaffold remained in the subchondral location, while surface cartilage was regenerated. The cross section of the knees of both the control and experimental pigs were subjected to hematoxylin and eosin staining. The cartilage of the knee in the experimental pig was partially matured, e.g., few chondrocyte cells were enclosed in the lacunae. In the knee of the control pig, the defect was fully grown with fibrocartilage. In another in vivo experiment in a rabbit and a pig, the composite of the TGF-β1-loaded hydrogel and scaffolds was found to regenerate hyaline cartilage. However, scaffolds that remain in the subchondral lesion potentially delay the healing process. Therefore, the structural design of the scaffold should be reconsidered to match the regeneration process of both cartilage and subchondral bone. Full article
(This article belongs to the Special Issue Novel Biomaterials for Tissue Engineering 2018)
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21 pages, 27990 KiB  
Article
β-Nicotinamide Adenine Dinucleotide (β-NAD) Inhibits ATP-Dependent IL-1β Release from Human Monocytic Cells
by Sebastian Daniel Hiller, Sarah Heldmann, Katrin Richter, Innokentij Jurastow, Mira Küllmar, Andreas Hecker, Sigrid Wilker, Gabriele Fuchs-Moll, Ivan Manzini, Günther Schmalzing, Wolfgang Kummer, Winfried Padberg, J. Michael McIntosh, Jelena Damm, Anna Zakrzewicz and Veronika Grau
Int. J. Mol. Sci. 2018, 19(4), 1126; https://doi.org/10.3390/ijms19041126 - 10 Apr 2018
Cited by 13 | Viewed by 6583
Abstract
While interleukin-1β (IL-1β) is a potent pro-inflammatory cytokine essential for host defense, high systemic levels cause life-threatening inflammatory syndromes. ATP, a stimulus of IL-1β maturation, is released from damaged cells along with β-nicotinamide adenine dinucleotide (β-NAD). Here, we tested the hypothesis that β-NAD [...] Read more.
While interleukin-1β (IL-1β) is a potent pro-inflammatory cytokine essential for host defense, high systemic levels cause life-threatening inflammatory syndromes. ATP, a stimulus of IL-1β maturation, is released from damaged cells along with β-nicotinamide adenine dinucleotide (β-NAD). Here, we tested the hypothesis that β-NAD controls ATP-signaling and, hence, IL-1β release. Lipopolysaccharide-primed monocytic U937 cells and primary human mononuclear leukocytes were stimulated with 2′(3′)-O-(4-benzoyl-benzoyl)ATP trieethylammonium salt (BzATP), a P2X7 receptor agonist, in the presence or absence of β-NAD. IL-1β was measured in cell culture supernatants. The roles of P2Y receptors, nicotinic acetylcholine receptors (nAChRs), and Ca2+-independent phospholipase A2 (iPLA2β, PLA2G6) were investigated using specific inhibitors and gene-silencing. Exogenous β-NAD signaled via P2Y receptors and dose-dependently (IC50 = 15 µM) suppressed the BzATP-induced IL-1β release. Signaling involved iPLA2β, release of a soluble mediator, and nAChR subunit α9. Patch-clamp experiments revealed that β-NAD inhibited BzATP-induced ion currents. In conclusion, we describe a novel triple membrane-passing signaling cascade triggered by extracellular β-NAD that suppresses ATP-induced release of IL-1β by monocytic cells. This cascade links activation of P2Y receptors to non-canonical metabotropic functions of nAChRs that inhibit P2X7 receptor function. The biomedical relevance of this mechanism might be the control of trauma-associated systemic inflammation. Full article
(This article belongs to the Special Issue Purinergic Signalling in Cancer and Inflammation)
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13 pages, 38053 KiB  
Article
In Vitro and In Vivo Osteogenic Activity of Titanium Implants Coated by Pulsed Laser Deposition with a Thin Film of Fluoridated Hydroxyapatite
by Luyuan Chen, Satoshi Komasa, Yoshiya Hashimoto, Shigeki Hontsu and Joji Okazaki
Int. J. Mol. Sci. 2018, 19(4), 1127; https://doi.org/10.3390/ijms19041127 - 10 Apr 2018
Cited by 32 | Viewed by 4860
Abstract
To enhance biocompatibility, osteogenesis, and osseointegration, we coated titanium implants, by krypton fluoride (KrF) pulsed laser deposition, with a thin film of fluoridated hydroxyapatite (FHA). Coating was confirmed by scanning electron microscopy (SEM) and scanning probe microscopy (SPM), while physicochemical properties were evaluated [...] Read more.
To enhance biocompatibility, osteogenesis, and osseointegration, we coated titanium implants, by krypton fluoride (KrF) pulsed laser deposition, with a thin film of fluoridated hydroxyapatite (FHA). Coating was confirmed by scanning electron microscopy (SEM) and scanning probe microscopy (SPM), while physicochemical properties were evaluated by attenuated reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Calcium deposition, osteocalcin production, and expression of osteoblast genes were significantly higher in rat bone marrow mesenchymal stem cells seeded on FHA-coated titanium than in cells seeded on uncoated titanium. Implantation into rat femurs also showed that the FHA-coated material had superior osteoinductive and osseointegration activity in comparison with that of traditional implants, as assessed by microcomputed tomography and histology. Thus, titanium coated with FHA holds promise as a dental implant material. Full article
(This article belongs to the Special Issue Bioactive Nanoparticles)
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10 pages, 3412 KiB  
Article
Irradiation-Induced Cardiac Connexin-43 and miR-21 Responses Are Hampered by Treatment with Atorvastatin and Aspirin
by Csilla Viczenczova, Branislav Kura, Tamara Egan Benova, Chang Yin, Rakesh C. Kukreja, Jan Slezak, Narcis Tribulova and Barbara Szeiffova Bacova
Int. J. Mol. Sci. 2018, 19(4), 1128; https://doi.org/10.3390/ijms19041128 - 10 Apr 2018
Cited by 21 | Viewed by 4142
Abstract
Radiation of the chest during cancer therapy is deleterious to the heart, mostly due to oxidative stress and inflammation related injury. A single sub-lethal dose of irradiation has been shown to result in compensatory up-regulation of the myocardial connexin-43 (Cx43), activation of the [...] Read more.
Radiation of the chest during cancer therapy is deleterious to the heart, mostly due to oxidative stress and inflammation related injury. A single sub-lethal dose of irradiation has been shown to result in compensatory up-regulation of the myocardial connexin-43 (Cx43), activation of the protein kinase C (PKC) signaling along with the decline of microRNA (miR)-1 and an increase of miR-21 levels in the left ventricle (LV). We investigated whether drugs with antioxidant, anti-inflammatory or vasodilating properties, such as aspirin, atorvastatin, and sildenafil, may affect myocardial response in the LV and right ventricle (RV) following chest irradiation. Adult, male Wistar rats were subjected to a single sub-lethal dose of chest radiation at 25 Gy and treated with aspirin (3 mg/day), atorvastatin (0.25 mg/day), and sildenafil (0.3 mg/day) for six weeks. Cx43, PKCε and PKCδ proteins expression and levels of miR-1 as well as miR-21 were determined in the LV and RV. Results showed that the suppression of miR-1 was associated with an increase of total and phosphorylated forms of Cx43 as well as PKCε expression in the LV while having no effect in the RV post-irradiation as compared to the non-irradiated rats. Treatment with aspirin and atorvastatin prevented an increase in the expression of Cx43 and PKCε without change in the miR-1 levels. Furthermore, treatment with aspirin, atorvastatin, and sildenafil completely prevented an increase of miR-21 in the LV while having partial effect in the RV post irradiation. The increase in pro-apoptotic PKCδ was not affected by any of the used treatment. In conclusion, irradiation and drug-induced changes were less pronounced in the RV as compared to the LV. Treatment with aspirin and atorvastatin interfered with irradiation-induced compensatory changes in myocardial Cx43 protein and miR-21 by preventing their elevation, possibly via amelioration of oxidative stress and inflammation. Full article
(This article belongs to the Special Issue Interplay of Connexins and Pannexins in Tissue Function and Disease)
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16 pages, 5157 KiB  
Article
An Organic Solvent-Tolerant Lipase with Both Hydrolytic and Synthetic Activities from the Oleaginous Fungus Mortierella echinosphaera
by Alexandra Kotogán, Carolina Zambrano, Anita Kecskeméti, Mónika Varga, András Szekeres, Tamás Papp, Csaba Vágvölgyi and Miklós Takó
Int. J. Mol. Sci. 2018, 19(4), 1129; https://doi.org/10.3390/ijms19041129 - 10 Apr 2018
Cited by 9 | Viewed by 4019
Abstract
Lipase enzymes of the oleaginous fungal group Mortierella are rarely studied. However, considering that most commercial lipases are derived from filamentous fungal sources, their investigation can contribute to the cost-effective development of new biotechnological processes. Here, an extracellular lipase with a molecular mass [...] Read more.
Lipase enzymes of the oleaginous fungal group Mortierella are rarely studied. However, considering that most commercial lipases are derived from filamentous fungal sources, their investigation can contribute to the cost-effective development of new biotechnological processes. Here, an extracellular lipase with a molecular mass of 30 kDa was isolated from Mortierella echinosphaera CBS 575.75 and characterized. The purified lipase exhibited an optimal p-nitrophenyl palmitate (pNPP)-hydrolyzing activity at 25 °C and pH 6.6–7.0 and proved to be highly stable at temperatures up to 40 °C and under broad pH conditions. The enzyme was active under low temperatures, retaining 32.5% of its activity at 10 °C, and was significantly stable in polar and non-polar organic solvents. The Km, Vmax, and kcat for pNPP were 0.336 mM, 30.4 μM/min, and 45.7 1/min for pNPP and 0.333 mM, 36.9 μM/min, and 55.6 1/min for pNP-decanoate, respectively. The pNPP hydrolysis was inhibited by Hg2+, N-bromosuccinimide, and sodium dodecyl sulfate, while ethylenediaminetetraacetic acid and metal ions, such as Ca2+, Mg2+, Na+, and K+ enhanced the activity. The purified lipase had non-regioselective activity and wide substrate specificity, showing a clear preference for medium-chained p-nitrophenyl esters. Besides its good transesterification activity, the enzyme appeared as a suitable biocatalyst to operate selective esterification reactions to long-chained alkyl esters. Adsorption to Accurel MP1000 improved the storage stability of the enzyme at 5 °C. The immobilized lipase displayed tolerance to a non-aqueous environment and was reusable for up to five cycles without significant loss in its synthetic and hydrolytic activities. These findings confirm the applicability of both the free and the immobilized enzyme preparations in future research. Full article
(This article belongs to the Special Issue Microbial Enzymes)
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29 pages, 21370 KiB  
Article
Mitochondrial Biogenesis in Diverse Cauliflower Cultivars under Mild and Severe Drought. Impaired Coordination of Selected Transcript and Proteomic Responses, and Regulation of Various Multifunctional Proteins
by Michał Rurek, Magdalena Czołpińska, Tomasz Andrzej Pawłowski, Aleksandra Maria Staszak, Witold Nowak, Włodzimierz Krzesiński and Tomasz Spiżewski
Int. J. Mol. Sci. 2018, 19(4), 1130; https://doi.org/10.3390/ijms19041130 - 10 Apr 2018
Cited by 9 | Viewed by 5234
Abstract
Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis) cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly) in [...] Read more.
Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis) cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly) in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Respiratory (e.g., complex II, IV (CII, CIV) and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e.g., components of RNA editing machinery) were diversely affected in their abundance under two drought levels. Western immunoassays showed additional cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides (found in several 2D spots) immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The abundance of selected mRNAs participating in drought response was also determined. We conclude that mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars, and associated with drought tolerance at the proteomic and functional levels. However, discussed alternative oxidase (AOX) regulation at the RNA and protein level were largely uncoordinated due to the altered availability of transcripts for translation, mRNA/ribosome interactions, and/or miRNA impact on transcript abundance and translation. Full article
(This article belongs to the Special Issue Plant Mitochondria)
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11 pages, 6900 KiB  
Article
Crystal Structure of the Isocitrate Dehydrogenase 2 from Acinetobacter baumannii (AbIDH2) Reveals a Novel Dimeric Structure with Two Monomeric-IDH-Like Subunits
by Peng Wang, Yatao Wu, Jie Liu, Ping Song, Shan Li, Xinxin Zhou and Guoping Zhu
Int. J. Mol. Sci. 2018, 19(4), 1131; https://doi.org/10.3390/ijms19041131 - 10 Apr 2018
Cited by 8 | Viewed by 3736
Abstract
Monomeric isocitrate dehydrogenases (IDHs) have a single polypeptide sizing around 85 kDa. The IDH2 from the opportunistic bacterium Acinetobacter baumannii (AbIDH2) with a mass of 83 kDa was formerly recognized as a typical monomeric IDH. However, both size exclusion chromatography and analytical ultracentrifugation [...] Read more.
Monomeric isocitrate dehydrogenases (IDHs) have a single polypeptide sizing around 85 kDa. The IDH2 from the opportunistic bacterium Acinetobacter baumannii (AbIDH2) with a mass of 83 kDa was formerly recognized as a typical monomeric IDH. However, both size exclusion chromatography and analytical ultracentrifugation analysis indicated that AbIDH2 exists as a homodimer in solution. The crystallographic study of the substrate/coenzyme-free AbIDH2 gave a dimeric structure and each subunit contained a domain I and a domain II. The dimeric assembly is mainly stabilized by hydrophobic interactions (16 hydrogen bonds and 11 salt bridges) from the dimer’s interface platform, which centered around the three parallel helices (α4, α12, and α17) and one loop from the domain II. Kinetic analysis showed that the dimeric AbIDH2 showed much lower catalytic efficiency (0.39 μM−1·s−1) as compared to the typical monomeric IDHs (~15 μM−1·s−1). Key residues crucial for dimer formation were simultaneously changed to generate the mutant mAbIDH2. The disruption of the hydrophobic forces disassociated the dimeric AbIDH2, making mAbIDH2 a monomeric enzyme. mAbIDH2 sustained specific activity (21.9 ± 2 U/mg) comparable to AbIDH2 (25.4 ± 0.7 U/mg). However, mAbIDH2 proved to be a thermolabile enzyme, indicating that the thermostable dimeric AbIDH2 may have a physiological significance for the growth and pathogenesis of A. baumannii. Phylogenetic analysis demonstrated the existence of numerous AbIDH2 homologous proteins, thus expanding the monomeric IDH protein family. Full article
(This article belongs to the Section Biochemistry)
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13 pages, 3523 KiB  
Article
The Effects of Long-Term, Low- and High-Dose Beta-Carotene Treatment in Zucker Diabetic Fatty Rats: The Role of HO-1
by Evelin Csepanyi, Attila Czompa, Peter Szabados-Furjesi, Istvan Lekli, Jozsef Balla, Gyorgy Balla, Arpad Tosaki and Istvan Bak
Int. J. Mol. Sci. 2018, 19(4), 1132; https://doi.org/10.3390/ijms19041132 - 10 Apr 2018
Cited by 12 | Viewed by 4530
Abstract
Nowadays, there is a growing interest in compounds derived from plants as potential raw materials for drug development. One of the most studied compounds is beta-carotene (BC). Several clinical studies can be found investigating the cardiovascular effects of BC, however, all these results [...] Read more.
Nowadays, there is a growing interest in compounds derived from plants as potential raw materials for drug development. One of the most studied compounds is beta-carotene (BC). Several clinical studies can be found investigating the cardiovascular effects of BC, however, all these results are controversial. There is an increasing body of evidence showing that besides the well-known antioxidant properties, under strong oxidative circumstances, BC could become prooxidant as well. In this study, we investigated the effects of long-term, low- and high-dose BC treatment in ischemic/reperfused (ISA/REP) hearts isolated from Zucker diabetic fatty (ZDF) rats. The animals were treated with various daily doses of BC for 4 weeks and then hearts were isolated and subjected to 30 min of global ischemia (ISA) followed by 120 min of reperfusion (REP). Blood glucose levels were measured before, after two weeks, and at the end of the treatment. In isolated hearts, the myocardial function was registered. At the end of the reperfusion period, the infarct size (IS) and heme oxygenase-1 (HO-1) expression were measured. The results showed that a low dose of BC treatment significantly improved postischemic recovery, which was reflected in a decreased IS. Interestingly, when BC was applied at high concentrations, the observed protective effects were lost. Although BC treatment increased HO-1 expression, we did not observe a better heart function and/or decreased IS in the high-dose-treated group. Glucose tolerance tests showed a concentration-independent decrease in blood glucose levels. Our results suggest that long-term, low-dose BC treatment could be effective in the treatment of type-2-diabetes and related cardiovascular diseases. Full article
(This article belongs to the Special Issue Oxidative Stress in Cardiovascular Disease 2018)
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14 pages, 28997 KiB  
Article
Allosteric Activation of GDP-Bound Ras Isoforms by Bisphenol Derivative Plasticisers
by Miriam Schöpel, Oleksandr Shkura, Jana Seidel, Klaus Kock, Xueyin Zhong, Stefanie Löffek, Iris Helfrich, Hagen S. Bachmann, Jürgen Scherkenbeck, Christian Herrmann and Raphael Stoll
Int. J. Mol. Sci. 2018, 19(4), 1133; https://doi.org/10.3390/ijms19041133 - 10 Apr 2018
Cited by 11 | Viewed by 6724
Abstract
The protein family of small GTPases controls cellular processes by acting as a binary switch between an active and an inactive state. The most prominent family members are H-Ras, N-Ras, and K-Ras isoforms, which are highly related and frequently mutated in cancer. Bisphenols [...] Read more.
The protein family of small GTPases controls cellular processes by acting as a binary switch between an active and an inactive state. The most prominent family members are H-Ras, N-Ras, and K-Ras isoforms, which are highly related and frequently mutated in cancer. Bisphenols are widespread in modern life because of their industrial application as plasticisers. Bisphenol A (BPA) is the best-known member and has gained significant scientific as well as public attention as an endocrine disrupting chemical, a fact that eventually led to its replacement. However, compounds used to replace BPA still contain the molecular scaffold of bisphenols. BPA, BPAF, BPB, BPE, BPF, and an amine-substituted BPAF-derivate all interact with all GDP-bound Ras-Isoforms through binding to a common site on these proteins. NMR-, SOScat-, and GDI- assay-based data revealed a new bisphenol-induced, allosterically activated GDP-bound Ras conformation that define these plasticisers as Ras allosteric agonists. Full article
(This article belongs to the Special Issue Advances in the Research of Endocrine Disrupting Chemicals)
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16 pages, 17447 KiB  
Article
Assessment of Ab Initio and Density Functional Theory Methods for the Excitations of Donor-Acceptor Complexes: The Case of the Benzene-Tetracyanoethylene Model
by Peng Xu, Cai-Rong Zhang, Wei Wang, Ji-Jun Gong, Zi-Jiang Liu and Hong-Shan Chen
Int. J. Mol. Sci. 2018, 19(4), 1134; https://doi.org/10.3390/ijms19041134 - 10 Apr 2018
Cited by 10 | Viewed by 4026
Abstract
The understanding of the excited-state properties of electron donors, acceptors and their interfaces in organic optoelectronic devices is a fundamental issue for their performance optimization. In order to obtain a balanced description of the different excitation types for electron-donor-acceptor systems, including the singlet [...] Read more.
The understanding of the excited-state properties of electron donors, acceptors and their interfaces in organic optoelectronic devices is a fundamental issue for their performance optimization. In order to obtain a balanced description of the different excitation types for electron-donor-acceptor systems, including the singlet charge transfer (CT), local excitations, and triplet excited states, several ab initio and density functional theory (DFT) methods for excited-state calculations were evaluated based upon the selected model system of benzene-tetracyanoethylene (B-TCNE) complexes. On the basis of benchmark calculations of the equation-of-motion coupled-cluster with single and double excitations method, the arithmetic mean of the absolute errors and standard errors of the electronic excitation energies for the different computational methods suggest that the M11 functional in DFT is superior to the other tested DFT functionals, and time-dependent DFT (TDDFT) with the Tamm–Dancoff approximation improves the accuracy of the calculated excitation energies relative to that of the full TDDFT. The performance of the M11 functional underlines the importance of kinetic energy density, spin-density gradient, and range separation in the development of novel DFT functionals. According to the TDDFT results, the performances of the different TDDFT methods on the CT properties of the B-TCNE complexes were also analyzed. Full article
(This article belongs to the Section Molecular Biophysics)
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17 pages, 6754 KiB  
Article
Neuroprotective Effects of Four Phenylethanoid Glycosides on H2O2-Induced Apoptosis on PC12 Cells via the Nrf2/ARE Pathway
by Maiquan Li, Tao Xu, Fei Zhou, Mengmeng Wang, Huaxin Song, Xing Xiao and Baiyi Lu
Int. J. Mol. Sci. 2018, 19(4), 1135; https://doi.org/10.3390/ijms19041135 - 10 Apr 2018
Cited by 63 | Viewed by 6230
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a key transcription factor against oxidative stress and neurodegenerative disorders. Phenylethanoid glycosides (PhGs; salidroside, acteoside, isoacteoside, and echinacoside) exhibit antioxidant and neuroprotective bioactivities. This study was performed to investigate the neuroprotective effect and molecular mechanism [...] Read more.
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a key transcription factor against oxidative stress and neurodegenerative disorders. Phenylethanoid glycosides (PhGs; salidroside, acteoside, isoacteoside, and echinacoside) exhibit antioxidant and neuroprotective bioactivities. This study was performed to investigate the neuroprotective effect and molecular mechanism of PhGs. PhGs pretreatment significantly suppressed H2O2-induced cytotoxicity in PC12 cells by triggering the nuclear translocation of Nrf2 and reversing the downregulated protein expression of heme oxygenase 1 (HO-1), NAD(P)H quinone oxidoreductase 1 (NQO1), glutamate cysteine ligase-catalytic subunit (GCLC), and glutamate-cysteine ligase modifier subunit (GCLM). Nrf2 siRNA or HO-1 inhibitor zinc protoporphyrin (ZnPP) reduced the neuroprotective effect. PhGs showed potential interaction with the Nrf2 binding site in Kelch-like ECH-association protein 1 (Keap1). This result may support the hypothesis that PhGs are activators of Nrf2. We demonstrated the potential binding between PhGs and the Keap1-activated Nrf2/ARE pathway, and that PhGs with more glycosides had enhanced effects. Full article
(This article belongs to the Special Issue Plant Natural Products for Human Health)
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13 pages, 12464 KiB  
Article
Rhodobacter sphaeroides Extract Lycogen™ Attenuates Testosterone-Induced Benign Prostate Hyperplasia in Rats
by Chiang-Ting Wang, Ya-Yun Wang, Wen-Sheng Liu, Chun-Ming Cheng, Kuo-Hsun Chiu, Li-Lian Liu, Xue-Zhu Liu, Zhi-Hong Wen, Ya-Huey Chen and Tsung-Ming Chen
Int. J. Mol. Sci. 2018, 19(4), 1137; https://doi.org/10.3390/ijms19041137 - 10 Apr 2018
Cited by 10 | Viewed by 5063
Abstract
Benign prostate hyperplasia (BPH) is one of the most common urological problems in mid-aged to elderly men. Risk factors of BPH include family history, obesity, type 2 diabetes, and high oxidative stress. The main medication classes for BPH management are alpha blockers and [...] Read more.
Benign prostate hyperplasia (BPH) is one of the most common urological problems in mid-aged to elderly men. Risk factors of BPH include family history, obesity, type 2 diabetes, and high oxidative stress. The main medication classes for BPH management are alpha blockers and 5α-reductase inhibitors. However, these conventional medicines cause adverse effects. Lycogen™, extracted from Rhodobacter sphaeroides WL-APD911, is an anti-oxidant and anti-inflammatory compound. In this study, the effect of Lycogen™ was evaluated in rats with testosterone-induced benign prostate hyperplasia (BPH). Testosterone injections and Lycogen™ administration were carried out for 28 days, and body weights were recorded twice per week. The testosterone injection successfully induced a prostate enlargement. BPH-induced rats treated with different doses of Lycogen™ exhibited a significantly decreased prostate index (PI). Moreover, the Lycogen™ administration recovered the histological abnormalities observed in the prostate of BPH rats. In conclusion, these findings support a dose-dependent preventing effect of Lycogen™ on testosterone-induced BPH in rats and suggest that Lycogen™ may be favorable to the prevention and management of benign prostate hyperplasia. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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13 pages, 12493 KiB  
Article
17β-Hydroxysteroid Dehydrogenase Type 2 Expression Is Induced by Androgen Signaling in Endometrial Cancer
by Chiaki Hashimoto, Yasuhiro Miki, Sota Tanaka, Kiyoshi Takagi, Misaki Fue, Zhulanqiqige Doe, Bin Li, Nobuo Yaegashi, Takashi Suzuki and Kiyoshi Ito
Int. J. Mol. Sci. 2018, 19(4), 1139; https://doi.org/10.3390/ijms19041139 - 10 Apr 2018
Cited by 15 | Viewed by 4528
Abstract
Endometrial cancer is one of the most common female pelvic cancers and has been considered an androgen-related malignancy. Several studies have demonstrated the anti-cell proliferative effect of androgen on endometrial cancer cells; however, the mechanisms of the anti-cancer effect of androgen remain largely [...] Read more.
Endometrial cancer is one of the most common female pelvic cancers and has been considered an androgen-related malignancy. Several studies have demonstrated the anti-cell proliferative effect of androgen on endometrial cancer cells; however, the mechanisms of the anti-cancer effect of androgen remain largely unclear. 17β-hydroxysteroid dehydrogenase type 2 (17β-HSD2), which catalyzes the conversion of E2 to E1, is known to be upregulated by androgen treatment in breast cancer cells. In this study, we therefore focused on the role of androgen on estrogen dependence in endometrial cancer. Dihydrotestosterone (DHT) was found to induce 17β-HSD2 mRNA and protein expression in HEC-1B endometrial cancer cells. DHT could also inhibit cell proliferation of HEC-1B when induced by estradiol treatment. In 19 endometrioid endometrial adenocarcinoma (EEA) tissues, intratumoral DHT concentration was measured by liquid chromatography/electrospray tandem mass spectrometry and was found to be significantly correlated with 17β-HSD2 immunohistochemical status. We further examined the correlations between 17β-HSD2 immunoreactivity and clinicopathological parameters in 53 EEA tissues. 17β-HSD2 status was inversely associated with the histological grade, clinical stage, and cell proliferation marker Ki-67, and positively correlated with progesterone receptor expression. 17β-HSD2 status tended to be positively associated with androgen receptor status. In 53 EEA cases, the 17β-HSD2-positive group tended to have better prognosis than that for the negative group with respect to progression-free survival and endometrial cancer-specific survival. These findings suggest that androgen suppresses the estrogen dependence of endometrial cancer through the induction of 17β-HSD2 in endometrial cancer. Full article
(This article belongs to the Special Issue Hormones-Dependent Cancers: New Aspects on Biochemistry and Molecular Pathology)
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20 pages, 29073 KiB  
Article
Aging and Intermittent Fasting Impact on Transcriptional Regulation and Physiological Responses of Adult Drosophila Neuronal and Muscle Tissues
by Sharon Zhang, Eric P. Ratliff, Brandon Molina, Nadja El-Mecharrafie, Jessica Mastroianni, Roxanne W. Kotzebue, Madhulika Achal, Ruth E. Mauntz, Arysa Gonzalez, Ayeh Barekat, William A. Bray, Andrew M. Macias, Daniel Daugherty, Greg L. Harris, Robert A. Edwards and Kim D. Finley
Int. J. Mol. Sci. 2018, 19(4), 1140; https://doi.org/10.3390/ijms19041140 - 10 Apr 2018
Cited by 15 | Viewed by 9011
Abstract
The progressive decline of the nervous system, including protein aggregate formation, reflects the subtle dysregulation of multiple functional pathways. Our previous work has shown intermittent fasting (IF) enhances longevity, maintains adult behaviors and reduces aggregates, in part, by promoting autophagic function in the [...] Read more.
The progressive decline of the nervous system, including protein aggregate formation, reflects the subtle dysregulation of multiple functional pathways. Our previous work has shown intermittent fasting (IF) enhances longevity, maintains adult behaviors and reduces aggregates, in part, by promoting autophagic function in the aging Drosophila brain. To clarify the impact that IF-treatment has upon aging, we used high throughput RNA-sequencing technology to examine the changing transcriptome in adult Drosophila tissues. Principle component analysis (PCA) and other analyses showed ~1200 age-related transcriptional differences in head and muscle tissues, with few genes having matching expression patterns. Pathway components showing age-dependent expression differences were involved with stress response, metabolic, neural and chromatin remodeling functions. Middle-aged tissues also showed a significant increase in transcriptional drift-variance (TD), which in the CNS included multiple proteolytic pathway components. Overall, IF-treatment had a demonstrably positive impact on aged transcriptomes, partly ameliorating both fold and variance changes. Consistent with these findings, aged IF-treated flies displayed more youthful metabolic, behavioral and basal proteolytic profiles that closely correlated with transcriptional alterations to key components. These results indicate that even modest dietary changes can have therapeutic consequences, slowing the progressive decline of multiple cellular systems, including proteostasis in the aging nervous system. Full article
(This article belongs to the Special Issue Molecular and Cellular Mechanisms of Aging and Age-Related Disorders)
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13 pages, 26395 KiB  
Article
Bio-Based Cellulose Acetate Films Reinforced with Lignin and Glycerol
by Patricia Gontijo de Melo, Mariana Fornazier Borges, Jéssica Afonso Ferreira, Matheus Vicente Barbosa Silva and Reinaldo Ruggiero
Int. J. Mol. Sci. 2018, 19(4), 1143; https://doi.org/10.3390/ijms19041143 - 10 Apr 2018
Cited by 13 | Viewed by 6354
Abstract
Two sets of four cellulose acetate (degree of substitution = 2.2) were incorporated with lignin extracted from the macaúba endocarp, before and after being chemically modified to sodium carboxymethyl-lignin and aluminum carboxymethyl-lignin, respectively. The eight membranes were prepared by the casting method after [...] Read more.
Two sets of four cellulose acetate (degree of substitution = 2.2) were incorporated with lignin extracted from the macaúba endocarp, before and after being chemically modified to sodium carboxymethyl-lignin and aluminum carboxymethyl-lignin, respectively. The eight membranes were prepared by the casting method after dissolution in acetone and embedded with lignins (0.1% w/w), one without modification (CAc-Lig) and two chemically modified (CAc-CMLNa) and (CAc-CMLAl), compared to membranes of pure acetate (CAc). In group II, in the four membranes prepared, glycerol was added (10% w/w) as a plasticizer. The membranes were characterized by a number of techniques: thermal (differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA)), morphological (scanning electron microscope (SEM) and atomic force microscopy (AFM)), structural (X-ray powder diffraction (XRD)), hydrophobic (contact angle and water vapor permeability), and thermomechanical (dynamic thermal mechanical analysis and tensile tests). The results show that despite some incompatibility with the cellulose acetate, the incorporation of the lignin in a concentration of 0.1% w/w acts as a reinforcement in the membrane, greatly increasing the tension rupture of the material. The presence of glycerol in a concentration of 10% w/w also acts as a reinforcement in all membranes, in addition to increasing the tension rupture. In this study, glycerol and acetate both increased the compatibility of the membranes. Full article
(This article belongs to the Special Issue The Lignin Challenge: Exploring Innovative Applications)
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22 pages, 15912 KiB  
Article
Structural Requirements of Alkylglyceryl-l-Ascorbic Acid Derivatives for Melanogenesis Inhibitory Activity
by Norihisa Taira, Yushi Katsuyama, Masato Yoshioka, Osamu Muraoka and Toshio Morikawa
Int. J. Mol. Sci. 2018, 19(4), 1144; https://doi.org/10.3390/ijms19041144 - 10 Apr 2018
Cited by 10 | Viewed by 7912
Abstract
l-Ascorbic acid has multifunctional benefits on skin aesthetics, including inhibition of melanin production, and is widely used in cosmetics. It, however, has low stability and poor skin penetration. We hypothesize that alkylglyceryl-l-ascorbic acid derivatives, highly stable vitamin C–alkylglycerol conjugates, would [...] Read more.
l-Ascorbic acid has multifunctional benefits on skin aesthetics, including inhibition of melanin production, and is widely used in cosmetics. It, however, has low stability and poor skin penetration. We hypothesize that alkylglyceryl-l-ascorbic acid derivatives, highly stable vitamin C–alkylglycerol conjugates, would have similar anti-melanogenic activity with better stability and penetration. We test 28 alkylglyceryl-l-ascorbic acid derivatives (1–28) on theophylline-stimulated B16 melanoma 4A5 cells to determine if they inhibit melanogenesis and establish any structure–function relationships. Although not the most potent inhibitors, 3-O-(2,3-dihydroxypropyl)-2-O-hexyl-l-ascorbic acid (6, IC50 = 81.4 µM) and 2-O-(2,3-dihydroxypropyl)-3-O-hexyl-l-ascorbic acid (20, IC50 = 117 µM) are deemed the best candidate derivatives based on their inhibitory activities and low toxicities. These derivatives are also found to be more stable than l-ascorbic acid and to have favorable characteristics for skin penetration. The following structural requirements for inhibitory activity of alkylglyceryl-l-ascorbic acid derivatives are also determined: (i) alkylation of glyceryl-l-ascorbic acid is essential for inhibitory activity; (ii) the 3-O-alkyl-derivatives (2–14) exhibit stronger inhibitory activity than the corresponding 2-O-alkyl-derivatives (16–28); and (iii) derivatives with longer alkyl chains have stronger inhibitory activities. Mechanistically, our studies suggest that l-ascorbic acid derivatives exert their effects by suppressing the mRNA expression of tyrosinase and tyrosine-related protein-1. Full article
(This article belongs to the Special Issue Melanins and Melanogenesis: From Nature to Applications)
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14 pages, 40267 KiB  
Article
CD147 Promotes CXCL1 Expression and Modulates Liver Fibrogenesis
by Wen-Pu Shi, Di Ju, Hao Li, Lin Yuan, Jian Cui, Dan Luo, Zhi-Nan Chen and Huijie Bian
Int. J. Mol. Sci. 2018, 19(4), 1145; https://doi.org/10.3390/ijms19041145 - 10 Apr 2018
Cited by 36 | Viewed by 6186
Abstract
Activated hepatic stellate cells (HSCs) release pro-inflammatory and pro-fibrogenic factors. CXC chemokine-ligand-1 (CXCL1) is expressed on HSCs. We previously found that the CD147 is overexpressed in activated HSCs. In this study, we showed an important role of CD147 in promoting liver fibrosis by [...] Read more.
Activated hepatic stellate cells (HSCs) release pro-inflammatory and pro-fibrogenic factors. CXC chemokine-ligand-1 (CXCL1) is expressed on HSCs. We previously found that the CD147 is overexpressed in activated HSCs. In this study, we showed an important role of CD147 in promoting liver fibrosis by activating HSCs and upregulating expression of chemokines. Specifically, we found that CD147 specific deletion in HSCs mice alleviated CCl4-induced liver fibrosis and inhibited HSCs activation. Overexpression of CD147 upregulated the secretion of CXCL1. Meanwhile, CXCL1 promoted HSCs activation through autocrine. Treating with PI3K/AKT inhibitor could effectively suppress CD147-induced CXCL1 expression. Taken together, these findings suggest that CD147 regulates CXCL1 release in HSCs by PI3K/AKT signaling. Inhibition of CD147 attenuates CCl4-induced liver fibrosis and inflammation. Therefore, administration of targeting CD147 could be a promising therapeutic strategy in liver fibrosis. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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10 pages, 6853 KiB  
Communication
Localization Microscopy of Actin Cytoskeleton in Human Platelets
by Sandra Mayr, Fabian Hauser, Anja Peterbauer, Andreas Tauscher, Christoph Naderer, Markus Axmann, Birgit Plochberger and Jaroslaw Jacak
Int. J. Mol. Sci. 2018, 19(4), 1150; https://doi.org/10.3390/ijms19041150 - 11 Apr 2018
Cited by 16 | Viewed by 6771
Abstract
Here, we measure the actin cytoskeleton arrangement of different morphological states of human platelets using a new protocol for photo-switching of rhodamine class fluorophores. A new medium composition was established for imaging the cytoskeleton using Alexa Fluor 488 conjugated to phalloidin. Morphological states [...] Read more.
Here, we measure the actin cytoskeleton arrangement of different morphological states of human platelets using a new protocol for photo-switching of rhodamine class fluorophores. A new medium composition was established for imaging the cytoskeleton using Alexa Fluor 488 conjugated to phalloidin. Morphological states of platelets bound to a glass substrate are visualized and quantified by two-dimensional localization microscopy at nanoscopic resolution. Marker-less drift correction yields localization of individual Alexa 488 conjugated to phalloidin with a positional accuracy of 12 nm. Full article
(This article belongs to the Special Issue Single Cell Technology)
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16 pages, 2397 KiB  
Article
DK1 Induces Apoptosis via Mitochondria-Dependent Signaling Pathway in Human Colon Carcinoma Cell Lines In Vitro
by Yazmin Hussin, Muhammad Nazirul Mubin Aziz, Nurul Fattin Che Rahim, Swee Keong Yeap, Nurul Elyani Mohamad, Mas Jaffri Masarudin, Noraini Nordin, Nik Mohd Afizan-Nik Abd Rahman, Chean Yeah Yong, Muhammad Nadeem Akhtar, Siti Noor Hajar Zamrus and Noorjahan Banu Alitheen
Int. J. Mol. Sci. 2018, 19(4), 1151; https://doi.org/10.3390/ijms19041151 - 11 Apr 2018
Cited by 17 | Viewed by 5044
Abstract
Extensive research has been done in the search for innovative treatments against colon adenocarcinomas; however, the incidence rate of patients remains a major cause of cancer-related deaths in Malaysia. Natural bioactive compounds such as curcumin have been substantially studied as an alternative to [...] Read more.
Extensive research has been done in the search for innovative treatments against colon adenocarcinomas; however, the incidence rate of patients remains a major cause of cancer-related deaths in Malaysia. Natural bioactive compounds such as curcumin have been substantially studied as an alternative to anticancer drug therapies and have been surmised as a potent agent but, nevertheless, remain deficient due to its poor cellular uptake. Therefore, efforts now have shifted toward mimicking curcumin to synthesize novel compounds sharing similar effects. A synthetic analog, (Z)-3-hydroxy-1-(2-hydroxyphenyl)-3-phenylprop-2-ene-1-one (DK1), was recently synthesized and reported to confer improved bioavailability and selectivity toward human breast cancer cells. This study, therefore, aims to assess the anticancer mechanism of DK1 in relation to the induction of in vitro cell death in selected human colon cancer cell lines. Using the3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide(MTT) assay, the cytotoxicity of DK1 towards HT29 and SW620 cell lines were investigated. Acridine orange/propidium iodide (AO/PI) dual-staining assay and flow cytometry analyses (cell cycle analysis, Annexin/V-FITC and JC-1 assays) were incorporated to determine the mode of cell death. To further determine the mechanism of cell death, quantitative real-time polymerase chain reaction (qRT-PCR) and proteome profiling were conducted. Results from this study suggest that DK1 induced changes in cell morphology, leading to a decrease in cell viability and subsequent induction of apoptosis. DK1 treatment inhibited cell viability and proliferation 48 h post treatment with IC50 values of 7.5 ± 1.6 µM for HT29 cells and 14.5 ± 4.3 µM for SW620 cells, causing cell cycle arrest with increased accumulation of cell populations at the sub-G0/G1phaseof 74% and 23%, respectively. Flow cytometry analyses showed that DK1 treatment in cancer cells induced apoptosis, as indicated by DNA fragmentation and depolarization of the mitochondrial membrane. qRT-PCR results show significant upregulation in the expression of caspase-9 in both HT29 and SW620 cell lines, further supporting that cell death induction by DK1 is via an intrinsic pathway. These outcomes, therefore, demonstrate DK1 as a potential anticancer agent for colon adenocarcinoma due to its anti-apoptotic attributes. Full article
(This article belongs to the Special Issue Natural Bioactives and Phytochemicals in Cancer Prevention)
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14 pages, 3376 KiB  
Article
Glucose-Dependent Insulinotropic Polypeptide Mitigates 6-OHDA-Induced Behavioral Impairments in Parkinsonian Rats
by Yu-Wen Yu, Shih-Chang Hsueh, Jing-Huei Lai, Yen-Hua Chen, Shuo-Jhen Kang, Kai-Yun Chen, Tsung-Hsun Hsieh, Barry J. Hoffer, Yazhou Li, Nigel H. Greig and Yung-Hsiao Chiang
Int. J. Mol. Sci. 2018, 19(4), 1153; https://doi.org/10.3390/ijms19041153 - 11 Apr 2018
Cited by 13 | Viewed by 4838
Abstract
In the present study, the effectiveness of glucose-dependent insulinotropic polypeptide (GIP) was evaluated by behavioral tests in 6-hydroxydopamine (6-OHDA) hemi-parkinsonian (PD) rats. Pharmacokinetic measurements of GIP were carried out at the same dose studied behaviorally, as well as at a lower dose used [...] Read more.
In the present study, the effectiveness of glucose-dependent insulinotropic polypeptide (GIP) was evaluated by behavioral tests in 6-hydroxydopamine (6-OHDA) hemi-parkinsonian (PD) rats. Pharmacokinetic measurements of GIP were carried out at the same dose studied behaviorally, as well as at a lower dose used previously. GIP was delivered by subcutaneous administration (s.c.) using implanted ALZET micro-osmotic pumps. After two days of pre-treatment, male Sprague Dawley rats received a single unilateral injection of 6-OHDA into the medial forebrain bundle (MFB). The neuroprotective effects of GIP were evaluated by apomorphine-induced contralateral rotations, as well as by locomotor and anxiety-like behaviors in open-field tests. Concentrations of human active and total GIP were measured in plasma during a five-day treatment period by ELISA and were found to be within a clinically translatable range. GIP pretreatment reduced behavioral abnormalities induced by the unilateral nigrostriatal dopamine (DA) lesion produced by 6-OHDA, and thus may be a novel target for PD therapeutic development. Full article
(This article belongs to the Special Issue Molecular Research on Neurodegenerative Diseases)
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21 pages, 35363 KiB  
Article
Identification and Evolution of TGF-β Signaling Pathway Members in Twenty-Four Animal Species and Expression in Tilapia
by Shuqing Zheng, Juan Long, Zhilong Liu, Wenjing Tao and Deshou Wang
Int. J. Mol. Sci. 2018, 19(4), 1154; https://doi.org/10.3390/ijms19041154 - 11 Apr 2018
Cited by 51 | Viewed by 5805
Abstract
Transforming growth factor β (TGF-β) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-β pathway members in 24 representative animal species. The appearance of the TGF-β pathway [...] Read more.
Transforming growth factor β (TGF-β) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-β pathway members in 24 representative animal species. The appearance of the TGF-β pathway was intrinsically linked to the emergence of metazoan. The total number of TGF-β ligands, receptors, and smads changed slightly in all invertebrates and jawless vertebrates analyzed. In contrast, expansion of the pathway members, especially ligands, was observed in jawed vertebrates most likely due to the second round of whole genome duplication (2R) and additional rounds in teleosts. Duplications of TGFB2, TGFBR2, ACVR1, SMAD4 and SMAD6, which were resulted from 2R, were first isolated. Type II receptors may be originated from the ACVR2-like ancestor. Interestingly, AMHR2 was not identified in Chimaeriformes and Cypriniformes even though they had the ligand AMH. Based on transcriptome data, TGF-β ligands exhibited a tissue-specific expression especially in the heart and gonads. However, most receptors and smads were expressed in multiple tissues indicating they were shared by different ligands. Spatial and temporal expression profiles of 8 genes in gonads of different developmental stages provided a fundamental clue for understanding their important roles in sex determination and reproduction. Taken together, our findings provided a global insight into the phylogeny and expression patterns of the TGF-β pathway genes, and hence contribute to the greater understanding of their biological roles in the organism especially in teleosts. Full article
(This article belongs to the Section Biochemistry)
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22 pages, 21992 KiB  
Article
Delivery of Proapoptotic Agents in Glioma Cell Lines by TSPO Ligand–Dextran Nanogels
by Antonio Lopalco, Annalisa Cutrignelli, Nunzio Denora, Mara Perrone, Rosa Maria Iacobazzi, Elisabetta Fanizza, Angela Lopedota, Nicoletta Depalo, Modesto De Candia, Massimo Franco and Valentino Laquintana
Int. J. Mol. Sci. 2018, 19(4), 1155; https://doi.org/10.3390/ijms19041155 - 11 Apr 2018
Cited by 20 | Viewed by 4150
Abstract
Translocator protein 18-kDa (TSPO) is a versatile mitochondrial target for molecular imaging and therapy. Moreover, selective TSPO ligands have been widely investigated for diagnostic purposes and explored to target drug delivery systems directed to cancer cells overexpressing TSPO. Indeed, poly(d,l [...] Read more.
Translocator protein 18-kDa (TSPO) is a versatile mitochondrial target for molecular imaging and therapy. Moreover, selective TSPO ligands have been widely investigated for diagnostic purposes and explored to target drug delivery systems directed to cancer cells overexpressing TSPO. Indeed, poly(d,l-lactic-co-glycolic acid (PLGA) polymers and nanocarriers decorated with TSPO ligands are capable of transporting TSPO ligands inside cancer cells, inducing survival inhibition in cancer cells and producing mitochondrial morphology modification. The aim of this work was to prepare nanogels (NGs) made with TSPO ligand dextran conjugates (TSPO-Dex) that are useful as potential delivery systems of two TSPO ligands as apoptotic agents. Synthesis and complete characterization of TSPO–dextran conjugates, an average molecular weights analysis, TSPO ligand release profiles, thermal behaviour and swelling studies were achieved. NG preparation, characterization and in vitro biological studies were also performed. The release of TSPO ligands released from dextran conjugates at 37 °C occurred in human serum at a faster rate than that detected in phosphate buffer. Cytotoxicity studies demonstrated that NGs produced from TSPO ligand–dextran conjugates induce survival inhibition in rat C6 glioma cell lines. Cellular uptake was also proven by fluorescence microscopy. Full article
(This article belongs to the Special Issue Translocator Protein (TSPO) in Drug Delivery and Imaging of Pathological Disorders)
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11 pages, 30025 KiB  
Article
Identification of an ACE-Inhibitory Peptide from Walnut Protein and Its Evaluation of the Inhibitory Mechanism
by Cong Wang, Maolin Tu, Di Wu, Hui Chen, Cheng Chen, Zhenyu Wang and Lianzhou Jiang
Int. J. Mol. Sci. 2018, 19(4), 1156; https://doi.org/10.3390/ijms19041156 - 11 Apr 2018
Cited by 51 | Viewed by 6328
Abstract
In the present study, a novel angiotensin I-converting enzyme inhibitory (ACE inhibitory) peptide, EPNGLLLPQY, derived from walnut seed storage protein, fragment residues 80–89, was identified by ultra-high performance liquid chromatography electrospray ionization quadrupole time of flight mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) from walnut protein hydrolysate. [...] Read more.
In the present study, a novel angiotensin I-converting enzyme inhibitory (ACE inhibitory) peptide, EPNGLLLPQY, derived from walnut seed storage protein, fragment residues 80–89, was identified by ultra-high performance liquid chromatography electrospray ionization quadrupole time of flight mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) from walnut protein hydrolysate. The IC50 value of the peptide was 233.178 μM, which was determined by the high performance liquid chromatography method by measuring the amount of hippuric acid (HA) generated from the ACE decomposition substrate (hippuryl-l-histidyl-l-leucine (HHL) to assess the ACE activity. Enzyme inhibitory kinetics of the peptide against ACE were also conducted, by which the inhibitory mechanism of ACE-inhibitory peptide was confirmed. Moreover, molecular docking was simulated by Discovery Studio 2017 R2 software to provide the potential mechanisms underlying the ACE-inhibitory activity of EPNGLLLPQY. Full article
(This article belongs to the Special Issue Selected Papers from 3-ISPMF, 3rd International Symposium on Phytochemicals in Medicine and Food (Kunming, 2018))
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22 pages, 8653 KiB  
Article
iTRAQ Quantitative Proteomic Analysis of Vitreous from Patients with Retinal Detachment
by Fátima Milhano Santos, Leonor Mesquita Gaspar, Sergio Ciordia, Ana Sílvia Rocha, João Paulo Castro e Sousa, Alberto Paradela, Luís António Passarinha and Cândida Teixeira Tomaz
Int. J. Mol. Sci. 2018, 19(4), 1157; https://doi.org/10.3390/ijms19041157 - 11 Apr 2018
Cited by 19 | Viewed by 5485
Abstract
Rhegmatogenous retinal detachment (RRD) is a potentially blinding condition characterized by a physical separation between neurosensory retina and retinal pigment epithelium. Quantitative proteomics can help to understand the changes that occur at the cellular level during RRD, providing additional information about the molecular [...] Read more.
Rhegmatogenous retinal detachment (RRD) is a potentially blinding condition characterized by a physical separation between neurosensory retina and retinal pigment epithelium. Quantitative proteomics can help to understand the changes that occur at the cellular level during RRD, providing additional information about the molecular mechanisms underlying its pathogenesis. In the present study, iTRAQ labeling was combined with two-dimensional LC-ESI-MS/MS to find expression changes in the proteome of vitreous from patients with RRD when compared to control samples. A total of 150 proteins were found differentially expressed in the vitreous of patients with RRD, including 96 overexpressed and 54 underexpressed. Several overexpressed proteins, several such as glycolytic enzymes (fructose-bisphosphate aldolase A, gamma-enolase, and phosphoglycerate kinase 1), glucose transporters (GLUT-1), growth factors (metalloproteinase inhibitor 1), and serine protease inhibitors (plasminogen activator inhibitor 1) are regulated by HIF-1, which suggests that HIF-1 signaling pathway can be triggered in response to RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Nevertheless, the differentially expressed proteins found in this study suggest that different mechanisms are activated after RRD to promote the survival of retinal cells through complex cellular responses. Full article
(This article belongs to the Special Issue Retinal Diseases: Bridging Basic and Clinical Research)
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16 pages, 38666 KiB  
Article
Antitumor Effect of Calcium-Mediated Destabilization of Epithelial Growth Factor Receptor on Non-Small Cell Lung Carcinoma
by In Un Kim, In Sung Sung, Jae Jun Sim, Minhee Park, Keun-Yeong Jeong and Hwan Mook Kim
Int. J. Mol. Sci. 2018, 19(4), 1158; https://doi.org/10.3390/ijms19041158 - 11 Apr 2018
Cited by 3 | Viewed by 3312
Abstract
Despite the development of numerous therapeutics targeting the epithelial growth factor receptor (EGFR) for non-small cell lung carcinoma (NSCLC), the application of these drugs is limited because of drug resistance. Here, we investigated the antitumor effect of calcium-mediated degradation of EGFR pathway-associated proteins [...] Read more.
Despite the development of numerous therapeutics targeting the epithelial growth factor receptor (EGFR) for non-small cell lung carcinoma (NSCLC), the application of these drugs is limited because of drug resistance. Here, we investigated the antitumor effect of calcium-mediated degradation of EGFR pathway-associated proteins on NSCLC. First, lactate calcium salt (LCS) was utilized for calcium supplementation. Src, α-tubulin and EGFR levels were measured after LSC treatment, and the proteins were visualized by immunocytochemistry. Calpeptin was used to confirm the calcium-mediated effect of LCS on NSCLC. Nuclear expression of c-Myc and cyclin D1 was determined to understand the underlying mechanism of signal inhibition following EGFR and Src destabilization. The colony formation assay and a xenograft animal model were used to confirm the in vitro and in vivo antitumor effects, respectively. LCS supplementation reduced Src and α-tubulin expression in NSCLC cells. EGFR was destabilized because of proteolysis of Src and α-tubulin. c-Myc and cyclin D1 expression levels were also reduced following the decrease in the transcriptional co-activation of EGFR and Src. Clonogenic ability and tumor growth were significantly inhibited by LSC treatment-induced EGFR destabilization. These results suggest that other than specifically targeting EGFR, proteolysis of associated molecules such as Src or α-tubulin may effectively exert an antitumor effect on NSCLC via EGFR destabilization. Therefore, LCS is expected to be a good candidate for developing novel anti-NSCLC therapeutics overcoming chemoresistance. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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19 pages, 2880 KiB  
Article
Opposing Roles of Calcium and Intracellular ATP on Gating of the Purinergic P2X2 Receptor Channel
by Milos B. Rokic, Patricio Castro, Elias Leiva-Salcedo, Melanija Tomic, Stanko S. Stojilkovic and Claudio Coddou
Int. J. Mol. Sci. 2018, 19(4), 1161; https://doi.org/10.3390/ijms19041161 - 11 Apr 2018
Cited by 4 | Viewed by 5545
Abstract
P2X2 receptors (P2X2R) exhibit a slow desensitization during the initial ATP application and a progressive, calcium-dependent increase in rates of desensitization during repetitive stimulation. This pattern is observed in whole-cell recordings from cells expressing recombinant and native P2X2R. However, desensitization is not observed [...] Read more.
P2X2 receptors (P2X2R) exhibit a slow desensitization during the initial ATP application and a progressive, calcium-dependent increase in rates of desensitization during repetitive stimulation. This pattern is observed in whole-cell recordings from cells expressing recombinant and native P2X2R. However, desensitization is not observed in perforated-patched cells and in two-electrode voltage clamped oocytes. Addition of ATP, but not ATPγS or GTP, in the pipette solution also abolishes progressive desensitization, whereas intracellular injection of apyrase facilitates receptor desensitization. Experiments with injection of alkaline phosphatase or addition of staurosporine and ATP in the intracellular solution suggest a role for a phosphorylation-dephosphorylation in receptor desensitization. Mutation of residues that are potential phosphorylation sites identified a critical role of the S363 residue in the intracellular ATP action. These findings indicate that intracellular calcium and ATP have opposing effects on P2X2R gating: calcium allosterically facilitates receptor desensitization and ATP covalently prevents the action of calcium. Single cell measurements further revealed that intracellular calcium stays elevated after washout in P2X2R-expressing cells and the blockade of mitochondrial sodium/calcium exchanger lowers calcium concentrations during washout periods to basal levels, suggesting a role of mitochondria in this process. Therefore, the metabolic state of the cell can influence P2X2R gating. Full article
(This article belongs to the Special Issue Calcium Signaling in Human Health and Diseases)
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16 pages, 9277 KiB  
Article
CA 19-9 Pancreatic Tumor Marker Fluorescence Immunosensing Detection via Immobilized Carbon Quantum Dots Conjugated Gold Nanocomposite
by Nawal Ahmad Alarfaj, Maha Farouk El-Tohamy and Hesham Farouk Oraby
Int. J. Mol. Sci. 2018, 19(4), 1162; https://doi.org/10.3390/ijms19041162 - 11 Apr 2018
Cited by 117 | Viewed by 12453
Abstract
The clinical detection of carbohydrate antigen 19-9 (CA 19-9), a tumor marker in biological samples, improves and facilitates the rapid screening and diagnosis of pancreatic cancer. A simple, low cost, fast, and green synthesis method to prepare a viable carbon quantum dots/gold (CQDs/Au) [...] Read more.
The clinical detection of carbohydrate antigen 19-9 (CA 19-9), a tumor marker in biological samples, improves and facilitates the rapid screening and diagnosis of pancreatic cancer. A simple, low cost, fast, and green synthesis method to prepare a viable carbon quantum dots/gold (CQDs/Au) nanocomposite fluorescence immunosensing solution for the detection of CA 19-9 was reported. The present method is conducted by preparing glucose-derived CQDs using a microwave-assisted method. CQDs were employed as reducing and stabilizing agents for the preparation of a CQDs/Au nanocomposite. The immobilized anti-CA 19-9-labeled horseradish peroxidase enzyme (Ab–HRP) was anchored to the surface of a CQDs/Au nanocomposite by a peptide interaction between the carboxylic and amine active groups. The CA 19-9 antigen was trapped by another monoclonal antibody that was coated on the surface of microtiter wells. The formed sandwich capping antibody–antigen–antibody enzyme complex had tunable fluorescence properties that were detected under excitation and emission wavelengths of 420 and 530 nm. The increase in fluorescence intensities of the immunoassay sensing solution was proportional to the CA 19-9 antigen concentration in the linear range of 0.01–350 U mL−1 and had a lower detection limit of 0.007 U mL−1. The proposed CQDs/Au nanocomposite immunoassay method provides a promising tool for detecting CA 19-9 in human serum. Full article
(This article belongs to the Special Issue Translating Gold Nanoparticles to Diagnostics and Therapeutics)
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11 pages, 1587 KiB  
Communication
Non-Coding Transcript Heterogeneity in Mesothelioma: Insights from Asbestos-Exposed Mice
by Emanuela Felley-Bosco and Hubert Rehrauer
Int. J. Mol. Sci. 2018, 19(4), 1163; https://doi.org/10.3390/ijms19041163 - 11 Apr 2018
Cited by 7 | Viewed by 4061
Abstract
Mesothelioma is an aggressive, rapidly fatal cancer and a better understanding of its molecular heterogeneity may help with making more efficient therapeutic strategies. Non-coding RNAs represent a larger part of the transcriptome but their contribution to diseases is not fully understood yet. We [...] Read more.
Mesothelioma is an aggressive, rapidly fatal cancer and a better understanding of its molecular heterogeneity may help with making more efficient therapeutic strategies. Non-coding RNAs represent a larger part of the transcriptome but their contribution to diseases is not fully understood yet. We used recently obtained RNA-seq data from asbestos-exposed mice and performed data mining of publicly available datasets in order to evaluate how non-coding RNA contribute to mesothelioma heterogeneity. Nine non-coding RNAs are specifically elevated in mesothelioma tumors and contribute to human mesothelioma heterogeneity. Because some of them have known oncogenic properties, this study supports the concept of non-coding RNAs as cancer progenitor genes. Full article
(This article belongs to the Special Issue Mesothelioma Heterogeneity: Potential Mechanisms)
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17 pages, 27563 KiB  
Article
A Novel Synthetic Material, BMM, Accelerates Wound Repair by Stimulating Re-Epithelialization and Fibroblast Activation
by Ga Young Seo, Changlim Hyun, Dongsoo Koh, Sanggyu Park, Yoongho Lim, Young Mee Kim and Moonjae Cho
Int. J. Mol. Sci. 2018, 19(4), 1164; https://doi.org/10.3390/ijms19041164 - 11 Apr 2018
Cited by 14 | Viewed by 5075
Abstract
Cutaneous wound repair is an intricate process whereby the skin reprograms itself after injury. In the mid-phase of wound repair, the proliferation, migration, and differentiation of cells are the major mechanisms to lead remodeling. We investigated the effect of BMM ((1E,2E)-1,2-bis((6-bromo-2H-chromen-3-yl)methylene)hydrazine), a novel [...] Read more.
Cutaneous wound repair is an intricate process whereby the skin reprograms itself after injury. In the mid-phase of wound repair, the proliferation, migration, and differentiation of cells are the major mechanisms to lead remodeling. We investigated the effect of BMM ((1E,2E)-1,2-bis((6-bromo-2H-chromen-3-yl)methylene)hydrazine), a novel synthetic material, on the migration and viability of keratinocytes or fibroblasts using the in vitro scratch woundhealing, electric cell-substrate imedance sensing (ECIS), invasion, and MTT assays. Cell migration-related factors were analyzed using western blot, and we found that treatment with BMM stimulated the EMT pathway and focal adhesion kinase (FAK)/Src signaling. Differentiation of HaCaT keratinocyte and fibroblast cells was also stimulated by BMM and specifically, NOX2/4 contributed to the activation of fibroblasts for wound healing. Furthermore, BMM treated HaCaT keratinocyte and fibroblast-co-cultured cells increased migration and differentiation. TGF-β and Cyr61 were also secreted to a greater extent than in single cultured cells. In vivo experiments showed that treatment with BMM promotes wound closure by promoting re-epithelialization. In this study, we demonstrated that a novel synthetic material, BMM, is capable of promoting wound healing via the stimulation of re-epithelialization in the epidermis and the activation of fibroblasts in the dermis, in particular, via the acceleration of the interaction between the epidermis and dermis. Full article
(This article belongs to the Section Biochemistry)
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15 pages, 10733 KiB  
Article
Beneficial Phytochemicals with Anti-Tumor Potential Revealed through Metabolic Profiling of New Red Pigmented Lettuces (Lactuca sativa L.)
by Xiao-Xiao Qin, Ming-Yue Zhang, Ying-Yan Han, Jing-Hong Hao, Chao-Jie Liu and Shuang-Xi Fan
Int. J. Mol. Sci. 2018, 19(4), 1165; https://doi.org/10.3390/ijms19041165 - 11 Apr 2018
Cited by 23 | Viewed by 5492
Abstract
The present study aimed to compare polyphenols among red lettuce cultivars and identify suitable cultivars for the development and utilization of healthy vegetables. Polyphenols, mineral elements, and antioxidant activity were analyzed in the leaves of six red pigmented lettuce (Lactuca sativa L.) [...] Read more.
The present study aimed to compare polyphenols among red lettuce cultivars and identify suitable cultivars for the development and utilization of healthy vegetables. Polyphenols, mineral elements, and antioxidant activity were analyzed in the leaves of six red pigmented lettuce (Lactuca sativa L.) cultivars; thereafter, we assessed the anti-tumor effects of cultivar B-2, which displayed the highest antioxidant activity. Quadrupole–Orbitrap mass spectrometry analysis revealed four classes of polyphenols in these cultivars. The composition and contents of these metabolites varied significantly among cultivars and primarily depended on leaf color. The B-2 cultivar had the highest antioxidant potential than others because it contained the highest levels of polyphenols, especially anthocyanin, flavone, and phenolic acid; furthermore, this cultivar displayed anti-tumor effects against the human lung adenocarcinoma cell line A549, human hepatoma cell line Bel7402, human cancer colorectal adenoma cell line HCT-8, and HT-29 human colon cancer cell line. Hence, the new red-leaf lettuce cultivar B-2 has a distinct metabolite profile, with high potential for development and utilization of natural phytochemical and mineral resources in lettuces and can be used as a nutrient-dense food product. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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10 pages, 3934 KiB  
Article
Glyteer, Soybean Tar, Impairs IL-4/Stat6 Signaling in Murine Bone Marrow-Derived Dendritic Cells: The Basis of Its Therapeutic Effect on Atopic Dermatitis
by Masaki Takemura, Takeshi Nakahara, Akiko Hashimoto-Hachiya, Masutaka Furue and Gaku Tsuji
Int. J. Mol. Sci. 2018, 19(4), 1169; https://doi.org/10.3390/ijms19041169 - 12 Apr 2018
Cited by 32 | Viewed by 5419
Abstract
Atopic dermatitis (AD) is a common inflammatory skin disease. Recent studies have revealed the involvement of T helper (Th)2 cytokines including Interleukin 4 (IL-4) in the pathogenesis of AD. Since epidermal Langerhans cells (LCs) and dermal myeloid dendritic cells (DCs) produce CCL17 and [...] Read more.
Atopic dermatitis (AD) is a common inflammatory skin disease. Recent studies have revealed the involvement of T helper (Th)2 cytokines including Interleukin 4 (IL-4) in the pathogenesis of AD. Since epidermal Langerhans cells (LCs) and dermal myeloid dendritic cells (DCs) produce CCL17 and CCL22 that chemoattract Th2 cells, interfering with CCL17 and CCL22 production from LCs and dermal myeloid DCs may be beneficial in the treatment of AD. To investigate this, we stimulated murine bone marrow-derived DCs (BMDCs) with IL-4. IL-4 stimulation produced Ccl17 and Ccl22, which was attenuated by soybean tar Glyteer, a known aryl hydrocarbon receptor (Ahr) activator. Notably, Glyteer treatment blocked the nuclear translocation of Stat6 induced by IL-4 stimulation, suggesting that this treatment impairs the IL-4/Stat6 signaling pathway in BMDCs. Unexpectedly, Glyteer treatment did not potently upregulate the expression of Cyp1a1, a specific Ahr-responsive gene, suggesting that its inhibitory machinery for Ccl17 and Ccl22 expression is likely to operate in an Ahr-independent manner. These findings indicate that Glyteer may exhibit therapeutic potential for AD by downregulating the CCL17 and CCL22 production from DCs in a Th2-deviated microenvironment. Full article
(This article belongs to the Special Issue Aryl Hydrocarbon Receptor in Biology and Toxicology)
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16 pages, 15763 KiB  
Article
MicroRNA Expression Analysis of In Vitro Dedifferentiated Human Pancreatic Islet Cells Reveals the Activation of the Pluripotency-Related MicroRNA Cluster miR-302s
by Guido Sebastiani, Giuseppina Emanuela Grieco, Noemi Brusco, Giuliana Ventriglia, Caterina Formichi, Lorella Marselli, Piero Marchetti and Francesco Dotta
Int. J. Mol. Sci. 2018, 19(4), 1170; https://doi.org/10.3390/ijms19041170 - 12 Apr 2018
Cited by 14 | Viewed by 4411
Abstract
β-cell dedifferentiation has been recently suggested as an additional mechanism contributing to type-1 and to type-2 diabetes pathogenesis. Moreover, several studies demonstrated that in vitro culture of native human pancreatic islets derived from non-diabetic donors resulted in the generation of an undifferentiated cell [...] Read more.
β-cell dedifferentiation has been recently suggested as an additional mechanism contributing to type-1 and to type-2 diabetes pathogenesis. Moreover, several studies demonstrated that in vitro culture of native human pancreatic islets derived from non-diabetic donors resulted in the generation of an undifferentiated cell population. Additional evidence from in vitro human β-cell lineage tracing experiments, demonstrated that dedifferentiated cells derive from β-cells, thus representing a potential in vitro model of β-cell dedifferentiation. Here, we report the microRNA expression profiles analysis of in vitro dedifferentiated islet cells in comparison to mature human native pancreatic islets. We identified 13 microRNAs upregulated and 110 downregulated in islet cells upon in vitro dedifferentiation. Interestingly, among upregulated microRNAs, we observed the activation of microRNA miR-302s cluster, previously defined as pluripotency-associated. Bioinformatic analysis indicated that miR-302s are predicted to target several genes involved in the control of β-cell/epithelial phenotype maintenance; accordingly, such genes were downregulated upon human islet in vitro dedifferentiation. Moreover, we uncovered that cell–cell contacts are needed to maintain low/null expression levels of miR-302. In conclusion, we showed that miR-302 microRNA cluster genes are involved in in vitro dedifferentiation of human pancreatic islet cells and inhibits the expression of multiple genes involved in the maintenance of β-cell mature phenotype. Full article
(This article belongs to the Special Issue The Role of MicroRNAs in Human Diseases)
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19 pages, 15813 KiB  
Article
Perineuronal Nets in Spinal Motoneurones: Chondroitin Sulphate Proteoglycan around Alpha Motoneurones
by Sian F. Irvine and Jessica C. F. Kwok
Int. J. Mol. Sci. 2018, 19(4), 1172; https://doi.org/10.3390/ijms19041172 - 12 Apr 2018
Cited by 30 | Viewed by 6967
Abstract
Perineuronal nets (PNNs) are extracellular matrix structures surrounding neuronal sub-populations throughout the central nervous system, regulating plasticity. Enzymatically removing PNNs successfully enhances plasticity and thus functional recovery, particularly in spinal cord injury models. While PNNs within various brain regions are well studied, much [...] Read more.
Perineuronal nets (PNNs) are extracellular matrix structures surrounding neuronal sub-populations throughout the central nervous system, regulating plasticity. Enzymatically removing PNNs successfully enhances plasticity and thus functional recovery, particularly in spinal cord injury models. While PNNs within various brain regions are well studied, much of the composition and associated populations in the spinal cord is yet unknown. We aim to investigate the populations of PNN neurones involved in this functional motor recovery. Immunohistochemistry for choline acetyltransferase (labelling motoneurones), PNNs using Wisteria floribunda agglutinin (WFA) and chondroitin sulphate proteoglycans (CSPGs), including aggrecan, was performed to characterise the molecular heterogeneity of PNNs in rat spinal motoneurones (Mns). CSPG-positive PNNs surrounded ~70–80% of Mns. Using WFA, only ~60% of the CSPG-positive PNNs co-localised with WFA in the spinal Mns, while ~15–30% of Mns showed CSPG-positive but WFA-negative PNNs. Selective labelling revealed that aggrecan encircled ~90% of alpha Mns. The results indicate that (1) aggrecan labels spinal PNNs better than WFA, and (2) there are differences in PNN composition and their associated neuronal populations between the spinal cord and cortex. Insights into the role of PNNs and their molecular heterogeneity in the spinal motor pools could aid in designing targeted strategies to enhance functional recovery post-injury. Full article
(This article belongs to the Special Issue Therapeutic Strategies to Spinal Cord Injury)
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20 pages, 8521 KiB  
Article
Response of Myeloid Leukemia Cells to Luteolin is Modulated by Differentially Expressed Pituitary Tumor-Transforming Gene 1 (PTTG1) Oncoprotein
by Pei-Yi Chen, Hsin-Jung Tien, Shih-Fen Chen, Chi-Ting Horng, Huei-Lin Tang, Hui-Ling Jung, Ming-Jiuan Wu and Jui-Hung Yen
Int. J. Mol. Sci. 2018, 19(4), 1173; https://doi.org/10.3390/ijms19041173 - 12 Apr 2018
Cited by 15 | Viewed by 6207
Abstract
Luteolin, a flavonoid nutraceutical abundant in vegetables and fruits, exhibits a wide range of bioactive properties, including antioxidant, anti-inflammatory and anti-cancer activities. Pituitary tumor-transforming gene 1 (PTTG1), an oncoprotein that regulates cell proliferation, is highly expressed in several types of cancer cells including [...] Read more.
Luteolin, a flavonoid nutraceutical abundant in vegetables and fruits, exhibits a wide range of bioactive properties, including antioxidant, anti-inflammatory and anti-cancer activities. Pituitary tumor-transforming gene 1 (PTTG1), an oncoprotein that regulates cell proliferation, is highly expressed in several types of cancer cells including leukemia. In this study, we aim to investigate the anti-cancer effects of luteolin on cells with differential PTTG1 expression and their underlying mechanisms in human myeloid leukemia cells. Methyl thiazolyl tetrazolium (MTT) assay data showed that luteolin (25–100 μM) significantly reduced cell viability in THP-1, HL-60 and K562 cells but did not affect normal peripheral blood mononuclear cells (PBMCs). Flow cytometric analysis and Western blot data demonstrated that luteolin induced a stronger apoptosis on undifferentiated myeloid leukemia cells with higher PTTG1 protein levels than on 12-myristate 13-acetate (PMA)- or all-trans-retinoic acid (ATRA)-differentiated cells with lower PTTG1 expression. Furthermore, PTTG1 knockdown by shRNA in leukemia cells suppressed cell proliferation, arrested cell-cycle progression and impaired the effectiveness of luteolin on cell-cycle regulation. Moreover, PTTG1-knockdown cells with luteolin exposure presented a reduction of the apoptotic proteins and maintained higher levels of the anti-apoptotic proteins such as Mcl-1, Bcl-2 and p21, which exhibited greater resistance to apoptosis. Finally, microarray analysis showed that 20 genes associated with cell proliferation, such as CXCL10, VEGFA, TNF, TP63 and FGFR1, were dramatically down-regulated in PTTG1-knockdown cells. Our current findings clearly demonstrate that luteolin-triggered leukemic cell apoptosis is modulated by the differential expression of the PTTG1. PTTG1 oncoprotein overexpression may modulate cell proliferation-related regulators and enhance the response of myeloid leukemia cells to luteolin. Luteolin is beneficial for the treatment of cancer cells with highly expressed PTTG1 oncoprotein. Full article
(This article belongs to the Special Issue Natural Bioactives and Phytochemicals in Cancer Prevention)
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10 pages, 9466 KiB  
Article
Triclosan Lacks (Anti-)Estrogenic Effects in Zebrafish Cells but Modulates Estrogen Response in Zebrafish Embryos
by Hélène Serra, François Brion, Jean-Marc Porcher, Hélène Budzinski and Selim Aït-Aïssa
Int. J. Mol. Sci. 2018, 19(4), 1175; https://doi.org/10.3390/ijms19041175 - 12 Apr 2018
Cited by 18 | Viewed by 4775
Abstract
Triclosan (TCS), an antimicrobial agent widely found in the aquatic environment, is suspected to act as an endocrine disrupting compound, however mechanistic information is lacking in regards to aquatic species. This study assessed the ability of TCS to interfere with estrogen receptor (ER) [...] Read more.
Triclosan (TCS), an antimicrobial agent widely found in the aquatic environment, is suspected to act as an endocrine disrupting compound, however mechanistic information is lacking in regards to aquatic species. This study assessed the ability of TCS to interfere with estrogen receptor (ER) transcriptional activity, in zebrafish-specific in vitro and in vivo reporter gene assays. We report that TCS exhibits a lack of either agonistic or antagonistic effects on a panel of ER-expressing zebrafish (ZELH-zfERα and -zfERβ) and human (MELN) cell lines. At the organism level, TCS at concentrations of up to 0.3 µM had no effect on ER-regulated brain aromatase gene expression in transgenic cyp19a1b-GFP zebrafish embryos. At a concentration of 1 µM, TCS interfered with the E2 response in an ambivalent manner by potentializing a low E2 response (0.625 nM), but decreasing a high E2 response (10 nM). Altogether, our study suggests that while modulation of ER-regulated genes by TCS may occur in zebrafish, it does so irrespective of a direct binding and activation of zfERs. Full article
(This article belongs to the Special Issue Molecular Pathways of Estrogen Receptor Action)
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14 pages, 4249 KiB  
Article
Tumor-Associated Macrophages and Mast Cells Positive to Tryptase Are Correlated with Angiogenesis in Surgically-Treated Gastric Cancer Patients
by Giuseppe Sammarco, Cosmo Damiano Gadaleta, Valeria Zuccalà, Emre Albayrak, Rosa Patruno, Pietro Milella, Rosario Sacco, Michele Ammendola and Girolamo Ranieri
Int. J. Mol. Sci. 2018, 19(4), 1176; https://doi.org/10.3390/ijms19041176 - 12 Apr 2018
Cited by 36 | Viewed by 3729
Abstract
Mast cells and macrophages can play a role in tumor angiogenesis by stimulating microvascular density (MVD). The density of mast cells positive to tryptase (MCDPT), tumor-associated macrophages (TAMs), and MVD were evaluated in a series of 86 gastric cancer (GC) tissue samples from [...] Read more.
Mast cells and macrophages can play a role in tumor angiogenesis by stimulating microvascular density (MVD). The density of mast cells positive to tryptase (MCDPT), tumor-associated macrophages (TAMs), and MVD were evaluated in a series of 86 gastric cancer (GC) tissue samples from patients who had undergone potential curative surgery. MCDPT, TAMs, and MVD were assessed in tumor tissue (TT) and in adjacent normal tissue (ANT) by immunohistochemistry and image analysis. Each of the above parameters was correlated with the others and, in particular for TT, with important clinico-pathological features. In TT, a significant correlation between MCDPT, TAMs, and MVD was found by Pearson t-test analysis (p ranged from 0.01 to 0.02). No correlation to the clinico-pathological features was found. A significant difference in terms of mean MCDPT, TAMs, and MVD between TT and ANT was found (p ranged from 0.001 to 0.002). Obtained data suggest MCDPT, TAMs, and MVD increased from ANT to TT. Interestingly, MCDPT and TAMs are linked in the tumor microenvironment and they play a role in GC angiogenesis in a synergistic manner. The assessment of the combination of MCDPT and TAMs could represent a surrogate marker of angiogenesis and could be evaluated as a target of novel anti-angiogenic therapies in GC patients. Full article
(This article belongs to the Special Issue Angiogenesis and Anti-Angiogenesis in Oncology: From Bench to Translational Research and Bedside Investigation)
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16 pages, 6115 KiB  
Article
Development and Characterization of Novel Genic-SSR Markers in Apple-Juniper Rust Pathogen Gymnosporangium yamadae (Pucciniales: Pucciniaceae) Using Next-Generation Sequencing
by Si-Qi Tao, Bin Cao, Cheng-Ming Tian and Ying-Mei Liang
Int. J. Mol. Sci. 2018, 19(4), 1178; https://doi.org/10.3390/ijms19041178 - 12 Apr 2018
Cited by 9 | Viewed by 4422
Abstract
The Apple-Juniper rust, Gymnosporangium yamadae, is an economically important pathogen of apples and junipers in Asia. The absence of markers has hampered the study of the genetic diversity of this widespread pathogen. In our study, we developed twenty-two novel microsatellite markers for [...] Read more.
The Apple-Juniper rust, Gymnosporangium yamadae, is an economically important pathogen of apples and junipers in Asia. The absence of markers has hampered the study of the genetic diversity of this widespread pathogen. In our study, we developed twenty-two novel microsatellite markers for G. yamadae from randomly sequenced regions of the transcriptome, using next-generation sequencing methods. These polymorphic markers were also tested on 96 G. yamadae individuals from two geographical populations. The allele numbers ranged from 2 to 9 with an average value of 6 per locus. The polymorphism information content (PIC) values ranged from 0.099 to 0.782 with an average value of 0.48. Furthermore, the observed (HO) and expected (HE) heterozygosity ranged from 0.000 to 0.683 and 0.04 to 0.820, respectively. These novel developed microsatellites provide abundant molecular markers for investigating the genetic structure and genetic diversity of G. yamadae, which will help us to better understand disease epidemics and the origin and migration routes of the Apple-Juniper rust pathogen. Further studies will also be completed to dissect how human activities influence the formation of current population structures. Furthermore, these SSR (simple sequence repeat) markers can also be used as tools to identify virulence by mapping the whole genomes of different virulent populations. These markers will, thus, assist the development of effective risk-assessment models and management systems for the Apple-Juniper rust pathogen. Full article
(This article belongs to the Special Issue Plant–Fungal Interactions)
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20 pages, 26911 KiB  
Article
Establishing a Split Luciferase Assay for Proteinkinase G (PKG) Interaction Studies
by Andrea Schramm, Philip Mueller-Thuemen, Timo Littmann, Manuela Harloff, Takeaki Ozawa and Jens Schlossmann
Int. J. Mol. Sci. 2018, 19(4), 1180; https://doi.org/10.3390/ijms19041180 - 12 Apr 2018
Cited by 4 | Viewed by 5489
Abstract
Nitric oxide (NO/cyclic guanosine monophosphate (cGMP)-regulated cellular mechanisms are involved in a variety of (patho-) physiological processes. One of the main effector molecules in this system, proteinkinase G (PKG), serves as a molecular switch by phosphorylating different target proteins and thereby turning them [...] Read more.
Nitric oxide (NO/cyclic guanosine monophosphate (cGMP)-regulated cellular mechanisms are involved in a variety of (patho-) physiological processes. One of the main effector molecules in this system, proteinkinase G (PKG), serves as a molecular switch by phosphorylating different target proteins and thereby turning them on or off. To date, only a few interaction partners of PKG have been described although the identification of protein–protein interactions (PPI) is indispensable for the understanding of cellular processes and diseases. Conventionally used methods to detect PPIs exhibit several disadvantages, e.g., co-immunoprecipitations, which depend on suitable high-affinity antibodies. Therefore, we established a cell-based protein-fragment complementation assay (PCA) for the identification of PKG target proteins. Here, a reporter protein (click beetle luciferase) is split into two fragments and fused to two different possible interaction partners. If interaction occurs, the reporter protein is functionally complemented and the catalyzed reaction can then be quantitatively measured. By using this technique, we confirmed the regulator of G-Protein signaling 2 (RGS2) as an interaction partner of PKGIα (a PKG-isoform) following stimulation with 8-Br-cGMP and 8-pCPT-cGMP. Hence, our results support the conclusion that the established approach could serve as a novel tool for the rapid, easy and cost-efficient detection of novel PKG target proteins. Full article
(This article belongs to the Special Issue cGMP-Signalling in Cells: Molecular and Functional Features)
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16 pages, 9239 KiB  
Article
An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking
by Boxin Guan, Changsheng Zhang and Yuhai Zhao
Int. J. Mol. Sci. 2018, 19(4), 1181; https://doi.org/10.3390/ijms19041181 - 13 Apr 2018
Cited by 10 | Viewed by 3820
Abstract
Protein–ligand docking is a process of searching for the optimal binding conformation between the receptor and the ligand. Automated docking plays an important role in drug design, and an efficient search algorithm is needed to tackle the docking problem. To tackle the protein–ligand [...] Read more.
Protein–ligand docking is a process of searching for the optimal binding conformation between the receptor and the ligand. Automated docking plays an important role in drug design, and an efficient search algorithm is needed to tackle the docking problem. To tackle the protein–ligand docking problem more efficiently, An ABC_DE_based hybrid algorithm (ADHDOCK), integrating artificial bee colony (ABC) algorithm and differential evolution (DE) algorithm, is proposed in the article. ADHDOCK applies an adaptive population partition (APP) mechanism to reasonably allocate the computational resources of the population in each iteration process, which helps the novel method make better use of the advantages of ABC and DE. The experiment tested fifty protein–ligand docking problems to compare the performance of ADHDOCK, ABC, DE, Lamarckian genetic algorithm (LGA), running history information guided genetic algorithm (HIGA), and swarm optimization for highly flexible protein–ligand docking (SODOCK). The results clearly exhibit the capability of ADHDOCK toward finding the lowest energy and the smallest root-mean-square deviation (RMSD) on most of the protein–ligand docking problems with respect to the other five algorithms. Full article
(This article belongs to the Section Molecular Biophysics)
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13 pages, 8094 KiB  
Article
Expressing OsMPK4 Impairs Plant Growth but Enhances the Resistance of Rice to the Striped Stem Borer Chilo suppressalis
by Xiaoli Liu, Jiancai Li, Liping Xu, Qi Wang and Yonggen Lou
Int. J. Mol. Sci. 2018, 19(4), 1182; https://doi.org/10.3390/ijms19041182 - 13 Apr 2018
Cited by 28 | Viewed by 5397
Abstract
Mitogen-activated protein kinases (MPKs) play a central role not only in plant growth and development, but also in plant responses to abiotic and biotic stresses, including pathogens. Yet, their role in herbivore-induced plant defenses and their underlying mechanisms remain largely unknown. Here, we [...] Read more.
Mitogen-activated protein kinases (MPKs) play a central role not only in plant growth and development, but also in plant responses to abiotic and biotic stresses, including pathogens. Yet, their role in herbivore-induced plant defenses and their underlying mechanisms remain largely unknown. Here, we cloned a rice MPK gene, OsMPK4, whose expression was induced by mechanical wounding, infestation of the striped stem borer (SSB) Chilo suppressalis, and treatment with jasmonic acid (JA), but not by treatment with salicylic acid (SA). The overexpression of OsMPK4 (oe-MPK4) enhanced constitutive and/or SSB-induced levels of JA, jasmonoyl-l-isoleucine (JA-Ile), ethylene (ET), and SA, as well as the activity of elicited trypsin proteinase inhibitors (TrypPIs), and reduced SSB performance. On the other hand, compared to wild-type plants, oe-MPK4 lines in the greenhouse showed growth retardation. These findings suggest that OsMPK4, by regulating JA-, ET-, and SA-mediated signaling pathways, functions as a positive regulator of rice resistance to the SSB and a negative regulator of rice growth. Full article
(This article belongs to the Special Issue Plant Innate Immunity 2.0)
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12 pages, 15408 KiB  
Article
The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding
by Ana Sara Gomes, Filipa Trovão, Benedita Andrade Pinheiro, Filipe Freire, Sara Gomes, Carla Oliveira, Lucília Domingues, Maria João Romão, Lucília Saraiva and Ana Luísa Carvalho
Int. J. Mol. Sci. 2018, 19(4), 1184; https://doi.org/10.3390/ijms19041184 - 13 Apr 2018
Cited by 16 | Viewed by 6123
Abstract
The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and [...] Read more.
The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and maintenance. For these reasons, the reactivation of p53 function is regarded as a promising strategy to halt cancer. In the present work, the recombinant mutant p53R280K DNA binding domain (DBD) was produced for the first time, and its crystal structure was determined in the absence of DNA to a resolution of 2.0 Å. The solved structure contains four molecules in the asymmetric unit, four zinc(II) ions, and 336 water molecules. The structure was compared with the wild-type p53 DBD structure, isolated and in complex with DNA. These comparisons contributed to a deeper understanding of the mutant p53R280K structure, as well as the loss of DNA binding related to halted transcriptional activity. The structural information derived may also contribute to the rational design of mutant p53 reactivating molecules with potential application in cancer treatment. Full article
(This article belongs to the Section Molecular Biophysics)
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13 pages, 8126 KiB  
Article
Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers
by Liling Zhao, Zanxia Cao, Yunqiang Bian, Guodong Hu, Jihua Wang and Yaoqi Zhou
Int. J. Mol. Sci. 2018, 19(4), 1186; https://doi.org/10.3390/ijms19041186 - 13 Apr 2018
Cited by 51 | Viewed by 7664
Abstract
Cathelicidins are a large family of cationic antimicrobial peptides (AMPs) found in mammals with broad spectrum antimicrobial activity. LL-37 is the sole amphipathic α-helical AMP from human Cathelicidins family. In addition to its bactericidal capability, LL-37 has antiviral, anti-tumor, and immunoregulatory activity. Despite [...] Read more.
Cathelicidins are a large family of cationic antimicrobial peptides (AMPs) found in mammals with broad spectrum antimicrobial activity. LL-37 is the sole amphipathic α-helical AMP from human Cathelicidins family. In addition to its bactericidal capability, LL-37 has antiviral, anti-tumor, and immunoregulatory activity. Despite many experimental studies, its molecular mechanism of action is not yet fully understood. Here, we performed three independent molecular dynamics simulations (600 ns or more) of a LL-37 peptide in the presence of 256 lipid bilayers with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) mimicking bacterial and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) mimicking mammalian membranes. We found that LL-37 can be quickly absorbed onto the POPG bilayer without loss of its helical conformation in the core region and with the helix lying in parallel to the bilayer. The POPG bilayer was deformed. In contrast, LL-37 is slower in reaching the POPC surface and loss much of its helical conformation during the interaction with the bilayer. LL-37 only partially entered the POPC bilayer without significant deformation of the membrane. The observed difference for different bilayers is largely due to the fact that LL-37 is positively charged, POPG is negatively charged, and POPC is neutral. Our simulation results demonstrated the initial stage of disruption of the bacterial membrane by LL-37 in atomic details. Comparison to experimental results on LL-37 and simulation studies in other systems was made. Full article
(This article belongs to the Special Issue Computational Studies of Structure-Dynamics-Function Relationships in Biomolecules)
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15 pages, 12684 KiB  
Article
Molecular and Ultrastructural Mechanisms Underlying Yellow Dwarf Symptom Formation in Wheat after Infection of Barley Yellow Dwarf Virus
by Wei Rong, Xindong Wang, Xifeng Wang, Sebastien Massart and Zengyan Zhang
Int. J. Mol. Sci. 2018, 19(4), 1187; https://doi.org/10.3390/ijms19041187 - 13 Apr 2018
Cited by 18 | Viewed by 5233
Abstract
Wheat (Tritium aestivum L.) production is essential for global food security. Infection of barley yellow dwarf virus-GAV (BYDV-GAV) results in wheat showing leaf yellowing and plant dwarfism symptom. To explore the molecular and ultrastructural mechanisms underlying yellow dwarf symptom formation in BYDV-GAV-infected [...] Read more.
Wheat (Tritium aestivum L.) production is essential for global food security. Infection of barley yellow dwarf virus-GAV (BYDV-GAV) results in wheat showing leaf yellowing and plant dwarfism symptom. To explore the molecular and ultrastructural mechanisms underlying yellow dwarf symptom formation in BYDV-GAV-infected wheat, we investigated the chloroplast ultrastructure via transmission electron microscopy (TEM), examined the contents of the virus, H2O2, and chlorophyll in Zhong8601, and studied the comparative transcriptome through microarray analyses in the susceptible wheat line Zhong8601 after virus infection. TEM images indicated that chloroplasts in BYDV-GAV-infected Zhong8601 leaf cells were fragmentized. Where thylakoids were not well developed, starch granules and plastoglobules were rare. Compared with mock-inoculated Zhong8601, chlorophyll content was markedly reduced, but the virus and H2O2 contents were significantly higher in BYDV-GAV-infected Zhong8601. The transcriptomic analyses revealed that chlorophyll biosynthesis and chloroplast related transcripts, encoding chlorophyll a/b binding protein, glucose-6-phosphate/phosphate translocator 2, and glutamyl-tRNA reductase 1, were down-regulated in BYDV-GAV-infected Zhong8601. Some phytohormone signaling-related transcripts, including abscisic acid (ABA) signaling factors (phospholipase D alpha 1 and calcineurin B-like protein 9) and nine ethylene response factors, were up-regulated. Additionally, reactive oxygen species (ROS)-related genes were transcriptionally regulated in BYDV-GAV infected Zhong8601, including three up-regulated transcripts encoding germin-like proteins (promoting ROS accumulation) and four down-regulated transcripts encoding peroxides (scavenging ROS). These results clearly suggest that the yellow dwarf symptom formation is mainly attributed to reduced chlorophyll content and fragmentized chloroplasts caused by down-regulation of the chlorophyll and chloroplast biosynthesis related genes, ROS excessive accumulation, and precisely transcriptional regulation of the above-mentioned ABA and ethylene signaling- and ROS-related genes in susceptible wheat infected by BYDV-GAV. Full article
(This article belongs to the Special Issue Plant Defense Genes Against Biotic Stresses)
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15 pages, 35521 KiB  
Article
A Lipophilic IR-780 Dye-Encapsulated Zwitterionic Polymer-Lipid Micellar Nanoparticle for Enhanced Photothermal Therapy and NIR-Based Fluorescence Imaging in a Cervical Tumor Mouse Model
by Santhosh Kalash Rajendrakumar, Ning-Chu Chang, Adityanarayan Mohapatra, Saji Uthaman, Byeong-Il Lee, Wei-bor Tsai and In-Kyu Park
Int. J. Mol. Sci. 2018, 19(4), 1189; https://doi.org/10.3390/ijms19041189 - 13 Apr 2018
Cited by 29 | Viewed by 8326
Abstract
To prolong blood circulation and avoid the triggering of immune responses, nanoparticles in the bloodstream require conjugation with polyethylene glycol (PEG). However, PEGylation hinders the interaction between the nanoparticles and the tumor cells and therefore limits the applications of PEGylated nanoparticles for therapeutic [...] Read more.
To prolong blood circulation and avoid the triggering of immune responses, nanoparticles in the bloodstream require conjugation with polyethylene glycol (PEG). However, PEGylation hinders the interaction between the nanoparticles and the tumor cells and therefore limits the applications of PEGylated nanoparticles for therapeutic drug delivery. To overcome this limitation, zwitterionic materials can be used to enhance the systemic blood circulation and tumor-specific delivery of hydrophobic agents such as IR-780 iodide dye for photothermal therapy. Herein, we developed micellar nanoparticles using the amphiphilic homopolymer poly(12-(methacryloyloxy)dodecyl phosphorylcholine) (PCB-lipid) synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization. The PCB-lipid can self-assemble into micelles and encapsulate IR-780 dye (PCB-lipid–IR-780). Our results demonstrated that PCB-lipid–IR-780 nanoparticle (NP) exhibited low cytotoxicity and remarkable photothermal cytotoxicity to cervical cancer cells (TC-1) upon near-infrared (NIR) laser irradiation. The biodistribution of PCB-lipid–IR-780 showed higher accumulation of PCB-lipid–IR-780 than that of free IR-780 in the TC-1 tumor. Furthermore, following NIR laser irradiation of the tumor region, the PCB-lipid–IR-780 accumulated in the tumor facilitated enhanced tumor ablation and subsequent tumor regression in the TC-1 xenograft model. Hence, these zwitterionic polymer-lipid hybrid micellar nanoparticles show great potential for cancer theranostics and might be beneficial for clinical applications. Full article
(This article belongs to the Special Issue Smart Polymers for Biomedical Applications)
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13 pages, 3324 KiB  
Article
iAPSL-IF: Identification of Apoptosis Protein Subcellular Location Using Integrative Features Captured from Amino Acid Sequences
by Yadong Tang, Lu Xie and Lanming Chen
Int. J. Mol. Sci. 2018, 19(4), 1190; https://doi.org/10.3390/ijms19041190 - 13 Apr 2018
Cited by 2 | Viewed by 2923
Abstract
Apoptosis proteins (APs) control normal tissue homeostasis by regulating the balance between cell proliferation and death. The function of APs is strongly related to their subcellular location. To date, computational methods have been reported that reliably identify the subcellular location of APs, however, [...] Read more.
Apoptosis proteins (APs) control normal tissue homeostasis by regulating the balance between cell proliferation and death. The function of APs is strongly related to their subcellular location. To date, computational methods have been reported that reliably identify the subcellular location of APs, however, there is still room for improvement of the prediction accuracy. In this study, we developed a novel method named iAPSL-IF (identification of apoptosis protein subcellular location—integrative features), which is based on integrative features captured from Markov chains, physicochemical property matrices, and position-specific score matrices (PSSMs) of amino acid sequences. The matrices with different lengths were transformed into fixed-length feature vectors using an auto cross-covariance (ACC) method. An optimal subset of the features was chosen using a recursive feature elimination (RFE) algorithm method, and the sequences with these features were trained by a support vector machine (SVM) classifier. Based on three datasets ZD98, CL317, and ZW225, the iAPSL-IF was examined using a jackknife cross-validation test. The resulting data showed that the iAPSL-IF outperformed the known predictors reported in the literature: its overall accuracy on the three datasets was 98.98% (ZD98), 94.95% (CL317), and 97.33% (ZW225), respectively; the Matthews correlation coefficient, sensitivity, and specificity for several classes of subcellular location proteins (e.g., membrane proteins, cytoplasmic proteins, endoplasmic reticulum proteins, nuclear proteins, and secreted proteins) in the datasets were 0.92–1.0, 94.23–100%, and 97.07–100%, respectively. Overall, the results of this study provide a high throughput and sequence-based method for better identification of the subcellular location of APs, and facilitates further understanding of programmed cell death in organisms. Full article
(This article belongs to the Section Molecular Biophysics)
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19 pages, 11317 KiB  
Article
gga-miR-451 Negatively Regulates Mycoplasma gallisepticum (HS Strain)-Induced Inflammatory Cytokine Production via Targeting YWHAZ
by Yabo Zhao, Kang Zhang, Mengyun Zou, Yingfei Sun and Xiuli Peng
Int. J. Mol. Sci. 2018, 19(4), 1191; https://doi.org/10.3390/ijms19041191 - 13 Apr 2018
Cited by 24 | Viewed by 3841
Abstract
Mycoplasma gallisepticum (MG) is the most economically significant mycoplasma pathogen of poultry that causes chronic respiratory disease (CRD) in chickens. Although miRNAs have been identified as a major regulator effect on inflammatory response, it is largely unclear how they regulate MG-induced inflammation. The [...] Read more.
Mycoplasma gallisepticum (MG) is the most economically significant mycoplasma pathogen of poultry that causes chronic respiratory disease (CRD) in chickens. Although miRNAs have been identified as a major regulator effect on inflammatory response, it is largely unclear how they regulate MG-induced inflammation. The aim of this study was to investigate the functional roles of gga-miR-451 and identify downstream targets regulated by gga-miR-451 in MG infection of chicken. We found that the expression of gga-miR-451 was significantly up-regulated during MG infection of chicken embryo fibroblast cells (DF-1) and chicken embryonic lungs. Overexpression of gga-miR-451 decreased the MG-induced inflammatory cytokine production, including tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6), whereas inhibition of gga-miR-451 had the opposite effect. Gene expression data combined with luciferase reporter assays demonstrated that tyrosine3-monooxygenase/tryptophan5-monooxygenase activation protein zeta (YWHAZ) was identified as a direct target of gga-miR-451 in the context of MG infection. Furthermore, upregulation of gga-miR-451 significantly inhibited the MG-infected DF-1 cells proliferation, induced cell-cycle arrest, and promoted apoptosis. Collectively, our results demonstrate that gga-miR-451 negatively regulates the MG-induced production of inflammatory cytokines via targeting YWHAZ, inhibits the cell cycle progression and cell proliferation, and promotes cell apoptosis. This study provides a better understanding of the molecular mechanisms of MG infection. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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14 pages, 3426 KiB  
Article
Separate and Combined Response to UV-B Radiation and Jasmonic Acid on Photosynthesis and Growth Characteristics of Scutellaria baicalensis
by Jiaxin Quan, Shanshan Song, Kadir Abdulrashid, Yongfu Chai, Ming Yue and Xiao Liu
Int. J. Mol. Sci. 2018, 19(4), 1194; https://doi.org/10.3390/ijms19041194 - 13 Apr 2018
Cited by 17 | Viewed by 4225
Abstract
The negative effects of enhanced ultraviolet-B (UV-B) on plant growth and development have been reported with many species. Considering the ability of jasmonic acid (JA) to improve plant stress tolerance, the hypothesis that JA pretreatment could alleviate the adverse effects of UV-B on [...] Read more.
The negative effects of enhanced ultraviolet-B (UV-B) on plant growth and development have been reported with many species. Considering the ability of jasmonic acid (JA) to improve plant stress tolerance, the hypothesis that JA pretreatment could alleviate the adverse effects of UV-B on S. baicalensis was tested in this study with photosynthesis and growth characteristics. The results showed that UV-B or JA alone both induced photosynthesis inhibition and decreased biomass in stems and leaves. However, the photosynthetic reduction caused by increased UV-B was mainly related to the effect of nonstomatal-limitation, while that of JA was a stomatal-limitation effect. JA pretreatment prior to UV-B could remit the photosynthetic inhibition via the recovery of chlorophyll content, stomatal conductance; and intercellular CO2 concentration (especially the maximum electron transport rate increase). Furthermore, the coaction of JA and enhanced UV-B alleviated some disadvantageous effects on the leaf and did not aggravate the growth damage induced by their separate actions. Full article
(This article belongs to the Special Issue Phytohormones and Their Crosstalk during Plant Growth, Development and Environmental Stress Adaptation)
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15 pages, 2581 KiB  
Article
Inhibitory Effects of Human Primary Intervertebral Disc Cells on Human Primary Osteoblasts in a Co-Culture System
by Rahel D. May, Daniela A. Frauchiger, Christoph E. Albers, Lorin M. Benneker, Sandro Kohl and Benjamin Gantenbein
Int. J. Mol. Sci. 2018, 19(4), 1195; https://doi.org/10.3390/ijms19041195 - 13 Apr 2018
Cited by 10 | Viewed by 3731
Abstract
Spinal fusion is a common surgical procedure to address a range of spinal pathologies, like damaged or degenerated discs. After the removal of the intervertebral disc (IVD), a structural spacer is positioned followed by internal fixation, and fusion of the degenerated segment by [...] Read more.
Spinal fusion is a common surgical procedure to address a range of spinal pathologies, like damaged or degenerated discs. After the removal of the intervertebral disc (IVD), a structural spacer is positioned followed by internal fixation, and fusion of the degenerated segment by natural bone growth. Due to their osteoinductive properties, bone morphogenetic proteins (BMP) are applied to promote spinal fusion. Although spinal fusion is successful in most patients, the rates of non-unions after lumbar spine fusion range from 5% to 35%. Clinical observations and recent studies indicate, that the incomplete removal of disc tissue might lead to failure of spinal fusion. Yet, it is still unknown if a secretion of BMP antagonists in intervertebral disc (IVD) cells could be the reason of inhibition in bone formation. In this study, we co-cultured human primary osteoblasts (OB) and IVD cells i.e., nucleus pulposus (NPC), annulus fibrosus (AFC) and cartilaginous endplate cells (CEPC), to test the possible inhibitory effect from IVD cells on OB. Although we could see a trend in lower matrix mineralization in OB co-cultured with IVD cells, results of alkaline phosphatase (ALP) activity and gene expression of major bone genes were inconclusive. However, in NPC, AFC and CEPC beads, an up-regulation of several BMP antagonist genes could be detected. Despite being able to show several indicators for an inhibition of osteoinductive effects due to IVD cells, the reasons for pseudarthrosis after spinal fusion remain unclear. Full article
(This article belongs to the Special Issue Musculoskeletal Diseases Therapy)
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17 pages, 11576 KiB  
Article
Calsenilin, a Presenilin Interactor, Regulates RhoA Signaling and Neurite Outgrowth
by Hee-Jun Kim, Won-Haeng Lee, Mo-Jong Kim, Sunmee Shin, Byungki Jang, Jae-Bong Park, Wilma Wasco, Joseph D. Buxbaum, Yong-Sun Kim and Eun-Kyoung Choi
Int. J. Mol. Sci. 2018, 19(4), 1196; https://doi.org/10.3390/ijms19041196 - 13 Apr 2018
Cited by 4 | Viewed by 5095
Abstract
Calsenilin modulates A-type potassium channels, regulates presenilin-mediated γ-secretase activity, and represses prodynorphin and c-fos genes expression. RhoA is involved in various cellular functions including proliferation, differentiation, migration, transcription, and regulation of the actin cytoskeleton. Although recent studies demonstrate that calsenilin can directly interact [...] Read more.
Calsenilin modulates A-type potassium channels, regulates presenilin-mediated γ-secretase activity, and represses prodynorphin and c-fos genes expression. RhoA is involved in various cellular functions including proliferation, differentiation, migration, transcription, and regulation of the actin cytoskeleton. Although recent studies demonstrate that calsenilin can directly interact with RhoA and that RhoA inactivation is essential for neuritogenesis, it is uncertain whether there is a link between calsenilin and RhoA-regulated neuritogenesis. Here, we investigated the role of calsenilin in RhoA-regulated neuritogenesis using in vitro and in vivo systems. We found that calsenilin induced RhoA inactivation, which accompanied RhoA phosphorylation and the reduced phosphorylation levels of LIM kinase (LIMK) and cofilin. Interestingly, PC12 cells overexpressing either full-length (FL) or the caspase 3-derived C-terminal fragment (CTF) of calsenilin significantly inactivated RhoA through its interaction with RhoA and p190 Rho GTPase-activating protein (p190RhoGAP). In addition, cells expressing FL and the CTF of calsenilin had increased neurite outgrowth compared to cells expressing the N-terminal fragment (NTF) of calsenilin or vector alone. Moreover, Tat-C3 and Y27632 treatment significantly increased the percentage of neurite-bearing cells, neurite length, and the number of neurites in cells. Finally, calsenilin deficiency in the brains of calsenilin-knockout mice significantly interfered with RhoA inactivation. These findings suggest that calsenilin contributes to neuritogenesis through RhoA inactivation. Full article
(This article belongs to the Special Issue Calcium Binding Proteins)
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22 pages, 7581 KiB  
Article
Hyperinsulinemia Promotes Esophageal Cancer Development in a Surgically-Induced Duodeno-Esophageal Reflux Murine Model
by Diletta Arcidiacono, Arben Dedja, Cinzia Giacometti, Matteo Fassan, Daniele Nucci, Simona Francia, Federico Fabris, Alice Zaramella, Emily J. Gallagher, Mauro Cassaro, Massimo Rugge, Derek LeRoith, Alfredo Alberti and Stefano Realdon
Int. J. Mol. Sci. 2018, 19(4), 1198; https://doi.org/10.3390/ijms19041198 - 14 Apr 2018
Cited by 18 | Viewed by 4865
Abstract
Hyperinsulinemia could have a role in the growing incidence of esophageal adenocarcinoma (EAC) and its pre-cancerous lesion, Barrett’s Esophagus, a possible consequence of Gastro-Esophageal Reflux Disease. Obesity is known to mediate esophageal carcinogenesis through different mechanisms including insulin-resistance leading to hyperinsulinemia, which may [...] Read more.
Hyperinsulinemia could have a role in the growing incidence of esophageal adenocarcinoma (EAC) and its pre-cancerous lesion, Barrett’s Esophagus, a possible consequence of Gastro-Esophageal Reflux Disease. Obesity is known to mediate esophageal carcinogenesis through different mechanisms including insulin-resistance leading to hyperinsulinemia, which may mediate cancer progression via the insulin/insulin-like growth factor axis. We used the hyperinsulinemic non-obese FVB/N (Friend leukemia virus B strain) MKR (muscle (M)-IGF1R-lysine (K)-arginine (R) mouse model to evaluate the exclusive role of hyperinsulinemia in the pathogenesis of EAC related to duodeno-esophageal reflux. FVB/N wild-type (WT) and MKR mice underwent jejunum-esophageal anastomosis side—to end with the exclusion of the stomach. Thirty weeks after surgery, the esophagus was processed for histological, immunological and insulin/Insulin-like growth factor 1 (IGF1) signal transduction analyses. Most of the WT mice (63.1%) developed dysplasia, whereas most of the MKR mice (74.3%) developed squamous cell and adenosquamous carcinomas, both expressing Human Epidermal growth factor receptor 2 (HER2). Hyperinsulinemia significantly increased esophageal cancer incidence in the presence of duodenal-reflux. Insulin receptor (IR) and IGF1 receptor (IGF1R) were overexpressed in the hyperinsulinemic condition. IGF1R, through ERK1/2 mitogenic pattern activation, seems to be involved in cancer onset. Hyperinsulinemia-induced IGF1R and HER2 up-regulation could also increase the possibility of forming of IGF1R/HER2 heterodimers to support cell growth/proliferation/progression in esophageal carcinogenesis. Full article
(This article belongs to the Special Issue Insulin and Insulin Receptor in Diseases)
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11 pages, 6179 KiB  
Article
Serum Is Not Necessary for Prior Pharmacological Activation of AMPK to Increase Insulin Sensitivity of Mouse Skeletal Muscle
by Nicolas O. Jørgensen, Jørgen F. P. Wojtaszewski and Rasmus Kjøbsted
Int. J. Mol. Sci. 2018, 19(4), 1201; https://doi.org/10.3390/ijms19041201 - 15 Apr 2018
Cited by 5 | Viewed by 4503
Abstract
Exercise, contraction, and pharmacological activation of AMP-activated protein kinase (AMPK) by 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) have all been shown to increase muscle insulin sensitivity for glucose uptake. Intriguingly, improvements in insulin sensitivity following contraction of isolated rat and mouse skeletal muscle and prior AICAR [...] Read more.
Exercise, contraction, and pharmacological activation of AMP-activated protein kinase (AMPK) by 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) have all been shown to increase muscle insulin sensitivity for glucose uptake. Intriguingly, improvements in insulin sensitivity following contraction of isolated rat and mouse skeletal muscle and prior AICAR stimulation of isolated rat skeletal muscle seem to depend on an unknown factor present in serum. One study recently questioned this requirement of a serum factor by showing serum-independency with muscle from old rats. Whether a serum factor is necessary for prior AICAR stimulation to increase insulin sensitivity of mouse skeletal muscle is not known. Therefore, we investigated the necessity of serum for this effect of AICAR in mouse skeletal muscle. We found that the ability of prior AICAR stimulation to improve insulin sensitivity of mouse skeletal muscle did not depend on the presence of serum during AICAR stimulation. Although prior AICAR stimulation did not enhance proximal insulin signaling, insulin-stimulated phosphorylation of Tre-2/BUB2/CDC16- domain family member 4 (TBC1D4) Ser711 was greater in prior AICAR-stimulated muscle compared to all other groups. These results imply that the presence of a serum factor is not necessary for prior AMPK activation by AICAR to enhance insulin sensitivity of mouse skeletal muscle. Full article
(This article belongs to the Special Issue AMP-Activated Protein Kinase Signalling)
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15 pages, 7262 KiB  
Article
Nitrate Reductases Are Relocalized to the Nucleus by AtSIZ1 and Their Levels Are Negatively Regulated by COP1 and Ammonium
by Joo Yong Kim, Bong Soo Park, Sang Woo Park, Han Yong Lee, Jong Tae Song and Hak Soo Seo
Int. J. Mol. Sci. 2018, 19(4), 1202; https://doi.org/10.3390/ijms19041202 - 15 Apr 2018
Cited by 20 | Viewed by 5003
Abstract
Nitrate reductases (NRs) catalyze the first step in the reduction of nitrate to ammonium. NR activity is regulated by sumoylation through the E3 ligase activity of AtSIZ1. However, it is not clear how NRs interact with AtSIZ1 in the cell, or how nitrogen [...] Read more.
Nitrate reductases (NRs) catalyze the first step in the reduction of nitrate to ammonium. NR activity is regulated by sumoylation through the E3 ligase activity of AtSIZ1. However, it is not clear how NRs interact with AtSIZ1 in the cell, or how nitrogen sources affect NR levels and their cellular localization. Here, we show that the subcellular localization of NRs is modulated by the E3 SUMO (Small ubiquitin-related modifier) ligase AtSIZ1 and that NR protein levels are regulated by nitrogen sources. Transient expression analysis of GFP fusion proteins in onion epidermal cells showed that the NRs NIA1 and NIA2 localize to the cytoplasmic membrane, and that AtSIZ1 localizes to the nucleoplasm, including nuclear bodies, when expressed separately, whereas NRs and AtSIZ1 localize to the nucleus when co-expressed. Nitrate did not affect the subcellular localization of the NRs, but it caused AtSIZ1 to move from the nucleus to the cytoplasm. NRs were not detected in ammonium-treated cells, whereas the localization of AtSIZ1 was not altered by ammonium treatment. NR protein levels increased in response to nitrate but decreased in response to ammonium. In addition, NR protein levels increased in response to a 26S proteasome inhibitor and in cop1-4 and DN-COP1-overexpressing transgenic plants. NR protein degradation occurred later in cop1-4 than in the wild-type, although the NR proteins did not interact with COP1. Therefore, AtSIZ1 controls nuclear localization of NR proteins, and ammonium negatively regulates their levels. The function and stability of NR proteins might be post-translationally modulated by ubiquitination. Full article
(This article belongs to the Section Molecular Plant Sciences)
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17 pages, 47618 KiB  
Article
Cloning, Characterization, and Functional Investigation of VaHAESA from Vitis amurensis Inoculated with Plasmopara viticola
by Shaoli Liu, Chi Zhang, Nan Chao, Jiang Lu and Yali Zhang
Int. J. Mol. Sci. 2018, 19(4), 1204; https://doi.org/10.3390/ijms19041204 - 16 Apr 2018
Cited by 9 | Viewed by 4577
Abstract
Plant pattern recognition receptors (PRRs) are essential for immune responses and establishing symbiosis. Plants detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by PRRs. This phenomenon is termed PAMP-triggered immunity (PTI). We investigated disease resistance in Vitis amurensis to identify PRRs [...] Read more.
Plant pattern recognition receptors (PRRs) are essential for immune responses and establishing symbiosis. Plants detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by PRRs. This phenomenon is termed PAMP-triggered immunity (PTI). We investigated disease resistance in Vitis amurensis to identify PRRs that are important for resistance against downy mildew, analyzed the PRRs that were upregulated by incompatible Plasmopara viticola infection, and cloned the full-length cDNA of the VaHAESA gene. We then analyzed the structure, subcellular localization, and relative disease resistance of VaHAESA. VaHAESA and PRR-receptor-like kinase 5 (RLK5) are highly similar, belonging to the leucine-rich repeat (LRR)-RLK family and localizing to the plasma membrane. The expression of PRR genes changed after the inoculation of V. amurensis with compatible and incompatible P. viticola; during early disease development, transiently transformed V. vinifera plants expressing VaHAESA were more resistant to pathogens than those transformed with the empty vector and untransformed controls, potentially due to increased H2O2, NO, and callose levels in the transformants. Furthermore, transgenic Arabidopsis thaliana showed upregulated expression of genes related to the PTI pathway and improved disease resistance. These results show that VaHAESA is a positive regulator of resistance against downy mildew in grapevines. Full article
(This article belongs to the Special Issue Plant Innate Immunity 2.0)
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14 pages, 12398 KiB  
Article
Transient Recombinant Protein Production in Glycoengineered Nicotiana benthamiana Cell Suspension Culture
by Sara C. Sukenik, Kalimuthu Karuppanan, Qiongyu Li, Carlito B. Lebrilla, Somen Nandi and Karen A. McDonald
Int. J. Mol. Sci. 2018, 19(4), 1205; https://doi.org/10.3390/ijms19041205 - 16 Apr 2018
Cited by 26 | Viewed by 7162
Abstract
Transient recombinant protein production is a promising alternative to stable transgenic systems, particularly for emergency situations in which rapid production of novel therapeutics is needed. In plants, Agrobacterium tumefaciens can be used as a gene delivery vector for transient expression. A potential barrier [...] Read more.
Transient recombinant protein production is a promising alternative to stable transgenic systems, particularly for emergency situations in which rapid production of novel therapeutics is needed. In plants, Agrobacterium tumefaciens can be used as a gene delivery vector for transient expression. A potential barrier for plant-based production of human therapeutics is that different glycosylation patterns are found on plant and mammalian proteins. Since glycosylation can affect the efficacy, safety and stability of a therapeutic protein, methods to control glycan structures and distributions in plant-based systems would be beneficial. In these studies, we performed Agrobacterium-mediated transient expression in glycoengineered plant cell suspension cultures. To reduce the presence of plant-specific glycans on the product, we generated and characterized cell suspension cultures from β-1,2-xylosyltransferase and α-1,3-fucosyltransferase knockdown Nicotiana benthamiana. An anthrax decoy fusion protein was transiently produced in these glycoengineered plant cell suspension cultures through co-culture with genetically engineered Agrobacterium. The mass ratio of Agrobacterium to plant cells used was shown to impact recombinant protein expression levels. N-glycosylation analysis on the anthrax decoy fusion protein produced in glycoengineered N. benthamiana showed a dramatic reduction in plant-specific N-glycans. Overall, the results presented here demonstrate the feasibility of a simple, rapid and scalable process for transient production of recombinant proteins without plant-specific glycans in a glycoengineered plant cell culture host. Full article
(This article belongs to the Special Issue Recombinant Proteins)
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12 pages, 5672 KiB  
Article
MicroRNAs Targeting Caspase-3 and -7 in PANC-1 Cells
by Jong Kook Park, Andrea I. Doseff and Thomas D. Schmittgen
Int. J. Mol. Sci. 2018, 19(4), 1206; https://doi.org/10.3390/ijms19041206 - 16 Apr 2018
Cited by 29 | Viewed by 9051
Abstract
MicroRNAs (miRNAs), a critical part of the RNA silencing machinery, are known to play important regulatory roles in cancer. However, the consequence of miRNA deregulation in cancer is unknown for many miRNAs. Here, we define that miRNAs, miR-17-5p, miR-132-3p/-212-3p, and miR-337-3p are significantly [...] Read more.
MicroRNAs (miRNAs), a critical part of the RNA silencing machinery, are known to play important regulatory roles in cancer. However, the consequence of miRNA deregulation in cancer is unknown for many miRNAs. Here, we define that miRNAs, miR-17-5p, miR-132-3p/-212-3p, and miR-337-3p are significantly up-regulated in the pancreatic ductal adenocarcinomas (PDAC) compared to the normal and benign tissues. Furthermore, by using PANC-1 cells, we demonstrate that overexpressed miR-337-3p and miR-17-5p/miR-132-3p/-212-3p can regulate executioner caspases-3 and -7, respectively. In addition, over-expression of miRNAs, especially miR-337-3p, attenuates tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) cytotoxicity in PANC-1 cells. Our findings unveil an important biological function for miRNAs up-regulated in PDAC in coordinately regulating caspases, potentially contributing to the malignant progression of PDAC. Full article
(This article belongs to the Special Issue Non-Coding RNAs and Epigenetics in Cancer & Selected Papers from the 2nd International Symposium on Frontiers in Molecular Science)
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22 pages, 5246 KiB  
Article
Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data
by Katarzyna Ropka-Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, Katarzyna Piórkowska, Grzegorz Żak, Artur Gurgul, Natalia Derebecka and Joanna Wesoły
Int. J. Mol. Sci. 2018, 19(4), 1208; https://doi.org/10.3390/ijms19041208 - 16 Apr 2018
Cited by 21 | Viewed by 4837
Abstract
Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, [...] Read more.
Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Pietrain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-β signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs. Full article
(This article belongs to the Special Issue Cell Growth Regulation)
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12 pages, 2957 KiB  
Article
Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia
by Lanmei Wang, Wenbin Zhu, Zaijie Dong, Feibiao Song, Juanjuan Dong and Jianjun Fu
Int. J. Mol. Sci. 2018, 19(4), 1209; https://doi.org/10.3390/ijms19041209 - 16 Apr 2018
Cited by 47 | Viewed by 6228
Abstract
Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs [...] Read more.
Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log2(fold change)| ≥ 1 and q-value ≤ 0.001) were identified. Target prediction and functional analysis of color-related miRNAs showed that a variety of putative target genes—including slc7a11, mc1r and asip—played potential roles in pigmentation. Moreover; the miRNA-mRNA regulatory network was illustrated to elucidate the pigmentation differentiation, in which miR-138-5p and miR-722 were predicted to play important roles in regulating the pigmentation process. These results advance our understanding of the molecular mechanisms of skin pigmentation differentiation in red tilapia. Full article
(This article belongs to the Section Biochemistry)
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20 pages, 7962 KiB  
Article
Antibacterial Efficacy of Silver Nanoparticles on Endometritis Caused by Prevotella melaninogenica and Arcanobacterum pyogenes in Dairy Cattle
by Sangiliyandi Gurunathan, Yun-Jung Choi and Jin-Hoi Kim
Int. J. Mol. Sci. 2018, 19(4), 1210; https://doi.org/10.3390/ijms19041210 - 16 Apr 2018
Cited by 70 | Viewed by 7103
Abstract
Bovine postpartum diseases remain one of the most significant and highly prevalent illnesses with negative effects on the productivity, survival, and welfare of dairy cows. Antibiotics are generally considered beneficial in the treatment of endometritis; however, frequent usage of each antibiotic drug is [...] Read more.
Bovine postpartum diseases remain one of the most significant and highly prevalent illnesses with negative effects on the productivity, survival, and welfare of dairy cows. Antibiotics are generally considered beneficial in the treatment of endometritis; however, frequent usage of each antibiotic drug is reason for the emergence of multidrug resistance (MDR) of the pathogenic microorganisms, representing a major impediment for the successful diagnosis and management of infectious diseases in both humans and animals. We synthesized silver nanoparticles (AgNPs) with an average size of 10 nm using the novel biomolecule apigenin as a reducing and stabilizing agent, and evaluated the efficacy of the AgNPs on the MDR pathogenic bacteria Prevotella melaninogenica and Arcanobacterium pyogenes isolated from uterine secretion samples. AgNPs inhibited cell viability and biofilm formation in a dose- and time-dependent manner. Moreover, the metabolic toxicity of the AgNPs was assessed through various cellular assays. The major toxic effect of cell death was caused by an increase in oxidative stress, as evidenced by the increased generation of reactive oxygen species (ROS), malondialdehyde, protein carbonyl content, and nitric oxide. The formation of ROS is considered to be the primary mechanism of bacterial death. Therefore, the biomolecule-mediated synthesis of AgNPs shows potential as an alternative antimicrobial therapy for bovine metritis and endometritis. Full article
(This article belongs to the Section Molecular Toxicology)
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14 pages, 20675 KiB  
Article
Brca1 Is Upregulated by 5-Aza-CdR and Promotes DNA Repair and Cell Survival, and Inhibits Neurite Outgrowth in Rat Retinal Neurons
by Qiyun Wang, Lijun Xu, Pei Chen, Zhuojun Xu, Jin Qiu, Jian Ge, Keming Yu and Jing Zhuang
Int. J. Mol. Sci. 2018, 19(4), 1214; https://doi.org/10.3390/ijms19041214 - 17 Apr 2018
Cited by 9 | Viewed by 3403
Abstract
Previous studies have reported that Brca1 acts as a “hinge” in the development of the central nervous system (CNS). However, the precise role of Brca1 in rat retinal neurons remains unclear. Here, we found that Brca1 is developmentally downregulated and silenced in adult [...] Read more.
Previous studies have reported that Brca1 acts as a “hinge” in the development of the central nervous system (CNS). However, the precise role of Brca1 in rat retinal neurons remains unclear. Here, we found that Brca1 is developmentally downregulated and silenced in adult retina. Brca1 was upregulated in rat primary retinal neurons by 5-Aza-2′-deoxycytidine (5-Aza-CdR) treatment. Moreover, the upregulation of Brca1 by both 5-Aza-CdR and transgenic Brca1 promoted genomic stability and improved cell viability following exposure to ionizing radiation (IR). Furthermore, transgenic Brca1 significantly inhibited neurite outgrowth of retinal neurons, which implicates that Brca1 silencing promotes cell differentiation and determines neuronal morphology. Taken together, our results reveal a biological function of Brca1 in retinal development. Full article
(This article belongs to the Section Biochemistry)
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15 pages, 9442 KiB  
Article
Mechanisms of Diabetes-Induced Endothelial Cell Senescence: Role of Arginase 1
by Esraa Shosha, Zhimin Xu, S. Priya Narayanan, Tahira Lemtalsi, Abdelrahman Y. Fouda, Modesto Rojas, Ji Xing, David Fulton, R. William Caldwell and Ruth B. Caldwell
Int. J. Mol. Sci. 2018, 19(4), 1215; https://doi.org/10.3390/ijms19041215 - 17 Apr 2018
Cited by 54 | Viewed by 6874
Abstract
We have recently found that diabetes-induced premature senescence of retinal endothelial cells is accompanied by NOX2-NADPH oxidase-induced increases in the ureohydrolase enzyme arginase 1 (A1). Here, we used genetic strategies to determine the specific involvement of A1 in diabetes-induced endothelial cell senescence. We [...] Read more.
We have recently found that diabetes-induced premature senescence of retinal endothelial cells is accompanied by NOX2-NADPH oxidase-induced increases in the ureohydrolase enzyme arginase 1 (A1). Here, we used genetic strategies to determine the specific involvement of A1 in diabetes-induced endothelial cell senescence. We used A1 knockout mice and wild type mice that were rendered diabetic with streptozotocin and retinal endothelial cells (ECs) exposed to high glucose or transduced with adenovirus to overexpress A1 for these experiments. ABH [2(S)-Amino-6-boronohexanoic acid] was used to inhibit arginase activity. We used Western blotting, immunolabeling, quantitative PCR, and senescence associated β-galactosidase (SA β-Gal) activity to evaluate senescence. Analyses of retinal tissue extracts from diabetic mice showed significant increases in mRNA expression of the senescence-related proteins p16INK4a, p21, and p53 when compared with non-diabetic mice. SA β-Gal activity and p16INK4a immunoreactivity were also increased in retinal vessels from diabetic mice. A1 gene deletion or pharmacological inhibition protected against the induction of premature senescence. A1 overexpression or high glucose treatment increased SA β-Gal activity in cultured ECs. These results demonstrate that A1 is critically involved in diabetes-induced senescence of retinal ECs. Inhibition of arginase activity may therefore be an effective therapeutic strategy to alleviate diabetic retinopathy by preventing premature senescence. Full article
(This article belongs to the Special Issue Diabetic Retinopathy: Mechanisms underlying Pathophysiology and Therapies)
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17 pages, 25726 KiB  
Article
Identification, Expression Analysis of the Hsf Family, and Characterization of Class A4 in Sedum Alfredii Hance under Cadmium Stress
by Shuang-Shuang Chen, Jing Jiang, Xiao-Jiao Han, Yun-Xing Zhang and Ren-Ying Zhuo
Int. J. Mol. Sci. 2018, 19(4), 1216; https://doi.org/10.3390/ijms19041216 - 17 Apr 2018
Cited by 31 | Viewed by 4500
Abstract
Sedum alfredii Hance, a cadmium (Cd)/zinc (Zn)/lead (Pb) co-hyperaccumulating species, is a promising phytoremediation candidate because it accumulates substantial amounts of heavy metal ions without showing any obvious signs of poisoning. The heat shock transcription factor (Hsf) family plays crucial roles in plant [...] Read more.
Sedum alfredii Hance, a cadmium (Cd)/zinc (Zn)/lead (Pb) co-hyperaccumulating species, is a promising phytoremediation candidate because it accumulates substantial amounts of heavy metal ions without showing any obvious signs of poisoning. The heat shock transcription factor (Hsf) family plays crucial roles in plant growth, development, and stress responses. Although the roles of some Hsfs in abiotic stress have been well studied in model plants, the Hsf family has not been systematically investigated in heavy metal hyperaccumulators. Here, we comprehensively analyzed the Hsf gene family in S. alfredii based on a transcriptome under Cd stress. There were 22 Hsf members that were identified and phylogenetically clustered into three classes, namely, SaHsfA, SaHsfB, and SaHsfC. All of the three classes shared similar motifs. The expression profiles of the 22 Hsf members showed significant differences: 18 SaHsfs were responsive to Cd stress, as were multiple SaHsp genes, including SaHsp18.1, SaHsp22, SaHsp26.5, SaHsp70, SaHsp90, and SaHsp101. Two class A4 members, SaHsfA4a and SaHsfA4c, exhibited transcriptional activation activities. Overexpression of SaHsfA4a and SaHsfA4c in transgenic yeast indicated an improved tolerance to Cd stress and Cd accumulation. Our results suggest SaHsfs play important regulatory roles in heavy metal stress responses, and provide a reference for further studies on the mechanism of heavy metal stress regulation by SaHsfs. Full article
(This article belongs to the Section Molecular Plant Sciences)
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15 pages, 1602 KiB  
Article
Assembly and Functional Analysis of an S/MAR Based Episome with the Cystic Fibrosis Transmembrane Conductance Regulator Gene
by Davide De Rocco, Barbara Pompili, Stefano Castellani, Elena Morini, Luca Cavinato, Giuseppe Cimino, Maria A Mariggiò, Simone Guarnieri, Massimo Conese, Paola Del Porto and Fiorentina Ascenzioni
Int. J. Mol. Sci. 2018, 19(4), 1220; https://doi.org/10.3390/ijms19041220 - 17 Apr 2018
Cited by 9 | Viewed by 4737
Abstract
Improving the efficacy of gene therapy vectors is still an important goal toward the development of safe and efficient gene therapy treatments. S/MAR (scaffold/matrix attached region)-based vectors are maintained extra-chromosomally in numerous cell types, which is similar to viral-based vectors. Additionally, when established [...] Read more.
Improving the efficacy of gene therapy vectors is still an important goal toward the development of safe and efficient gene therapy treatments. S/MAR (scaffold/matrix attached region)-based vectors are maintained extra-chromosomally in numerous cell types, which is similar to viral-based vectors. Additionally, when established as an episome, they show a very high mitotic stability. In the present study we tested the idea that addition of an S/MAR element to a CFTR (cystic fibrosis transmembrane conductance regulator) expression vector, may allow the establishment of a CFTR episome in bronchial epithelial cells. Starting from the observation that the S/MAR vector pEPI-EGFP (enhanced green fluorescence protein) is maintained as an episome in human bronchial epithelial cells, we assembled the CFTR vector pBQ-S/MAR. This vector, transfected in bronchial epithelial cells with mutated CFTR, supported long term wt CFTR expression and activity, which in turn positively impacted on the assembly of tight junctions in polarized epithelial cells. Additionally, the recovery of intact pBQ-S/MAR, but not the parental vector lacking the S/MAR element, from transfected cells after extensive proliferation, strongly suggested that pBQ-S/MAR was established as an episome. These results add a new element, the S/MAR, that can be considered to improve the persistence and safety of gene therapy vectors for cystic fibrosis pulmonary disease. Full article
(This article belongs to the Special Issue Gene Therapy)
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14 pages, 3474 KiB  
Communication
Proinflammatory Markers, Chemokines, and Enkephalin in Patients Suffering from Dry Eye Disease
by Pierre Nicolle, Hong Liang, Elodie Reboussin, Ghislaine Rabut, Elise Warcoin, Françoise Brignole-Baudouin, Stéphane Melik-Parsadaniantz, Christophe Baudouin, Antoine Labbe and Annabelle Reaux-Le Goazigo
Int. J. Mol. Sci. 2018, 19(4), 1221; https://doi.org/10.3390/ijms19041221 - 17 Apr 2018
Cited by 43 | Viewed by 6015
Abstract
Dry eye symptoms are among the leading complaints in ophthalmology. Dry eye disease (DED) is associated with significant pain affecting quality of life. Cellular and molecular mechanisms underlying ocular pain associated with DED are not fully understood. In this study, we investigated the [...] Read more.
Dry eye symptoms are among the leading complaints in ophthalmology. Dry eye disease (DED) is associated with significant pain affecting quality of life. Cellular and molecular mechanisms underlying ocular pain associated with DED are not fully understood. In this study, we investigated the ocular surface of patients with DED using in vivo confocal microscopy (IVCM) to quantify corneal nerve density and its relation with corneal inflammation. Gene expression of the proinflammatory markers HLA-DR, IL-6, CXCL12, and CCL2 and the receptors CXCR4 and CCR2, as well as PENK (enkephalin precursor), was therefore quantified in conjunctival impression cytology specimens. Thirty-two patients with DED and 15 age-matched controls were included. Subbasal nerve density was significantly lower in DED patients compared to controls. IVCM analysis revealed that DED patients had a significantly higher corneal dendritic cell density compared to controls. Conjunctival impression cytology analysis revealed that HLA-DR, IL-6, CXCR4, and CCL2/CCR2 mRNA levels were significantly increased in DED patients compared to controls, whereas PENK mRNA levels were significantly decreased. Similar results were obtained in vitro on immortalized human conjunctiva-derived epithelial cells challenged with osmotic stress that mimics the DED condition. These results demonstrate that proinflammatory molecules and endogenous enkephalin have opposite gene regulation during DED. Full article
(This article belongs to the Special Issue Pain and Inflammation)
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17 pages, 5556 KiB  
Article
Bone Cell Activity in Clinical Prostate Cancer Bone Metastasis and Its Inverse Relation to Tumor Cell Androgen Receptor Activity
by Annika Nordstrand, Erik Bovinder Ylitalo, Elin Thysell, Emma Jernberg, Sead Crnalic, Anders Widmark, Anders Bergh, Ulf H. Lerner and Pernilla Wikström
Int. J. Mol. Sci. 2018, 19(4), 1223; https://doi.org/10.3390/ijms19041223 - 18 Apr 2018
Cited by 25 | Viewed by 5117
Abstract
Advanced prostate cancer frequently metastasizes to bone and induces a mixed osteoblastic/osteolytic bone response. Standard treatment for metastatic prostate cancer is androgen-deprivation therapy (ADT) that also affects bone biology. Treatment options for patients relapsing after ADT are limited, particularly in cases where castration-resistance [...] Read more.
Advanced prostate cancer frequently metastasizes to bone and induces a mixed osteoblastic/osteolytic bone response. Standard treatment for metastatic prostate cancer is androgen-deprivation therapy (ADT) that also affects bone biology. Treatment options for patients relapsing after ADT are limited, particularly in cases where castration-resistance does not depend on androgen receptor (AR) activity. Patients with non-AR driven metastases may, however, benefit from therapies targeting the tumor microenvironment. Therefore, the current study specifically investigated bone cell activity in clinical bone metastases in relation to tumor cell AR activity, in order to gain novel insight into biological heterogeneities of possible importance for patient stratification into bone-targeting therapies. Metastasis tissue obtained from treatment-naïve (n = 11) and castration-resistant (n = 28) patients was characterized using whole-genome expression analysis followed by multivariate modeling, functional enrichment analysis, and histological evaluation. Bone cell activity was analyzed by measuring expression levels of predefined marker genes representing osteoclasts (ACP5, CTSK, MMP9), osteoblasts (ALPL, BGLAP, RUNX2) and osteocytes (SOST). Principal component analysis indicated a positive correlation between osteoblast and osteoclast activity and a high variability in bone cell activity between different metastases. Immunohistochemistry verified a positive correlation between runt-related transcription factor 2 (RUNX2) positive osteoblasts and tartrate-resistant acid phosphatase (TRAP, encoded by ACP5) positive osteoclasts lining the metastatic bone surface. No difference in bone cell activity was seen between treatment-naïve and castration-resistant patients. Importantly, bone cell activity was inversely correlated to tumor cell AR activity (measured as AR, FOXA1, HOXB13, KLK2, KLK3, NKX3-1, STEAP2, and TMPRSS2 expression) and to patient serum prostate-specific antigen (PSA) levels. Functional enrichment analysis indicated high bone morphogenetic protein (BMP) signaling in metastases with high bone cell activity and low tumor cell AR activity. This was confirmed by BMP4 immunoreactivity in tumor cells of metastases with ongoing bone formation, as determined by histological evaluation of van Gieson-stained sections. In conclusion, the inverse relation observed between bone cell activity and tumor cell AR activity in prostate cancer bone metastasis may be of importance for patient response to AR and/or bone targeting therapies, but needs to be evaluated in clinical settings in relation to serum markers for bone remodeling, radiography and patient response to therapy. The importance of BMP signaling in the development of sclerotic metastasis lesions deserves further exploration. Full article
(This article belongs to the Special Issue Bone Metastasis: Pathophysiology and Molecular Mechanisms)
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22 pages, 13778 KiB  
Article
Lack of the α1,3-Fucosyltransferase Gene (Osfuct) Affects Anther Development and Pollen Viability in Rice
by Joon-Soo Sim, Mahipal Singh Kesawat, Manu Kumar, Su-Yeon Kim, Vimalraj Mani, Parthiban Subramanian, Soyoung Park, Chang-Muk Lee, Seong-Ryong Kim and Bum-Soo Hahn
Int. J. Mol. Sci. 2018, 19(4), 1225; https://doi.org/10.3390/ijms19041225 - 18 Apr 2018
Cited by 14 | Viewed by 6033
Abstract
N-linked glycosylation is one of the key post-translational modifications. α1,3-Fucosyltransferase (OsFucT) is responsible for transferring α1,3-linked fucose residues to the glycoprotein N-glycan in plants. We characterized an Osfuct mutant that displayed pleiotropic developmental defects, such as impaired anther and pollen development, [...] Read more.
N-linked glycosylation is one of the key post-translational modifications. α1,3-Fucosyltransferase (OsFucT) is responsible for transferring α1,3-linked fucose residues to the glycoprotein N-glycan in plants. We characterized an Osfuct mutant that displayed pleiotropic developmental defects, such as impaired anther and pollen development, diminished growth, shorter plant height, fewer tillers, and shorter panicle length and internodes under field conditions. In addition, the anthers were curved, the pollen grains were shriveled, and pollen viability and pollen number per anther decreased dramatically in the mutant. Matrix-assisted laser desorption/ionization time-of-flight analyses of the N-glycans revealed that α1,3-fucose was lacking in the N-glycan structure of the mutant. Mutant complementation revealed that the phenotype was caused by loss of Osfuct function. Transcriptome profiling also showed that several genes essential for plant developmental processes were significantly altered in the mutant, including protein kinases, transcription factors, genes involved in metabolism, genes related to protein synthesis, and hypothetical proteins. Moreover, the mutant exhibited sensitivity to an increased concentration of salt. This study facilitates a further understanding of the function of genes mediating N-glycan modification and anther and pollen development in rice. Full article
(This article belongs to the Section Molecular Plant Sciences)
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12 pages, 3326 KiB  
Article
Transient Overexpression of HvSERK2 Improves Barley Resistance to Powdery Mildew
by Yingbo Li, Qingwei Li, Guimei Guo, Ting He, Runhong Gao, Muhammad Faheem, Jianhua Huang, Ruiju Lu and Chenghong Liu
Int. J. Mol. Sci. 2018, 19(4), 1226; https://doi.org/10.3390/ijms19041226 - 18 Apr 2018
Cited by 10 | Viewed by 4004
Abstract
Somatic embryogenesis receptor-like kinases (SERKs) play an essential role in plant response to pathogen infection. Here we identified three SERK genes (HvSERK1/2/3) from barley, and aimed to determine their implication in defense responses to barley powdery mildew (Bgh). Although [...] Read more.
Somatic embryogenesis receptor-like kinases (SERKs) play an essential role in plant response to pathogen infection. Here we identified three SERK genes (HvSERK1/2/3) from barley, and aimed to determine their implication in defense responses to barley powdery mildew (Bgh). Although HvSERK1/2/3 share the characteristic domains of the SERK family, only HvSERK2 was significantly induced in barley leaves during Bgh infection. The expression of HvSERK2 was rapidly induced by hydrogen peroxide (H2O2) treatment, but not by treatment with salicylic acid (SA), methyl jasmonate (MeJA), ethephon (ETH), or abscisic acid (ABA). Bioinformatics analysis of the cloned HvSERK2 promoter revealed that it contains several elements responsible for defense responses against pathogens. Promoter functional analysis showed that the HvSERK2 promoter was induced by Bgh and H2O2. Subcellular localization analysis of HvSERK2 indicated that it is mainly located on the plasma membrane. Transient overexpression of HvSERK2 in epidermal cells of the susceptible barley cultivar Hua 30 reduced the Bgh haustorium index from 58.6% to 43.2%. This study suggests that the HvSERK2 gene plays a positive role in the improvement of barley resistance to powdery mildew, and provides new insight into the function of SERK genes in the biotic stress response of plants. Full article
(This article belongs to the Special Issue Plant Defense Genes Against Biotic Stresses)
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12 pages, 9872 KiB  
Article
The Adenosine A3 Receptor Regulates Differentiation of Glioblastoma Stem-Like Cells to Endothelial Cells under Hypoxia
by René Rocha, Ángelo Torres, Karina Ojeda, Daniel Uribe, Dellis Rocha, José Erices, Ignacio Niechi, Pamela Ehrenfeld, Rody San Martín and Claudia Quezada
Int. J. Mol. Sci. 2018, 19(4), 1228; https://doi.org/10.3390/ijms19041228 - 18 Apr 2018
Cited by 35 | Viewed by 4726
Abstract
Glioblastoma (GBM) is a neoplasm characterized by an extensive blood vessel network. Hypoxic niches of GBM can induce tumorigenic properties of a small cell subpopulation called Glioblastoma stem-like cells (GSCs) and can also increase extracellular adenosine generation which activates the A3 adenosine [...] Read more.
Glioblastoma (GBM) is a neoplasm characterized by an extensive blood vessel network. Hypoxic niches of GBM can induce tumorigenic properties of a small cell subpopulation called Glioblastoma stem-like cells (GSCs) and can also increase extracellular adenosine generation which activates the A3 adenosine receptor (A3AR). Moreover, GSCs potentiates the persistent neovascularization in GBM. The aim of this study was to determine if A3AR blockade can reduce the vasculogenesis mediated by the differentiation of GSCs to Endothelial Cells (ECs) under hypoxia. We evaluated the expression of endothelial cell markers (CD31, CD34, CD144, and vWF) by fluorescence-activated cell sorting (FACS), and vascular endothelial growth factor (VEGF) secretion by ELISA using MRS1220 (A3AR antagonist) under hypoxia. We validate our results using U87MG-GSCs A3AR knockout (GSCsA3-KO). The effect of MRS1220 on blood vessel formation was evaluated in vivo using a subcutaneous GSCs-tumor model. GSCs increased extracellular adenosine production and A3AR expression under hypoxia. Hypoxia also increased the percentage of GSCs positive for endothelial cell markers and VEGF secretion, which was in turn prevented when using MRS1220 and in GSCsA3-KO. Finally, in vivo treatment with MRS1220 reduced tumor size and blood vessel formation. Blockade of A3AR decreases the differentiation of GSCs to ECs under hypoxia and in vivo blood vessel formation. Full article
(This article belongs to the Special Issue Angiogenesis and Anti-Angiogenesis in Oncology: From Bench to Translational Research and Bedside Investigation)
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15 pages, 10853 KiB  
Article
Identification of Placental Aspartic Proteinase in the Eurasian Beaver (Castor fiber L.)
by Aleksandra Lipka, Grzegorz Panasiewicz, Marta Majewska, Lukasz Paukszto, Martyna Bieniek-Kobuszewska and Bozena Szafranska
Int. J. Mol. Sci. 2018, 19(4), 1229; https://doi.org/10.3390/ijms19041229 - 18 Apr 2018
Cited by 4 | Viewed by 4116
Abstract
Aspartic proteinases (AP) form a multigenic group widely distributed in various organisms and includes pepsins (pep), cathepsins D and E, pregnancy associated glycoproteins (PAGs) as well as plant, fungal, and retroviral proteinases. This study describes the transcript identification and expression localization of the [...] Read more.
Aspartic proteinases (AP) form a multigenic group widely distributed in various organisms and includes pepsins (pep), cathepsins D and E, pregnancy associated glycoproteins (PAGs) as well as plant, fungal, and retroviral proteinases. This study describes the transcript identification and expression localization of the AP within the discoid placenta of the Castor fiber. We identified 1257 bp of the AP cDNA sequence, encoding 391 amino acids (aa) of the polypeptide precursor composed of 16 aa signal peptide, 46 aa pro-piece, and 329 aa of the mature protein. Within the AP precursor, one site of potential N-glycosylation (NPS119–121) and two Asp residues (D) specific for the catalytic cleft of AP were identified (VLFDTGSSNLWV91–102 and GIVDTGTSLLTV277–288). The highest homology of the identified placental AP nucleotide and aa sequence was to mouse pepsinogen C (75.8% and 70.1%, respectively). Identified AP also shared high homology with other superfamily members: PAGs, cathepsins, and napsins. The AP identified in this study was named as pepsinogen/PAG-Like (pep/PAG-L). Diversified pep/PAG-L protein profiles with a dominant 58 kDa isoform were identified. Immune reactive signals of the pep/PAG-L were localized within the trophectodermal cells of the beaver placenta. This is the first report describing the placental AP (pep/PAG-L) in the C. fiber. Full article
(This article belongs to the Section Biochemistry)
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13 pages, 17152 KiB  
Article
Three-Dimensional Architecture and Mechanical Properties of Bovine Bone Mixed with Autologous Platelet Liquid, Blood, or Physiological Water: An In Vitro Study
by Antonio Scarano, Francesco Inchingolo, Giovanna Murmura, Tonino Traini, Adriano Piattelli and Felice Lorusso
Int. J. Mol. Sci. 2018, 19(4), 1230; https://doi.org/10.3390/ijms19041230 - 18 Apr 2018
Cited by 77 | Viewed by 4767
Abstract
In recent years, several techniques and material options have been investigated and developed for bone defect repair and regeneration. The progress in studies of composite graft materials and autologous platelet-derived growth factors for bone regeneration in dentistry and their biological and biomechanical properties [...] Read more.
In recent years, several techniques and material options have been investigated and developed for bone defect repair and regeneration. The progress in studies of composite graft materials and autologous platelet-derived growth factors for bone regeneration in dentistry and their biological and biomechanical properties has improved clinical strategies and results. The aim of this study was to evaluate the three-dimensional architecture and mechanical properties of three different combinations of composite bovine graft, adding autologous platelet liquid (APL), blood, or physiological water. One experimental group for each combination of biomaterials was created. In particular, in Group I, the bovine graft was mixed with APL; in Group II, it was mixed with blood, and in Group III, the biomaterial graft was combined with physiological water. Then, the composite biomaterials were evaluated by scanning electron microscopy (SEM), and a compression-loading test was conducted. The evaluation showed a statistical significance (p < 0.01) of the elastic regime of deformation resistance, in which the combination of APL with bone graft resulted in an 875% increase in the mechanical resistance. The protocol of APL mixed with bovine bone graft produced a composite sticky graft block that was capable of increasing the mechanical properties in order to improve its clinical use in the treatment of the maxillary bone defects. Full article
(This article belongs to the Special Issue Head Tissues Regeneration)
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18 pages, 16345 KiB  
Article
Testosterone-Dependent miR-26a-5p and let-7g-5p Act as Signaling Mediators to Regulate Sperm Apoptosis via Targeting PTEN and PMAIP1
by Jideng Ma, Yu Fan, Jinwei Zhang, Siyuan Feng, Zihui Hu, Wanling Qiu, Keren Long, Long Jin, Qianzi Tang, Xun Wang, Qi Zhou, Yiren Gu, Weihang Xiao, Lingyan Liu, Xuewei Li and Mingzhou Li
Int. J. Mol. Sci. 2018, 19(4), 1233; https://doi.org/10.3390/ijms19041233 - 18 Apr 2018
Cited by 41 | Viewed by 5751
Abstract
Recent evidence suggests that testosterone deficiency can dramatically decrease the quality of sperm. MicroRNAs (miRNAs) are conserved mediators of post-transcriptional gene regulation in eukaryotes. However, the systemic regulation and function of miRNAs in sperm quality decline induced by testosterone deficiency has not been [...] Read more.
Recent evidence suggests that testosterone deficiency can dramatically decrease the quality of sperm. MicroRNAs (miRNAs) are conserved mediators of post-transcriptional gene regulation in eukaryotes. However, the systemic regulation and function of miRNAs in sperm quality decline induced by testosterone deficiency has not been investigated. Here, we found that the sperm apoptosis was significantly enhanced and the sperm motility was dramatically decreased in hemicastrated pigs. We then used small RNA sequencing to detect miRNA profiles of sperm from pigs with prepubertal hemicastration (HC) and compared them with control libraries. We identified 16 differentially expressed (DE) miRNAs between the sperm of prepubertal HC and control (CT) pigs. Functional enrichment analysis indicated that the target genes of these DE miRNAs were mainly enriched in apoptosis-related pathways including the p53, mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR) pathways. Furthermore, gain- and loss-of-function analyses demonstrated potential anti-apoptotic effects of the DE miRNAs miR-26a-5p and let-7g-5p on sperm cells. The luciferase reporter assay confirmed that PTEN and PMAIP1 are targets of miR-26a-5p and let-7g-5p, respectively. Spearman’s correlation analysis revealed significantly positive correlations between the sperm and its corresponding seminal plasma exosomes regarding the miRNA expression levels. In conclusion, testosterone deficiency-induced changes in the miRNA components of seminal plasma exosomes secreted by the genital tract may partially elucidate sperm miRNAome alterations, which are further responsible for the decline of sperm motility. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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13 pages, 1611 KiB  
Article
Isolation and Identification of Putative Protein Substrates of the AAA+ Molecular Chaperone ClpB from the Pathogenic Spirochaete Leptospira interrogans
by Joanna Krajewska, Zbigniew Arent, Michal Zolkiewski and Sabina Kędzierska-Mieszkowska
Int. J. Mol. Sci. 2018, 19(4), 1234; https://doi.org/10.3390/ijms19041234 - 18 Apr 2018
Cited by 13 | Viewed by 5288
Abstract
Bacterial ClpB is an ATP-dependent Hsp100 chaperone that reactivates aggregated proteins in cooperation with the DnaK chaperone system and promotes survival of bacteria under stress conditions. A large number of publications also indicate that ClpB supports the virulence of bacteria, including a pathogenic [...] Read more.
Bacterial ClpB is an ATP-dependent Hsp100 chaperone that reactivates aggregated proteins in cooperation with the DnaK chaperone system and promotes survival of bacteria under stress conditions. A large number of publications also indicate that ClpB supports the virulence of bacteria, including a pathogenic spirochaete Leptospira interrogans responsible for leptospirosis in both animals and humans. However, the exact role of ClpB in bacterial pathogenicity remains poorly characterized. It can be assumed that ClpB, due to its role as the molecular chaperone, mediates refolding of essential bacterial proteins, including the known virulence factors, which may become prone to aggregation under infection-induced stresses. In this study, we identified putative substrates of ClpB from L. interrogans (ClpBLi). For this purpose, we used a proteomic approach combining the ClpB-Trap affinity pull-down assays, Liquid chromatography-tandem mass spectrometry (LC-MS-MS/MS), and bioinformatics analyses. Most of the identified proteins were enzymes predominantly associated with major metabolic pathways like the tricarboxylic acid (TCA) cycle, glycolysis–gluconeogenesis and amino acid and fatty acid metabolism. Based on our proteomic study, we suggest that ClpB can support the virulence of L. interrogans by protecting the conformational integrity and catalytic activity of multiple metabolic enzymes, thus maintaining energy homeostasis in pathogen cells. Full article
(This article belongs to the Special Issue Molecular Chaperones)
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18 pages, 2432 KiB  
Article
Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis
by Hao Liu, Haifen Li, Jianzhong Gu, Li Deng, Li Ren, Yanbin Hong, Qing Lu, Xiaoping Chen and Xuanqiang Liang
Int. J. Mol. Sci. 2018, 19(4), 1235; https://doi.org/10.3390/ijms19041235 - 18 Apr 2018
Cited by 28 | Viewed by 4947
Abstract
Peanuts (Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the [...] Read more.
Peanuts (Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the high content of OA in peanut oil is beneficial for human health and long-term storage due to its antioxidant activity. However, the dynamic changes in proteomics related to OA accumulation during seed development still remain largely unexplored. In the present study, a comparative proteome analysis based on iTRAQ (isobaric Tags for Relative and Absolute Quantification) was performed to identify the critical candidate factors involved in OA formation. A total of 389 differentially expressed proteins (DEPs) were identified between high-oleate cultivar Kainong176 and low-oleate cultivar Kainong70. Among these DEPs, 201 and 188 proteins were upregulated and downregulated, respectively. In addition, these DEPs were categorized into biosynthesis pathways of unsaturated FAs at the early stage during the high-oleic peanut seed development, and several DEPs involved in lipid oxidation pathway were found at the stage of seed maturation. Meanwhile, 28 DEPs were sporadically distributed in distinct stages of seed formation, and their molecular functions were directly correlated to FA biosynthesis and degradation. Fortunately, the expression of FAB2 (stearoyl-acyl carrier protein desaturase), the rate-limiting enzyme in the upstream biosynthesis process of OA, was significantly increased in the early stage and then decreased in the late stage of seed development in the high-oleate cultivar Kainong176. Furthermore, real-time PCR verified the expression pattern of FAB2 at the mRNA level, which was consistent with its protein abundance. However, opposite results were found for the low-oleate cultivar Kainong70. Overall, the comparative proteome analysis provided valuable insight into the molecular dynamics of OA accumulation during peanut seed development. Full article
(This article belongs to the Section Molecular Plant Sciences)
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17 pages, 3120 KiB  
Article
CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization
by Michaela Frolikova, Pavla Manaskova-Postlerova, Jiri Cerny, Jana Jankovicova, Ondrej Simonik, Alzbeta Pohlova, Petra Secova, Jana Antalikova and Katerina Dvorakova-Hortova
Int. J. Mol. Sci. 2018, 19(4), 1236; https://doi.org/10.3390/ijms19041236 - 19 Apr 2018
Cited by 31 | Viewed by 8551
Abstract
Proteins CD9 and CD81 are members of the tetraspanin superfamily and were detected in mammalian sperm, where they are suspected to form an active tetraspanin web and to participate in sperm–egg membrane fusion. The importance of these two proteins during the early stages [...] Read more.
Proteins CD9 and CD81 are members of the tetraspanin superfamily and were detected in mammalian sperm, where they are suspected to form an active tetraspanin web and to participate in sperm–egg membrane fusion. The importance of these two proteins during the early stages of fertilization is supported by the complete sterility of CD9/CD81 double null female mice. In this study, the putative mechanism of CD9/CD81 involvement in tetraspanin web formation in sperm and its activity prior to fertilization was addressed. Confocal microscopy and colocalization assay was used to determine a mutual CD9/CD81 localization visualised in detail by super-resolution microscopy, and their interaction was address by co-immunoprecipitation. The species-specific traits in CD9 and CD81 distribution during sperm maturation were compared between mice and humans. A mutual position of CD9/CD81 is shown in human spermatozoa in the acrosomal cap, however in mice, CD9 and CD81 occupy a distinct area. During the acrosome reaction in human sperm, only CD9 is relocated, compared to the relocation of both proteins in mice. The structural modelling of CD9 and CD81 homologous and possibly heterologous network formation was used to propose their lateral Cis as well as Trans interactions within the sperm membrane and during sperm–egg membrane fusion. Full article
(This article belongs to the Special Issue Membrane Fusion)
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11 pages, 3748 KiB  
Article
PIN7 Auxin Carrier Has a Preferential Role in Terminating Radial Root Expansion in Arabidopsis thaliana
by Michel Ruiz Rosquete, Sascha Waidmann and Jürgen Kleine-Vehn
Int. J. Mol. Sci. 2018, 19(4), 1238; https://doi.org/10.3390/ijms19041238 - 19 Apr 2018
Cited by 40 | Viewed by 7782
Abstract
Directional growth of lateral roots is critical for radial expansion and soil coverage. Despite its importance, almost nothing is known about its molecular determinants. Initially, young lateral roots (LRs) grow away from the parental root, maintaining the angle acquired shortly after emergence. A [...] Read more.
Directional growth of lateral roots is critical for radial expansion and soil coverage. Despite its importance, almost nothing is known about its molecular determinants. Initially, young lateral roots (LRs) grow away from the parental root, maintaining the angle acquired shortly after emergence. A second downwards bending response to gravity terminates the so-called plateau phase and thereby limits radial root expansion. Here, we show that the exit from the plateau phase correlates with an increase in auxin signalling at the tip of the LRs. Moreover, the increase in auxin levels induces the termination of the plateau phase, which requires PIN-FORMED (PIN) auxin efflux carriers. Our data suggests that the developmental increase in auxin triggers the preferential derepression of PIN7 in gravity-sensing columella cells. The subsequent polarization of PIN7 heralds the bending towards gravity and, hence, the exit from the plateau phase. This developmental framework reveals the distinct roles of PIN auxin efflux carriers in controlling the radial growth of root systems. Full article
(This article belongs to the Special Issue Auxin)
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14 pages, 15646 KiB  
Article
Telomerase Inhibition by a New Synthetic Derivative of the Aporphine Alkaloid Boldine
by Sakineh Kazemi Noureini, Mitra Kheirabadi, Fatima Masoumi, Farve Khosrogerdi, Younes Zarei, Cristian Suárez-Rozas, Julio Salas-Norambuena and Bruce Kennedy Cassels
Int. J. Mol. Sci. 2018, 19(4), 1239; https://doi.org/10.3390/ijms19041239 - 19 Apr 2018
Cited by 12 | Viewed by 5336
Abstract
Telomerase, the enzyme responsible for cell immortality, is an important target in anti-cancer drug discovery. Boldine, an abundant aporphine alkaloid of Peumus boldus, is known to inhibit telomerase at non-toxic concentrations. Cytotoxicity of N-benzylsecoboldine hydrochloride (BSB), a synthetic derivative of boldine, [...] Read more.
Telomerase, the enzyme responsible for cell immortality, is an important target in anti-cancer drug discovery. Boldine, an abundant aporphine alkaloid of Peumus boldus, is known to inhibit telomerase at non-toxic concentrations. Cytotoxicity of N-benzylsecoboldine hydrochloride (BSB), a synthetic derivative of boldine, was determined using the MTT method in MCF7 and MDA-MB231 cells. Aliquots of cell lysates were incubated with various concentrations of BSB in qTRAP (quantitative telomere repeat amplification protocol)-ligand experiments before substrate elongation by telomerase or amplification by hot-start Taq polymerase. The crystal structure of TERT, the catalytic subunit of telomerase from Tribolium castaneum, was used for docking and molecular dynamics analysis. The qTRAP-ligand data gave an IC50 value of about 0.17 ± 0.1 µM for BSB, roughly 400 times stronger than boldine, while the LD50 in the cytotoxicity assays were 12.5 and 21.88 µM, respectively, in cells treated for 48 h. Although both compounds interacted well with the active site, MD analysis suggests a second binding site with which BSB interacts via two hydrogen bonds, much more strongly than boldine. Theoretical analyses also evaluated the IC50 for BSB as submicromolar. BSB, with greater hydrophobicity and flexibility than boldine, represents a promising structure to inhibit telomerase at non-toxic concentrations. Full article
(This article belongs to the Special Issue Role of Telomeres and Telomerase in Cancer and Aging)
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13 pages, 7367 KiB  
Article
Activation of ER Stress-Dependent miR-216b Has a Critical Role in Salvia miltiorrhiza Ethanol-Extract-Induced Apoptosis in U266 and U937 Cells
by Changmin Kim, Hyo-Sook Song, Hojung Park and Bonglee Kim
Int. J. Mol. Sci. 2018, 19(4), 1240; https://doi.org/10.3390/ijms19041240 - 19 Apr 2018
Cited by 25 | Viewed by 8582
Abstract
Although Salvia miltiorrhiza has been reported to have anti-cancer mechanisms, such as caspase activation, cell cycle arrest, an anti-angiogenesis effect, and Bcl-2 family regulation, its underlying mechanism of endoplasmic reticulum (ER) stress-mediated apoptosis has never been demonstrated. Thus, in this current study, ER [...] Read more.
Although Salvia miltiorrhiza has been reported to have anti-cancer mechanisms, such as caspase activation, cell cycle arrest, an anti-angiogenesis effect, and Bcl-2 family regulation, its underlying mechanism of endoplasmic reticulum (ER) stress-mediated apoptosis has never been demonstrated. Thus, in this current study, ER stress-related apoptosis via miR-216b of the ethanol extract of Salvia miltiorrhiza (SM) is elucidated for the first time. SM treatment inhibited the viability of U266 and U937 cells in a concentration-dependent manner. However, SM-exposed Raw264.7 cells were intact compared to U266 or U937 cells. Treatment with SM significantly elevated the generation of reactive oxygen species (ROS). The anti-proliferative effect of SM was reversed by pretreatment with the ROS scavenger, N-acetyl-l-cysteine (NAC), compared to cells treated only with SM. Also, SM treatment increased the ER stress by elevation of phosphorylated activating transcription factor 4 (p-ATF4), phosphorylated eukaryotic Initiation Factor 2 (p-eIF2), and phosphorylated protein kinase RNA-like endoplasmic reticulum kinase (p-PERK) expression. Caspase-3 and Poly (ADP-ribose) polymerase (PARP) were cleaved and CCAAT-enhancer-binding protein homologous protein (CHOP) was activated by SM treatment. PARP cleavage and CHOP activation were attenuated by NAC pretreatment. Furthermore, SM increased the tumor suppressor, miR-216b, and suppressed its target, c-Jun. miR-216b inhibitor attenuated the apoptotic effect of SM. Taken together, SM treatment induced apoptosis through regulation of miR-216b and ROS/ER stress pathways. SM could be a potential drug for treatment of multiple myeloma and myeloid leukemia. Full article
(This article belongs to the Special Issue Traditional Medicine – Unraveling Its Molecular Mechanism)
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18 pages, 2070 KiB  
Article
Proteomic Identification of the Galectin-1-Involved Molecular Pathways in Urinary Bladder Urothelial Carcinoma
by Chien-Feng Li, Kun-Hung Shen, Lan-Hsiang Chien, Cheng-Hao Huang, Ting-Feng Wu and Hong-Lin He
Int. J. Mol. Sci. 2018, 19(4), 1242; https://doi.org/10.3390/ijms19041242 - 19 Apr 2018
Cited by 8 | Viewed by 4180
Abstract
Among various heterogeneous types of bladder tumors, urothelial carcinoma is the most prevalent lesion. Some of the urinary bladder urothelial carcinomas (UBUCs) develop local recurrence and may cause distal invasion. Galectin-1 de-regulation significantly affects cell transformation, cell proliferation, angiogenesis, and cell invasiveness. In [...] Read more.
Among various heterogeneous types of bladder tumors, urothelial carcinoma is the most prevalent lesion. Some of the urinary bladder urothelial carcinomas (UBUCs) develop local recurrence and may cause distal invasion. Galectin-1 de-regulation significantly affects cell transformation, cell proliferation, angiogenesis, and cell invasiveness. In continuation of our previous investigation on the role of galectin-1 in UBUC tumorigenesis, in this study, proteomics strategies were implemented in order to find more galectin-1-associated signaling pathways. The results of this study showed that galectin-1 knockdown could induce 15 down-regulated proteins and two up-regulated proteins in T24 cells. These de-regulated proteins might participate in lipid/amino acid/energy metabolism, cytoskeleton, cell proliferation, cell-cell interaction, cell apoptosis, metastasis, and protein degradation. The aforementioned dys-regulated proteins were confirmed by western immunoblotting. Proteomics results were further translated to prognostic markers by analyses of biopsy samples. Results of cohort studies demonstrated that over-expressions of glutamine synthetase, alcohol dehydrogenase (NADP+), fatty acid binding protein 4, and toll interacting protein in clinical specimens were all significantly associated with galectin-1 up-regulation. Univariate analyses showed that de-regulations of glutamine synthetase and fatty acid binding protein 4 in clinical samples were respectively linked to disease-specific survival and metastasis-free survival. Full article
(This article belongs to the Special Issue Galectins in Cancer and Translational Medicine)
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19 pages, 6719 KiB  
Article
4-Hydroxypiperidines and Their Flexible 3-(Amino)propyloxy Analogues as Non-Imidazole Histamine H3 Receptor Antagonist: Further Structure–Activity Relationship Exploration and In Vitro and In Vivo Pharmacological Evaluation
by Beata Olszewska, Anna Stasiak, Daniel McNaught Flores, Wiesława Agnieszka Fogel, Rob Leurs and Krzysztof Walczyński
Int. J. Mol. Sci. 2018, 19(4), 1243; https://doi.org/10.3390/ijms19041243 - 19 Apr 2018
Cited by 6 | Viewed by 4366
Abstract
Presynaptic histamine H3 receptors (H3R) act as auto- or heteroreceptors controlling, respectively, the release of histamine and of other neurotransmitters in the central nervous system (CNS). The extracellular levels of several neurotransmitters are enhanced by H3R antagonists, and [...] Read more.
Presynaptic histamine H3 receptors (H3R) act as auto- or heteroreceptors controlling, respectively, the release of histamine and of other neurotransmitters in the central nervous system (CNS). The extracellular levels of several neurotransmitters are enhanced by H3R antagonists, and there is a great interest for potent, brain-penetrating H3 receptor antagonists/inverse agonists to compensate for the neurotransmitter deficits present in various neurological disorders. We have shown that 1-[(benzylfuran-2-yl)methyl]piperidinyl-4-oxyl- and benzyl- derivatives of N-propylpentan-1-amines exhibit high in vitro potencies toward the guinea pig H3 receptor (jejunum), with pA2 = 8.47 and 7.79, respectively (the reference compound used was thioperamide with pA2 = 8.67). Furthermore, following the replacement of 4-hydroxypiperidine with a 3-(methylamino)propyloxy chain, the pA2 value for the first group decreased, whereas it increased for the second group. Here, we present data on the impact of elongating the aliphatic chain between the nitrogen of 4-hydroxypiperidine or 3-(methylamino)propan-1-ol and the lipophilic residue. Additionally, the most active compound in this series of non-imidazole H3 receptor antagonists/inverse agonists, i.e., ADS-003, was evaluated for its affinity to the recombinant rat and human histamine H3 receptors transiently expressed in HEK-293T cells. It was shown that ADS-003, given parenterally for 5 days, reduced the food intake of rats, as well as changed histamine and noradrenaline concentrations in the rats’ brain in a manner and degree similar to the reference H3 antagonist Ciproxifan. Full article
(This article belongs to the Section Molecular Toxicology)
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24 pages, 41100 KiB  
Article
Molecular Modeling Studies on Carbazole Carboxamide Based BTK Inhibitors Using Docking and Structure-Based 3D-QSAR
by Rui Li, Yongli Du, Zhipei Gao and Jingkang Shen
Int. J. Mol. Sci. 2018, 19(4), 1244; https://doi.org/10.3390/ijms19041244 - 19 Apr 2018
Cited by 8 | Viewed by 5091
Abstract
Rheumatoid arthritis (RA) is the second common rheumatic immune disease with chronic, invasive inflammatory characteristics. Non-steroidal anti-inflammatory drugs (NSAIDs), slow-acting anti-rheumatic drugs (SAARDs), or glucocorticoid drugs can improve RA patients’ symptoms, but fail to cure. Broton’s tyrosine kinase (BTK) inhibitors have been proven [...] Read more.
Rheumatoid arthritis (RA) is the second common rheumatic immune disease with chronic, invasive inflammatory characteristics. Non-steroidal anti-inflammatory drugs (NSAIDs), slow-acting anti-rheumatic drugs (SAARDs), or glucocorticoid drugs can improve RA patients’ symptoms, but fail to cure. Broton’s tyrosine kinase (BTK) inhibitors have been proven to be an efficacious target against autoimmune indications and B-cell malignancies. Among the current 11 clinical drugs, only BMS-986142, classified as a carbazole derivative, is used for treating RA. To design novel and highly potent carbazole inhibitors, molecular docking and three dimensional quantitative structure–activity relationship (3D-QSAR) were applied to explore a dataset of 132 new carbazole carboxamide derivatives. The established comparative molecular field analysis (CoMFA) (q2 = 0.761, r2 = 0.933) and comparative molecular similarity indices analysis (CoMSIA) (q2 = 0.891, r2 = 0.988) models obtained high predictive and satisfactory values. CoMFA/CoMSIA contour maps demonstrated that bulky substitutions and hydrogen-bond donors were preferred at R1 and 1-position, respectively, and introducing hydrophilic substitutions at R1 and R4 was important for improving BTK inhibitory activities. These results will contribute to the design of novel and highly potent BTK inhibitors. Full article
(This article belongs to the Special Issue Computational Studies of Structure-Dynamics-Function Relationships in Biomolecules)
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16 pages, 2020 KiB  
Article
Detrimental Effects of Helium Ion Irradiation on Cognitive Performance and Cortical Levels of MAP-2 in B6D2F1 Mice
by Jacob Raber, Eileen Ruth S. Torres, Tunde Akinyeke, Joanne Lee, Sydney J. Weber Boutros, Mitchell S. Turker and Amy Kronenberg
Int. J. Mol. Sci. 2018, 19(4), 1247; https://doi.org/10.3390/ijms19041247 - 20 Apr 2018
Cited by 18 | Viewed by 4533
Abstract
The space radiation environment includes helium (4He) ions that may impact brain function. As little is known about the effects of exposures to 4He ions on the brain, we assessed the behavioral and cognitive performance of C57BL/6J × DBA2/J F1 [...] Read more.
The space radiation environment includes helium (4He) ions that may impact brain function. As little is known about the effects of exposures to 4He ions on the brain, we assessed the behavioral and cognitive performance of C57BL/6J × DBA2/J F1 (B6D2F1) mice three months following irradiation with 4He ions (250 MeV/n; linear energy transfer (LET) = 1.6 keV/μm; 0, 21, 42 or 168 cGy). Sham-irradiated mice and mice irradiated with 21 or 168 cGy showed novel object recognition, but mice irradiated with 42 cGy did not. In the passive avoidance test, mice received a slight foot shock in a dark compartment, and latency to re-enter that compartment was assessed 24 h later. Sham-irradiated mice and mice irradiated with 21 or 42 cGy showed a higher latency on Day 2 than Day 1, but the latency to enter the dark compartment in mice irradiated with 168 cGy was comparable on both days. 4He ion irradiation, at 42 and 168 cGy, reduced the levels of the dendritic marker microtubule-associated protein-2 (MAP-2) in the cortex. There was an effect of radiation on apolipoprotein E (apoE) levels in the hippocampus and cortex, with higher apoE levels in mice irradiated at 42 cGy than 168 cGy and a trend towards higher apoE levels in mice irradiated at 21 than 168 cGy. In addition, in the hippocampus, there was a trend towards a negative correlation between MAP-2 and apoE levels. While reduced levels of MAP-2 in the cortex might have contributed to the altered performance in the passive avoidance test, it does not seem sufficient to do so. The higher hippocampal and cortical apoE levels in mice irradiated at 42 than 168 cGy might have served as a compensatory protective response preserving their passive avoidance memory. Thus, there were no alterations in behavioral performance in the open filed or depressive-like behavior in the forced swim test, while cognitive impairments were seen in the object recognition and passive avoidance tests, but not in the contextual or cued fear conditioning tests. Taken together, the results indicate that some aspects of cognitive performance are altered in male mice exposed to 4He ions, but that the response is task-dependent. Furthermore, the sensitive doses can vary within each task in a non-linear fashion. This highlights the importance of assessing the cognitive and behavioral effects of charged particle exposure with a variety of assays and at multiple doses, given the possibility that lower doses may be more damaging due to the absence of induced compensatory mechanisms at higher doses. Full article
(This article belongs to the Special Issue Advances and Challenges in Biomolecular Radiation Research)
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13 pages, 2255 KiB  
Article
Molecular Evolution and Expression Divergence of HMT Gene Family in Plants
by Man Zhao, Peng Chen, Wenyi Wang, Fengjie Yuan, Danhua Zhu, Zhao Wang and Xiangxian Ying
Int. J. Mol. Sci. 2018, 19(4), 1248; https://doi.org/10.3390/ijms19041248 - 20 Apr 2018
Cited by 9 | Viewed by 4387
Abstract
Homocysteine methyltransferase (HMT) converts homocysteine to methionine using S-methylmethionine (SMM) or S-adenosylmethionine (SAM) as methyl donors in organisms, playing an important role in supplying methionine for the growth and the development of plants. To better understand the functions of the HMT [...] Read more.
Homocysteine methyltransferase (HMT) converts homocysteine to methionine using S-methylmethionine (SMM) or S-adenosylmethionine (SAM) as methyl donors in organisms, playing an important role in supplying methionine for the growth and the development of plants. To better understand the functions of the HMT genes in plants, we conducted a wide evolution and expression analysis of these genes. Reconstruction of the phylogenetic relationship showed that the HMT gene family was divided into Class 1 and Class 2. In Class 1, HMTs were only found in seed plants, while Class 2 presented in all land plants, which hinted that the HMT genes might have diverged in seed plants. The analysis of gene structures and selection pressures showed that they were relatively conserved during evolution. However, type I functional divergence had been detected in the HMTs. Furthermore, the expression profiles of HMTs showed their distinct expression patterns in different tissues, in which some HMTs were widely expressed in various organs, whereas the others were highly expressed in some specific organs, such as seeds or leaves. Therefore, according to our results in the evolution, functional divergence, and expression, the HMT genes might have diverged during evolution. Further analysis in the expression patterns of AthHMTs with their methyl donors suggested that the diverged HMTs might be related to supply methionine for the development of plant seeds. Full article
(This article belongs to the Section Molecular Plant Sciences)
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13 pages, 1825 KiB  
Article
Molecular Characterization and the Function of Argonaute3 in RNAi Pathway of Plutella xylostella
by Muhammad Salman Hameed, Zhengbing Wang, Liette Vasseur and Guang Yang
Int. J. Mol. Sci. 2018, 19(4), 1249; https://doi.org/10.3390/ijms19041249 - 20 Apr 2018
Cited by 9 | Viewed by 4385
Abstract
Argonaute (Ago) protein family plays a key role in the RNA interference (RNAi) process in different insects including Lepidopteran. However, the role of Ago proteins in the RNAi pathway of Plutella xylostella is still unknown. We cloned an Argonaute3 gene in P. xylostella [...] Read more.
Argonaute (Ago) protein family plays a key role in the RNA interference (RNAi) process in different insects including Lepidopteran. However, the role of Ago proteins in the RNAi pathway of Plutella xylostella is still unknown. We cloned an Argonaute3 gene in P. xylostella (PxAgo3) with the complete coding sequence of 2832 bp. The encoded protein had 935 amino acids with an expected molecular weight of 108.9 kDa and an isoelectric point of 9.29. It contained a PAZ (PIWI/Argonaute/Zwile) domain and PIWI (P-element-induced whimpy testes) domain. PxAgo3 was classified into the Piwi subfamily of Ago proteins with a high similarity of 93.0% with Bombyx mori Ago3 (BmAgo3). The suppression of PxAgo3 by dsPxAgo3 was observed 3 h after treatment and was maintained until 24 h. Knockdown of PxAgo3 decreased the suppression level of PxActin by dsPxActin in P. xylostella cells, while overexpression of PxAgo3 increased the RNAi efficiency. Our results suggest that PxAgo3 play a key role in the double stranded RNA (dsRNA)-regulated RNAi pathway in P. xylostella. Full article
(This article belongs to the Special Issue Molecular Entomology of Insects of Economic Importance)
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22 pages, 1443 KiB  
Article
In Vitro Identification of New Transcriptomic and miRNomic Profiles Associated with Pulmonary Fibrosis Induced by High Doses Everolimus: Looking for New Pathogenetic Markers and Therapeutic Targets
by Simona Granata, Gloria Santoro, Valentina Masola, Paola Tomei, Fabio Sallustio, Paola Pontrelli, Matteo Accetturo, Nadia Antonucci, Pierluigi Carratù, Antonio Lupo and Gianluigi Zaza
Int. J. Mol. Sci. 2018, 19(4), 1250; https://doi.org/10.3390/ijms19041250 - 20 Apr 2018
Cited by 8 | Viewed by 4663
Abstract
The administration of Everolimus (EVE), a mTOR inhibitor used in transplantation and cancer, is often associated with adverse effects including pulmonary fibrosis. Although the underlying mechanism is not fully clarified, this condition could be in part caused by epithelial to mesenchymal transition (EMT) [...] Read more.
The administration of Everolimus (EVE), a mTOR inhibitor used in transplantation and cancer, is often associated with adverse effects including pulmonary fibrosis. Although the underlying mechanism is not fully clarified, this condition could be in part caused by epithelial to mesenchymal transition (EMT) of airway cells. To improve our knowledge, primary bronchial epithelial cells (BE63/3) were treated with EVE (5 and 100 nM) for 24 h. EMT markers (α-SMA, vimentin, fibronectin) were measured by RT-PCR. Transepithelial resistance was measured by Millicell-ERS ohmmeter. mRNA and microRNA profiling were performed by Illumina and Agilent kit, respectively. Only high dose EVE increased EMT markers and reduced the transepithelial resistance of BE63/3. Bioinformatics showed 125 de-regulated genes that, according to enrichment analysis, were implicated in collagen synthesis/metabolism. Connective tissue growth factor (CTGF) was one of the higher up-regulated mRNA. Five nM EVE was ineffective on the pro-fibrotic machinery. Additionally, 3 miRNAs resulted hyper-expressed after 100 nM EVE and able to regulate 31 of the genes selected by the transcriptomic analysis (including CTGF). RT-PCR and western blot for MMP12 and CTGF validated high-throughput results. Our results revealed a complex biological network implicated in EVE-related pulmonary fibrosis and underlined new potential disease biomarkers and therapeutic targets. Full article
(This article belongs to the Special Issue mTOR in Human Diseases)
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13 pages, 5824 KiB  
Article
SPAG17 Is Required for Male Germ Cell Differentiation and Fertility
by Elizabeth Kazarian, HyunYoung Son, Paulene Sapao, Wei Li, Zhibing Zhang, Jerome F. Strauss III and Maria E. Teves
Int. J. Mol. Sci. 2018, 19(4), 1252; https://doi.org/10.3390/ijms19041252 - 21 Apr 2018
Cited by 39 | Viewed by 8255
Abstract
Spag17 encodes a protein present in the axoneme central pair complex of motile cilia and flagella. A mutation in this gene has been reported to be associated with infertility caused by defects in sperm motility. Here, we report that Spag17 knockout mice are [...] Read more.
Spag17 encodes a protein present in the axoneme central pair complex of motile cilia and flagella. A mutation in this gene has been reported to be associated with infertility caused by defects in sperm motility. Here, we report that Spag17 knockout mice are infertile because of a severe defect in spermatogenesis. The histological evaluation of testis sections from mutant mice revealed seminiferous tubules with spermatogenesis arrested at the spermatid stage and cell debris in the cauda epididymis. The few sperm collected from the cauda epididymis were immotile and displayed abnormal tail and head morphology. Immunofluorescence analysis of Spag17 knockout germ cells showed spermatids with abnormally long manchette structures and morphological defects in the head. Electron microscopy showed altered manchette microtubules, reduced chromatin condensation, irregular nuclear shape, and detached acrosomes. Additionally, the transport of proteins (Pcdp1 and IFT20) along the manchette microtubules was disrupted in the knockout elongating spermatids. Our results show for the first time that Spag17 is essential for normal manchette structure, protein transport, and formation of the sperm head and flagellum, in addition to its role in sperm motility. Full article
(This article belongs to the Section Biochemistry)
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10 pages, 515 KiB  
Article
Mesenchylmal Stem Cell Culture on Poly(N-isopropylacrylamide) Hydrogel with Repeated Thermo-Stimulation
by Aya Mizutani Akimoto, Erika Hasuike Niitsu, Kenichi Nagase, Teruo Okano, Hideko Kanazawa and Ryo Yoshida
Int. J. Mol. Sci. 2018, 19(4), 1253; https://doi.org/10.3390/ijms19041253 - 21 Apr 2018
Cited by 26 | Viewed by 5843
Abstract
We prepared thermoresponsive hydrogels by mixing poly(N-isopropylacrylamide) (PNIPAAm) derivatives as the main chain components, octa-arm polyethylene glycol (PEG) as a crosslinker, and the Arg-Gly-Asp-Ser (RGDS) peptides as cell adhesion units. Human bone marrow-derived mesenchymal stem cells (hbmMSCs) were cultured on the [...] Read more.
We prepared thermoresponsive hydrogels by mixing poly(N-isopropylacrylamide) (PNIPAAm) derivatives as the main chain components, octa-arm polyethylene glycol (PEG) as a crosslinker, and the Arg-Gly-Asp-Ser (RGDS) peptides as cell adhesion units. Human bone marrow-derived mesenchymal stem cells (hbmMSCs) were cultured on the hydrogels. The PNIPAAm gel prepared by the post-crosslinking gelation method was revealed to be cytocompatible and showed temperature-dependent changes in mechanical properties. Repeated changes in the swelling ratio of the PNIPAAm gel affected the shape of the hbmMSCs. With respect to both cytocompatibility and reversibility of changes in mechanical properties, the PNIPAAm gel system could be potentially useful for the analysis of cell mechanobiology. Full article
(This article belongs to the Special Issue Smart Polymers for Biomedical Applications)
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16 pages, 1764 KiB  
Article
Memory Function in Feeding Habit Transformation of Mandarin Fish (Siniperca chuatsi)
by Yaqi Dou, Shan He, Xu-Fang Liang, Wenjing Cai, Jie Wang, Linjie Shi and Jiao Li
Int. J. Mol. Sci. 2018, 19(4), 1254; https://doi.org/10.3390/ijms19041254 - 22 Apr 2018
Cited by 19 | Viewed by 6302
Abstract
Mandarin fish refuse dead prey fish or artificial diets and can be trained to transform their inborn feeding habit. To investigate the effect of memory on feeding habit transformation, we compared the reaction time to dead prey fish and the success rate of [...] Read more.
Mandarin fish refuse dead prey fish or artificial diets and can be trained to transform their inborn feeding habit. To investigate the effect of memory on feeding habit transformation, we compared the reaction time to dead prey fish and the success rate of feeding habit transformation to dead prey fish with training of mandarin fish in the 1st experimental group (trained once) and the 2nd experimental group (trained twice). The mandarin fish in the 2nd group had higher success rate of feeding habit transformation (100%) than those in the 1st group (67%), and shorter reaction time to dead prey fish (<1 s) than those in the 1st group (>1 s). Gene expression of cAMP responsive element binding protein I (Creb I), brain-derived neurotrophic factor (Bdnf), CCAAT enhancer binding protein delta (C/EBPD), fos-related antigen 2 (Fra2), and proto-oncogenes c-fos (c-fos) involved in long-term memory formation were significantly increased in the 2nd group after repeated training, and taste 1 receptor member 1 (T1R1), involved in feeding habit formation, was significantly increased in brains of the 2nd group after repeated training. DNA methylation levels at five candidate CpG (cytosine–guanine) sites contained in the predicted CpG island in the 5′-flanking region of T1R1 were significantly decreased in brains of the 2nd group compared with that of the 1st group. These results indicated that the repeated training can improve the feeding habit transformation through the memory formation of accepting dead prey fish. DNA methylation of the T1R1 might be a regulatory factor for feeding habit transformation from live prey fish to dead prey fish in mandarin fish. Full article
(This article belongs to the Special Issue DNA Methylation)
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18 pages, 4373 KiB  
Article
Theoretical Studies Applied to the Evaluation of the DFPase Bioremediation Potential against Chemical Warfare Agents Intoxication
by Flávia V. Soares, Alexandre A. De Castro, Ander F. Pereira, Daniel H. S. Leal, Daiana T. Mancini, Ondrej Krejcar, Teodorico C. Ramalho, Elaine F. F. Da Cunha and Kamil Kuca
Int. J. Mol. Sci. 2018, 19(4), 1257; https://doi.org/10.3390/ijms19041257 - 23 Apr 2018
Cited by 21 | Viewed by 4807
Abstract
Organophosphorus compounds (OP) are part of a group of compounds that may be hazardous to health. They are called neurotoxic agents because of their action on the nervous system, inhibiting the acetylcholinesterase (AChE) enzyme and resulting in a cholinergic crisis. Their high toxicity [...] Read more.
Organophosphorus compounds (OP) are part of a group of compounds that may be hazardous to health. They are called neurotoxic agents because of their action on the nervous system, inhibiting the acetylcholinesterase (AChE) enzyme and resulting in a cholinergic crisis. Their high toxicity and rapid action lead to irreversible damage to the nervous system, drawing attention to developing new treatment methods. The diisopropyl fluorophosphatase (DFPase) enzyme has been considered as a potent biocatalyst for the hydrolysis of toxic OP and has potential for bioremediation of this kind of intoxication. In order to investigate the degradation process of the nerve agents Tabun, Cyclosarin and Soman through the wild-type DFPase, and taking into account their stereochemistry, theoretical studies were carried out. The intermolecular interaction energy and other parameters obtained from the molecular docking calculations were used to construct a data matrix, which were posteriorly treated by statistical analyzes of chemometrics, using the PCA (Principal Components Analysis) multivariate analysis. The analyzed parameters seem to be quite important for the reaction mechanisms simulation (QM/MM). Our findings showed that the wild-type DFPase enzyme is stereoselective in hydrolysis, showing promising results for the catalytic degradation of the neurotoxic agents under study, with the degradation mechanism performed through two proposed pathways. Full article
(This article belongs to the Special Issue Computational Studies of Structure-Dynamics-Function Relationships in Biomolecules)
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17 pages, 3727 KiB  
Article
Liu Jun Zi Tang—A Potential, Multi-Herbal Complementary Therapy for Chemotherapy-Induced Neurotoxicity
by Chun-Tang Chiou, Kaw-Chen Wang, Ying-Chen Yang, Chuen-Lin Huang, Sien-Hung Yang, Yao-Haur Kuo and Nai-Kuei Huang
Int. J. Mol. Sci. 2018, 19(4), 1258; https://doi.org/10.3390/ijms19041258 - 23 Apr 2018
Cited by 18 | Viewed by 6262
Abstract
Liu Jun Zi Tang (LJZT) has been used to treat functional dyspepsia and depression, suggesting its effects on gastrointestinal and neurological functions. LJZT is currently used as a complementary therapy to attenuate cisplatin-induced side effects, such as dyspepsia. However, its effect on chemotherapy-induced [...] Read more.
Liu Jun Zi Tang (LJZT) has been used to treat functional dyspepsia and depression, suggesting its effects on gastrointestinal and neurological functions. LJZT is currently used as a complementary therapy to attenuate cisplatin-induced side effects, such as dyspepsia. However, its effect on chemotherapy-induced neuropathic pain or neurotoxicity has rarely been studied. Thus, we explored potential mechanisms underlying LJZT protection against cisplatin-induced neurotoxicity. We observed that LJZT attenuated cisplatin-induced thermal hyperalgesia in mice and apoptosis in human neuroblastoma SH-SY5Y cells. Furthermore, it also attenuated cisplatin-induced cytosolic and mitochondrial free radical formation, reversed the cisplatin-induced decrease in mitochondrial membrane potential, and increased the release of mitochondrial pro-apoptotic factors. LJZT not only activated the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) promoter region, but also attenuated the cisplatin-induced reduction of PGC-1α expression. Silencing of the PGC-1α gene counteracted the protection of LJZT. Taken together, LJZT mediated, through anti-oxidative effect and mitochondrial function regulation, to prevent cisplatin-induced neurotoxicity. Full article
(This article belongs to the Special Issue Traditional Medicine – Unraveling Its Molecular Mechanism)
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12 pages, 3901 KiB  
Article
Cytokine Expression and Macrophage Localization in Xenograft and Allograft Tumor Models Stimulated with Lipopolysaccharide
by Junko Masuda, Tsukasa Shigehiro, Takuma Matsumoto, Ayano Satoh, Akifumi Mizutani, Chiho Umemura, Shoki Saito, Mayumi Kijihira, Eiji Takayama, Akimasa Seno, Hiroshi Murakami and Masaharu Seno
Int. J. Mol. Sci. 2018, 19(4), 1261; https://doi.org/10.3390/ijms19041261 - 23 Apr 2018
Cited by 17 | Viewed by 7526
Abstract
T cell-deficient mice such as nude mice are often used to generate tumor xenograft for the development of anticancer agents. However, the functionality of the other immune cells including macrophages, dendritic cells (DCs), and myeloid-derived suppressor cells (MDSCs) in the xenograft are largely [...] Read more.
T cell-deficient mice such as nude mice are often used to generate tumor xenograft for the development of anticancer agents. However, the functionality of the other immune cells including macrophages, dendritic cells (DCs), and myeloid-derived suppressor cells (MDSCs) in the xenograft are largely unknown. Macrophages and dendritic cells (DCs) acquire functionally distinct properties in response to various environmental stimuli; the interaction of these cells with MDSCs in tumor microenvironments regulates cancer progression. Nude mice are less likely to reject human cancer cells because of major histocompatibility complex (MHC) mismatches. The tumor microenvironment in a xenograft, comprising human and mouse cells, exhibits more complex bidirectional signaling and function than that of allograft. Here, we evaluated the differences of myeloid cells between them. Plasma interferon-γ and interleukin-18 concentrations in the xenograft tumor model after lipopolysaccharide (LPS) administration were significantly higher than those in the allograft tumor model. MHC class I, II, and CD80 expression levels were increased in CD11b+ and MDSC populations after LPS administration in the spleen of a xenograft tumor model but not in that of an allograft tumor model. Additionally, the number of CD80- and mannose receptor C type 1 (MRC1)-expressing cells was decreased upon LPS administration in the tumor of the xenograft tumor. These results suggest that functions of macrophages and DCs are sustained in the xenograft, whereas their functions in response to LPS were suppressed in the allograft. The findings will encourage the consideration of the effects of myeloid cells in the xenograft for drug development. Full article
(This article belongs to the Section Biochemistry)
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17 pages, 5976 KiB  
Article
Erythropoietin Intensifies the Proapoptotic Activity of LFM-A13 in Cells and in a Mouse Model of Colorectal Cancer
by Anna Tankiewicz-Kwedlo, Justyna Magdalena Hermanowicz, Krystyna Pawlak, Robert Czarnomysy, Krzysztof Bielawski, Izabela Prokop and Dariusz Pawlak
Int. J. Mol. Sci. 2018, 19(4), 1262; https://doi.org/10.3390/ijms19041262 - 23 Apr 2018
Cited by 4 | Viewed by 4399
Abstract
The Bruton’s tyrosine kinase (BTK) inhibitor LFM-A13 has been widely employed as an antileukemic agent, but applications in solid cancer have been found recently. The compound promotes apoptosis, has an antiproliferative effect, and increases cancer cell sensitivity to chemotherapy drugs. We decided to [...] Read more.
The Bruton’s tyrosine kinase (BTK) inhibitor LFM-A13 has been widely employed as an antileukemic agent, but applications in solid cancer have been found recently. The compound promotes apoptosis, has an antiproliferative effect, and increases cancer cell sensitivity to chemotherapy drugs. We decided to assess the impact of the simultaneous use of erythropoietin (Epo) and LFM-A13 on signal transduction in colon DLD-1 and HT-29 cells, as well as in tumor xenografts. The induction of apoptosis by Epo and LFM-A-13 in the cells was confirmed by phosphatidylserine externalization, loss of mitochondrial membrane potential, and modulation of the expression of apoptotic protein BAX and antiapoptotic protein BCL-2 in colon adenocarcinoma cells. Nude mice were inoculated with adenocarcinoma cells and treated with Epo and LFM-A13 in order to evaluate the degree of tumor regression. The simultaneous use of Epo and LFM-A13 severely inhibited cell growth, activated apoptosis, and also inhibited tumor growth in xenografts. The addition of Epo to LFM-A13 intensified the antiproliferative effect of LFM-A13, confirmed by the loss of mitochondrial membrane potential and the accumulation of apoptotic colon cancer cells with externalized phosphatidylserine (PS). These preclinical results suggest that the combination of Epo and LFM-A13 has a high proapoptotic activity and should be tested in the clinic for the treatment of solid tumors such as colon cancer. Full article
(This article belongs to the Special Issue Tumor Targeting Therapy and Selective Killing 2018)
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Review

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19 pages, 705 KiB  
Review
Non-Coding RNA in the Pathogenesis, Progression and Treatment of Hypertension
by Christiana Leimena and Hongyu Qiu
Int. J. Mol. Sci. 2018, 19(4), 927; https://doi.org/10.3390/ijms19040927 - 21 Mar 2018
Cited by 47 | Viewed by 5974
Abstract
Hypertension is a complex, multifactorial disease that involves the coexistence of multiple risk factors, environmental factors and physiological systems. The complexities extend to the treatment and management of hypertension, which are still the pursuit of many researchers. In the last two decades, various [...] Read more.
Hypertension is a complex, multifactorial disease that involves the coexistence of multiple risk factors, environmental factors and physiological systems. The complexities extend to the treatment and management of hypertension, which are still the pursuit of many researchers. In the last two decades, various genes have emerged as possible biomarkers and have become the target for investigations of specialized drug design based on its risk factors and the primary cause. Owing to the growing technology of microarrays and next-generation sequencing, the non-protein-coding RNAs (ncRNAs) have increasingly gained attention, and their status of redundancy has flipped to importance in normal cellular processes, as well as in disease progression. The ncRNA molecules make up a significant portion of the human genome, and their role in diseases continues to be uncovered. Specifically, the cellular role of these ncRNAs has played a part in the pathogenesis of hypertension and its progression to heart failure. This review explores the function of the ncRNAs, their types and biology, the current update of their association with hypertension pathology and the potential new therapeutic regime for hypertension. Full article
(This article belongs to the Special Issue Role of Genomics in the Management of Hypertension)
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19 pages, 747 KiB  
Review
Sirtuins as Mediator of the Anti-Ageing Effects of Calorie Restriction in Skeletal and Cardiac Muscle
by Alberto Zullo, Emanuela Simone, Maddalena Grimaldi, Vincenzina Musto and Francesco Paolo Mancini
Int. J. Mol. Sci. 2018, 19(4), 928; https://doi.org/10.3390/ijms19040928 - 21 Mar 2018
Cited by 47 | Viewed by 9812
Abstract
Fighting diseases and controlling the signs of ageing are the major goals of biomedicine. Sirtuins, enzymes with mainly deacetylating activity, could be pivotal targets of novel preventive and therapeutic strategies to reach such aims. Scientific proofs are accumulating in experimental models, but, to [...] Read more.
Fighting diseases and controlling the signs of ageing are the major goals of biomedicine. Sirtuins, enzymes with mainly deacetylating activity, could be pivotal targets of novel preventive and therapeutic strategies to reach such aims. Scientific proofs are accumulating in experimental models, but, to a minor extent, also in humans, that the ancient practice of calorie restriction could prove an effective way to prevent several degenerative diseases and to postpone the detrimental signs of ageing. In the present review, we summarize the evidence about the central role of sirtuins in mediating the beneficial effects of calorie restriction in skeletal and cardiac muscle since these tissues are greatly damaged by diseases and advancing years. Moreover, we entertain the possibility that the identification of sirtuin activators that mimic calorie restriction could provide the benefits without the inconvenience of this dietary style. Full article
(This article belongs to the Special Issue Sirtuins and Epigenetics in Aging and Diseases)
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11 pages, 326 KiB  
Review
Induced Tissue-Specific Stem Cells and Epigenetic Memory in Induced Pluripotent Stem Cells
by Hirofumi Noguchi, Chika Miyagi-Shiohira and Yoshiki Nakashima
Int. J. Mol. Sci. 2018, 19(4), 930; https://doi.org/10.3390/ijms19040930 - 21 Mar 2018
Cited by 45 | Viewed by 7471
Abstract
Induced pluripotent stem (iPS) cells have significant implications for overcoming most of the ethical issues associated with embryonic stem (ES) cells. The pattern of expressed genes, DNA methylation, and covalent histone modifications in iPS cells are very similar to those in ES cells. [...] Read more.
Induced pluripotent stem (iPS) cells have significant implications for overcoming most of the ethical issues associated with embryonic stem (ES) cells. The pattern of expressed genes, DNA methylation, and covalent histone modifications in iPS cells are very similar to those in ES cells. However, it has recently been shown that, following the reprogramming of mouse/human iPS cells, epigenetic memory is inherited from the parental cells. These findings suggest that the phenotype of iPS cells may be influenced by their cells of origin and that their skewed differentiation potential may prove useful in the generation of differentiated cell types that are currently difficult to produce from ES/iPS cells for the treatment of human diseases. Our recent study demonstrated the generation of induced tissue-specific stem (iTS) cells by transient overexpression of the reprogramming factors combined with tissue-specific selection. iTS cells are cells that inherit numerous components of epigenetic memory from donor tissue and acquire self-renewal potential. This review describes the “epigenetic memory” phenomenon in iPS and iTS cells and the possible clinical applications of these stem cells. Full article
(This article belongs to the Special Issue Cell Reprogramming)
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14 pages, 1904 KiB  
Review
Application of CRISPR-Cas9 Based Genome-Wide Screening Approaches to Study Cellular Signalling Mechanisms
by Sumana Sharma and Evangelia Petsalaki
Int. J. Mol. Sci. 2018, 19(4), 933; https://doi.org/10.3390/ijms19040933 - 21 Mar 2018
Cited by 43 | Viewed by 10572
Abstract
The cellular signalling process is a highly complex mechanism, involving multiple players, which together orchestrate the cell’s response to environmental changes and perturbations. Given the multitude of genes that participate in the process of cellular signalling, its study in a genome-wide manner has [...] Read more.
The cellular signalling process is a highly complex mechanism, involving multiple players, which together orchestrate the cell’s response to environmental changes and perturbations. Given the multitude of genes that participate in the process of cellular signalling, its study in a genome-wide manner has proven challenging. Recent advances in gene editing technologies, including clustered regularly-interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) approaches, have opened new opportunities to investigate global regulatory signalling programs of cells in an unbiased manner. In this review, we focus on how the application of pooled genetic screening approaches using the CRISPR/Cas9 system has contributed to a systematic understanding of cellular signalling processes in normal and disease contexts. Full article
(This article belongs to the Special Issue Genome Editing 2018)
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14 pages, 9238 KiB  
Review
Microfabrication-Based Three-Dimensional (3-D) Extracellular Matrix Microenvironments for Cancer and Other Diseases
by Kena Song, Zirui Wang, Ruchuan Liu, Guo Chen and Liyu Liu
Int. J. Mol. Sci. 2018, 19(4), 935; https://doi.org/10.3390/ijms19040935 - 21 Mar 2018
Cited by 13 | Viewed by 6002
Abstract
Exploring the complicated development of tumors and metastases needs a deep understanding of the physical and biological interactions between cancer cells and their surrounding microenvironments. One of the major challenges is the ability to mimic the complex 3-D tissue microenvironment that particularly influences [...] Read more.
Exploring the complicated development of tumors and metastases needs a deep understanding of the physical and biological interactions between cancer cells and their surrounding microenvironments. One of the major challenges is the ability to mimic the complex 3-D tissue microenvironment that particularly influences cell proliferation, migration, invasion, and apoptosis in relation to the extracellular matrix (ECM). Traditional cell culture is unable to create 3-D cell scaffolds resembling tissue complexity and functions, and, in the past, many efforts were made to realize the goal of obtaining cell clusters in hydrogels. However, the available methods still lack a precise control of cell external microenvironments. Recently, the rapid development of microfabrication techniques, such as 3-D printing, microfluidics, and photochemistry, has offered great advantages in reconstructing 3-D controllable cancer cell microenvironments in vitro. Consequently, various biofunctionalized hydrogels have become the ideal candidates to help the researchers acquire some new insights into various diseases. Our review will discuss some important studies and the latest progress regarding the above approaches for the production of 3-D ECM structures for cancer and other diseases. Especially, we will focus on new discoveries regarding the impact of the ECM on different aspects of cancer metastasis, e.g., collective invasion, enhanced intravasation by stress and aligned collagen fibers, angiogenesis regulation, as well as on drug screening. Full article
(This article belongs to the Special Issue Extracellular Matrix in Development and Disease)
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17 pages, 799 KiB  
Review
Disease Modeling Using 3D Organoids Derived from Human Induced Pluripotent Stem Cells
by Beatrice Xuan Ho, Nicole Min Qian Pek and Boon-Seng Soh
Int. J. Mol. Sci. 2018, 19(4), 936; https://doi.org/10.3390/ijms19040936 - 21 Mar 2018
Cited by 117 | Viewed by 18161
Abstract
The rising interest in human induced pluripotent stem cell (hiPSC)-derived organoid culture has stemmed from the manipulation of various combinations of directed multi-lineage differentiation and morphogenetic processes that mimic organogenesis. Organoids are three-dimensional (3D) structures that are comprised of multiple cell types, self-organized [...] Read more.
The rising interest in human induced pluripotent stem cell (hiPSC)-derived organoid culture has stemmed from the manipulation of various combinations of directed multi-lineage differentiation and morphogenetic processes that mimic organogenesis. Organoids are three-dimensional (3D) structures that are comprised of multiple cell types, self-organized to recapitulate embryonic and tissue development in vitro. This model has been shown to be superior to conventional two-dimensional (2D) cell culture methods in mirroring functionality, architecture, and geometric features of tissues seen in vivo. This review serves to highlight recent advances in the 3D organoid technology for use in modeling complex hereditary diseases, cancer, host–microbe interactions, and possible use in translational and personalized medicine where organoid cultures were used to uncover diagnostic biomarkers for early disease detection via high throughput pharmaceutical screening. In addition, this review also aims to discuss the advantages and shortcomings of utilizing organoids in disease modeling. In summary, studying human diseases using hiPSC-derived organoids may better illustrate the processes involved due to similarities in the architecture and microenvironment present in an organoid, which also allows drug responses to be properly recapitulated in vitro. Full article
(This article belongs to the Special Issue Disease Modeling Using Human Induced Pluripotent Stem Cells)
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30 pages, 16180 KiB  
Review
The Role of Endothelial Ca2+ Signaling in Neurovascular Coupling: A View from the Lumen
by Germano Guerra, Angela Lucariello, Angelica Perna, Laura Botta, Antonio De Luca and Francesco Moccia
Int. J. Mol. Sci. 2018, 19(4), 938; https://doi.org/10.3390/ijms19040938 - 21 Mar 2018
Cited by 71 | Viewed by 7733
Abstract
Background: Neurovascular coupling (NVC) is the mechanism whereby an increase in neuronal activity (NA) leads to local elevation in cerebral blood flow (CBF) to match the metabolic requirements of firing neurons. Following synaptic activity, an increase in neuronal and/or astrocyte Ca2+ concentration [...] Read more.
Background: Neurovascular coupling (NVC) is the mechanism whereby an increase in neuronal activity (NA) leads to local elevation in cerebral blood flow (CBF) to match the metabolic requirements of firing neurons. Following synaptic activity, an increase in neuronal and/or astrocyte Ca2+ concentration leads to the synthesis of multiple vasoactive messengers. Curiously, the role of endothelial Ca2+ signaling in NVC has been rather neglected, although endothelial cells are known to control the vascular tone in a Ca2+-dependent manner throughout peripheral vasculature. Methods: We analyzed the literature in search of the most recent updates on the potential role of endothelial Ca2+ signaling in NVC. Results: We found that several neurotransmitters (i.e., glutamate and acetylcholine) and neuromodulators (e.g., ATP) can induce dilation of cerebral vessels by inducing an increase in endothelial Ca2+ concentration. This, in turn, results in nitric oxide or prostaglandin E2 release or activate intermediate and small-conductance Ca2+-activated K+ channels, which are responsible for endothelial-dependent hyperpolarization (EDH). In addition, brain endothelial cells express multiple transient receptor potential (TRP) channels (i.e., TRPC3, TRPV3, TRPV4, TRPA1), which induce vasodilation by activating EDH. Conclusions: It is possible to conclude that endothelial Ca2+ signaling is an emerging pathway in the control of NVC. Full article
(This article belongs to the Special Issue Calcium Signaling in Human Health and Diseases)
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24 pages, 5545 KiB  
Review
Phytochemicals in Skin Cancer Prevention and Treatment: An Updated Review
by Chau Yee Ng, Hsi Yen, Hui-Yi Hsiao and Shih-Chi Su
Int. J. Mol. Sci. 2018, 19(4), 941; https://doi.org/10.3390/ijms19040941 - 22 Mar 2018
Cited by 67 | Viewed by 10863
Abstract
Skin is the largest human organ, our protection against various environmental assaults and noxious agents. Accumulation of these stress events may lead to the formation of skin cancers, including both melanoma and non-melanoma skin cancers. Although modern targeted therapies have ameliorated the management [...] Read more.
Skin is the largest human organ, our protection against various environmental assaults and noxious agents. Accumulation of these stress events may lead to the formation of skin cancers, including both melanoma and non-melanoma skin cancers. Although modern targeted therapies have ameliorated the management of cutaneous malignancies, a safer, more affordable, and more effective strategy for chemoprevention and treatment is clearly needed for the improvement of skin cancer care. Phytochemicals are biologically active compounds derived from plants and herbal products. These agents appear to be beneficial in the battle against cancer as they exert anti-carcinogenic effects and are widely available, highly tolerated, and cost-effective. Evidence has indicated that the anti-carcinogenic properties of phytochemicals are due to their anti-oxidative, anti-inflammatory, anti-proliferative, and anti-angiogenic effects. In this review, we discuss the preventive potential, therapeutic effects, bioavailability, and structure–activity relationship of these selected phytochemicals for the management of skin cancers. The knowledge compiled here will provide clues for future investigations on novel oncostatic phytochemicals and additional anti-skin cancer mechanisms. Full article
(This article belongs to the Special Issue Natural Bioactives and Phytochemicals in Cancer Prevention)
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31 pages, 1541 KiB  
Review
Role of Inflammation in Diabetic Retinopathy
by Anne Rübsam, Sonia Parikh and Patrice E. Fort
Int. J. Mol. Sci. 2018, 19(4), 942; https://doi.org/10.3390/ijms19040942 - 22 Mar 2018
Cited by 527 | Viewed by 19458
Abstract
Diabetic retinopathy is a common complication of diabetes and remains the leading cause of blindness among the working-age population. For decades, diabetic retinopathy was considered only a microvascular complication, but the retinal microvasculature is intimately associated with and governed by neurons and glia, [...] Read more.
Diabetic retinopathy is a common complication of diabetes and remains the leading cause of blindness among the working-age population. For decades, diabetic retinopathy was considered only a microvascular complication, but the retinal microvasculature is intimately associated with and governed by neurons and glia, which are affected even prior to clinically detectable vascular lesions. While progress has been made to improve the vascular alterations, there is still no treatment to counteract the early neuro-glial perturbations in diabetic retinopathy. Diabetes is a complex metabolic disorder, characterized by chronic hyperglycemia along with dyslipidemia, hypoinsulinemia and hypertension. Increasing evidence points to inflammation as one key player in diabetes-associated retinal perturbations, however, the exact underlying molecular mechanisms are not yet fully understood. Interlinked molecular pathways, such as oxidative stress, formation of advanced glycation end-products and increased expression of vascular endothelial growth factor have received a lot of attention as they all contribute to the inflammatory response. In the current review, we focus on the involvement of inflammation in the pathophysiology of diabetic retinopathy with special emphasis on the functional relationships between glial cells and neurons. Finally, we summarize recent advances using novel targets to inhibit inflammation in diabetic retinopathy. Full article
(This article belongs to the Special Issue Diabetic Retinopathy: Mechanisms underlying Pathophysiology and Therapies)
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17 pages, 3131 KiB  
Review
Mesenchymal Stem Cells of Dental Origin for Inducing Tissue Regeneration in Periodontitis: A Mini-Review
by Beatriz Hernández-Monjaraz, Edelmiro Santiago-Osorio, Alberto Monroy-García, Edgar Ledesma-Martínez and Víctor Manuel Mendoza-Núñez
Int. J. Mol. Sci. 2018, 19(4), 944; https://doi.org/10.3390/ijms19040944 - 22 Mar 2018
Cited by 89 | Viewed by 10796
Abstract
Periodontitis is a chronic disease that begins with a period of inflammation of the supporting tissues of the teeth table and then progresses, destroying the tissues until loss of the teeth occurs. The restoration of the damaged dental support apparatus is an extremely [...] Read more.
Periodontitis is a chronic disease that begins with a period of inflammation of the supporting tissues of the teeth table and then progresses, destroying the tissues until loss of the teeth occurs. The restoration of the damaged dental support apparatus is an extremely complex process due to the regeneration of the cementum, the periodontal ligament, and the alveolar bone. Conventional treatment relies on synthetic materials that fill defects and replace lost dental tissue, but these approaches are not substitutes for a real regeneration of tissue. To address this, there are several approaches to tissue engineering for regenerative dentistry, among them, the use of stem cells. Mesenchymal stem cells (MSC) can be obtained from various sources of adult tissues, such as bone marrow, adipose tissue, skin, and tissues of the orofacial area. MSC of dental origin, such as those found in the bone marrow, have immunosuppressive and immunotolerant properties, multipotency, high proliferation rates, and the capacity for tissue repair. However, they are poorly used as sources of tissue for therapeutic purposes. Their accessibility makes them an attractive source of mesenchymal stem cells, so this review describes the field of dental stem cell research and proposes a potential mechanism involved in periodontal tissue regeneration induced by dental MSC. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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14 pages, 1266 KiB  
Review
Pivotal Roles of Peroxisome Proliferator-Activated Receptors (PPARs) and Their Signal Cascade for Cellular and Whole-Body Energy Homeostasis
by Shreekrishna Lamichane, Babita Dahal Lamichane and Sang-Mo Kwon
Int. J. Mol. Sci. 2018, 19(4), 949; https://doi.org/10.3390/ijms19040949 - 22 Mar 2018
Cited by 109 | Viewed by 9220
Abstract
Peroxisome proliferator-activated receptors (PPARs), members of the nuclear receptor superfamily, are important in whole-body energy metabolism. PPARs are classified into three isoforms, namely, PPARα, β/δ, and γ. They are collectively involved in fatty acid oxidation, as well as glucose and lipid metabolism throughout [...] Read more.
Peroxisome proliferator-activated receptors (PPARs), members of the nuclear receptor superfamily, are important in whole-body energy metabolism. PPARs are classified into three isoforms, namely, PPARα, β/δ, and γ. They are collectively involved in fatty acid oxidation, as well as glucose and lipid metabolism throughout the body. Importantly, the three isoforms of PPARs have complementary and distinct metabolic activities for energy balance at a cellular and whole-body level. PPARs also act with other co-regulators to maintain energy homeostasis. When endogenous ligands bind with these receptors, they regulate the transcription of genes involved in energy homeostasis. However, the exact molecular mechanism of PPARs in energy metabolism remains unclear. In this review, we summarize the importance of PPAR signals in multiple organs and focus on the pivotal roles of PPAR signals in cellular and whole-body energy homeostasis. Full article
(This article belongs to the Special Issue PPARs in Cellular and Whole Body Energy Metabolism)
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21 pages, 1555 KiB  
Review
The Role of Auxin in Cell Wall Expansion
by Mateusz Majda and Stéphanie Robert
Int. J. Mol. Sci. 2018, 19(4), 951; https://doi.org/10.3390/ijms19040951 - 22 Mar 2018
Cited by 266 | Viewed by 19036
Abstract
Plant cells are surrounded by cell walls, which are dynamic structures displaying a strictly regulated balance between rigidity and flexibility. Walls are fairly rigid to provide support and protection, but also extensible, to allow cell growth, which is triggered by a high intracellular [...] Read more.
Plant cells are surrounded by cell walls, which are dynamic structures displaying a strictly regulated balance between rigidity and flexibility. Walls are fairly rigid to provide support and protection, but also extensible, to allow cell growth, which is triggered by a high intracellular turgor pressure. Wall properties regulate the differential growth of the cell, resulting in a diversity of cell sizes and shapes. The plant hormone auxin is well known to stimulate cell elongation via increasing wall extensibility. Auxin participates in the regulation of cell wall properties by inducing wall loosening. Here, we review what is known on cell wall property regulation by auxin. We focus particularly on the auxin role during cell expansion linked directly to cell wall modifications. We also analyze downstream targets of transcriptional auxin signaling, which are related to the cell wall and could be linked to acid growth and the action of wall-loosening proteins. All together, this update elucidates the connection between hormonal signaling and cell wall synthesis and deposition. Full article
(This article belongs to the Special Issue Auxin)
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26 pages, 8662 KiB  
Review
Plant Growth Promoting and Biocontrol Activity of Streptomyces spp. as Endophytes
by Sai Shiva Krishna Prasad Vurukonda, Davide Giovanardi and Emilio Stefani
Int. J. Mol. Sci. 2018, 19(4), 952; https://doi.org/10.3390/ijms19040952 - 22 Mar 2018
Cited by 413 | Viewed by 26776
Abstract
There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often [...] Read more.
There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often lead to resistance in plant pathogens. In agriculture, plant growth-promoting and biocontrol microorganisms have emerged as safe alternatives to chemical pesticides. Streptomyces spp. and their metabolites may have great potential as excellent agents for controlling various fungal and bacterial phytopathogens. Streptomycetes belong to the rhizosoil microbial communities and are efficient colonizers of plant tissues, from roots to the aerial parts. They are active producers of antibiotics and volatile organic compounds, both in soil and in planta, and this feature is helpful for identifying active antagonists of plant pathogens and can be used in several cropping systems as biocontrol agents. Additionally, their ability to promote plant growth has been demonstrated in a number of crops, thus inspiring the wide application of streptomycetes as biofertilizers to increase plant productivity. The present review highlights Streptomyces spp.-mediated functional traits, such as enhancement of plant growth and biocontrol of phytopathogens. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 2017)
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16 pages, 1033 KiB  
Review
Branched Chain Amino Acids: Beyond Nutrition Metabolism
by Cunxi Nie, Ting He, Wenju Zhang, Guolong Zhang and Xi Ma
Int. J. Mol. Sci. 2018, 19(4), 954; https://doi.org/10.3390/ijms19040954 - 23 Mar 2018
Cited by 474 | Viewed by 37126
Abstract
Branched chain amino acids (BCAAs), including leucine (Leu), isoleucine (Ile), and valine (Val), play critical roles in the regulation of energy homeostasis, nutrition metabolism, gut health, immunity and disease in humans and animals. As the most abundant of essential amino acids (EAAs), BCAAs [...] Read more.
Branched chain amino acids (BCAAs), including leucine (Leu), isoleucine (Ile), and valine (Val), play critical roles in the regulation of energy homeostasis, nutrition metabolism, gut health, immunity and disease in humans and animals. As the most abundant of essential amino acids (EAAs), BCAAs are not only the substrates for synthesis of nitrogenous compounds, they also serve as signaling molecules regulating metabolism of glucose, lipid, and protein synthesis, intestinal health, and immunity via special signaling network, especially phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signal pathway. Current evidence supports BCAAs and their derivatives as the potential biomarkers of diseases such as insulin resistance (IR), type 2 diabetes mellitus (T2DM), cancer, and cardiovascular diseases (CVDs). These diseases are closely associated with catabolism and balance of BCAAs. Hence, optimizing dietary BCAA levels should have a positive effect on the parameters associated with health and diseases. This review focuses on recent findings of BCAAs in metabolic pathways and regulation, and underlying the relationship of BCAAs to related disease processes. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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14 pages, 657 KiB  
Review
Neuroimmune Tau Mechanisms: Their Role in the Progression of Neuronal Degeneration
by Nicole Cortés, Víctor Andrade, Leonardo Guzmán-Martínez, Matías Estrella and Ricardo B. Maccioni
Int. J. Mol. Sci. 2018, 19(4), 956; https://doi.org/10.3390/ijms19040956 - 23 Mar 2018
Cited by 33 | Viewed by 5511
Abstract
Progressive neurodegenerative pathologies in aged populations are an issue of major concern worldwide. The microtubule-associated protein tau is able to self-aggregate to form abnormal supramolecular structures that include small oligomers up to complex polymers. Tauopathies correspond to a group of diseases that share [...] Read more.
Progressive neurodegenerative pathologies in aged populations are an issue of major concern worldwide. The microtubule-associated protein tau is able to self-aggregate to form abnormal supramolecular structures that include small oligomers up to complex polymers. Tauopathies correspond to a group of diseases that share tau pathology as a common etiological agent. Since microglial cells play a preponderant role in innate immunity and are the main source of proinflammatory factors in the central nervous system (CNS), the alterations in the cross-talks between microglia and neuronal cells are the main focus of studies concerning the origins of tauopathies. According to evidence from a series of studies, these changes generate a feedback mechanism reactivating microglia and provoking constant cellular damage. Thus, the previously summarized mechanisms could explain the onset and progression of different tauopathies and their functional/behavioral effects, opening the window towards an understanding of the molecular basis of anomalous tau interactions. Despite clinical and pathological differences, increasing experimental evidence indicates an overlap between tauopathies and synucleinopathies, considering that neuroinflammatory events are involved and the existence of protein misfolding. Neurofibrillary tangles of pathological tau (NFT) and Lewy bodies appear to coexist in certain brain areas. Thus, the co-occurrence of synucleinopathies with tauopathies is evidenced by several investigations, in which NFT were found in the substantia nigra of patients with Parkinson’s disease, suggesting that the pathologies share some common features at the level of neuroinflammatory events. Full article
(This article belongs to the Special Issue Tau Function and Dysfunctional Tauopathies)
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15 pages, 7773 KiB  
Review
Micro-Economics of Apoptosis in Cancer: ncRNAs Modulation of BCL-2 Family Members
by Lidia Villanova, Silvia Careccia, Ruggero De Maria and Micol E. Fiori
Int. J. Mol. Sci. 2018, 19(4), 958; https://doi.org/10.3390/ijms19040958 - 23 Mar 2018
Cited by 22 | Viewed by 6368
Abstract
In the last few years, non-coding RNAs (ncRNAs) have been a hot topic in cancer research. Many ncRNAs were found to regulate the apoptotic process and to play a role in tumor cell resistance to treatment. The apoptotic program is on the frontline [...] Read more.
In the last few years, non-coding RNAs (ncRNAs) have been a hot topic in cancer research. Many ncRNAs were found to regulate the apoptotic process and to play a role in tumor cell resistance to treatment. The apoptotic program is on the frontline as self-defense from cancer onset, and evasion of apoptosis has been classified as one of the hallmarks of cancer responsible for therapy failure. The B-cell lymphoma 2 (BCL-2) family members are key players in the regulation of apoptosis and mediate the activation of the mitochondrial death machinery in response to radiation, chemotherapeutic agents and many targeted therapeutics. The balance between the pro-survival and the pro-apoptotic BCL-2 proteins is strictly controlled by ncRNAs. Here, we highlight the most common mechanisms exerted by microRNAs, long non-coding RNAs and circular RNAs on the main mediators of the intrinsic apoptotic cascade with particular focus on their significance in cancer biology. Full article
(This article belongs to the Special Issue The Role of MicroRNAs in Human Diseases)
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20 pages, 17560 KiB  
Review
Compressive Force Spectroscopy: From Living Cells to Single Proteins
by Jiabin Wang, Meijun Liu, Yi Shen, Jielin Sun, Zhifeng Shao and Daniel Mark Czajkowsky
Int. J. Mol. Sci. 2018, 19(4), 960; https://doi.org/10.3390/ijms19040960 - 23 Mar 2018
Cited by 5 | Viewed by 4336
Abstract
One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities [...] Read more.
One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these “tensile” force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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23 pages, 12939 KiB  
Review
Roles of Chloroplast Retrograde Signals and Ion Transport in Plant Drought Tolerance
by Chenchen Zhao, Anthony M. Haigh, Paul Holford and Zhong-Hua Chen
Int. J. Mol. Sci. 2018, 19(4), 963; https://doi.org/10.3390/ijms19040963 - 23 Mar 2018
Cited by 23 | Viewed by 8060
Abstract
Worldwide, drought affects crop yields; therefore, understanding plants’ strategies to adapt to drought is critical. Chloroplasts are key regulators of plant responses, and signals from chloroplasts also regulate nuclear gene expression during drought. However, the interactions between chloroplast-initiated retrograde signals and ion channels [...] Read more.
Worldwide, drought affects crop yields; therefore, understanding plants’ strategies to adapt to drought is critical. Chloroplasts are key regulators of plant responses, and signals from chloroplasts also regulate nuclear gene expression during drought. However, the interactions between chloroplast-initiated retrograde signals and ion channels under stress are still not clear. In this review, we summarise the retrograde signals that participate in regulating plant stress tolerance. We compare chloroplastic transporters that modulate retrograde signalling through retrograde biosynthesis or as critical components in retrograde signalling. We also discuss the roles of important plasma membrane and tonoplast ion transporters that are involved in regulating stomatal movement. We propose how retrograde signals interact with ion transporters under stress. Full article
(This article belongs to the Special Issue Plasma-Membrane Transport)
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18 pages, 10615 KiB  
Review
State-of-the-Art Fluorescence Fluctuation-Based Spectroscopic Techniques for the Study of Protein Aggregation
by Akira Kitamura and Masataka Kinjo
Int. J. Mol. Sci. 2018, 19(4), 964; https://doi.org/10.3390/ijms19040964 - 23 Mar 2018
Cited by 35 | Viewed by 7330
Abstract
Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, are devastating proteinopathies with misfolded protein aggregates accumulating in neuronal cells. Inclusion bodies of protein aggregates are frequently observed in the neuronal cells of patients. Investigation of the underlying [...] Read more.
Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, are devastating proteinopathies with misfolded protein aggregates accumulating in neuronal cells. Inclusion bodies of protein aggregates are frequently observed in the neuronal cells of patients. Investigation of the underlying causes of neurodegeneration requires the establishment and selection of appropriate methodologies for detailed investigation of the state and conformation of protein aggregates. In the current review, we present an overview of the principles and application of several methodologies used for the elucidation of protein aggregation, specifically ones based on determination of fluctuations of fluorescence. The discussed methods include fluorescence correlation spectroscopy (FCS), imaging FCS, image correlation spectroscopy (ICS), photobleaching ICS (pbICS), number and brightness (N&B) analysis, super-resolution optical fluctuation imaging (SOFI), and transient state (TRAST) monitoring spectroscopy. Some of these methodologies are classical protein aggregation analyses, while others are not yet widely used. Collectively, the methods presented here should help the future development of research not only into protein aggregation but also neurodegenerative diseases. Full article
(This article belongs to the Special Issue Laser Application in Life Sciences 2018)
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13 pages, 1523 KiB  
Review
DNA Damage, Mutagenesis and Cancer
by Ashis K. Basu
Int. J. Mol. Sci. 2018, 19(4), 970; https://doi.org/10.3390/ijms19040970 - 23 Mar 2018
Cited by 320 | Viewed by 24697
Abstract
A large number of chemicals and several physical agents, such as UV light and γ-radiation, have been associated with the etiology of human cancer. Generation of DNA damage (also known as DNA adducts or lesions) induced by these agents is an important first [...] Read more.
A large number of chemicals and several physical agents, such as UV light and γ-radiation, have been associated with the etiology of human cancer. Generation of DNA damage (also known as DNA adducts or lesions) induced by these agents is an important first step in the process of carcinogenesis. Evolutionary processes gave rise to DNA repair tools that are efficient in repairing damaged DNA; yet replication of damaged DNA may take place prior to repair, particularly when they are induced at a high frequency. Damaged DNA replication may lead to gene mutations, which in turn may give rise to altered proteins. Mutations in an oncogene, a tumor-suppressor gene, or a gene that controls the cell cycle can generate a clonal cell population with a distinct advantage in proliferation. Many such events, broadly divided into the stages of initiation, promotion, and progression, which may occur over a long period of time and transpire in the context of chronic exposure to carcinogens, can lead to the induction of human cancer. This is exemplified in the long-term use of tobacco being responsible for an increased risk of lung cancer. This mini-review attempts to summarize this wide area that centers on DNA damage as it relates to the development of human cancer. Full article
(This article belongs to the Special Issue Chemically-Induced DNA Damage, Mutagenesis, and Cancer)
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24 pages, 30261 KiB  
Review
Survivin-Based Treatment Strategies for Squamous Cell Carcinoma
by Andrea Santarelli, Marco Mascitti, Lucio Lo Russo, Davide Sartini, Giuseppe Troiano, Monica Emanuelli and Lorenzo Lo Muzio
Int. J. Mol. Sci. 2018, 19(4), 971; https://doi.org/10.3390/ijms19040971 - 24 Mar 2018
Cited by 42 | Viewed by 7010
Abstract
Survivin, an anti-apoptotic molecule abundantly expressed in most human neoplasms, has been reported to contribute to cancer initiation and drug resistance in a wide variety of human tumors. Efficient downregulation of survivin can sensitize tumor cells to various therapeutic interventions, generating considerable efforts [...] Read more.
Survivin, an anti-apoptotic molecule abundantly expressed in most human neoplasms, has been reported to contribute to cancer initiation and drug resistance in a wide variety of human tumors. Efficient downregulation of survivin can sensitize tumor cells to various therapeutic interventions, generating considerable efforts in its validation as a new target in cancer therapy. This review thoroughly analyzes up-to-date information on the potential of survivin as a therapeutic target for new anticancer treatments. The literature dealing with the therapeutic targeting of survivin will be reviewed, discussing specifically squamous cell carcinomas (SCCs), and with emphasis on the last clinical trials. This review gives insight into the recent developments undertaken in validating various treatment strategies that target survivin in SCCs and analyze the translational possibility, identifying those strategies that seem to be the closest to being incorporated into clinical practice. The most recent developments, such as dominant-negative survivin mutants, RNA interference, anti-sense oligonucleotides, small-molecule inhibitors, and peptide-based immunotherapy, seem to be helpful for effectively downregulating survivin expression and reducing tumor growth potential, increasing the apoptotic rate, and sensitizing tumor cells to chemo- and radiotherapy. However, selective and efficient targeting of survivin in clinical trials still poses a major challenge. Full article
(This article belongs to the Special Issue Oral Cancer—Diagnosis and Therapeutics)
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26 pages, 22429 KiB  
Review
Mammalian Plakins, Giant Cytolinkers: Versatile Biological Functions and Roles in Cancer
by Lifang Hu, Zizhan Huang, Zixiang Wu, Arshad Ali and Airong Qian
Int. J. Mol. Sci. 2018, 19(4), 974; https://doi.org/10.3390/ijms19040974 - 24 Mar 2018
Cited by 19 | Viewed by 4925
Abstract
Cancer is a highly lethal disease that is characterized by aberrant cell proliferation, migration, and adhesion, which are closely related to the dynamic changes of cytoskeletons and cytoskeletal-adhesion. These will further result in cell invasion and metastasis. Plakins are a family of giant [...] Read more.
Cancer is a highly lethal disease that is characterized by aberrant cell proliferation, migration, and adhesion, which are closely related to the dynamic changes of cytoskeletons and cytoskeletal-adhesion. These will further result in cell invasion and metastasis. Plakins are a family of giant cytolinkers that connect cytoskeletal elements with each other and to junctional complexes. With various isoforms composed of different domain structures, mammalian plakins are broadly expressed in numerous tissues. They play critical roles in many cellular processes, including cell proliferation, migration, adhesion, and signaling transduction. As these cellular processes are key steps in cancer development, mammalian plakins have in recent years attracted more and more attention for their potential roles in cancer. Current evidence shows the importance of mammalian plakins in various human cancers and demonstrates mammalian plakins as potential biomarkers for cancer. Here, we introduce the basic characteristics of mammalian plakins, review the recent advances in understanding their biological functions, and highlight their roles in human cancers, based on studies performed by us and others. This will provide researchers with a comprehensive understanding of mammalian plakins, new insights into the development of cancer, and novel targets for cancer diagnosis and therapy. Full article
(This article belongs to the Section Biochemistry)
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14 pages, 9183 KiB  
Review
Galectin-3 in Atrial Fibrillation: Mechanisms and Therapeutic Implications
by Nicolas Clementy, Eric Piver, Arnaud Bisson, Clémentine Andre, Anne Bernard, Bertrand Pierre, Laurent Fauchier and Dominique Babuty
Int. J. Mol. Sci. 2018, 19(4), 976; https://doi.org/10.3390/ijms19040976 - 25 Mar 2018
Cited by 51 | Viewed by 7197
Abstract
Maintenance of atrial fibrillation is a complex mechanism, including extensive electrical and structural remodeling of the atria which involves progressive fibrogenesis. Galectin-3 is a biomarker of fibrosis, and, thus, may be involved in atrial remodeling in atrial fibrillation patients. We review the role [...] Read more.
Maintenance of atrial fibrillation is a complex mechanism, including extensive electrical and structural remodeling of the atria which involves progressive fibrogenesis. Galectin-3 is a biomarker of fibrosis, and, thus, may be involved in atrial remodeling in atrial fibrillation patients. We review the role of galectin-3 in AF mechanisms and its potential therapeutic implications. Full article
(This article belongs to the Special Issue Galectins in Cancer and Translational Medicine)
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24 pages, 10960 KiB  
Review
Multifaced Roles of the αvβ3 Integrin in Ehlers–Danlos and Arterial Tortuosity Syndromes’ Dermal Fibroblasts
by Nicoletta Zoppi, Nicola Chiarelli, Marco Ritelli and Marina Colombi
Int. J. Mol. Sci. 2018, 19(4), 982; https://doi.org/10.3390/ijms19040982 - 26 Mar 2018
Cited by 30 | Viewed by 7829
Abstract
The αvβ3 integrin, an endothelial cells’ receptor-binding fibronectin (FN) in the extracellular matrix (ECM) of blood vessels, regulates ECM remodeling during migration, invasion, angiogenesis, wound healing and inflammation, and is also involved in the epithelial mesenchymal transition. In vitro-grown human control fibroblasts organize [...] Read more.
The αvβ3 integrin, an endothelial cells’ receptor-binding fibronectin (FN) in the extracellular matrix (ECM) of blood vessels, regulates ECM remodeling during migration, invasion, angiogenesis, wound healing and inflammation, and is also involved in the epithelial mesenchymal transition. In vitro-grown human control fibroblasts organize a fibrillar network of FN, which is preferentially bound on the entire cell surface to its canonical α5β1 integrin receptor, whereas the αvβ3 integrin is present only in rare patches in focal contacts. We report on the preferential recruitment of the αvβ3 integrin, due to the lack of FN–ECM and its canonical integrin receptor, in dermal fibroblasts from Ehlers–Danlos syndromes (EDS) and arterial tortuosity syndrome (ATS), which are rare multisystem connective tissue disorders. We review our previous findings that unraveled different biological mechanisms elicited by the αvβ3 integrin in fibroblasts derived from patients affected with classical (cEDS), vascular (vEDS), hypermobile EDS (hEDS), hypermobility spectrum disorders (HSD), and ATS. In cEDS and vEDS, respectively, due to defective type V and type III collagens, αvβ3 rescues patients’ fibroblasts from anoikis through a paxillin-p60Src-mediated cross-talk with the EGF receptor. In hEDS and HSD, without a defined molecular basis, the αvβ3 integrin transduces to the ILK-Snail1-axis inducing a fibroblast-to-myofibroblast-transition. In ATS cells, the deficiency of the dehydroascorbic acid transporter GLUT10 leads to redox imbalance, ECM disarray together with the activation of a non-canonical αvβ3 integrin-TGFBRII signaling, involving p125FAK/p60Src/p38MAPK. The characterization of these different biological functions triggered by αvβ3 provides insights into the multifaced nature of this integrin, at least in cultured dermal fibroblasts, offering future perspectives for research in this field. Full article
(This article belongs to the Special Issue Integrins and Human Pathologies)
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14 pages, 6025 KiB  
Review
The Sealing Zone in Osteoclasts: A Self-Organized Structure on the Bone
by Jiro Takito, Satoshi Inoue and Masanori Nakamura
Int. J. Mol. Sci. 2018, 19(4), 984; https://doi.org/10.3390/ijms19040984 - 26 Mar 2018
Cited by 77 | Viewed by 7661
Abstract
Osteoclasts form a specialized cell–matrix adhesion structure, known as the “sealing zone”, during bone resorption. The sealing zone is a dynamic actin-rich structure that defines the resorption area of the bone. The detailed dynamics and fine structure of the sealing zone have been [...] Read more.
Osteoclasts form a specialized cell–matrix adhesion structure, known as the “sealing zone”, during bone resorption. The sealing zone is a dynamic actin-rich structure that defines the resorption area of the bone. The detailed dynamics and fine structure of the sealing zone have been elusive. Osteoclasts plated on glass do not form a sealing zone, but generate a separate supra-molecular structure called the “podosome belt”. Podosomes are integrin-based adhesion complexes involved in matrix adhesion, cell migration, matrix degradation, and mechanosensing. Invadopodia, podosome-like protrusions in cancer cells, are involved in cell invasion into other tissues by promoting matrix degradation. Both podosomes and invadopodia exhibit actin pattern transitions during maturation. We previously found that Arp2/3-dependent actin flow occurs in all observed assembly patterns of podosomes in osteoclasts on glass. It is known that the actin wave in Dictyostelium cells exhibits a similar pattern transition in its evolution. Because of significant advances in our understanding regarding the mechanism of podosomes/invadopodia formation over the last decade, we revisited the structure and function of the sealing zone in this review, highlighting the possible involvement of self-organized actin waves in the organogenesis of the sealing zone. Full article
(This article belongs to the Section Biochemistry)
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18 pages, 7896 KiB  
Review
NF2/Merlin Inactivation and Potential Therapeutic Targets in Mesothelioma
by Tatsuhiro Sato and Yoshitaka Sekido
Int. J. Mol. Sci. 2018, 19(4), 988; https://doi.org/10.3390/ijms19040988 - 26 Mar 2018
Cited by 76 | Viewed by 11268
Abstract
The neurofibromatosis type 2 (NF2) gene encodes merlin, a tumor suppressor protein frequently inactivated in schwannoma, meningioma, and malignant mesothelioma (MM). The sequence of merlin is similar to that of ezrin/radixin/moesin (ERM) proteins which crosslink actin with the plasma membrane, suggesting [...] Read more.
The neurofibromatosis type 2 (NF2) gene encodes merlin, a tumor suppressor protein frequently inactivated in schwannoma, meningioma, and malignant mesothelioma (MM). The sequence of merlin is similar to that of ezrin/radixin/moesin (ERM) proteins which crosslink actin with the plasma membrane, suggesting that merlin plays a role in transducing extracellular signals to the actin cytoskeleton. Merlin adopts a distinct closed conformation defined by specific intramolecular interactions and regulates diverse cellular events such as transcription, translation, ubiquitination, and miRNA biosynthesis, many of which are mediated through Hippo and mTOR signaling, which are known to be closely involved in cancer development. MM is a very aggressive tumor associated with asbestos exposure, and genetic alterations in NF2 that abrogate merlin’s functional activity are found in about 40% of MMs, indicating the importance of NF2 inactivation in MM development and progression. In this review, we summarize the current knowledge of molecular events triggered by NF2/merlin inactivation, which lead to the development of mesothelioma and other cancers, and discuss potential therapeutic targets in merlin-deficient mesotheliomas. Full article
(This article belongs to the Special Issue Mesothelioma Heterogeneity: Potential Mechanisms)
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18 pages, 723 KiB  
Review
The Horizon of a Therapy for Rare Genetic Diseases: A “Druggable” Future for Fibrodysplasia Ossificans Progressiva
by Serena Cappato, Francesca Giacopelli, Roberto Ravazzolo and Renata Bocciardi
Int. J. Mol. Sci. 2018, 19(4), 989; https://doi.org/10.3390/ijms19040989 - 26 Mar 2018
Cited by 27 | Viewed by 7316
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a rare genetic condition characterized by progressive extra-skeletal ossification leading to cumulative and severe disability. FOP has an extremely variable and episodic course and can be induced by trauma, infections, iatrogenic harms, immunization or can occur in an [...] Read more.
Fibrodysplasia ossificans progressiva (FOP) is a rare genetic condition characterized by progressive extra-skeletal ossification leading to cumulative and severe disability. FOP has an extremely variable and episodic course and can be induced by trauma, infections, iatrogenic harms, immunization or can occur in an unpredictable way, without any recognizable trigger. The causative gene is ACVR1, encoding the Alk-2 type I receptor for bone morphogenetic proteins (BMPs). The signaling is initiated by BMP binding to a receptor complex consisting of type I and II molecules and can proceed into the cell through two main pathways, a canonical, SMAD-dependent signaling and a p38-mediated cascade. Most FOP patients carry the recurrent R206H substitution in the receptor Glycine-Serine rich (GS) domain, whereas a few other mutations are responsible for a limited number of cases. Mutations cause a dysregulation of the downstream BMP-dependent pathway and make mutated ACVR1 responsive to a non-canonical ligand, Activin A. There is no etiologic treatment for FOP. However, many efforts are currently ongoing to find specific therapies targeting the receptor activity and the downstream aberrant pathway at different levels or targeting cellular components and/or processes that are important in modifying the local environment leading to bone neo-formation. Full article
(This article belongs to the Special Issue Rare Diseases: Molecular Mechanisms and Therapeutic Strategies)
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11 pages, 223 KiB  
Review
Gut Microbiota and Type 1 Diabetes
by Hui Han, Yuying Li, Jun Fang, Gang Liu, Jie Yin, Tiejun Li and Yulong Yin
Int. J. Mol. Sci. 2018, 19(4), 995; https://doi.org/10.3390/ijms19040995 - 27 Mar 2018
Cited by 145 | Viewed by 12537
Abstract
Recently, the onset of type 1 diabetes (T1D) has increased rapidly and became a major public health concern worldwide. Various factors are associated with the development of T1D, such as diet, genome, and intestinal microbiota. The gastrointestinal (GI) tract harbors a complex and [...] Read more.
Recently, the onset of type 1 diabetes (T1D) has increased rapidly and became a major public health concern worldwide. Various factors are associated with the development of T1D, such as diet, genome, and intestinal microbiota. The gastrointestinal (GI) tract harbors a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host homeostasis and metabolic diseases. Recent evidence shows that altered gut bacterial composition (dysbiosis) is highly associated with the pathogenesis of insulin dysfunction and T1D and, thus, targeting gut microbiota may serve as a therapeutic potential for T1D patients. In this study, we updated the effect of gut microbiota on T1D and potential mechanisms were discussed. Full article
(This article belongs to the Special Issue The Mechanism of Action of Food Components in Disease Prevention 2017)
13 pages, 2083 KiB  
Review
The Neurotoxic Role of Extracellular Tau Protein
by Álvaro Sebastián-Serrano, Laura De Diego-García and Miguel Díaz-Hernández
Int. J. Mol. Sci. 2018, 19(4), 998; https://doi.org/10.3390/ijms19040998 - 27 Mar 2018
Cited by 52 | Viewed by 5961
Abstract
Tauopathies are a class of neurodegenerative diseases associated with the microtubule-associated protein tau, with Alzheimer’s disease (AD) being the most prevalent related disorder. Neurofibrillary tangles (NFTs) are one of the neuropathological hallmarks present in the brains of AD patients. Because NFTs are aberrant [...] Read more.
Tauopathies are a class of neurodegenerative diseases associated with the microtubule-associated protein tau, with Alzheimer’s disease (AD) being the most prevalent related disorder. Neurofibrillary tangles (NFTs) are one of the neuropathological hallmarks present in the brains of AD patients. Because NFTs are aberrant intracellular inclusions formed by hyperphosphorylated tau, it was initially proposed that phosphorylated and/or aggregated intracellular tau protein was causative of neuronal death. However, recent studies suggest a toxic role for non-phosphorylated and non-aggregated tau when it is located in the brain extracellular space. In this work, we will discuss the neurotoxic role of extracellular tau as well its involvement in the spreading of tau pathologies. Full article
(This article belongs to the Special Issue Tau Function and Dysfunctional Tauopathies)
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37 pages, 3535 KiB  
Review
The Different Facets of Extracellular Calcium Sensors: Old and New Concepts in Calcium-Sensing Receptor Signalling and Pharmacology
by Andrea Gerbino and Matilde Colella
Int. J. Mol. Sci. 2018, 19(4), 999; https://doi.org/10.3390/ijms19040999 - 27 Mar 2018
Cited by 37 | Viewed by 8201
Abstract
The current interest of the scientific community for research in the field of calcium sensing in general and on the calcium-sensing Receptor (CaR) in particular is demonstrated by the still increasing number of papers published on this topic. The extracellular calcium-sensing receptor is [...] Read more.
The current interest of the scientific community for research in the field of calcium sensing in general and on the calcium-sensing Receptor (CaR) in particular is demonstrated by the still increasing number of papers published on this topic. The extracellular calcium-sensing receptor is the best-known G-protein-coupled receptor (GPCR) able to sense external Ca2+ changes. Widely recognized as a fundamental player in systemic Ca2+ homeostasis, the CaR is ubiquitously expressed in the human body where it activates multiple signalling pathways. In this review, old and new notions regarding the mechanisms by which extracellular Ca2+ microdomains are created and the tools available to measure them are analyzed. After a survey of the main signalling pathways triggered by the CaR, a special attention is reserved for the emerging concepts regarding CaR function in the heart, CaR trafficking and pharmacology. Finally, an overview on other Ca2+ sensors is provided. Full article
(This article belongs to the Special Issue Calcium Signaling in Human Health and Diseases)
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15 pages, 349 KiB  
Review
Extracellular Matrix as a Regulator of Epidermal Stem Cell Fate
by Elina Chermnykh, Ekaterina Kalabusheva and Ekaterina Vorotelyak
Int. J. Mol. Sci. 2018, 19(4), 1003; https://doi.org/10.3390/ijms19041003 - 27 Mar 2018
Cited by 59 | Viewed by 7878
Abstract
Epidermal stem cells reside within the specific anatomic location, called niche, which is a microenvironment that interacts with stem cells to regulate their fate. Regulation of many important processes, including maintenance of stem cell quiescence, self-renewal, and homeostasis, as well as the regulation [...] Read more.
Epidermal stem cells reside within the specific anatomic location, called niche, which is a microenvironment that interacts with stem cells to regulate their fate. Regulation of many important processes, including maintenance of stem cell quiescence, self-renewal, and homeostasis, as well as the regulation of division and differentiation, are common functions of the stem cell niche. As it was shown in multiple studies, extracellular matrix (ECM) contributes a lot to stem cell niches in various tissues, including that of skin. In epidermis, ECM is represented, primarily, by a highly specialized ECM structure, basement membrane (BM), which separates the epidermal and dermal compartments. Epidermal stem cells contact with BM, but when they lose the contact and migrate to the overlying layers, they undergo terminal differentiation. When considering all of these factors, ECM is of fundamental importance in regulating epidermal stem cells maintenance, proper mobilization, and differentiation. Here, we summarize the remarkable progress that has recently been made in the research of ECM role in regulating epidermal stem cell fate, paying special attention to the hair follicle stem cell niche. We show that the destruction of ECM components impairs epidermal stem cell morphogenesis and homeostasis. A deep understanding of ECM molecular structure as well as the development of in vitro system for stem cell maintaining by ECM proteins may bring us to developing new approaches for regenerative medicine. Full article
(This article belongs to the Special Issue Molecular Research of Epidermal Stem Cells 2017)
19 pages, 3042 KiB  
Review
Role of Macrophages in Brain Tumor Growth and Progression
by Elia Guadagno, Ivan Presta, Domenico Maisano, Annalidia Donato, Caterina Krizia Pirrone, Gabriella Cardillo, Simona Domenica Corrado, Chiara Mignogna, Teresa Mancuso, Giuseppe Donato, Marialaura Del Basso De Caro and Natalia Malara
Int. J. Mol. Sci. 2018, 19(4), 1005; https://doi.org/10.3390/ijms19041005 - 27 Mar 2018
Cited by 83 | Viewed by 8805
Abstract
The role of macrophages in the growth and the progression of tumors has been extensively studied in recent years. A large body of data demonstrates that macrophage polarization plays an essential role in the growth and progression of brain tumors, such as gliomas, [...] Read more.
The role of macrophages in the growth and the progression of tumors has been extensively studied in recent years. A large body of data demonstrates that macrophage polarization plays an essential role in the growth and progression of brain tumors, such as gliomas, meningiomas, and medulloblastomas. The brain neoplasm cells have the ability to influence the polarization state of the tumor associated macrophages. In turn, innate immunity cells have a decisive role through regulation of the acquired immune response, but also through humoral cross-talking with cancer cells in the tumor microenvironment. Neoangiogenesis, which is an essential element in glial tumor progression, is even regulated by the tumor associated macrophages, whose activity is linked to other factors, such as hypoxia. In addition, macrophages play a decisive role in establishing the entry into the bloodstream of cancer cells. As is well known, the latter phenomenon is also present in brain tumors, even if they only rarely metastasize. Looking ahead in the future, we can imagine that characterizing the relationships between tumor and tumor associated macrophage, as well as the study of circulating tumor cells, could give us useful tools in prognostic evaluation and therapy. More generally, the study of innate immunity in brain tumors can boost the development of new forms of immunotherapy. Full article
(This article belongs to the Special Issue Macrophages in Inflammation)
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12 pages, 5207 KiB  
Review
Particulate Guanylyl Cyclase A/cGMP Signaling Pathway in the Kidney: Physiologic and Therapeutic Indications
by Yang Chen and John C. Burnett
Int. J. Mol. Sci. 2018, 19(4), 1006; https://doi.org/10.3390/ijms19041006 - 27 Mar 2018
Cited by 32 | Viewed by 8741
Abstract
The particulate guanylyl cyclase A (pGC-A)/cGMP pathway plays important roles in regulating renal physiological function and as well as in counteracting pathophysiological conditions. Naturally occurring peptide pGC-A activators consist of atrial natriuretic peptide (ANP), b-type NP (BNP), and urodilatin (URO). These activators bind [...] Read more.
The particulate guanylyl cyclase A (pGC-A)/cGMP pathway plays important roles in regulating renal physiological function and as well as in counteracting pathophysiological conditions. Naturally occurring peptide pGC-A activators consist of atrial natriuretic peptide (ANP), b-type NP (BNP), and urodilatin (URO). These activators bind and activate pGC-A, generating the second messenger cyclic 3′,5′ guanosine monophosphate (cGMP). Cyclic GMP binds to downstream pathway effector molecules including protein kinase G (PKG), cGMP-gated ion channels, and phosphodiesterases (PDEs). These mediators result in a variety of physiological actions in the kidney, including diuresis, natriuresis, increased glomerular filtration rate (GFR) and organ protection, thus, opposing renal cellular injury and remodeling. Downstream proteins regulated by PKG include collagen 1 (Col-1), transforming growth factor beta (TGF-β) and apoptosis-related proteins. In addition to their physiological regulatory effects, pGC-A/cGMP signaling is critical for preserving renal homeostasis in different renal diseases such as acute kidney injury (AKI). Regarding therapeutic options, native pGC-A activators have short half-lives and their activity can be further enhanced by advances in innovative peptide engineering. Thus, novel designer peptide pGC-A activators with enhanced renal activity are under development. Full article
(This article belongs to the Special Issue cGMP-Signalling in Cells: Molecular and Functional Features)
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17 pages, 3375 KiB  
Review
The Role of Circulating Free DNA and MicroRNA in Non-Invasive Diagnosis of HBV- and HCV-Related Hepatocellular Carcinoma
by Francesca Pezzuto, Luigi Buonaguro, Franco Maria Buonaguro and Maria Lina Tornesello
Int. J. Mol. Sci. 2018, 19(4), 1007; https://doi.org/10.3390/ijms19041007 - 28 Mar 2018
Cited by 53 | Viewed by 9632
Abstract
Hepatocellular carcinoma (HCC) is the third and the fifth leading cause of cancer related death worldwide in men and in women, respectively. HCC generally has a poor prognosis, with a very low 5-year overall survival, due to delayed diagnosis and treatment. Early tumour [...] Read more.
Hepatocellular carcinoma (HCC) is the third and the fifth leading cause of cancer related death worldwide in men and in women, respectively. HCC generally has a poor prognosis, with a very low 5-year overall survival, due to delayed diagnosis and treatment. Early tumour detection and timely intervention are the best strategies to reduce morbidity and mortality in HCC patients. Histological evaluation of liver biopsies is the gold standard for cancer diagnosis, although it is an invasive, time-consuming and expensive procedure. Recently, the analysis of circulating free DNA (cfDNA) and RNA molecules released by tumour cells in body fluids, such as blood serum, saliva and urine, has attracted great interest for development of diagnostic assays based on circulating liver cancer molecular biomarkers. Such “liquid biopsies” have shown to be useful for the identification of specific molecular signatures in nucleic acids released by cancer cells, such as gene mutations and altered methylation of DNA as well as variations in the levels of circulating microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Body fluids analysis may represent a valuable strategy to monitor liver disease progression in subjects chronically infected with hepatitis viruses or cancer relapse in HCC treated patients. Several studies showed that qualitative and quantitative assays evaluating molecular profiles of circulating cell-free nucleic acids could be successfully employed for early diagnosis and therapeutic management of HCC patients. This review describes the state of art on the use of liquid biopsy for cancer driver gene mutations, deregulated DNA methylation as well as miRNA levels in HCC diagnosis. Full article
(This article belongs to the Special Issue MicroRNA as Biomarkers in Cancer Diagnostics and Therapy)
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11 pages, 2209 KiB  
Review
The Impact of Carnitine on Dietary Fiber and Gut Bacteria Metabolism and Their Mutual Interaction in Monogastrics
by Abdallah Ghonimy, Dong Ming Zhang, Mohammed Hamdy Farouk and Qiuju Wang
Int. J. Mol. Sci. 2018, 19(4), 1008; https://doi.org/10.3390/ijms19041008 - 28 Mar 2018
Cited by 38 | Viewed by 7870
Abstract
Carnitine has vital roles in the endogenous metabolism of short chain fatty acids. It can protect and support gut microbial species, and some dietary fibers can reduce the available iron involved in the bioactivity of carnitine. There is also an antagonistic relationship between [...] Read more.
Carnitine has vital roles in the endogenous metabolism of short chain fatty acids. It can protect and support gut microbial species, and some dietary fibers can reduce the available iron involved in the bioactivity of carnitine. There is also an antagonistic relationship between high microbial populations and carnitine bioavailability. This review shows the interactions between carnitine and gut microbial composition. It also elucidates the role of carnitine bacterial metabolism, mitochondrial function, fiber fermentability, and short chain fatty acids (SCFAs). Full article
(This article belongs to the Special Issue Dietary Fibre: New Insights on Biochemistry and Health Benefits)
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15 pages, 2896 KiB  
Review
Contributions of Bioactive Molecules in Stem Cell-Based Periodontal Regeneration
by An-Qi Liu, Cheng-Hu Hu, Fang Jin, Li-Shu Zhang and Kun Xuan
Int. J. Mol. Sci. 2018, 19(4), 1016; https://doi.org/10.3390/ijms19041016 - 28 Mar 2018
Cited by 17 | Viewed by 7043
Abstract
Periodontal disease is a widespread disease, which without proper treatment, may lead to tooth loss in adults. Because stem cells from the inflammatory microenvironment created by periodontal disease exhibit impaired regeneration potential even under favorable conditions, it is difficult to obtain satisfactory therapeutic [...] Read more.
Periodontal disease is a widespread disease, which without proper treatment, may lead to tooth loss in adults. Because stem cells from the inflammatory microenvironment created by periodontal disease exhibit impaired regeneration potential even under favorable conditions, it is difficult to obtain satisfactory therapeutic outcomes using traditional treatments, which only focus on the control of inflammation. Therefore, a new stem cell-based therapy known as cell aggregates/cell sheets technology has emerged. This approach provides sufficient numbers of stem cells with high viability for treating the defective site and offers new hope in the field of periodontal regeneration. However, it is not sufficient for regenerating periodontal tissues by delivering cell aggregates/cell sheets to the impaired microenvironment in order to suppress the function of resident cells. In the present review, we summarize some promising bioactive molecules that act as cellular signals, which recreate a favorable microenvironment for tissue regeneration, recruit endogenous cells into the defective site and enhance the viability of exogenous cells. Full article
(This article belongs to the Special Issue Advances in the Research of Endocrine Disrupting Chemicals)
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20 pages, 15941 KiB  
Review
EP4 as a Therapeutic Target for Aggressive Human Breast Cancer
by Mousumi Majumder, Pinki Nandi, Ahmed Omar, Kingsley Chukwunonso Ugwuagbo and Peeyush K. Lala
Int. J. Mol. Sci. 2018, 19(4), 1019; https://doi.org/10.3390/ijms19041019 - 29 Mar 2018
Cited by 56 | Viewed by 14300
Abstract
G-protein-coupled receptors (GPCRs, also called seven-transmembrane or heptahelical receptors) are a superfamily of cell surface receptor proteins that bind to many extracellular ligands and transmit signals to an intracellular guanine nucleotide-binding protein (G-protein). When a ligand binds, the receptor activates the attached G-protein [...] Read more.
G-protein-coupled receptors (GPCRs, also called seven-transmembrane or heptahelical receptors) are a superfamily of cell surface receptor proteins that bind to many extracellular ligands and transmit signals to an intracellular guanine nucleotide-binding protein (G-protein). When a ligand binds, the receptor activates the attached G-protein by causing the exchange of Guanosine-5′-triphosphate (GTP) for guanosine diphosphate (GDP). They play a major role in many physiological functions, as well as in the pathology of many diseases, including cancer progression and metastasis. Only a few GPCR members have been exploited as targets for developing drugs with therapeutic benefit in cancer. Present review briefly summarizes the signaling pathways utilized by the EP (prostaglandin E receptor) family of GPCR, their physiological and pathological roles in carcinogenesis, with special emphasis on the roles of EP4 in breast cancer progression. We make a case for EP4 as a promising newer therapeutic target for treating breast cancer. We show that an aberrant over-expression of cyclooxygenase (COX)-2, which is an inflammation-associated enzyme, occurring in 40–50% of breast cancer patients leads to tumor progression and metastasis due to multiple cellular events resulting from an increased prostaglandin (PG) E2 production in the tumor milieu. They include inactivation of host anti-tumor immune cells, such as Natural Killer (NK) and T cells, increased immuno-suppressor function of tumor-associated macrophages, promotion of tumor cell migration, invasiveness and tumor-associated angiogenesis, due to upregulation of multiple angiogenic factors including Vascular Endothelial Growth Factor (VEGF)-A, increased lymphangiogenesis (due to upregulation of VEGF-C/D), and a stimulation of stem-like cell (SLC) phenotype in cancer cells. All of these events were primarily mediated by activation of the Prostaglandin (PG) E receptor EP4 on tumor or host cells. We show that selective EP4 antagonists (EP4A) could mitigate all of these events tested with cells in vitro as well as in vivo in syngeneic COX-2 expressing mammary cancer bearing mice or immune-deficient mice bearing COX-2 over-expressing human breast cancer xenografts. We suggest that EP4A can avoid thrombo-embolic side effects of long term use of COX-2 inhibitors by sparing cardio-protective roles of PGI2 via IP receptor activation or PGE2 via EP3 receptor activation. Furthermore, we identified two COX-2/EP4 induced oncogenic and SLC-stimulating microRNAs—miR526b and miR655, one of which (miR655) appears to be a potential blood biomarker in breast cancer patients for monitoring SLC-ablative therapies, such as with EP4A. We suggest that EP4A will likely produce the highest benefit in aggressive breast cancers, such as COX-2 expressing triple-negative breast cancers, when combined with other newer agents, such as inhibitors of programmed cell death (PD)-1 or PD-L1. Full article
(This article belongs to the Special Issue Cancer-Driver G Protein-Coupled Receptors as Therapeutic Targets)
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16 pages, 7688 KiB  
Review
Review on PACAP-Induced Transcriptomic and Proteomic Changes in Neuronal Development and Repair
by Adam Rivnyak, Peter Kiss, Andrea Tamas, Dorottya Balogh and Dora Reglodi
Int. J. Mol. Sci. 2018, 19(4), 1020; https://doi.org/10.3390/ijms19041020 - 29 Mar 2018
Cited by 23 | Viewed by 5255
Abstract
Pituitary adenylate cyclase activating polypeptide (PACAP) is a neuropeptide with widespread occurrence and diverse biological effects. Among its several different effects, of special importance is the action of PACAP on neuronal proliferation, differentiation and migration, and neuroprotection. The neuroprotective mechanism of PACAP is [...] Read more.
Pituitary adenylate cyclase activating polypeptide (PACAP) is a neuropeptide with widespread occurrence and diverse biological effects. Among its several different effects, of special importance is the action of PACAP on neuronal proliferation, differentiation and migration, and neuroprotection. The neuroprotective mechanism of PACAP is both direct and indirect, via neuronal and non-neuronal cells. Several research groups have performed transcriptomic and proteomic analysis on PACAP-mediated genes and proteins. Hundreds of proteins have been described as being involved in the PACAP-mediated neuroprotection. In the present review we summarize the few currently available transcriptomic data potentially leading to the proteomic changes in neuronal development and protection. Proteomic studies focusing on the neuroprotective role of PACAP are also reviewed and discussed in light of the most intriguing and promising effect of this neuropeptide, which may possibly have future therapeutic potential. Full article
(This article belongs to the Special Issue Advances in Proteomic Research for the Characterization of Bioactive Molecules)
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14 pages, 947 KiB  
Review
Stem Cells Therapy for Spinal Cord Injury
by Marina Gazdic, Vladislav Volarevic, C. Randall Harrell, Crissy Fellabaum, Nemanja Jovicic, Nebojsa Arsenijevic and Miodrag Stojkovic
Int. J. Mol. Sci. 2018, 19(4), 1039; https://doi.org/10.3390/ijms19041039 - 30 Mar 2018
Cited by 84 | Viewed by 16538
Abstract
Spinal cord injury (SCI), a serious public health issue, most likely occurs in previously healthy young adults. Current therapeutic strategies for SCI includes surgical decompression and pharmacotherapy, however, there is still no gold standard for the treatment of this devastating condition. Inefficiency and [...] Read more.
Spinal cord injury (SCI), a serious public health issue, most likely occurs in previously healthy young adults. Current therapeutic strategies for SCI includes surgical decompression and pharmacotherapy, however, there is still no gold standard for the treatment of this devastating condition. Inefficiency and adverse effects of standard therapy indicate that novel therapeutic strategies are required. Because of their neuroregenerative and neuroprotective properties, stem cells are a promising tool for the treatment of SCI. Herein, we summarize and discuss the promising therapeutic potential of human embryonic stem cells (hESC), induced pluripotent stem cells (iPSC) and ependymal stem/progenitor cells (epSPC) for SCI. Full article
(This article belongs to the Special Issue Therapeutic Strategies to Spinal Cord Injury)
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12 pages, 279 KiB  
Review
Heterogeneity in Immune Cell Content in Malignant Pleural Mesothelioma
by Jorien Minnema-Luiting, Heleen Vroman, Joachim Aerts and Robin Cornelissen
Int. J. Mol. Sci. 2018, 19(4), 1041; https://doi.org/10.3390/ijms19041041 - 30 Mar 2018
Cited by 56 | Viewed by 5219
Abstract
Malignant pleural mesothelioma (MPM) is a highly aggressive cancer with limited therapy options and dismal prognosis. In recent years, the role of immune cells within the tumor microenvironment (TME) has become a major area of interest. In this review, we discuss the current [...] Read more.
Malignant pleural mesothelioma (MPM) is a highly aggressive cancer with limited therapy options and dismal prognosis. In recent years, the role of immune cells within the tumor microenvironment (TME) has become a major area of interest. In this review, we discuss the current knowledge of heterogeneity in immune cell content and checkpoint expression in MPM in relation to prognosis and prediction of treatment efficacy. Generally, immune-suppressive cells such as M2 macrophages, myeloid-derived suppressor cells and regulatory T cells are present within the TME, with extensive heterogeneity in cell numbers. Infiltration of effector cells such as cytotoxic T cells, natural killer cells and T helper cells is commonly found, also with substantial patient to patient heterogeneity. PD-L1 expression also varied greatly (16–65%). The infiltration of immune cells in tumor and associated stroma holds key prognostic and predictive implications. As such, there is a strong rationale for thoroughly mapping the TME to better target therapy in mesothelioma. Researchers should be aware of the extensive possibilities that exist for a tumor to evade the cytotoxic killing from the immune system. Therefore, no “one size fits all” treatment is likely to be found and focus should lie on the heterogeneity of the tumors and TME. Full article
(This article belongs to the Special Issue Mesothelioma Heterogeneity: Potential Mechanisms)
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17 pages, 12742 KiB  
Review
The Potential for Connexin Hemichannels to Drive Breast Cancer Progression through Regulation of the Inflammatory Response
by J. Matthew Rhett and Elizabeth S. Yeh
Int. J. Mol. Sci. 2018, 19(4), 1043; https://doi.org/10.3390/ijms19041043 - 30 Mar 2018
Cited by 12 | Viewed by 4446
Abstract
Over the past few decades, connexin hemichannels have become recognized as major players in modulating the inflammatory response. Chronic inflammation is documented to promote tumorigenesis and is a critical component of tumor progression. Furthermore, inflammation is strongly linked to angiogenesis, immunotolerance, invasiveness, metastasis, [...] Read more.
Over the past few decades, connexin hemichannels have become recognized as major players in modulating the inflammatory response. Chronic inflammation is documented to promote tumorigenesis and is a critical component of tumor progression. Furthermore, inflammation is strongly linked to angiogenesis, immunotolerance, invasiveness, metastasis, and resistance in breast cancers. In this review, the literature on the role of connexin hemichannels in inflammation is summarized, and the potential role for hemichannel-mediated inflammation in driving breast cancer progression is discussed. Lastly, the potential for connexin-based therapeutics to modulate the inflammatory component of the tumor microenvironment as an avenue for the treatment of breast cancer is also discussed. Full article
(This article belongs to the Special Issue Involvement of Connexin Hemichannels in the Inflammatory Response of Chronic Diseases)
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20 pages, 9160 KiB  
Review
Annexin A1: Uncovering the Many Talents of an Old Protein
by Madeeha H. Sheikh and Egle Solito
Int. J. Mol. Sci. 2018, 19(4), 1045; https://doi.org/10.3390/ijms19041045 - 31 Mar 2018
Cited by 139 | Viewed by 15616
Abstract
Annexin A1 (ANXA1) has long been classed as an anti-inflammatory protein due to its control over leukocyte-mediated immune responses. However, it is now recognized that ANXA1 has widespread effects beyond the immune system with implications in maintaining the homeostatic environment within the entire [...] Read more.
Annexin A1 (ANXA1) has long been classed as an anti-inflammatory protein due to its control over leukocyte-mediated immune responses. However, it is now recognized that ANXA1 has widespread effects beyond the immune system with implications in maintaining the homeostatic environment within the entire body due to its ability to affect cellular signalling, hormonal secretion, foetal development, the aging process and development of disease. In this review, we aim to provide a global overview of the role of ANXA1 covering aspects of peripheral and central inflammation, immune repair and endocrine control with focus on the prognostic, diagnostic and therapeutic potential of the molecule in cancer, neurodegeneration and inflammatory-based disorders. Full article
(This article belongs to the Special Issue Annexins—Closing the Gap between Fundamental and Translational Research)
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29 pages, 2978 KiB  
Review
Transplantable Melanomas in Hamsters and Gerbils as Models for Human Melanoma. Sensitization in Melanoma Radiotherapy—From Animal Models to Clinical Trials
by Martyna Śniegocka, Ewa Podgórska, Przemysław M. Płonka, Martyna Elas, Bożena Romanowska-Dixon, Małgorzata Szczygieł, Michał A. Żmijewski, Mirosława Cichorek, Anna Markiewicz, Anna A. Brożyna, Andrzej T. Słominski and Krystyna Urbańska
Int. J. Mol. Sci. 2018, 19(4), 1048; https://doi.org/10.3390/ijms19041048 - 1 Apr 2018
Cited by 30 | Viewed by 7119
Abstract
The focus of the present review is to investigate the role of melanin in the radioprotection of melanoma and attempts to sensitize tumors to radiation by inhibiting melanogenesis. Early studies showed radical scavenging, oxygen consumption and adsorption as mechanisms of melanin radioprotection. Experimental [...] Read more.
The focus of the present review is to investigate the role of melanin in the radioprotection of melanoma and attempts to sensitize tumors to radiation by inhibiting melanogenesis. Early studies showed radical scavenging, oxygen consumption and adsorption as mechanisms of melanin radioprotection. Experimental models of melanoma in hamsters and in gerbils are described as well as their use in biochemical and radiobiological studies, including a spontaneously metastasizing ocular model. Some results from in vitro studies on the inhibition of melanogenesis are presented as well as radio-chelation therapy in experimental and clinical settings. In contrast to cutaneous melanoma, uveal melanoma is very successfully treated with radiation, both using photon and proton beams. We point out that the presence or lack of melanin pigmentation should be considered, when choosing therapeutic options, and that both the experimental and clinical data suggest that melanin could be a target for radiosensitizing melanoma cells to increase efficacy of radiotherapy against melanoma. Full article
(This article belongs to the Special Issue Animal Models of Melanoma)
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12 pages, 1146 KiB  
Review
MicroRNA Regulation of Telomerase Reverse Transcriptase (TERT): Micro Machines Pull Strings of Papier-Mâché Puppets
by Ammad Ahmad Farooqi, Qaisar Mansoor, Nada Alaaeddine and Baojun Xu
Int. J. Mol. Sci. 2018, 19(4), 1051; https://doi.org/10.3390/ijms19041051 - 1 Apr 2018
Cited by 22 | Viewed by 5696
Abstract
Substantial fraction of high-quality information is continuously being added into the existing pool of knowledge related to the biology of telomeres. Based on the insights gleaned from decades of research, it is clear that chromosomal stability needs a highly controlled and dynamic balance [...] Read more.
Substantial fraction of high-quality information is continuously being added into the existing pool of knowledge related to the biology of telomeres. Based on the insights gleaned from decades of research, it is clear that chromosomal stability needs a highly controlled and dynamic balance of DNA gain and loss in each terminal tract of telomeric repeats. Telomeres are formed by tandem repeats of TTAGGG sequences, which are gradually lost with each round of division of the cells. Targeted inhibition of telomerase to effectively induce apoptosis in cancer cells has attracted tremendous attention and overwhelmingly increasingly list of telomerase inhibitors truthfully advocates pharmacological significance of telomerase. Telomerase reverse transcriptase (TERT) is a multi-talented and catalytically active component of the telomerase-associated protein machinery. Different proteins of telomerase-associated machinery work in a synchronized and orchestrated manner to ensure proper maintenance of telomeric length of chromosomes. Rapidly emerging scientific findings about regulation of TERT by microRNAs has revolutionized our understanding related to the biology of telomeres and telomerase. In this review, we have comprehensively discussed how different miRNAs regulate TERT in different cancers. Use of miRNA-based therapeutics against TERT in different cancers needs detailed research in preclinical models for effective translation of laboratory findings to clinically effective therapeutics. Full article
(This article belongs to the Special Issue Role of Telomeres and Telomerase in Cancer and Aging)
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14 pages, 6006 KiB  
Review
The Role of Single-Molecule Force Spectroscopy in Unraveling Typical and Autoimmune Heparin-induced Thrombocytopenia
by Van-Chien Bui and Thi-Huong Nguyen
Int. J. Mol. Sci. 2018, 19(4), 1054; https://doi.org/10.3390/ijms19041054 - 2 Apr 2018
Cited by 7 | Viewed by 4656
Abstract
For the last two decades, heparins have been widely used as anticoagulants. Besides numerous advantages, up to 5% patients with heparin administration suffer from a major adverse drug effect known as heparin-induced thrombocytopenia (HIT). This typical HIT can result in deep vein thrombosis, [...] Read more.
For the last two decades, heparins have been widely used as anticoagulants. Besides numerous advantages, up to 5% patients with heparin administration suffer from a major adverse drug effect known as heparin-induced thrombocytopenia (HIT). This typical HIT can result in deep vein thrombosis, pulmonary embolism, occlusion of a limb artery, acute myocardial infarct, stroke, and a systemic reaction or skin necrosis. The basis of HIT may lead to clinical insights. Recent studies using single-molecule force spectroscopy (SMFS)-based atomic force microscopy revealed detailed binding mechanisms of the interactions between platelet factor 4 (PF4) and heparins of different lengths in typical HIT. Especially, SMFS results allowed identifying a new mechanism of the autoimmune HIT caused by a subset of human-derived antibodies in patients without heparin exposure. The findings proved that not only heparin but also a subset of antibodies induce thrombocytopenia. In this review, the role of SMFS in unraveling a major adverse drug effect and insights into molecular mechanisms inducing thrombocytopenia by both heparins and antibodies will be discussed. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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24 pages, 7350 KiB  
Review
Genetic and Epigenetic Control of CDKN1C Expression: Importance in Cell Commitment and Differentiation, Tissue Homeostasis and Human Diseases
by Emanuela Stampone, Ilaria Caldarelli, Alberto Zullo, Debora Bencivenga, Francesco Paolo Mancini, Fulvio Della Ragione and Adriana Borriello
Int. J. Mol. Sci. 2018, 19(4), 1055; https://doi.org/10.3390/ijms19041055 - 2 Apr 2018
Cited by 47 | Viewed by 8533
Abstract
The CDKN1C gene encodes the p57Kip2 protein which has been identified as the third member of the CIP/Kip family, also including p27Kip1 and p21Cip1. In analogy with these proteins, p57Kip2 is able to bind tightly and inhibit cyclin/cyclin-dependent [...] Read more.
The CDKN1C gene encodes the p57Kip2 protein which has been identified as the third member of the CIP/Kip family, also including p27Kip1 and p21Cip1. In analogy with these proteins, p57Kip2 is able to bind tightly and inhibit cyclin/cyclin-dependent kinase complexes and, in turn, modulate cell division cycle progression. For a long time, the main function of p57Kip2 has been associated only to correct embryogenesis, since CDKN1C-ablated mice are not vital. Accordingly, it has been demonstrated that CDKN1C alterations cause three human hereditary syndromes, characterized by altered growth rate. Subsequently, the p57Kip2 role in several cell phenotypes has been clearly assessed as well as its down-regulation in human cancers. CDKN1C lies in a genetic locus, 11p15.5, characterized by a remarkable regional imprinting that results in the transcription of only the maternal allele. The control of CDKN1C transcription is also linked to additional mechanisms, including DNA methylation and specific histone methylation/acetylation. Finally, long non-coding RNAs and miRNAs appear to play important roles in controlling p57Kip2 levels. This review mostly represents an appraisal of the available data regarding the control of CDKN1C gene expression. In addition, the structure and function of p57Kip2 protein are briefly described and correlated to human physiology and diseases. Full article
(This article belongs to the Special Issue Transcriptional Regulation: Molecules, Involved Mechanisms and Misregulation)
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17 pages, 6103 KiB  
Review
Potential Interplay between Hyperosmolarity and Inflammation on Retinal Pigmented Epithelium in Pathogenesis of Diabetic Retinopathy
by François Willermain, Lisa Scifo, Célia Weber, Laure Caspers, Jason Perret and Christine Delporte
Int. J. Mol. Sci. 2018, 19(4), 1056; https://doi.org/10.3390/ijms19041056 - 2 Apr 2018
Cited by 41 | Viewed by 6399
Abstract
Diabetic retinopathy is a frequent eyesight threatening complication of type 1 and type 2 diabetes. Under physiological conditions, the inner and the outer blood-retinal barriers protect the retina by regulating ion, protein, and water flux into and out of the retina. During diabetic [...] Read more.
Diabetic retinopathy is a frequent eyesight threatening complication of type 1 and type 2 diabetes. Under physiological conditions, the inner and the outer blood-retinal barriers protect the retina by regulating ion, protein, and water flux into and out of the retina. During diabetic retinopathy, many factors, including inflammation, contribute to the rupture of the inner and/or the outer blood-retinal barrier. This rupture leads the development of macular edema, a foremost cause of sight loss among diabetic patients. Under these conditions, it has been speculated that retinal pigmented epithelial cells, that constitute the outer blood-retinal barrier, may be subjected to hyperosmolar stress resulting from different mechanisms. Herein, we review the possible origins and consequences of hyperosmolar stress on retinal pigmented epithelial cells during diabetic retinopathy, with a special focus on the intimate interplay between inflammation and hyperosmolar stress, as well as the current and forthcoming new pharmacotherapies for the treatment of such condition. Full article
(This article belongs to the Special Issue Diabetic Retinopathy: Mechanisms underlying Pathophysiology and Therapies)
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16 pages, 7979 KiB  
Review
Emerging Roles of Vascular Cell Adhesion Molecule-1 (VCAM-1) in Immunological Disorders and Cancer
by Deok-Hoon Kong, Young Kwan Kim, Mi Ra Kim, Ji Hye Jang and Sukmook Lee
Int. J. Mol. Sci. 2018, 19(4), 1057; https://doi.org/10.3390/ijms19041057 - 2 Apr 2018
Cited by 420 | Viewed by 26455
Abstract
Tumor necrosis factor alpha (TNFα) is a pro-inflammatory cytokine that triggers the expression of inflammatory molecules, including other cytokines and cell adhesion molecules. TNFα induces the expression of intercellular cell adhesion molecule-1 and vascular cell adhesion molecule-1 (VCAM-1). VCAM-1 was originally identified as [...] Read more.
Tumor necrosis factor alpha (TNFα) is a pro-inflammatory cytokine that triggers the expression of inflammatory molecules, including other cytokines and cell adhesion molecules. TNFα induces the expression of intercellular cell adhesion molecule-1 and vascular cell adhesion molecule-1 (VCAM-1). VCAM-1 was originally identified as a cell adhesion molecule that helps regulate inflammation-associated vascular adhesion and the transendothelial migration of leukocytes, such as macrophages and T cells. Recent evidence suggests that VCAM-1 is closely associated with the progression of various immunological disorders, including rheumatoid arthritis, asthma, transplant rejection, and cancer. This review covers the role and relevance of VCAM-1 in inflammation, and also highlights the emerging potential of VCAM-1 as a novel therapeutic target in immunological disorders and cancer. Full article
(This article belongs to the Special Issue Tumor Necrosis Factor (TNF))
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14 pages, 11053 KiB  
Review
GFRA1: A Novel Molecular Target for the Prevention of Osteosarcoma Chemoresistance
by Mihwa Kim and Dae Joon Kim
Int. J. Mol. Sci. 2018, 19(4), 1078; https://doi.org/10.3390/ijms19041078 - 4 Apr 2018
Cited by 35 | Viewed by 8582
Abstract
The glycosylphosphatidylinositol-linked GDNF (glial cell derived neurotrophic factor) receptor alpha (GFRA), a coreceptor that recognizes the GDNF family of ligands, has a crucial role in the development and maintenance of the nervous system. Of the four identified GFRA isoforms, GFRA1 specifically recognizes GDNF [...] Read more.
The glycosylphosphatidylinositol-linked GDNF (glial cell derived neurotrophic factor) receptor alpha (GFRA), a coreceptor that recognizes the GDNF family of ligands, has a crucial role in the development and maintenance of the nervous system. Of the four identified GFRA isoforms, GFRA1 specifically recognizes GDNF and is involved in the regulation of proliferation, differentiation, and migration of neuronal cells. GFRA1 has also been implicated in cancer cell progression and metastasis. Recent findings show that GFRA1 can contribute to the development of chemoresistance in osteosarcoma. GFRA1 expression was induced following treatment of osteosarcoma cells with the popular anticancer drug, cisplatin and induction of GFRA1 expression significantly suppressed apoptosis mediated by cisplatin in osteosarcoma cells. GFRA1 expression promotes autophagy by activating the SRC-AMPK signaling axis following cisplatin treatment, resulting in enhanced osteosarcoma cell survival. GFRA1-induced autophagy promoted tumor growth in mouse xenograft models, suggesting a novel function of GFRA1 in osteosarcoma chemoresistance. Full article
(This article belongs to the Special Issue Current Advances in Soft Tissue and Bone Sarcoma)
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15 pages, 348 KiB  
Review
Teleosts Genomics: Progress and Prospects in Disease Prevention and Control
by Hetron Mweemba Munang’andu, Jorge Galindo-Villegas and Lior David
Int. J. Mol. Sci. 2018, 19(4), 1083; https://doi.org/10.3390/ijms19041083 - 4 Apr 2018
Cited by 23 | Viewed by 4414
Abstract
Genome wide studies based on conventional molecular tools and upcoming omics technologies are beginning to gain functional applications in the control and prevention of diseases in teleosts fish. Herein, we provide insights into current progress and prospects in the use genomics studies for [...] Read more.
Genome wide studies based on conventional molecular tools and upcoming omics technologies are beginning to gain functional applications in the control and prevention of diseases in teleosts fish. Herein, we provide insights into current progress and prospects in the use genomics studies for the control and prevention of fish diseases. Metagenomics has emerged to be an important tool used to identify emerging infectious diseases for the timely design of rational disease control strategies, determining microbial compositions in different aquatic environments used for fish farming and the use of host microbiota to monitor the health status of fish. Expounding the use of antimicrobial peptides (AMPs) as therapeutic agents against different pathogens as well as elucidating their role in tissue regeneration is another vital aspect of genomics studies that had taken precedent in recent years. In vaccine development, prospects made include the identification of highly immunogenic proteins for use in recombinant vaccine designs as well as identifying gene signatures that correlate with protective immunity for use as benchmarks in optimizing vaccine efficacy. Progress in quantitative trait loci (QTL) mapping is beginning to yield considerable success in identifying resistant traits against some of the highly infectious diseases that have previously ravaged the aquaculture industry. Altogether, the synopsis put forth shows that genomics studies are beginning to yield positive contribution in the prevention and control of fish diseases in aquaculture. Full article
(This article belongs to the Section Biochemistry)
26 pages, 1367 KiB  
Review
Plants and Surgery: The Protective Effects of Thymoquinone on Hepatic Injury—A Systematic Review of In Vivo Studies
by Aysun Tekbas, Jutta Huebner, Utz Settmacher and Uta Dahmen
Int. J. Mol. Sci. 2018, 19(4), 1085; https://doi.org/10.3390/ijms19041085 - 5 Apr 2018
Cited by 21 | Viewed by 5128
Abstract
Multimodal treatment concepts including liver transplantation for hepatocellular carcinoma (HCC), extended resection methods and neoadjuvant chemotherapy for colorectal liver metastasis significantly improve patients’ outcome. However, surgery-induced hepatic ischemia-reperfusion injury (IRI) and chemotherapy-associated hepatotoxicity result in hepatocellular damage and compromised liver function. Activation of [...] Read more.
Multimodal treatment concepts including liver transplantation for hepatocellular carcinoma (HCC), extended resection methods and neoadjuvant chemotherapy for colorectal liver metastasis significantly improve patients’ outcome. However, surgery-induced hepatic ischemia-reperfusion injury (IRI) and chemotherapy-associated hepatotoxicity result in hepatocellular damage and compromised liver function. Activation of common key pathways in ischemic liver and hepatotoxic injury results in oxidative stress, inflammatory responses and apoptosis causing organ damage. Controlling liver damage before and during surgery is essential for the postoperative outcome. Nigella sativa has a long tradition as a natural remedy. In the essential oil, Thymoquinone (TQ) was identified as the main component and responsible for most of the therapeutic effects. Therefore, this systematic review aimed to summarize the hepatoprotective effects of TQ and its potential suitability to improve surgical outcome by reducing surgical ischemic injury and hepatotoxicity of neoadjuvant chemotherapy. The key findings can be summarized as TQ having strong antioxidant, anti-inflammatory, antifibrotic, anti-/proapoptotic and anticarcinogenic effects. Almost no side effects were reported irrespective of a large dose range, suggesting a wide therapeutic window. These results give rise to the expectation that TQ could evolve to a novel powerful drug to reduce hepatic injury. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Pathophysiology of Ischemia-Reperfusion Injury)
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14 pages, 9160 KiB  
Review
Correcting Calcium Dysregulation in Chronic Heart Failure Using SERCA2a Gene Therapy
by T. Jake Samuel, Ryan P. Rosenberry, Seungyong Lee and Zui Pan
Int. J. Mol. Sci. 2018, 19(4), 1086; https://doi.org/10.3390/ijms19041086 - 5 Apr 2018
Cited by 31 | Viewed by 8808
Abstract
Chronic heart failure (CHF) is a major contributor to cardiovascular disease and is the leading cause of hospitalization for those over the age of 65, which is estimated to account for close to seventy billion dollars in healthcare costs by 2030 in the [...] Read more.
Chronic heart failure (CHF) is a major contributor to cardiovascular disease and is the leading cause of hospitalization for those over the age of 65, which is estimated to account for close to seventy billion dollars in healthcare costs by 2030 in the US alone. The successful therapies for preventing and reversing CHF progression are urgently required. One strategy under active investigation is to restore dysregulated myocardial calcium (Ca2+), a hallmark of CHF. It is well established that intracellular Ca2+ concentrations are tightly regulated to control efficient myocardial systolic contraction and diastolic relaxation. Among the many cell surface proteins and intracellular organelles that act as the warp and woof of the regulatory network controlling intracellular Ca2+ signals in cardiomyocytes, sarco/endoplasmic reticulum Ca2+ ATPase type 2a (SERCA2a) undoubtedly plays a central role. SERCA2a is responsible for sequestrating cytosolic Ca2+ back into the sarcoplasmic reticulum during diastole, allowing for efficient uncoupling of actin-myosin and subsequent ventricular relaxation. Accumulating evidence has demonstrated that the expression of SERCA2a is downregulated in CHF, which subsequently contributes to severe systolic and diastolic dysfunction. Therefore, restoring SERCA2a expression and improving cardiomyocyte Ca2+ handling provides an excellent alternative to currently used transplantation and mechanical assist devices in the treatment of CHF. Indeed, advancements in safe and effective gene delivery techniques have led to the emergence of SERCA2a gene therapy as a potential therapeutic choice for CHF patients. This mini-review will succinctly detail the progression of SERCA2a gene therapy from its inception in plasmid and animal models, to its clinical trials in CHF patients, highlighting potential avenues for future work along the way. Full article
(This article belongs to the Special Issue Calcium Signaling in Human Health and Diseases)
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17 pages, 514 KiB  
Review
Zebrafish as a Model System for Investigating the Compensatory Regulation of Ionic Balance during Metabolic Acidosis
by Lletta Lewis and Raymond W. M. Kwong
Int. J. Mol. Sci. 2018, 19(4), 1087; https://doi.org/10.3390/ijms19041087 - 5 Apr 2018
Cited by 18 | Viewed by 8580
Abstract
Zebrafish (Danio rerio) have become an important model for integrative physiological research. Zebrafish inhabit a hypo-osmotic environment; to maintain ionic and acid-base homeostasis, they must actively take up ions and secrete acid to the water. The gills in the adult and [...] Read more.
Zebrafish (Danio rerio) have become an important model for integrative physiological research. Zebrafish inhabit a hypo-osmotic environment; to maintain ionic and acid-base homeostasis, they must actively take up ions and secrete acid to the water. The gills in the adult and the skin at larval stage are the primary sites of ionic regulation in zebrafish. The uptake of ions in zebrafish is mediated by specific ion transporting cells termed ionocytes. Similarly, in mammals, ion reabsorption and acid excretion occur in specific cell types in the terminal region of the renal tubules (distal convoluted tubule and collecting duct). Previous studies have suggested that functional regulation of several ion transporters/channels in the zebrafish ionocytes resembles that in the mammalian renal cells. Additionally, several mechanisms involved in regulating the epithelial ion transport during metabolic acidosis are found to be similar between zebrafish and mammals. In this article, we systemically review the similarities and differences in ionic regulation between zebrafish and mammals during metabolic acidosis. We summarize the available information on the regulation of epithelial ion transporters during acidosis, with a focus on epithelial Na+, Cl− and Ca2+ transporters in zebrafish ionocytes and mammalian renal cells. We also discuss the neuroendocrine responses to acid exposure, and their potential role in ionic compensation. Finally, we identify several knowledge gaps that would benefit from further study. Full article
(This article belongs to the Special Issue Ion Transporters and Channels in Physiology and Pathophysiology)
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19 pages, 32485 KiB  
Review
Applications of CRISPR/Cas System to Bacterial Metabolic Engineering
by Suhyung Cho, Jongoh Shin and Byung-Kwan Cho
Int. J. Mol. Sci. 2018, 19(4), 1089; https://doi.org/10.3390/ijms19041089 - 5 Apr 2018
Cited by 119 | Viewed by 37456
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) adaptive immune system has been extensively used for gene editing, including gene deletion, insertion, and replacement in bacterial and eukaryotic cells owing to its simple, rapid, and efficient activities in unprecedented resolution. Furthermore, the CRISPR [...] Read more.
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) adaptive immune system has been extensively used for gene editing, including gene deletion, insertion, and replacement in bacterial and eukaryotic cells owing to its simple, rapid, and efficient activities in unprecedented resolution. Furthermore, the CRISPR interference (CRISPRi) system including deactivated Cas9 (dCas9) with inactivated endonuclease activity has been further investigated for regulation of the target gene transiently or constitutively, avoiding cell death by disruption of genome. This review discusses the applications of CRISPR/Cas for genome editing in various bacterial systems and their applications. In particular, CRISPR technology has been used for the production of metabolites of high industrial significance, including biochemical, biofuel, and pharmaceutical products/precursors in bacteria. Here, we focus on methods to increase the productivity and yield/titer scan by controlling metabolic flux through individual or combinatorial use of CRISPR/Cas and CRISPRi systems with introduction of synthetic pathway in industrially common bacteria including Escherichia coli. Further, we discuss additional useful applications of the CRISPR/Cas system, including its use in functional genomics. Full article
(This article belongs to the Special Issue Genome Editing 2018)
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18 pages, 15842 KiB  
Review
Emerging Roles of Estrogen-Related Receptors in the Brain: Potential Interactions with Estrogen Signaling
by Kenji Saito and Huxing Cui
Int. J. Mol. Sci. 2018, 19(4), 1091; https://doi.org/10.3390/ijms19041091 - 5 Apr 2018
Cited by 56 | Viewed by 12206
Abstract
In addition to their well-known role in the female reproductive system, estrogens can act in the brain to regulate a wide range of behaviors and physiological functions in both sexes. Over the past few decades, genetically modified animal models have greatly increased our [...] Read more.
In addition to their well-known role in the female reproductive system, estrogens can act in the brain to regulate a wide range of behaviors and physiological functions in both sexes. Over the past few decades, genetically modified animal models have greatly increased our knowledge about the roles of estrogen receptor (ER) signaling in the brain in behavioral and physiological regulations. However, less attention has been paid to the estrogen-related receptors (ERRs), the members of orphan nuclear receptors whose sequences are homologous to ERs but lack estrogen-binding ability. While endogenous ligands of ERRs remain to be determined, they seemingly share transcriptional targets with ERs and their expression can be directly regulated by ERs through the estrogen-response element embedded within the regulatory region of the genes encoding ERRs. Despite the broad expression of ERRs in the brain, we have just begun to understand the fundamental roles they play at molecular, cellular, and circuit levels. Here, we review recent research advancement in understanding the roles of ERs and ERRs in the brain, with particular emphasis on ERRs, and discuss possible cross-talk between ERs and ERRs in behavioral and physiological regulations. Full article
(This article belongs to the Special Issue Molecular Pathways of Estrogen Receptor Action)
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20 pages, 9400 KiB  
Review
Tau-Induced Pathology in Epilepsy and Dementia: Notions from Patients and Animal Models
by Marina P. Sánchez, Ana M. García-Cabrero, Gentzane Sánchez-Elexpuru, Daniel F. Burgos and José M. Serratosa
Int. J. Mol. Sci. 2018, 19(4), 1092; https://doi.org/10.3390/ijms19041092 - 5 Apr 2018
Cited by 45 | Viewed by 8409
Abstract
Patients with dementia present epilepsy more frequently than the general population. Seizures are more common in patients with Alzheimer’s disease (AD), dementia with Lewy bodies (LBD), frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP) than in other dementias. Missense mutations in the microtubule [...] Read more.
Patients with dementia present epilepsy more frequently than the general population. Seizures are more common in patients with Alzheimer’s disease (AD), dementia with Lewy bodies (LBD), frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP) than in other dementias. Missense mutations in the microtubule associated protein tau (MAPT) gene have been found to cause familial FTD and PSP, while the P301S mutation in MAPT has been associated with early-onset fast progressive dementia and the presence of seizures. Brains of patients with AD, LBD, FTD and PSP show hyperphosphorylated tau aggregates, amyloid-β plaques and neuropil threads. Increasing evidence suggests the existence of overlapping mechanisms related to the generation of network hyperexcitability and cognitive decline. Neuronal overexpression of tau with various mutations found in FTD with parkinsonism-linked to chromosome 17 (FTDP-17) in mice produces epileptic activity. On the other hand, the use of certain antiepileptic drugs in animal models with AD prevents cognitive impairment. Further efforts should be made to search for plausible common targets for both conditions. Moreover, attempts should also be made to evaluate the use of drugs targeting tau and amyloid-β as suitable pharmacological interventions in epileptic disorders. The diagnosis of dementia and epilepsy in early stages of those diseases may be helpful for the initiation of treatments that could prevent the generation of epileptic activity and cognitive deterioration. Full article
(This article belongs to the Special Issue Tau Function and Dysfunctional Tauopathies)
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16 pages, 10175 KiB  
Review
Squamous Cell Carcinoma Antigen 2 (SCCA2, SERPINB4): An Emerging Biomarker for Skin Inflammatory Diseases
by Kenji Izuhara, Yukie Yamaguchi, Shoichiro Ohta, Satoshi Nunomura, Yasuhiro Nanri, Yoshinori Azuma, Noriko Nomura, Yasuhiko Noguchi and Michiko Aihara
Int. J. Mol. Sci. 2018, 19(4), 1102; https://doi.org/10.3390/ijms19041102 - 6 Apr 2018
Cited by 42 | Viewed by 7098
Abstract
Squamous cell carcinoma antigens 1 and 2 (SCCA1 and 2, SERPIN B3 and B4), members of the ovalbumin serpin (ov-serpin)/clade B serpin family, were originally discovered as tumor-specific antigens and are used as tumor markers for various kinds of squamous cell carcinomas. Recently, [...] Read more.
Squamous cell carcinoma antigens 1 and 2 (SCCA1 and 2, SERPIN B3 and B4), members of the ovalbumin serpin (ov-serpin)/clade B serpin family, were originally discovered as tumor-specific antigens and are used as tumor markers for various kinds of squamous cell carcinomas. Recently, our understanding of the underlying mechanisms of how SCCA1/2 enhance tumor growth has greatly increased. Moreover, it has been shown that SCCA1/2 are involved in the pathogenesis of several inflammatory diseases: asthma, psoriasis, and atopic dermatitis (AD). IL-22 and IL-17, signature cytokines of type 17 inflammation, as well as IL-4 and IL-13, signature cytokines of type 2 inflammation, both of which are positively correlated with the pathogenesis of psoriasis and allergic diseases, respectively, can induce expression of SCCA1/2 in airway epithelial cells and/or keratinocytes, leading to high expression of SCCA1/2 in these diseases. Based on these findings, several trials have been performed to examine the potential of applying SCCA1/2 to biomarkers for these diseases. The findings show that SCCA2 is useful to aid diagnosis, estimate clinical severity and disease type, and assess responses to treatment in psoriasis and AD. These results suggest that SCCA2 has emerged as a novel biomarker for skin inflammatory diseases. Full article
(This article belongs to the Special Issue Molecular Research on Mucosal Immunity)
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19 pages, 4026 KiB  
Review
Molecular Consortia—Various Structural and Synthetic Concepts for More Effective Therapeutics Synthesis
by Anna Pawełczyk, Katarzyna Sowa-Kasprzak, Dorota Olender and Lucjusz Zaprutko
Int. J. Mol. Sci. 2018, 19(4), 1104; https://doi.org/10.3390/ijms19041104 - 6 Apr 2018
Cited by 57 | Viewed by 5473
Abstract
The design and discovery of novel drug candidates are the initial and most probably the crucial steps in the drug development process. One of the tasks of medicinal chemistry is to produce new molecules that have a desired biological effect. However, even today [...] Read more.
The design and discovery of novel drug candidates are the initial and most probably the crucial steps in the drug development process. One of the tasks of medicinal chemistry is to produce new molecules that have a desired biological effect. However, even today the search for new pharmaceuticals is a very complicated process that is hard to rationalize. Literature provides many scientific reports on future prospects of design of potentially useful drugs. Many trends have been proposed for the design of new drugs containing different structures (dimers, heterodimers, heteromers, adducts, associates, complexes, biooligomers, dendrimers, dual-, bivalent-, multifunction drugs and codrugs, identical or non-identical twin drugs, mixed or combo drugs, supramolecular particles and various nanoindividuals. Recently much attention has been paid to different strategies of molecular hybridization. In this paper, various molecular combinations were described e.g., drug–drug or drug-non-drug combinations which are expressed in a schematic multi-factor form called a molecular matrix, consisting of four factors: association mode, connection method, and the number of elements and linkers. One of the most popular trends is to create small–small molecule combinations such as different hybrids, codrugs, drug–drug conjugates (DDCs) and small-large molecule combinations such as antibody-drug conjugates (ADCs), polymer-drug conjugates (PDCs) or different prodrugs and macromolecular therapeutics. A review of the structural possibilities of active framework combinations indicates that a wide range of potentially effective novel-type compounds can be formed. What is particularly important is that new therapeutics can be obtained in fast, efficient, and selective methods using current trends in chemical synthesis and the design of drugs such as the “Lego” concept or rational green approach. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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40 pages, 28288 KiB  
Review
Antibacterial Free Fatty Acids and Monoglycerides: Biological Activities, Experimental Testing, and Therapeutic Applications
by Bo Kyeong Yoon, Joshua A. Jackman, Elba R. Valle-González and Nam-Joon Cho
Int. J. Mol. Sci. 2018, 19(4), 1114; https://doi.org/10.3390/ijms19041114 - 8 Apr 2018
Cited by 370 | Viewed by 22076
Abstract
Antimicrobial lipids such as fatty acids and monoglycerides are promising antibacterial agents that destabilize bacterial cell membranes, causing a wide range of direct and indirect inhibitory effects. The goal of this review is to introduce the latest experimental approaches for characterizing how antimicrobial [...] Read more.
Antimicrobial lipids such as fatty acids and monoglycerides are promising antibacterial agents that destabilize bacterial cell membranes, causing a wide range of direct and indirect inhibitory effects. The goal of this review is to introduce the latest experimental approaches for characterizing how antimicrobial lipids destabilize phospholipid membranes within the broader scope of introducing current knowledge about the biological activities of antimicrobial lipids, testing strategies, and applications for treating bacterial infections. To this end, a general background on antimicrobial lipids, including structural classification, is provided along with a detailed description of their targeting spectrum and currently understood antibacterial mechanisms. Building on this knowledge, different experimental approaches to characterize antimicrobial lipids are presented, including cell-based biological and model membrane-based biophysical measurement techniques. Particular emphasis is placed on drawing out how biological and biophysical approaches complement one another and can yield mechanistic insights into how the physicochemical properties of antimicrobial lipids influence molecular self-assembly and concentration-dependent interactions with model phospholipid and bacterial cell membranes. Examples of possible therapeutic applications are briefly introduced to highlight the potential significance of antimicrobial lipids for human health and medicine, and to motivate the importance of employing orthogonal measurement strategies to characterize the activity profile of antimicrobial lipids. Full article
(This article belongs to the Special Issue Molecular Signaling and Nanobiotechnology: Prospects for Future Antimicrobial Therapy)
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24 pages, 17252 KiB  
Review
Migration/Invasion of Malignant Gliomas and Implications for Therapeutic Treatment
by Ching-Ann Liu, Chia-Yu Chang, Kuo-Wei Hsueh, Hong-Lin Su, Tzyy-Wen Chiou, Shinn-Zong Lin and Horng-Jyh Harn
Int. J. Mol. Sci. 2018, 19(4), 1115; https://doi.org/10.3390/ijms19041115 - 8 Apr 2018
Cited by 81 | Viewed by 7294
Abstract
Malignant tumors of the central nervous system (CNS) are among cancers with the poorest prognosis, indicated by their association with tumors of high-level morbidity and mortality. Gliomas, the most common primary CNS tumors that arise from neuroglial stem or progenitor cells, have estimated [...] Read more.
Malignant tumors of the central nervous system (CNS) are among cancers with the poorest prognosis, indicated by their association with tumors of high-level morbidity and mortality. Gliomas, the most common primary CNS tumors that arise from neuroglial stem or progenitor cells, have estimated annual incidence of 6.6 per 100,000 individuals in the USA, and 3.5 per 100,000 individuals in Taiwan. Tumor invasion and metastasis are the major contributors to the deaths in cancer patients. Therapeutic goals including cancer stem cells (CSC), phenotypic shifts, EZH2/AXL/TGF-β axis activation, miRNAs and exosomes are relevant to GBM metastasis to develop novel targeted therapeutics for GBM and other brain cancers. Herein, we highlight tumor metastasis in our understanding of gliomas, and illustrate novel exosome therapeutic approaches in glioma, thereby paving the way towards innovative therapies in neuro-oncology. Full article
(This article belongs to the Special Issue Glioma Cell Invasion)
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34 pages, 15302 KiB  
Review
Mesenchymal Stromal Cells: Emerging Roles in Bone Metastasis
by Nicola Graham and Bin-Zhi Qian
Int. J. Mol. Sci. 2018, 19(4), 1121; https://doi.org/10.3390/ijms19041121 - 9 Apr 2018
Cited by 36 | Viewed by 7124
Abstract
Bone metastasis is the most advanced stage of many cancers and indicates a poor prognosis for patients due to resistance to anti-tumor therapies. The establishment of metastasis within the bone is a multistep process. To ensure survival within the bone marrow, tumor cells [...] Read more.
Bone metastasis is the most advanced stage of many cancers and indicates a poor prognosis for patients due to resistance to anti-tumor therapies. The establishment of metastasis within the bone is a multistep process. To ensure survival within the bone marrow, tumor cells must initially colonize a niche in which they can enter dormancy. Subsequently, reactivation permits the proliferation and growth of the tumor cells, giving rise to a macro-metastasis displayed clinically as a bone metastatic lesion. Here, we review the evidences that suggest mesenchymal stromal cells play an important role in each of these steps throughout the development of bone metastasis. Similarities between the molecular mechanisms implicated in these processes and those involved in the homeostasis of the bone indicate that the metastatic cells may exploit the homeostatic processes to their own advantage. Identifying the molecular interactions between the mesenchymal stromal cells and tumor cells that promote tumor development may offer insight into potential therapeutic targets that could be utilized to treat bone metastasis. Full article
(This article belongs to the Special Issue Bone Metastasis: Pathophysiology and Molecular Mechanisms)
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15 pages, 3346 KiB  
Review
DDX5 RNA Helicases: Emerging Roles in Viral Infection
by Wenyu Cheng, Guohua Chen, Huaijie Jia, Xiaobing He and Zhizhong Jing
Int. J. Mol. Sci. 2018, 19(4), 1122; https://doi.org/10.3390/ijms19041122 - 9 Apr 2018
Cited by 39 | Viewed by 6813
Abstract
Asp-Glu-Ala-Asp (DEAD)-box polypeptide 5 (DDX5), also called p68, is a prototypical member of the large ATP-dependent RNA helicases family and is known to participate in all aspects of RNA metabolism ranging from transcription to translation, RNA decay, and miRNA processing. The roles of [...] Read more.
Asp-Glu-Ala-Asp (DEAD)-box polypeptide 5 (DDX5), also called p68, is a prototypical member of the large ATP-dependent RNA helicases family and is known to participate in all aspects of RNA metabolism ranging from transcription to translation, RNA decay, and miRNA processing. The roles of DDX5 in cell cycle regulation, tumorigenesis, apoptosis, cancer development, adipogenesis, Wnt-β-catenin signaling, and viral infection have been established. Several RNA viruses have been reported to hijack DDX5 to facilitate various steps of their replication cycles. Furthermore, DDX5 can be bounded by the viral proteins of some viruses with unknown functions. Interestingly, an antiviral function of DDX5 has been reported during hepatitis B virus and myxoma virus infection. Thus, the precise roles of this apparently multifaceted protein remain largely obscure. Here, we provide a rapid and critical overview of the structure and functions of DDX5 with a particular emphasis on its role during virus infection. Full article
(This article belongs to the Section Biochemistry)
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15 pages, 18832 KiB  
Review
Comparative Genomics and Transcriptome Profiling in Primary Aldosteronism
by Elke Tatjana Aristizabal Prada, Isabella Castellano, Eva Sušnik, Yuhong Yang, Lucie S. Meyer, Martina Tetti, Felix Beuschlein, Martin Reincke and Tracy A. Williams
Int. J. Mol. Sci. 2018, 19(4), 1124; https://doi.org/10.3390/ijms19041124 - 9 Apr 2018
Cited by 13 | Viewed by 6153
Abstract
Primary aldosteronism is the most common form of endocrine hypertension with a prevalence of 6% in the general population with hypertension. The genetic basis of the four familial forms of primary aldosteronism (familial hyperaldosteronism FH types I–IV) and the majority of sporadic unilateral [...] Read more.
Primary aldosteronism is the most common form of endocrine hypertension with a prevalence of 6% in the general population with hypertension. The genetic basis of the four familial forms of primary aldosteronism (familial hyperaldosteronism FH types I–IV) and the majority of sporadic unilateral aldosterone-producing adenomas has now been resolved. Familial forms of hyperaldosteronism are, however, rare. The sporadic forms of the disease prevail and these are usually caused by either a unilateral aldosterone-producing adenoma or bilateral adrenal hyperplasia. Aldosterone-producing adenomas frequently carry a causative somatic mutation in either of a number of genes with the KCNJ5 gene, encoding an inwardly rectifying potassium channel, a recurrent target harboring mutations at a prevalence of more than 40% worldwide. Other than genetic variations, gene expression profiling of aldosterone-producing adenomas has shed light on the genes and intracellular signalling pathways that may play a role in the pathogenesis and pathophysiology of these tumors. Full article
(This article belongs to the Special Issue Role of Genomics in the Management of Hypertension)
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13 pages, 3114 KiB  
Review
The Role of Extracellular Vesicles in Bone Metastasis
by Michela Rossi, Giulia Battafarano, Matteo D’Agostini and Andrea Del Fattore
Int. J. Mol. Sci. 2018, 19(4), 1136; https://doi.org/10.3390/ijms19041136 - 10 Apr 2018
Cited by 36 | Viewed by 6759
Abstract
Multiple types of cancer have the specific ability to home to the bone microenvironment and cause metastatic lesions. Despite being the focus of intense investigation, the molecular and cellular mechanisms that regulate the metastasis of disseminated tumor cells still remain largely unknown. Bone [...] Read more.
Multiple types of cancer have the specific ability to home to the bone microenvironment and cause metastatic lesions. Despite being the focus of intense investigation, the molecular and cellular mechanisms that regulate the metastasis of disseminated tumor cells still remain largely unknown. Bone metastases severely impact quality of life since they are associated with pain, fractures, and bone marrow aplasia. In this review, we will summarize the recent discoveries on the role of extracellular vesicles (EV) in the regulation of bone remodeling activity and bone metastasis occurrence. Indeed, it was shown that extracellular vesicles, including exosomes and microvesicles, released from tumor cells can modify the bone microenvironment, allowing the formation of osteolytic, osteosclerotic, and mixed mestastases. In turn, bone-derived EV can stimulate the proliferation of tumor cells. The inhibition of EV-mediated crosstalk between cancer and bone cells could represent a new therapeutic target for bone metastasis. Full article
(This article belongs to the Special Issue Bone Metastasis: Pathophysiology and Molecular Mechanisms)
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21 pages, 3684 KiB  
Review
A Review of the Interactions between Wheat and Wheat Pathogens: Zymoseptoria tritici, Fusarium spp. and Parastagonospora nodorum
by Adrian Duba, Klaudia Goriewa-Duba and Urszula Wachowska
Int. J. Mol. Sci. 2018, 19(4), 1138; https://doi.org/10.3390/ijms19041138 - 10 Apr 2018
Cited by 35 | Viewed by 9840
Abstract
Zymoseptoria tritici is a hemibiotrophic pathogen which causes Septoria leaf blotch in wheat. The pathogenesis of the disease consists of a biotrophic phase and a necrotrophic phase. The pathogen infects the host plant by suppressing its immune response in the first stage of [...] Read more.
Zymoseptoria tritici is a hemibiotrophic pathogen which causes Septoria leaf blotch in wheat. The pathogenesis of the disease consists of a biotrophic phase and a necrotrophic phase. The pathogen infects the host plant by suppressing its immune response in the first stage of infection. Hemibiotrophic pathogens of the genus Fusarium cause Fusarium head blight, and the necrotrophic Parastagonospora nodorum is responsible for Septoria nodorum blotch in wheat. Cell wall-degrading enzymes in plants promote infections by necrotrophic and hemibiotrophic pathogens, and trichothecenes, secondary fungal metabolites, facilitate infections caused by fungi of the genus Fusarium. There are no sources of complete resistance to the above pathogens in wheat. Defense mechanisms in wheat are controlled by many genes encoding resistance traits. In the wheat genome, the characteristic features of loci responsible for resistance to pathogenic infections indicate that at least several dozen genes encode resistance to pathogens. The molecular interactions between wheat and Z. tritici, P. nodorum and Fusarium spp. pathogens have been insufficiently investigated. Most studies focus on the mechanisms by which the hemibiotrophic Z. tritici suppresses immune responses in plants and the role of mycotoxins and effector proteins in infections caused by P. nodorum and Fusarium spp. fungi. Trichothecene glycosylation and effector proteins, which are involved in defense responses in wheat, have been described at the molecular level. Recent advances in molecular biology have produced interesting findings which should be further elucidated in studies of molecular interactions between wheat and fungal pathogens. The Clustered Regularly-Interspaced Short Palindromic Repeats/ CRISPR associated (CRISPR/Cas) system can be used to introduce targeted mutations into the wheat genome and confer resistance to selected fungal diseases. Host-induced gene silencing and spray-induced gene silencing are also useful tools for analyzing wheat–pathogens interactions which can be used to develop new strategies for controlling fungal diseases. Full article
(This article belongs to the Special Issue Signal Transduction Pathways in Plants for Resistance Against Plant Pathogens)
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39 pages, 40443 KiB  
Review
Prospects of Understanding the Molecular Biology of Disease Resistance in Rice
by Pankaj Kumar Singh, Akshay Nag, Preeti Arya, Ritu Kapoor, Akshay Singh, Rajdeep Jaswal and Tilak Raj Sharma
Int. J. Mol. Sci. 2018, 19(4), 1141; https://doi.org/10.3390/ijms19041141 - 10 Apr 2018
Cited by 41 | Viewed by 10863
Abstract
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in [...] Read more.
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host–pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice. Full article
(This article belongs to the Special Issue Plant Defense Genes Against Biotic Stresses)
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18 pages, 5011 KiB  
Review
Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization
by Tatyana O. Pleshakova, Natalia S. Bukharina, Alexander I. Archakov and Yuri D. Ivanov
Int. J. Mol. Sci. 2018, 19(4), 1142; https://doi.org/10.3390/ijms19041142 - 10 Apr 2018
Cited by 53 | Viewed by 7347
Abstract
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination [...] Read more.
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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21 pages, 4101 KiB  
Review
Signals of Systemic Immunity in Plants: Progress and Open Questions
by Attila L. Ádám, Zoltán Á. Nagy, György Kátay, Emese Mergenthaler and Orsolya Viczián
Int. J. Mol. Sci. 2018, 19(4), 1146; https://doi.org/10.3390/ijms19041146 - 10 Apr 2018
Cited by 66 | Viewed by 10389
Abstract
Systemic acquired resistance (SAR) is a defence mechanism that induces protection against a wide range of pathogens in distant, pathogen-free parts of plants after a primary inoculation. Multiple mobile compounds were identified as putative SAR signals or important factors for influencing movement of [...] Read more.
Systemic acquired resistance (SAR) is a defence mechanism that induces protection against a wide range of pathogens in distant, pathogen-free parts of plants after a primary inoculation. Multiple mobile compounds were identified as putative SAR signals or important factors for influencing movement of SAR signalling elements in Arabidopsis and tobacco. These include compounds with very different chemical structures like lipid transfer protein DIR1 (DEFECTIVE IN INDUCED RESISTANCE1), methyl salicylate (MeSA), dehydroabietinal (DA), azelaic acid (AzA), glycerol-3-phosphate dependent factor (G3P) and the lysine catabolite pipecolic acid (Pip). Genetic studies with different SAR-deficient mutants and silenced lines support the idea that some of these compounds (MeSA, DIR1 and G3P) are activated only when SAR is induced in darkness. In addition, although AzA doubled in phloem exudate of tobacco mosaic virus (TMV) infected tobacco leaves, external AzA treatment could not induce resistance neither to viral nor bacterial pathogens, independent of light conditions. Besides light intensity and timing of light exposition after primary inoculation, spectral distribution of light could also influence the SAR induction capacity. Recent data indicated that TMV and CMV (cucumber mosaic virus) infection in tobacco, like bacteria in Arabidopsis, caused massive accumulation of Pip. Treatment of tobacco leaves with Pip in the light, caused a drastic and significant local and systemic decrease in lesion size of TMV infection. Moreover, two very recent papers, added in proof, demonstrated the role of FMO1 (FLAVIN-DEPENDENT-MONOOXYGENASE1) in conversion of Pip to N-hydroxypipecolic acid (NHP). NHP systemically accumulates after microbial attack and acts as a potent inducer of plant immunity to bacterial and oomycete pathogens in Arabidopsis. These results argue for the pivotal role of Pip and NHP as an important signal compound of SAR response in different plants against different pathogens. Full article
(This article belongs to the Special Issue Plant Innate Immunity 2.0)
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22 pages, 663 KiB  
Review
Multifaceted Role of Pneumolysin in the Pathogenesis of Myocardial Injury in Community-Acquired Pneumonia
by Ronald Anderson, Jan G. Nel and Charles Feldman
Int. J. Mol. Sci. 2018, 19(4), 1147; https://doi.org/10.3390/ijms19041147 - 11 Apr 2018
Cited by 34 | Viewed by 6979
Abstract
Pneumolysin (PLY), a member of the family of Gram-positive bacterial, cholesterol-dependent, β-barrel pore-forming cytolysins, is the major protein virulence factor of the dangerous respiratory pathogen, Streptococcus pneumoniae (pneumococcus). PLY plays a major role in the pathogenesis of community-acquired pneumonia (CAP), promoting colonization and [...] Read more.
Pneumolysin (PLY), a member of the family of Gram-positive bacterial, cholesterol-dependent, β-barrel pore-forming cytolysins, is the major protein virulence factor of the dangerous respiratory pathogen, Streptococcus pneumoniae (pneumococcus). PLY plays a major role in the pathogenesis of community-acquired pneumonia (CAP), promoting colonization and invasion of the upper and lower respiratory tracts respectively, as well as extra-pulmonary dissemination of the pneumococcus. Notwithstanding its role in causing acute lung injury in severe CAP, PLY has also been implicated in the development of potentially fatal acute and delayed-onset cardiovascular events, which are now recognized as being fairly common complications of this condition. This review is focused firstly on updating mechanisms involved in the immunopathogenesis of PLY-mediated myocardial damage, specifically the direct cardiotoxic and immunosuppressive activities, as well as the indirect pro-inflammatory/pro-thrombotic activities of the toxin. Secondly, on PLY-targeted therapeutic strategies including, among others, macrolide antibiotics, natural product antagonists, cholesterol-containing liposomes, and fully humanized monoclonal antibodies, as well as on vaccine-based preventive strategies. These sections are preceded by overviews of CAP in general, the role of the pneumococcus as the causative pathogen, the occurrence and types of CAP-associated cardiac complication, and the structure and biological activities of PLY. Full article
(This article belongs to the Special Issue Bacterial Protein Toxins: Enemies within or Unexpected Friends)
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23 pages, 6500 KiB  
Review
Deoxyribonucleic Acid Damage and Repair: Capitalizing on Our Understanding of the Mechanisms of Maintaining Genomic Integrity for Therapeutic Purposes
by Jolene Michelle Helena, Anna Margaretha Joubert, Simone Grobbelaar, Elsie Magdalena Nolte, Marcel Nel, Michael Sean Pepper, Magdalena Coetzee and Anne Elisabeth Mercier
Int. J. Mol. Sci. 2018, 19(4), 1148; https://doi.org/10.3390/ijms19041148 - 11 Apr 2018
Cited by 19 | Viewed by 11799
Abstract
Deoxyribonucleic acid (DNA) is the self-replicating hereditary material that provides a blueprint which, in collaboration with environmental influences, produces a structural and functional phenotype. As DNA coordinates and directs differentiation, growth, survival, and reproduction, it is responsible for life and the continuation of [...] Read more.
Deoxyribonucleic acid (DNA) is the self-replicating hereditary material that provides a blueprint which, in collaboration with environmental influences, produces a structural and functional phenotype. As DNA coordinates and directs differentiation, growth, survival, and reproduction, it is responsible for life and the continuation of our species. Genome integrity requires the maintenance of DNA stability for the correct preservation of genetic information. This is facilitated by accurate DNA replication and precise DNA repair. DNA damage may arise from a wide range of both endogenous and exogenous sources but may be repaired through highly specific mechanisms. The most common mechanisms include mismatch, base excision, nucleotide excision, and double-strand DNA (dsDNA) break repair. Concurrent with regulation of the cell cycle, these mechanisms are precisely executed to ensure full restoration of damaged DNA. Failure or inaccuracy in DNA repair contributes to genome instability and loss of genetic information which may lead to mutations resulting in disease or loss of life. A detailed understanding of the mechanisms of DNA damage and its repair provides insight into disease pathogeneses and may facilitate diagnosis and the development of targeted therapies. Full article
(This article belongs to the Special Issue DNA Replication Stress)
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28 pages, 3257 KiB  
Review
The Role, Involvement and Function(s) of Interleukin-35 and Interleukin-37 in Disease Pathogenesis
by Ramatu Omenesa Bello, Voon Kin Chin, Mohammad Faruq Abd Rachman Isnadi, Roslaini Abd Majid, Maizaton Atmadini Abdullah, Tze Yan Lee, Zainul Amiruddin Zakaria, Mohd Khairi Hussain and Rusliza Basir
Int. J. Mol. Sci. 2018, 19(4), 1149; https://doi.org/10.3390/ijms19041149 - 11 Apr 2018
Cited by 32 | Viewed by 7981
Abstract
The recently identified cytokines—interleukin (IL)-35 and interleukin (IL)-37—have been described for their anti-inflammatory and immune-modulating actions in numerous inflammatory diseases, auto-immune disorders, malignancies, infectious diseases and sepsis. Either cytokine has been reported to be reduced and in some cases elevated and consequently contributed [...] Read more.
The recently identified cytokines—interleukin (IL)-35 and interleukin (IL)-37—have been described for their anti-inflammatory and immune-modulating actions in numerous inflammatory diseases, auto-immune disorders, malignancies, infectious diseases and sepsis. Either cytokine has been reported to be reduced and in some cases elevated and consequently contributed towards disease pathogenesis. In view of the recent advances in utilizing cytokine profiles for the development of biological macromolecules, beneficial in the management of certain intractable immune-mediated disorders, these recently characterized cytokines (IL-35 and IL-37) offer potential as reasonable targets for the discovery of novel immune-modulating anti-inflammatory therapies. A detailed comprehension of their sophisticated regulatory mechanisms and patterns of expression may provide unique opportunities for clinical application as highly selective and target specific therapeutic agents. This review seeks to summarize the recent advancements in discerning the dynamics, mechanisms, immunoregulatory and anti-inflammatory actions of IL-35 and IL-37 as they relate to disease pathogenesis. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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12 pages, 2826 KiB  
Review
The JAK2 GGCC (46/1) Haplotype in Myeloproliferative Neoplasms: Causal or Random?
by Luisa Anelli, Antonella Zagaria, Giorgina Specchia and Francesco Albano
Int. J. Mol. Sci. 2018, 19(4), 1152; https://doi.org/10.3390/ijms19041152 - 11 Apr 2018
Cited by 16 | Viewed by 6296
Abstract
The germline JAK2 haplotype known as “GGCC or 46/1 haplotype” (haplotypeGGCC_46/1) consists of a combination of single nucleotide polymorphisms (SNPs) mapping in a region of about 250 kb, extending from the JAK2 intron 10 to the Insulin-like 4 (INLS4) [...] Read more.
The germline JAK2 haplotype known as “GGCC or 46/1 haplotype” (haplotypeGGCC_46/1) consists of a combination of single nucleotide polymorphisms (SNPs) mapping in a region of about 250 kb, extending from the JAK2 intron 10 to the Insulin-like 4 (INLS4) gene. Four main SNPs (rs3780367, rs10974944, rs12343867, and rs1159782) generating a “GGCC” combination are more frequently indicated to represent the JAK2 haplotype. These SNPs are inherited together and are frequently associated with the onset of myeloproliferative neoplasms (MPN) positive for both JAK2 V617 and exon 12 mutations. The association between the JAK2 haplotypeGGCC_46/1 and mutations in other genes, such as thrombopoietin receptor (MPL) and calreticulin (CALR), or the association with triple negative MPN, is still controversial. This review provides an overview of the frequency and the role of the JAK2 haplotypeGGCC_46/1 in the pathogenesis of different myeloid neoplasms and describes the hypothetical mechanisms at the basis of the association with JAK2 gene mutations. Moreover, possible clinical implications are discussed, as different papers reported contrasting data about the correlation between the JAK2 haplotypeGGCC_46/1 and blood cell count, survival, or disease progression. Full article
(This article belongs to the Section Biochemistry)
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15 pages, 1837 KiB  
Review
Conflicting Roles of Connexin43 in Tumor Invasion and Growth in the Central Nervous System
by Miaki Uzu, Wun Chey Sin, Ayaka Shimizu and Hiromi Sato
Int. J. Mol. Sci. 2018, 19(4), 1159; https://doi.org/10.3390/ijms19041159 - 11 Apr 2018
Cited by 23 | Viewed by 5714
Abstract
The tumor microenvironment is known to have increased levels of cytokines and metabolites, such as glutamate, due to their release from the surrounding cells. A normal cell around the tumor that responds to the inflammatory environment is likely to be subsequently altered. We [...] Read more.
The tumor microenvironment is known to have increased levels of cytokines and metabolites, such as glutamate, due to their release from the surrounding cells. A normal cell around the tumor that responds to the inflammatory environment is likely to be subsequently altered. We discuss how these abnormalities will support tumor survival via the actions of gap junctions (GJs) and hemichannels (HCs) which are composed of hexamer of connexin43 (Cx43) protein. In particular, we discuss how GJ intercellular communication (GJIC) in glioma cells, the primary brain tumor, is a regulatory factor and its attenuation leads to tumor invasion. In contrast, the astrocytes, which are normal cells around the glioma, are “hijacked” by tumor cells, either by receiving the transmission of malignant substances from the cancer cells via GJIC, or perhaps via astrocytic HC activity through the paracrine signaling which enable the delivery of these substances to the distal astrocytes. This astrocytic signaling would promote tumor expansion in the brain. In addition, brain metastasis from peripheral tissues has also been known to be facilitated by GJs formed between cerebral vascular endothelial cells and cancer cells. Astrocytes and microglia are generally thought to eliminate cancer cells at the blood–brain barrier. In contrast, some reports suggest they facilitate tumor progression as tumor cells take advantage of the normal functions of astrocytes that support the survival of the neurons by exchanging nutrients and metabolites. In summary, GJIC is essential for the normal physiological function of growth and allowing the diffusion of physiological substances. Therefore, whether GJIC is cancer promoting or suppressing may be dependent on what permeates through GJs, when it is active, and to which cells. The nature of GJs, which has been ambiguous in brain tumor progression, needs to be revisited and understood together with new findings on Cx proteins and HC activities. Full article
(This article belongs to the Special Issue Involvement of Connexin Hemichannels in the Inflammatory Response of Chronic Diseases)
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14 pages, 295 KiB  
Review
An Overview on the Clinical Development of Tau-Based Therapeutics
by Miguel Medina
Int. J. Mol. Sci. 2018, 19(4), 1160; https://doi.org/10.3390/ijms19041160 - 11 Apr 2018
Cited by 123 | Viewed by 9506
Abstract
Tauopathies such as Alzheimer’s disease (AD), frontotemporal lobar degeneration, or progressive supranuclear palsy constitute a group of brain disorders defined by neurodegeneration and the presence of tau aggregates in the affected brains regions. Tau is a microtubule-associated protein that accumulates in the cytosol [...] Read more.
Tauopathies such as Alzheimer’s disease (AD), frontotemporal lobar degeneration, or progressive supranuclear palsy constitute a group of brain disorders defined by neurodegeneration and the presence of tau aggregates in the affected brains regions. Tau is a microtubule-associated protein that accumulates in the cytosol under pathological conditions, steering the formation of aggregates or inclusions thought to be involved in the degeneration and neuronal death associated with these diseases. Despite a substantial and unmet medical need for novel, more effective disease-modifying therapies for the treatment of AD and tauopathies, the last couple of decades have seen numerous drug development undertakings primarily focused on β-amyloid, with disappointing results to date. On the other hand, tau-focused approaches have not received much attention until recently, notwithstanding that the presence of extensive tau pathology is fundamental for the disease and tau pathology shows a better correlation with impaired cognitive function than with amyloid pathology in AD patients. The last few years have brought us advances in our comprehension of tau biological functions beyond its well-established role as a microtubule-associated protein, unveiling novel physiological tau functions that may also be involved in pathogenesis and thus provide novel targets for therapeutic intervention. This review describes several emerging, encouraging therapeutic approaches aimed at tackling the underlying causes of tau pathology in AD and other tauopathies that have recently reached the clinical development stage. Full article
(This article belongs to the Special Issue Tau Function and Dysfunctional Tauopathies)
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13 pages, 2999 KiB  
Review
Defining Driver DNA Methylation Changes in Human Cancer
by Gerd P. Pfeifer
Int. J. Mol. Sci. 2018, 19(4), 1166; https://doi.org/10.3390/ijms19041166 - 12 Apr 2018
Cited by 228 | Viewed by 16394
Abstract
Human malignant tumors are characterized by pervasive changes in the patterns of DNA methylation. These changes include a globally hypomethylated tumor cell genome and the focal hypermethylation of numerous 5′-cytosine-phosphate-guanine-3′ (CpG) islands, many of them associated with gene promoters. It has been challenging [...] Read more.
Human malignant tumors are characterized by pervasive changes in the patterns of DNA methylation. These changes include a globally hypomethylated tumor cell genome and the focal hypermethylation of numerous 5′-cytosine-phosphate-guanine-3′ (CpG) islands, many of them associated with gene promoters. It has been challenging to link specific DNA methylation changes with tumorigenesis in a cause-and-effect relationship. Some evidence suggests that cancer-associated DNA hypomethylation may increase genomic instability. Promoter hypermethylation events can lead to silencing of genes functioning in pathways reflecting hallmarks of cancer, including DNA repair, cell cycle regulation, promotion of apoptosis or control of key tumor-relevant signaling networks. A convincing argument for a tumor-driving role of DNA methylation can be made when the same genes are also frequently mutated in cancer. Many of the most commonly hypermethylated genes encode developmental transcription factors, the methylation of which may lead to permanent gene silencing. Inactivation of such genes will deprive the cells in which the tumor may initiate from the option of undergoing or maintaining lineage differentiation and will lock them into a perpetuated stem cell-like state thus providing an additional window for cell transformation. Full article
(This article belongs to the Special Issue DNA Methylation)
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21 pages, 8978 KiB  
Review
Targeting the Adenosinergic Axis in Chronic Lymphocytic Leukemia: A Way to Disrupt the Tumor Niche?
by Tiziana Vaisitti, Francesca Arruga and Silvia Deaglio
Int. J. Mol. Sci. 2018, 19(4), 1167; https://doi.org/10.3390/ijms19041167 - 12 Apr 2018
Cited by 9 | Viewed by 5545
Abstract
Targeting adenosine triphosphate (ATP) metabolism and adenosinergic signaling in cancer is gaining momentum, as increasing evidence is showing their relevance in tumor immunology and biology. Chronic lymphocytic leukemia (CLL) results from the expansion of a population of mature B cells that progressively occupies [...] Read more.
Targeting adenosine triphosphate (ATP) metabolism and adenosinergic signaling in cancer is gaining momentum, as increasing evidence is showing their relevance in tumor immunology and biology. Chronic lymphocytic leukemia (CLL) results from the expansion of a population of mature B cells that progressively occupies the bone marrow (BM), the blood, and peripheral lymphoid organs. Notwithstanding significant progress in the treatment of these patients, the cure remains an unmet clinical need, suggesting that novel drugs or drug combinations are needed. A unique feature of CLL is its reliance on micro-environmental signals for proliferation and cell survival. We and others have shown that the lymphoid niche, an area of intense interactions between leukemic and bystander non-tumor cells, is a typically hypoxic environment. Here adenosine is generated by leukemic cells, as well as by cells of myeloid origin, acting through autocrine and paracrine mechanisms, ultimately affecting tumor growth, limiting drug responses, and skewing the immune cells towards a tolerant phenotype. Hence, understanding the mechanisms through which this complex network of enzymes, receptors, and metabolites functions in CLL, will pave the way to the use of pharmacological agents targeting the system, which, in combination with drugs targeting leukemic cells, may get us one step closer to curing these patients. Full article
(This article belongs to the Special Issue Purinergic Signalling in Cancer and Inflammation)
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18 pages, 1656 KiB  
Review
Pathobiologic Roles of Epstein–Barr Virus-Encoded MicroRNAs in Human Lymphomas
by Mohsen Navari, Maryam Etebari, Mostafa Ibrahimi, Lorenzo Leoncini and Pier Paolo Piccaluga
Int. J. Mol. Sci. 2018, 19(4), 1168; https://doi.org/10.3390/ijms19041168 - 12 Apr 2018
Cited by 32 | Viewed by 6526
Abstract
Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating [...] Read more.
Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating role—are of great importance. The genome of EBV encodes 44 mature microRNAs belonging to two different classes, including BamHI-A rightward transcript (BART) and Bam HI fragment H rightward open reading frame 1 (BHRF1), with different expression levels in different EBV latency types. These microRNAs might contribute to the pathogenetic effects exerted by EBV through targeting self mRNAs and host mRNAs and interfering with several important cellular mechanisms such as immunosurveillance, cell proliferation, and apoptosis. In addition, EBV microRNAs can regulate the surrounding microenvironment of the infected cells through exosomal transportation. Moreover, these small molecules could be potentially used as molecular markers. In this review, we try to present an updated and extensive view of the role of EBV-encoded miRNAs in human lymphomas. Full article
(This article belongs to the Special Issue The Role of MicroRNAs in Human Diseases)
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21 pages, 28041 KiB  
Review
Current Approaches Including Novel Nano/Microtechniques to Reduce Silicone Implant-Induced Contracture with Adverse Immune Responses
by Shin Hyuk Kang, Chanutchamon Sutthiwanjampa, Chan Yeong Heo, Woo Seob Kim, Soo-Hong Lee and Hansoo Park
Int. J. Mol. Sci. 2018, 19(4), 1171; https://doi.org/10.3390/ijms19041171 - 12 Apr 2018
Cited by 28 | Viewed by 7428
Abstract
Capsular contracture, which is the pathologic development of fibrous capsules around implants, is a major complication of reconstructive and aesthetic breast surgeries. Capsular contracture can cause implant failure with breast hardening, deformity, and severe pain. The exact mechanisms underlying this complication remain unclear. [...] Read more.
Capsular contracture, which is the pathologic development of fibrous capsules around implants, is a major complication of reconstructive and aesthetic breast surgeries. Capsular contracture can cause implant failure with breast hardening, deformity, and severe pain. The exact mechanisms underlying this complication remain unclear. In addition, anaplastic large cell lymphoma is now widely recognized as a very rare disease associated with breast implants. Foreign body reactions are an inevitable common denominator of capsular contracture. A number of studies have focused on the associated immune responses and their regulation. The present article provides an overview of the currently available techniques, including novel nano/microtechniques, to reduce silicone implant-induced contracture and associated foreign body responses. Full article
(This article belongs to the Special Issue Nano/Micro-Assisted Regenerative Medicine)
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17 pages, 480 KiB  
Review
DNA Methylation and Histone Modification in Hypertension
by Shaunrick Stoll, Charles Wang and Hongyu Qiu
Int. J. Mol. Sci. 2018, 19(4), 1174; https://doi.org/10.3390/ijms19041174 - 12 Apr 2018
Cited by 87 | Viewed by 16217
Abstract
Systemic hypertension, which eventually results in heart failure, renal failure or stroke, is a common chronic human disorder that particularly affects elders. Although many signaling pathways involved in the development of hypertension have been reported over the past decades, which has led to [...] Read more.
Systemic hypertension, which eventually results in heart failure, renal failure or stroke, is a common chronic human disorder that particularly affects elders. Although many signaling pathways involved in the development of hypertension have been reported over the past decades, which has led to the implementation of a wide variety of anti-hypertensive therapies, one half of all hypertensive patients still do not have their blood pressure controlled. The frontier in understanding the molecular mechanisms underlying hypertension has now advanced to the level of epigenomics. Particularly, increasing evidence is emerging that DNA methylation and histone modifications play an important role in gene regulation and are involved in alteration of the phenotype and function of vascular cells in response to environmental stresses. This review seeks to highlight the recent advances in our knowledge of the epigenetic regulations and mechanisms of hypertension, focusing on the role of DNA methylation and histone modification in the vascular wall. A better understanding of the epigenomic regulation in the hypertensive vessel may lead to the identification of novel target molecules that, in turn, may lead to novel drug discoveries for the treatment of hypertension. Full article
(This article belongs to the Special Issue Role of Genomics in the Management of Hypertension)
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18 pages, 25059 KiB  
Review
Structure-Function Relationship of Transporters in the Glutamate–Glutamine Cycle of the Central Nervous System
by Mariko Kato Hayashi
Int. J. Mol. Sci. 2018, 19(4), 1177; https://doi.org/10.3390/ijms19041177 - 12 Apr 2018
Cited by 42 | Viewed by 9149
Abstract
Many kinds of transporters contribute to glutamatergic excitatory synaptic transmission. Glutamate is loaded into synaptic vesicles by vesicular glutamate transporters to be released from presynaptic terminals. After synaptic vesicle release, glutamate is taken up by neurons or astrocytes to terminate the signal and [...] Read more.
Many kinds of transporters contribute to glutamatergic excitatory synaptic transmission. Glutamate is loaded into synaptic vesicles by vesicular glutamate transporters to be released from presynaptic terminals. After synaptic vesicle release, glutamate is taken up by neurons or astrocytes to terminate the signal and to prepare for the next signal. Glutamate transporters on the plasma membrane are responsible for transporting glutamate from extracellular fluid to cytoplasm. Glutamate taken up by astrocyte is converted to glutamine by glutamine synthetase and transported back to neurons through glutamine transporters on the plasma membranes of the astrocytes and then on neurons. Glutamine is converted back to glutamate by glutaminase in the neuronal cytoplasm and then loaded into synaptic vesicles again. Here, the structures of glutamate transporters and glutamine transporters, their conformational changes, and how they use electrochemical gradients of various ions for substrate transport are summarized. Pharmacological regulations of these transporters are also discussed. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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20 pages, 10295 KiB  
Review
Nanocoatings for Chronic Wound Repair—Modulation of Microbial Colonization and Biofilm Formation
by Mara Mădălina Mihai, Mădălina Preda, Iulia Lungu, Monica Cartelle Gestal, Mircea Ioan Popa and Alina Maria Holban
Int. J. Mol. Sci. 2018, 19(4), 1179; https://doi.org/10.3390/ijms19041179 - 12 Apr 2018
Cited by 88 | Viewed by 9119
Abstract
Wound healing involves a complex interaction between immunity and other natural host processes, and to succeed it requires a well-defined cascade of events. Chronic wound infections can be mono- or polymicrobial but their major characteristic is their ability to develop a biofilm. A [...] Read more.
Wound healing involves a complex interaction between immunity and other natural host processes, and to succeed it requires a well-defined cascade of events. Chronic wound infections can be mono- or polymicrobial but their major characteristic is their ability to develop a biofilm. A biofilm reduces the effectiveness of treatment and increases resistance. A biofilm is an ecosystem on its own, enabling the bacteria and the host to establish different social interactions, such as competition or cooperation. With an increasing incidence of chronic wounds and, implicitly, of chronic biofilm infections, there is a need for alternative therapeutic agents. Nanotechnology shows promising openings, either by the intrinsic antimicrobial properties of nanoparticles or their function as drug carriers. Nanoparticles and nanostructured coatings can be active at low concentrations toward a large variety of infectious agents; thus, they are unlikely to elicit emergence of resistance. Nanoparticles might contribute to the modulation of microbial colonization and biofilm formation in wounds. This comprehensive review comprises the pathogenesis of chronic wounds, the role of chronic wound colonization and infection in the healing process, the conventional and alternative topical therapeutic approaches designed to combat infection and stimulate healing, as well as revolutionizing therapies such as nanotechnology-based wound healing approaches. Full article
(This article belongs to the Special Issue Molecular Signaling and Nanobiotechnology: Prospects for Future Antimicrobial Therapy)
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15 pages, 1039 KiB  
Review
The Double Face of Exosome-Carried MicroRNAs in Cancer Immunomodulation
by Romina Alfonsi, Ludovica Grassi, Michele Signore and Désirée Bonci
Int. J. Mol. Sci. 2018, 19(4), 1183; https://doi.org/10.3390/ijms19041183 - 13 Apr 2018
Cited by 31 | Viewed by 5944
Abstract
In recent years many articles have underlined the key role of nanovesicles, i.e., exosomes, as information carriers among biological systems including cancer. Tumor-derived exosomes (TEXs) are key players in the dynamic crosstalk between cancer cells and the microenvironment while promote immune system control [...] Read more.
In recent years many articles have underlined the key role of nanovesicles, i.e., exosomes, as information carriers among biological systems including cancer. Tumor-derived exosomes (TEXs) are key players in the dynamic crosstalk between cancer cells and the microenvironment while promote immune system control evasion. In fact, tumors are undoubtedly capable of silencing the immune response through multiple mechanisms, including the release of exosomes. TEXs have been shown to boost tumor growth and promote progression and metastatic spreading via suppression or stimulation of the immune response towards cancer cells. The advantage of immunotherapeutic treatment alone over combining immuno- and conventional therapy is currently debated. Understanding the role of tumor exosome-cargo is of crucial importance for our full comprehension of neoplastic immonosuppression and for the construction of novel therapies and vaccines based on (nano-) vesicles. Furthermore, to devise new anti-cancer approaches, diverse groups investigated the possibility of engineering TEXs by conditioning cancer cells’ own cargo. In this review, we summarize the state of art of TEX-based immunomodulation with a particular focus on the molecular function of non-coding family genes, microRNAs. Finally, we will report on recent efforts in the study of potential applications of engineered exosomes in cancer immunotherapy. Full article
(This article belongs to the Special Issue The Role of MicroRNAs in Human Diseases)
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19 pages, 25914 KiB  
Review
Excessive Extracellular ATP Desensitizes P2Y2 and P2X4 ATP Receptors Provoking Surfactant Impairment Ending in Ventilation-Induced Lung Injury
by Djo Hasan, Joshua Satalin, Philip Van der Zee, Michaela Kollisch-Singule, Paul Blankman, Atsuko Shono, Peter Somhorst, Corstiaan Den Uil, Han Meeder, Toru Kotani and Gary F. Nieman
Int. J. Mol. Sci. 2018, 19(4), 1185; https://doi.org/10.3390/ijms19041185 - 13 Apr 2018
Cited by 21 | Viewed by 5734
Abstract
Stretching the alveolar epithelial type I (AT I) cells controls the intercellular signaling for the exocytosis of surfactant by the AT II cells through the extracellular release of adenosine triphosphate (ATP) (purinergic signaling). Extracellular ATP is cleared by extracellular ATPases, maintaining its homeostasis [...] Read more.
Stretching the alveolar epithelial type I (AT I) cells controls the intercellular signaling for the exocytosis of surfactant by the AT II cells through the extracellular release of adenosine triphosphate (ATP) (purinergic signaling). Extracellular ATP is cleared by extracellular ATPases, maintaining its homeostasis and enabling the lung to adapt the exocytosis of surfactant to the demand. Vigorous deformation of the AT I cells by high mechanical power ventilation causes a massive release of extracellular ATP beyond the clearance capacity of the extracellular ATPases. When extracellular ATP reaches levels >100 μM, the ATP receptors of the AT II cells become desensitized and surfactant impairment is initiated. The resulting alteration in viscoelastic properties and in alveolar opening and collapse time-constants leads to alveolar collapse and the redistribution of inspired air from the alveoli to the alveolar ducts, which become pathologically dilated. The collapsed alveoli connected to these dilated alveolar ducts are subject to a massive strain, exacerbating the ATP release. After reaching concentrations >300 μM extracellular ATP acts as a danger-associated molecular pattern, causing capillary leakage, alveolar space edema, and further deactivation of surfactant by serum proteins. Decreasing the tidal volume to 6 mL/kg or less at this stage cannot prevent further lung injury. Full article
(This article belongs to the Special Issue Purinergic Signalling in Cancer and Inflammation)
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33 pages, 9142 KiB  
Review
Sympathetic Nerve Hyperactivity in the Spleen: Causal for Nonpathogenic-Driven Chronic Immune-Mediated Inflammatory Diseases (IMIDs)?
by Denise L. Bellinger and Dianne Lorton
Int. J. Mol. Sci. 2018, 19(4), 1188; https://doi.org/10.3390/ijms19041188 - 13 Apr 2018
Cited by 60 | Viewed by 14964
Abstract
Immune-Mediated Inflammatory Diseases (IMIDs) is a descriptive term coined for an eclectic group of diseases or conditions that share common inflammatory pathways, and for which there is no definitive etiology. IMIDs affect the elderly most severely, with many older individuals having two or [...] Read more.
Immune-Mediated Inflammatory Diseases (IMIDs) is a descriptive term coined for an eclectic group of diseases or conditions that share common inflammatory pathways, and for which there is no definitive etiology. IMIDs affect the elderly most severely, with many older individuals having two or more IMIDs. These diseases include, but are not limited to, type-1 diabetes, obesity, hypertension, chronic pulmonary disease, coronary heart disease, inflammatory bowel disease, and autoimmunity, such as rheumatoid arthritis (RA), Sjőgren’s syndrome, systemic lupus erythematosus, psoriasis, psoriatic arthritis, and multiple sclerosis. These diseases are ostensibly unrelated mechanistically, but increase in frequency with age and share chronic systemic inflammation, implicating major roles for the spleen. Chronic systemic and regional inflammation underlies the disease manifestations of IMIDs. Regional inflammation and immune dysfunction promotes targeted end organ tissue damage, whereas systemic inflammation increases morbidity and mortality by affecting multiple organ systems. Chronic inflammation and skewed dysregulated cell-mediated immune responses drive many of these age-related medical disorders. IMIDs are commonly autoimmune-mediated or suspected to be autoimmune diseases. Another shared feature is dysregulation of the autonomic nervous system and hypothalamic pituitary adrenal (HPA) axis. Here, we focus on dysautonomia. In many IMIDs, dysautonomia manifests as an imbalance in activity/reactivity of the sympathetic and parasympathetic divisions of the autonomic nervous system (ANS). These major autonomic pathways are essential for allostasis of the immune system, and regulating inflammatory processes and innate and adaptive immunity. Pathology in ANS is a hallmark and causal feature of all IMIDs. Chronic systemic inflammation comorbid with stress pathway dysregulation implicate neural-immune cross-talk in the etiology and pathophysiology of IMIDs. Using a rodent model of inflammatory arthritis as an IMID model, we report disease-specific maladaptive changes in β2-adrenergic receptor (AR) signaling from protein kinase A (PKA) to mitogen activated protein kinase (MAPK) pathways in the spleen. Beta2-AR signal “shutdown” in the spleen and switching from PKA to G-coupled protein receptor kinase (GRK) pathways in lymph node cells drives inflammation and disease advancement. Based on these findings and the existing literature in other IMIDs, we present and discuss relevant literature that support the hypothesis that unresolvable immune stimulation from chronic inflammation leads to a maladaptive disease-inducing and perpetuating sympathetic response in an attempt to maintain allostasis. Since the role of sympathetic dysfunction in IMIDs is best studied in RA and rodent models of RA, this IMID is the primary one used to evaluate data relevant to our hypothesis. Here, we review the relevant literature and discuss sympathetic dysfunction as a significant contributor to the pathophysiology of IMIDs, and then discuss a novel target for treatment. Based on our findings in inflammatory arthritis and our understanding of common inflammatory process that are used by the immune system across all IMIDs, novel strategies to restore SNS homeostasis are expected to provide safe, cost-effective approaches to treat IMIDs, lower comorbidities, and increase longevity. Full article
(This article belongs to the Special Issue Spleen: Crossroad between Immune System, Metabolic Asset and Endocrine Function)
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15 pages, 3776 KiB  
Review
Oncosuppressors and Oncogenes: Role in Haemangioma Genesis and Potential for Therapeutic Targeting
by Peace Mabeta
Int. J. Mol. Sci. 2018, 19(4), 1192; https://doi.org/10.3390/ijms19041192 - 13 Apr 2018
Cited by 17 | Viewed by 4193
Abstract
Genetic lesions in proto-oncogenes result in the perturbation of angiogenesis, the formation of neovessels from a pre-existing microvasculature. Similarly, the subversion of tumor suppressor genes promotes tumor vascularization. Excessive neovessel formation is associated with various neoplasms such as infantile hemangiomas (IH). Hemangiomas are [...] Read more.
Genetic lesions in proto-oncogenes result in the perturbation of angiogenesis, the formation of neovessels from a pre-existing microvasculature. Similarly, the subversion of tumor suppressor genes promotes tumor vascularization. Excessive neovessel formation is associated with various neoplasms such as infantile hemangiomas (IH). Hemangiomas are the most common tumors in pediatric patients and at present have no definitive treatment. The pathogenesis of IH is not well understood; however, both vasculogenesis and angiogenesis are associated with hemangioma genesis. A number of factors that modulate angiogenesis and vasculogenesis have been shown to be dysregulated in IH. Several of the oncogenes and tumor suppressors linked to the promotion of angiogenesis are also altered in infantile hemangioma. In this review, the roles of oncogenes and tumor suppressor genes during neovascularization and hemangioma genesis are explored. In addition, the potential for targeting these genes in IH therapy is discussed. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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16 pages, 22405 KiB  
Review
Atomic Force Microscopy Based Tip-Enhanced Raman Spectroscopy in Biology
by Lizhen Gao, Huiling Zhao, Tianfeng Li, Peipei Huo, Dong Chen and Bo Liu
Int. J. Mol. Sci. 2018, 19(4), 1193; https://doi.org/10.3390/ijms19041193 - 13 Apr 2018
Cited by 24 | Viewed by 7928
Abstract
Most biological phenomena occur at the nanometer scale, which is not accessible by the conventional optical techniques because of the optical diffraction limitation. Tip-enhanced Raman spectroscopy (TERS), one of the burgeoning probing techniques, not only can provide the topography characterization with high resolution, [...] Read more.
Most biological phenomena occur at the nanometer scale, which is not accessible by the conventional optical techniques because of the optical diffraction limitation. Tip-enhanced Raman spectroscopy (TERS), one of the burgeoning probing techniques, not only can provide the topography characterization with high resolution, but also can deliver the chemical or molecular information of a sample beyond the optical diffraction limitation. Therefore, it has been widely used in various structural analyses pertaining to materials science, tissue engineering, biological processes and so on. Based on the different feedback mechanisms, TERS can be classified into three types: atomic force microscopy based TERS system (AFM-TERS), scanning tunneling microscopy based TERS system (STM-TERS) and shear force microscopy based TERS system (SFM-TERS). Among them, AFM-TERS is the most widely adopted feedback system by live biosamples because it can work in liquid and this allows the investigation of biological molecules under native conditions. In this review, we mainly focus on the applications of AFM-TERS in three biological systems: nucleic acids, proteins and pathogens. From the TERS characterization to the data analysis, this review demonstrates that AFM-TERS has great potential applications to visually characterizing the biomolecular structure and crucially detecting more nano-chemical information of biological systems. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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21 pages, 3116 KiB  
Review
PPAR Agonists and Metabolic Syndrome: An Established Role?
by Margherita Botta, Matteo Audano, Amirhossein Sahebkar, Cesare R. Sirtori, Nico Mitro and Massimiliano Ruscica
Int. J. Mol. Sci. 2018, 19(4), 1197; https://doi.org/10.3390/ijms19041197 - 14 Apr 2018
Cited by 179 | Viewed by 16304
Abstract
Therapeutic approaches to metabolic syndrome (MetS) are numerous and may target lipoproteins, blood pressure or anthropometric indices. Peroxisome proliferator-activated receptors (PPARs) are involved in the metabolic regulation of lipid and lipoprotein levels, i.e., triglycerides (TGs), blood glucose, and abdominal adiposity. PPARs may be [...] Read more.
Therapeutic approaches to metabolic syndrome (MetS) are numerous and may target lipoproteins, blood pressure or anthropometric indices. Peroxisome proliferator-activated receptors (PPARs) are involved in the metabolic regulation of lipid and lipoprotein levels, i.e., triglycerides (TGs), blood glucose, and abdominal adiposity. PPARs may be classified into the α, β/δ and γ subtypes. The PPAR-α agonists, mainly fibrates (including newer molecules such as pemafibrate) and omega-3 fatty acids, are powerful TG-lowering agents. They mainly affect TG catabolism and, particularly with fibrates, raise the levels of high-density lipoprotein cholesterol (HDL-C). PPAR-γ agonists, mainly glitazones, show a smaller activity on TGs but are powerful glucose-lowering agents. Newer PPAR-α/δ agonists, e.g., elafibranor, have been designed to achieve single drugs with TG-lowering and HDL-C-raising effects, in addition to the insulin-sensitizing and antihyperglycemic effects of glitazones. They also hold promise for the treatment of non-alcoholic fatty liver disease (NAFLD) which is closely associated with the MetS. The PPAR system thus offers an important hope in the management of atherogenic dyslipidemias, although concerns regarding potential adverse events such as the rise of plasma creatinine, gallstone formation, drug–drug interactions (i.e., gemfibrozil) and myopathy should also be acknowledged. Full article
(This article belongs to the Special Issue PPARs in Cellular and Whole Body Energy Metabolism)
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23 pages, 6508 KiB  
Review
MicroRNAs as Potential Regulators of Glutathione Peroxidases Expression and Their Role in Obesity and Related Pathologies
by Petra Matoušková, Barbora Hanousková and Lenka Skálová
Int. J. Mol. Sci. 2018, 19(4), 1199; https://doi.org/10.3390/ijms19041199 - 14 Apr 2018
Cited by 41 | Viewed by 5359
Abstract
Glutathione peroxidases (GPxs) belong to the eight-member family of phylogenetically related enzymes with different cellular localization, but distinct antioxidant function. Several GPxs are important selenoproteins. Dysregulated GPx expression is connected with severe pathologies, including obesity and diabetes. We performed a comprehensive bioinformatic analysis [...] Read more.
Glutathione peroxidases (GPxs) belong to the eight-member family of phylogenetically related enzymes with different cellular localization, but distinct antioxidant function. Several GPxs are important selenoproteins. Dysregulated GPx expression is connected with severe pathologies, including obesity and diabetes. We performed a comprehensive bioinformatic analysis using the programs miRDB, miRanda, TargetScan, and Diana in the search for hypothetical microRNAs targeting 3′untranslated regions (3´UTR) of GPxs. We cross-referenced the literature for possible intersections between our results and available reports on identified microRNAs, with a special focus on the microRNAs related to oxidative stress, obesity, and related pathologies. We identified many microRNAs with an association with oxidative stress and obesity as putative regulators of GPxs. In particular, miR-185-5p was predicted by a larger number of programs to target six GPxs and thus could play the role as their master regulator. This microRNA was altered by selenium deficiency and can play a role as a feedback control of selenoproteins’ expression. Through the bioinformatics analysis we revealed the potential connection of microRNAs, GPxs, obesity, and other redox imbalance related diseases. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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19 pages, 3675 KiB  
Review
Metabolic Features of Multiple Myeloma
by Chaima El Arfani, Kim De Veirman, Ken Maes, Elke De Bruyne and Eline Menu
Int. J. Mol. Sci. 2018, 19(4), 1200; https://doi.org/10.3390/ijms19041200 - 14 Apr 2018
Cited by 52 | Viewed by 8248
Abstract
Cancer is known for its cellular changes contributing to tumour growth and cell proliferation. As part of these changes, metabolic rearrangements are identified in several cancers, including multiple myeloma (MM), which is a condition whereby malignant plasma cells accumulate in the bone marrow [...] Read more.
Cancer is known for its cellular changes contributing to tumour growth and cell proliferation. As part of these changes, metabolic rearrangements are identified in several cancers, including multiple myeloma (MM), which is a condition whereby malignant plasma cells accumulate in the bone marrow (BM). These metabolic changes consist of generation, inhibition and accumulation of metabolites and metabolic shifts in MM cells. Changes in the BM micro-environment could be the reason for such adjustments. Enhancement of glycolysis and glutaminolysis is found in MM cells compared to healthy cells. Metabolites and enzymes can be upregulated or downregulated and play a crucial role in drug resistance. Therefore, this review will focus on changes in glucose and glutamine metabolism linked with the emergence of drug resistance. Moreover, metabolites do not only affect other metabolic components to benefit cancer development; they also interfere with transcription factors involved in proliferation and apoptotic regulation. Full article
(This article belongs to the Special Issue Novel Therapeutic Strategies in Multiple Myeloma)
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15 pages, 4124 KiB  
Review
Vascular Endothelial Growth Factor-A Exerts Diverse Cellular Effects via Small G Proteins, Rho and Rap
by Akio Shimizu, Dimitar P. Zankov, Misuzu Kurokawa-Seo and Hisakazu Ogita
Int. J. Mol. Sci. 2018, 19(4), 1203; https://doi.org/10.3390/ijms19041203 - 16 Apr 2018
Cited by 24 | Viewed by 6559
Abstract
Vascular endothelial growth factors (VEGFs) include five molecules (VEGF-A, -B, -C, -D, and placental growth factor), and have various roles that crucially regulate cellular functions in many kinds of cells and tissues. Intracellular signal transduction induced by VEGFs has been extensively studied and [...] Read more.
Vascular endothelial growth factors (VEGFs) include five molecules (VEGF-A, -B, -C, -D, and placental growth factor), and have various roles that crucially regulate cellular functions in many kinds of cells and tissues. Intracellular signal transduction induced by VEGFs has been extensively studied and is usually initiated by their binding to two classes of transmembrane receptors: receptor tyrosine kinase VEGF receptors (VEGF receptor-1, -2 and -3) and neuropilins (NRP1 and NRP2). In addition to many established results reported by other research groups, we have previously identified small G proteins, especially Ras homologue gene (Rho) and Ras-related protein (Rap), as important mediators of VEGF-A-stimulated signaling in cancer cells as well as endothelial cells. This review article describes the VEGF-A-induced signaling pathways underlying diverse cellular functions, including cell proliferation, migration, and angiogenesis, and the involvement of Rho, Rap, and their related molecules in these pathways. Full article
(This article belongs to the Special Issue Vascular Endothelial Growth Factor)
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35 pages, 34261 KiB  
Review
Tribute to Marcelle Grenson (1925–1996), A Pioneer in the Study of Amino Acid Transport in Yeast
by Bruno André
Int. J. Mol. Sci. 2018, 19(4), 1207; https://doi.org/10.3390/ijms19041207 - 16 Apr 2018
Cited by 3 | Viewed by 4468
Abstract
The year 2016 marked the 20th anniversary of the death of Marcelle Grenson and the 50th anniversary of her first publication on yeast amino acid transport, the topic to which, as Professor at the Free University of Brussels (ULB), she devoted the major [...] Read more.
The year 2016 marked the 20th anniversary of the death of Marcelle Grenson and the 50th anniversary of her first publication on yeast amino acid transport, the topic to which, as Professor at the Free University of Brussels (ULB), she devoted the major part of her scientific career. M. Grenson was the first scientist in Belgium to introduce and apply genetic analysis in yeast to dissect the molecular mechanisms that were underlying complex problems in biology. Today, M. Grenson is recognized for the pioneering character of her work on the diversity and regulation of amino acid transporters in yeast. The aim of this tribute is to review the major milestones of her forty years of scientific research that were conducted between 1950 and 1990. Full article
(This article belongs to the Special Issue Amino Acids Transport and Metabolism)
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19 pages, 1975 KiB  
Review
Therapeutic Potential of Annexin A1 in Ischemia Reperfusion Injury
by Junaid Ansari, Gaganpreet Kaur and Felicity N. E. Gavins
Int. J. Mol. Sci. 2018, 19(4), 1211; https://doi.org/10.3390/ijms19041211 - 16 Apr 2018
Cited by 53 | Viewed by 6179
Abstract
Cardiovascular disease (CVD) continues to be the leading cause of death in the world. Increased inflammation and an enhanced thrombotic milieu represent two major complications of CVD, which can culminate into an ischemic event. Treatment for these life-threatening complications remains reperfusion and restoration [...] Read more.
Cardiovascular disease (CVD) continues to be the leading cause of death in the world. Increased inflammation and an enhanced thrombotic milieu represent two major complications of CVD, which can culminate into an ischemic event. Treatment for these life-threatening complications remains reperfusion and restoration of blood flow. However, reperfusion strategies may result in ischemia–reperfusion injury (I/RI) secondary to various cardiovascular pathologies, including myocardial infarction and stroke, by furthering the inflammatory and thrombotic responses and delivering inflammatory mediators to the affected tissue. Annexin A1 (AnxA1) and its mimetic peptides are endogenous anti-inflammatory and pro-resolving mediators, known to have significant effects in resolving inflammation in a variety of disease models. Mounting evidence suggests that AnxA1, which interacts with the formyl peptide receptor (FPR) family, may have a significant role in mitigating I/RI associated complications. In this review article, we focus on how AnxA1 plays a protective role in the I/R based vascular pathologies. Full article
(This article belongs to the Special Issue Annexins—Closing the Gap between Fundamental and Translational Research)
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26 pages, 6757 KiB  
Review
Demyelination in Multiple Sclerosis: Reprogramming Energy Metabolism and Potential PPARγ Agonist Treatment Approaches
by Alexandre Vallée, Yves Lecarpentier, Rémy Guillevin and Jean-Noël Vallée
Int. J. Mol. Sci. 2018, 19(4), 1212; https://doi.org/10.3390/ijms19041212 - 16 Apr 2018
Cited by 46 | Viewed by 7745
Abstract
Demyelination in multiple sclerosis (MS) cells is the site of several energy metabolic abnormalities driven by dysregulation between the opposed interplay of peroxisome proliferator-activated receptor γ (PPARγ) and WNT/β-catenin pathways. We focus our review on the opposing interactions observed in demyelinating processes in [...] Read more.
Demyelination in multiple sclerosis (MS) cells is the site of several energy metabolic abnormalities driven by dysregulation between the opposed interplay of peroxisome proliferator-activated receptor γ (PPARγ) and WNT/β-catenin pathways. We focus our review on the opposing interactions observed in demyelinating processes in MS between the canonical WNT/β-catenin pathway and PPARγ and their reprogramming energy metabolism implications. Demyelination in MS is associated with chronic inflammation, which is itself associated with the release of cytokines by CD4+ Th17 cells, and downregulation of PPARγ expression leading to the upregulation of the WNT/β-catenin pathway. Upregulation of WNT/β-catenin signaling induces activation of glycolytic enzymes that modify their energy metabolic behavior. Then, in MS cells, a large portion of cytosolic pyruvate is converted into lactate. This phenomenon is called the Warburg effect, despite the availability of oxygen. The Warburg effect is the shift of an energy transfer production from mitochondrial oxidative phosphorylation to aerobic glycolysis. Lactate production is correlated with increased WNT/β-catenin signaling and demyelinating processes by inducing dysfunction of CD4+ T cells leading to axonal and neuronal damage. In MS, downregulation of PPARγ decreases insulin sensitivity and increases neuroinflammation. PPARγ agonists inhibit Th17 differentiation in CD4+ T cells and then diminish release of cytokines. In MS, abnormalities in the regulation of circadian rhythms stimulate the WNT pathway to initiate the demyelination process. Moreover, PPARγ contributes to the regulation of some key circadian genes. Thus, PPARγ agonists interfere with reprogramming energy metabolism by directly inhibiting the WNT/β-catenin pathway and circadian rhythms and could appear as promising treatments in MS due to these interactions. Full article
(This article belongs to the Special Issue PPARs in Cellular and Whole Body Energy Metabolism)
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26 pages, 1848 KiB  
Review
The Role of miRNAs in Virus-Mediated Oncogenesis
by Zuzana Vojtechova and Ruth Tachezy
Int. J. Mol. Sci. 2018, 19(4), 1217; https://doi.org/10.3390/ijms19041217 - 17 Apr 2018
Cited by 49 | Viewed by 6701
Abstract
To date, viruses are reported to be responsible for more than 15% of all tumors worldwide. The oncogenesis could be influenced directly by the activity of viral oncoproteins or by the chronic infection or inflammation. The group of human oncoviruses includes Epstein–Barr virus [...] Read more.
To date, viruses are reported to be responsible for more than 15% of all tumors worldwide. The oncogenesis could be influenced directly by the activity of viral oncoproteins or by the chronic infection or inflammation. The group of human oncoviruses includes Epstein–Barr virus (EBV), human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), human herpesvirus 8 (HHV-8) or polyomaviruses, and transregulating retroviruses such as HIV or HTLV-1. Most of these viruses express short noncoding RNAs called miRNAs to regulate their own gene expression or to influence host gene expression and thus contribute to the carcinogenic processes. In this review, we will focus on oncogenic viruses and summarize the role of both types of miRNAs, viral as well as host’s, in the oncogenesis. Full article
(This article belongs to the Special Issue The Role of MicroRNAs in Human Diseases)
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18 pages, 17641 KiB  
Review
Annexins in Glaucoma
by Timothy E. Yap, Benjamin Michael Davis, Li Guo, Eduardo M. Normando and Maria Francesca Cordeiro
Int. J. Mol. Sci. 2018, 19(4), 1218; https://doi.org/10.3390/ijms19041218 - 17 Apr 2018
Cited by 13 | Viewed by 5220
Abstract
Glaucoma is one of the leading causes of irreversible visual loss, which has been estimated to affect 3.5% of those over 40 years old and projected to affect a total of 112 million people by 2040. Such a dramatic increase in affected patients [...] Read more.
Glaucoma is one of the leading causes of irreversible visual loss, which has been estimated to affect 3.5% of those over 40 years old and projected to affect a total of 112 million people by 2040. Such a dramatic increase in affected patients demonstrates the need for continual improvement in the way we diagnose and treat this condition. Annexin A5 is a 36 kDa protein that is ubiquitously expressed in humans and is studied as an indicator of apoptosis in several fields. This molecule has a high calcium-dependent affinity for phosphatidylserine, a cell membrane phospholipid externalized to the outer cell membrane in early apoptosis. The DARC (Detection of Apoptosing Retinal Cells) project uses fluorescently-labelled annexin A5 to assess glaucomatous degeneration, the inherent process of which is the apoptosis of retinal ganglion cells. Furthermore, this project has conducted investigation of the retinal apoptosis in the neurodegenerative conditions of the eye and brain. In this present study, we summarized the use of annexin A5 as a marker of apoptosis in the eye. We also relayed the progress of the DARC project, developing real-time imaging of retinal ganglion cell apoptosis in vivo from the experimental models of disease and identifying mechanisms underlying neurodegeneration and its treatments, which has been applied to the first human clinical trials. DARC has potential as a biomarker in neurodegeneration, especially in the research of novel treatments, and could be a useful tool for the diagnosis and monitoring of glaucoma. Full article
(This article belongs to the Special Issue Annexins—Closing the Gap between Fundamental and Translational Research)
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30 pages, 4884 KiB  
Review
Polyamine Metabolism and Oxidative Protein Folding in the ER as ROS-Producing Systems Neglected in Virology
by Olga A. Smirnova, Birke Bartosch, Natalia F. Zakirova, Sergey N. Kochetkov and Alexander V. Ivanov
Int. J. Mol. Sci. 2018, 19(4), 1219; https://doi.org/10.3390/ijms19041219 - 17 Apr 2018
Cited by 29 | Viewed by 7366
Abstract
Reactive oxygen species (ROS) are produced in various cell compartments by an array of enzymes and processes. An excess of ROS production can be hazardous for normal cell functioning, whereas at normal levels, ROS act as vital regulators of many signal transduction pathways [...] Read more.
Reactive oxygen species (ROS) are produced in various cell compartments by an array of enzymes and processes. An excess of ROS production can be hazardous for normal cell functioning, whereas at normal levels, ROS act as vital regulators of many signal transduction pathways and transcription factors. ROS production is affected by a wide range of viruses. However, to date, the impact of viral infections has been studied only in respect to selected ROS-generating enzymes. The role of several ROS-generating and -scavenging enzymes or cellular systems in viral infections has never been addressed. In this review, we focus on the roles of biogenic polyamines and oxidative protein folding in the endoplasmic reticulum (ER) and their interplay with viruses. Polyamines act as ROS scavengers, however, their catabolism is accompanied by H2O2 production. Hydrogen peroxide is also produced during oxidative protein folding, with ER oxidoreductin 1 (Ero1) being a major source of oxidative equivalents. In addition, Ero1 controls Ca2+ efflux from the ER in response to e.g., ER stress. Here, we briefly summarize the current knowledge on the physiological roles of biogenic polyamines and the role of Ero1 at the ER, and present available data on their interplay with viral infections. Full article
(This article belongs to the Special Issue Free Radicals and Oxidants in Pathogenesis)
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16 pages, 10191 KiB  
Review
Mechanisms of ATP Release by Inflammatory Cells
by Michel Dosch, Joël Gerber, Fadi Jebbawi and Guido Beldi
Int. J. Mol. Sci. 2018, 19(4), 1222; https://doi.org/10.3390/ijms19041222 - 18 Apr 2018
Cited by 187 | Viewed by 9842
Abstract
Extracellular nucleotides (e.g., ATP, ADP, UTP, UDP) released by inflammatory cells interact with specific purinergic P2 type receptors to modulate their recruitment and activation. The focus of this review is on stimuli and mechanisms of extracellular nucleotide release and its consequences during inflammation. [...] Read more.
Extracellular nucleotides (e.g., ATP, ADP, UTP, UDP) released by inflammatory cells interact with specific purinergic P2 type receptors to modulate their recruitment and activation. The focus of this review is on stimuli and mechanisms of extracellular nucleotide release and its consequences during inflammation. Necrosis leads to non-specific release of nucleotides, whereas specific release mechanisms include vesicular exocytosis and channel-mediated release via connexin or pannexin hemichannels. These release mechanisms allow stimulated inflammatory cells such as macrophages, neutrophils, and endothelial cells to fine-tune autocrine/paracrine responses during acute and chronic inflammation. Key effector functions of inflammatory cells are therefore regulated by purinergic signaling in acute and chronic diseases, making extracellular nucleotide release a promising target for the development of new therapies. Full article
(This article belongs to the Special Issue Purinergic Signalling in Cancer and Inflammation)
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28 pages, 7021 KiB  
Review
Epigenetic Programming of Synthesis, Release, and/or Receptor Expression of Common Mediators Participating in the Risk/Resilience for Comorbid Stress-Related Disorders and Coronary Artery Disease
by Carlos Manuel Zapata-Martín del Campo, Martín Martínez-Rosas and Verónica Guarner-Lans
Int. J. Mol. Sci. 2018, 19(4), 1224; https://doi.org/10.3390/ijms19041224 - 18 Apr 2018
Cited by 11 | Viewed by 5312
Abstract
Corticotrophin releasing factor, vasopressin, oxytocin, natriuretic hormones, angiotensin, neuregulins, some purinergic substances, and some cytokines contribute to the long-term modulation and restructuring of cardiovascular regulation networks and, at the same time, have relevance in situations of comorbid abnormal stress responses. The synthesis, release, [...] Read more.
Corticotrophin releasing factor, vasopressin, oxytocin, natriuretic hormones, angiotensin, neuregulins, some purinergic substances, and some cytokines contribute to the long-term modulation and restructuring of cardiovascular regulation networks and, at the same time, have relevance in situations of comorbid abnormal stress responses. The synthesis, release, and receptor expression of these mediators seem to be under epigenetic control since early stages of life, possibly underlying the comorbidity to coronary artery disease (CAD) and stress-related disorders (SRD). The exposure to environmental conditions, such as stress, during critical periods in early life may cause epigenetic programming modifying the development of pathways that lead to stable and long-lasting alterations in the functioning of these mediators during adulthood, determining the risk of or resilience to CAD and SRD. However, in contrast to genetic information, epigenetic marks may be dynamically altered throughout the lifespan. Therefore, epigenetics may be reprogrammed if the individual accepts the challenge to undertake changes in their lifestyle. Alternatively, epigenetics may remain fixed and/or even be inherited in the next generation. In this paper, we analyze some of the common neuroendocrine functions of these mediators in CAD and SRD and summarize the evidence indicating that they are under early programming to put forward the theoretical hypothesis that the comorbidity of these diseases might be epigenetically programmed and modified over the lifespan of the individual. Full article
(This article belongs to the Special Issue Epigenetics of Neurodevelopmental Disorders)
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18 pages, 382 KiB  
Review
Extracellular Vesicles as Conveyors of Membrane-Derived Bioactive Lipids in Immune System
by Krizia Sagini, Eva Costanzi, Carla Emiliani, Sandra Buratta and Lorena Urbanelli
Int. J. Mol. Sci. 2018, 19(4), 1227; https://doi.org/10.3390/ijms19041227 - 18 Apr 2018
Cited by 68 | Viewed by 5535
Abstract
Over the last 20 years, extracellular vesicles (EVs) have been established as an additional way to transmit signals outside the cell. They are membrane-surrounded structures of nanometric size that can either originate from the membrane invagination of multivesicular bodies of the late endosomal [...] Read more.
Over the last 20 years, extracellular vesicles (EVs) have been established as an additional way to transmit signals outside the cell. They are membrane-surrounded structures of nanometric size that can either originate from the membrane invagination of multivesicular bodies of the late endosomal compartment (exosomes) or bud from the plasma membrane (microvesicles). They contain proteins, lipids, and nucleic acids—namely miRNA, but also mRNA and lncRNA—which are derived from the parental cell, and have been retrieved in every fluid of the body. As carriers of antigens, either alone or in association with major histocompatibility complex (MHC) class II and class I molecules, their immunomodulatory properties have been extensively investigated. Moreover, recent studies have shown that EVs may carry and deliver membrane-derived bioactive lipids that play an important function in the immune system and related pathologies, such as prostaglandins, leukotrienes, specialized pro-resolving mediators, and lysophospholipids. EVs protect bioactive lipids from degradation and play a role in the transcellular synthesis of prostaglandins and leukotrienes. Here, we summarized the role of EVs in the regulation of immune response, specifically focusing our attention on the emerging role of EVs as carriers of bioactive lipids, which is important for immune system function. Full article
(This article belongs to the Special Issue Signaling Pathway of Immune Cells and Immune Disorder)
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12 pages, 2903 KiB  
Review
Expression and Regulation of Thymic Stromal Lymphopoietin and Thymic Stromal Lymphopoietin Receptor Heterocomplex in the Innate–Adaptive Immunity of Pediatric Asthma
by Sheng-Chieh Lin, Fang-Yi Cheng, Jun-Jen Liu and Yi-Ling Ye
Int. J. Mol. Sci. 2018, 19(4), 1231; https://doi.org/10.3390/ijms19041231 - 18 Apr 2018
Cited by 17 | Viewed by 6785
Abstract
Asthma is a chronic inflammatory disease affecting the airway, and it is characterized by a wheezing breathing sound, variable airflow obstruction and the presence of inflammatory cells in the submucosa of the bronchi. Viral infection, pollutants and sensitivity to aeroallergens damage the epithelium [...] Read more.
Asthma is a chronic inflammatory disease affecting the airway, and it is characterized by a wheezing breathing sound, variable airflow obstruction and the presence of inflammatory cells in the submucosa of the bronchi. Viral infection, pollutants and sensitivity to aeroallergens damage the epithelium from childhood, which causes asthma. The pathogenesis of asthma includes pathways of innate stimulation by environmental microbes and irritant pathogens. Damaged epithelial cells produce thymic stromal lymphopoietin (TSLP) and stimulate myeloid dendritic cell maturation through the thymic stromal lymphopoietin receptor (TSLPR) heterocomplex. TSLP-activated myeloid dendritic cells promote naive CD4+ T cells to differentiate into T helper type 2 (Th2) phenotype CD4+ T cells. Re-exposure to allergens or environmental stimuli causes an adaptive immune response. TSLP-activated dendritic cells expressing the OX40 ligand (OX40L; CD252) trigger naive CD4+ T cells to differentiate into inflammatory Th2 effector cells secreting the cytokines interleukin-4, 5, 9, and 13 (IL-4, IL-5, IL-9 and IL-13), and the dendritic cells (DCs) promote the proliferation of allergen-specific Th2 memory cells. Allergen presentation by Th2 cells through its interaction with their receptors in the presence of major histocompatibility complex (MHC) class II on B cells and through costimulation involving CD40 and CD40L interactions results in immunoglobulin class switching from IgM to IgE. DCs and other blood cell subsets express the TSLPR heterocomplex. The regulatory mechanism of the TSLPR heterocomplex on these different cell subsets remains unclear. The TSLPR heterocomplex is composed of the IL-7Rα chain and TSLPR chain. Moreover, two isoforms of TSLP, short isoform TSLP (sfTSLP) and long isoform TSLP (lfTSLP), have roles in atopic and allergic development. Identifying and clarifying the regulation of TSLPR and IL-7Rα in pediatric asthma are still difficult, because the type of blood cell and the expression for each blood cell in different stages of atopic diseases are poorly understood. We believe that further integrated assessments of the regulation mechanism of the TSLP–TSLPR heterocomplex axis in vitro and in vivo can provide a faster and earlier diagnosis of pediatric asthma and promote the development of more effective preventive strategies at the onset of allergies. Full article
(This article belongs to the Special Issue Molecular Research on Mucosal Immunity)
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18 pages, 965 KiB  
Review
Resistance to Anti-Angiogenic Therapy in Cancer—Alterations to Anti-VEGF Pathway
by Yoshiro Itatani, Kenji Kawada, Takamasa Yamamoto and Yoshiharu Sakai
Int. J. Mol. Sci. 2018, 19(4), 1232; https://doi.org/10.3390/ijms19041232 - 18 Apr 2018
Cited by 230 | Viewed by 17382
Abstract
Anti-angiogenic therapy is one of the promising strategies for many types of solid cancers. Bevacizumab (Avastin), a recombinant humanized monoclonal antibody of vascular endothelial growth factor (VEGF) A, was approved for the first time as an anti-angiogenic drug for the treatment of metastatic [...] Read more.
Anti-angiogenic therapy is one of the promising strategies for many types of solid cancers. Bevacizumab (Avastin), a recombinant humanized monoclonal antibody of vascular endothelial growth factor (VEGF) A, was approved for the first time as an anti-angiogenic drug for the treatment of metastatic colorectal cancer (CRC) by the Food and Drug Administration (FDA) in 2004. In addition, the other VEGF pathway inhibitors including small molecule tyrosine kinase inhibitors (sunitinib, sorafenib, and pazopanib), a soluble VEGF decoy receptor (aflibercept), and a humanized monoclonal antibody of VEGF receptor 2 (VEGFR2) (ramucirumab) have been approved for cancer therapy. Although many types of VEGF pathway inhibitors can improve survival in most cancer patients, some patients have little or no beneficial effect from them. The primary or acquired resistance towards many oncological drugs, including anti-VEGF inhibitors, is a common problem in cancer treatment. This review summarizes the proposed alternative mechanisms of angiogenesis other than the VEGF pathway. These mechanisms are involved in the development of resistance to anti-VEGF therapies in cancer patients. Full article
(This article belongs to the Special Issue Alterations to Signalling Pathways in Cancer Cells 2018)
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26 pages, 434 KiB  
Review
Calcium and Nuclear Signaling in Prostate Cancer
by Ivan V. Maly and Wilma A. Hofmann
Int. J. Mol. Sci. 2018, 19(4), 1237; https://doi.org/10.3390/ijms19041237 - 19 Apr 2018
Cited by 24 | Viewed by 6856
Abstract
Recently, there have been a number of developments in the fields of calcium and nuclear signaling that point to new avenues for a more effective diagnosis and treatment of prostate cancer. An example is the discovery of new classes of molecules involved in [...] Read more.
Recently, there have been a number of developments in the fields of calcium and nuclear signaling that point to new avenues for a more effective diagnosis and treatment of prostate cancer. An example is the discovery of new classes of molecules involved in calcium-regulated nuclear import and nuclear calcium signaling, from the G protein-coupled receptor (GPCR) and myosin families. This review surveys the new state of the calcium and nuclear signaling fields with the aim of identifying the unifying themes that hold out promise in the context of the problems presented by prostate cancer. Genomic perturbations, kinase cascades, developmental pathways, and channels and transporters are covered, with an emphasis on nuclear transport and functions. Special attention is paid to the molecular mechanisms behind prostate cancer progression to the malignant forms and the unfavorable response to anti-androgen treatment. The survey leads to some new hypotheses that connect heretofore disparate results and may present a translational interest. Full article
(This article belongs to the Special Issue Calcium Signaling in Human Health and Diseases)
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14 pages, 3877 KiB  
Review
HIV Vaccination: A Roadmap among Advancements and Concerns
by Maria Trovato, Luciana D’Apice, Antonella Prisco and Piergiuseppe De Berardinis
Int. J. Mol. Sci. 2018, 19(4), 1241; https://doi.org/10.3390/ijms19041241 - 19 Apr 2018
Cited by 29 | Viewed by 7577
Abstract
Since the identification of the Human Immunodeficiency Virus type 1 (HIV-1) as the etiologic agent of AIDS (Acquired Immunodeficiency Syndrome), many efforts have been made to stop the AIDS pandemic. A major success of medical research has been the development of the highly [...] Read more.
Since the identification of the Human Immunodeficiency Virus type 1 (HIV-1) as the etiologic agent of AIDS (Acquired Immunodeficiency Syndrome), many efforts have been made to stop the AIDS pandemic. A major success of medical research has been the development of the highly active antiretroviral therapy and its availability to an increasing number of people worldwide, with a considerable effect on survival. However, a safe and effective vaccine able to prevent and eradicate the HIV pandemic is still lacking. Clinical trials and preclinical proof-of-concept studies in nonhuman primate (NHP) models have provided insights into potential correlates of protection against the HIV-1 infection, which include broadly neutralizing antibodies (bnAbs), non-neutralizing antibodies targeting the variable loops 1 and 2 (V1V2) regions of the HIV-1 envelope (Env), polyfunctional antibody, and Env-specific T-cell responses. In this review, we provide a brief overview of different HIV-1 vaccine approaches and discuss the current understanding of the cellular and humoral correlates of HIV-1 immunity. Full article
(This article belongs to the Special Issue New Advances in Human Vaccine)
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20 pages, 6074 KiB  
Review
NF-κB-Mediated Inflammation in the Pathogenesis of Intracranial Aneurysm and Subarachnoid Hemorrhage. Does Autophagy Play a Role?
by Elzbieta Pawlowska, Joanna Szczepanska, Karol Wisniewski, Paulina Tokarz, Dariusz J. Jaskólski and Janusz Blasiak
Int. J. Mol. Sci. 2018, 19(4), 1245; https://doi.org/10.3390/ijms19041245 - 19 Apr 2018
Cited by 64 | Viewed by 7078
Abstract
The rupture of saccular intracranial aneurysms (IA) is the commonest cause of non-traumatic subarachnoid hemorrhage (SAH)—the most serious form of stroke with a high mortality rate. Aneurysm walls are usually characterized by an active inflammatory response, and NF-κB (nuclear factor kappa-light-chain-enhancer of activated [...] Read more.
The rupture of saccular intracranial aneurysms (IA) is the commonest cause of non-traumatic subarachnoid hemorrhage (SAH)—the most serious form of stroke with a high mortality rate. Aneurysm walls are usually characterized by an active inflammatory response, and NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) has been identified as the main transcription factor regulating the induction of inflammation-related genes in IA lesions. This transcription factor has also been related to IA rupture and resulting SAH. We and others have shown that autophagy interacts with inflammation in many diseases, but there is no information of such interplay in IA. Moreover, NF-κB, which is a pivotal factor controlling inflammation, is regulated by autophagy-related proteins, and autophagy is regulated by NF-κB signaling. It was also shown that autophagy mediates the normal functioning of vessels, so its disturbance can be associated with vessel-related disorders. Early brain injury, delayed brain injury, and associated cerebral vasospasm are among the most serious consequences of IA rupture and are associated with impaired function of the autophagy–lysosomal system. Further studies on the role of the interplay between autophagy and NF-κB-mediated inflammation in IA can help to better understand IA pathogenesis and to identify IA patients with an increased SAH risk. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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15 pages, 615 KiB  
Review
Human Cancer and Platelet Interaction, a Potential Therapeutic Target
by Shike Wang, Zhenyu Li and Ren Xu
Int. J. Mol. Sci. 2018, 19(4), 1246; https://doi.org/10.3390/ijms19041246 - 20 Apr 2018
Cited by 62 | Viewed by 8170
Abstract
Cancer patients experience a four-fold increase in thrombosis risk, indicating that cancer development and progression are associated with platelet activation. Xenograft experiments and transgenic mouse models further demonstrate that platelet activation and platelet-cancer cell interaction are crucial for cancer metastasis. Direct or indirect [...] Read more.
Cancer patients experience a four-fold increase in thrombosis risk, indicating that cancer development and progression are associated with platelet activation. Xenograft experiments and transgenic mouse models further demonstrate that platelet activation and platelet-cancer cell interaction are crucial for cancer metastasis. Direct or indirect interaction of platelets induces cancer cell plasticity and enhances survival and extravasation of circulating cancer cells during dissemination. In vivo and in vitro experiments also demonstrate that cancer cells induce platelet aggregation, suggesting that platelet-cancer interaction is bidirectional. Therefore, understanding how platelets crosstalk with cancer cells may identify potential strategies to inhibit cancer metastasis and to reduce cancer-related thrombosis. Here, we discuss the potential function of platelets in regulating cancer progression and summarize the factors and signaling pathways that mediate the cancer cell-platelet interaction. Full article
(This article belongs to the Special Issue Extracellular Matrix in Development and Disease)
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17 pages, 2132 KiB  
Review
What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies
by Yann Guillermin, Jonathan Lopez, Kaddour Chabane, Sandrine Hayette, Claire Bardel, Gilles Salles, Pierre Sujobert and Sarah Huet
Int. J. Mol. Sci. 2018, 19(4), 1251; https://doi.org/10.3390/ijms19041251 - 20 Apr 2018
Cited by 9 | Viewed by 5612
Abstract
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role [...] Read more.
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS. We define the pre-analytical issues such as sequencing DNA obtained from formalin-fixed and paraffin-embedded tissue (FFPE), the acquisition of germline DNA, or the bioinformatic pitfalls, the analytical issues encountered and how to manage them. We describe the main constitutional and cancer databases, their characteristics and limitations, with an emphasis on variant interpretation in lymphoid malignancies. Finally, we discuss the challenges of predictions that one can make using in silico or in vitro modelling, pharmacogenomic screening, and the limits of those prediction tools. This description of the current status in genomic interpretation highlights the need for new large databases and international collaboration in the lymphoma field. Full article
(This article belongs to the Special Issue Translational Diagnostics in Lymphoproliferative and Plasma Cell Disorders)
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31 pages, 2344 KiB  
Review
Prostate Cancer Genomics: Recent Advances and the Prevailing Underrepresentation from Racial and Ethnic Minorities
by Shyh-Han Tan, Gyorgy Petrovics and Shiv Srivastava
Int. J. Mol. Sci. 2018, 19(4), 1255; https://doi.org/10.3390/ijms19041255 - 22 Apr 2018
Cited by 54 | Viewed by 11281
Abstract
Prostate cancer (CaP) is the most commonly diagnosed non-cutaneous cancer and the second leading cause of male cancer deaths in the United States. Among African American (AA) men, CaP is the most prevalent malignancy, with disproportionately higher incidence and mortality rates. Even after [...] Read more.
Prostate cancer (CaP) is the most commonly diagnosed non-cutaneous cancer and the second leading cause of male cancer deaths in the United States. Among African American (AA) men, CaP is the most prevalent malignancy, with disproportionately higher incidence and mortality rates. Even after discounting the influence of socioeconomic factors, the effect of molecular and genetic factors on racial disparity of CaP is evident. Earlier studies on the molecular basis for CaP disparity have focused on the influence of heritable mutations and single-nucleotide polymorphisms (SNPs). Most CaP susceptibility alleles identified based on genome-wide association studies (GWAS) were common, low-penetrance variants. Germline CaP-associated mutations that are highly penetrant, such as those found in HOXB13 and BRCA2, are usually rare. More recently, genomic studies enabled by Next-Gen Sequencing (NGS) technologies have focused on the identification of somatic mutations that contribute to CaP tumorigenesis. These studies confirmed the high prevalence of ERG gene fusions and PTEN deletions among Caucasian Americans and identified novel somatic alterations in SPOP and FOXA1 genes in early stages of CaP. Individuals with African ancestry and other minorities are often underrepresented in these large-scale genomic studies, which are performed primarily using tumors from men of European ancestry. The insufficient number of specimens from AA men and other minority populations, together with the heterogeneity in the molecular etiology of CaP across populations, challenge the generalizability of findings from these projects. Efforts to close this gap by sequencing larger numbers of tumor specimens from more diverse populations, although still at an early stage, have discovered distinct genomic alterations. These research findings can have a direct impact on the diagnosis of CaP, the stratification of patients for treatment, and can help to address the disparity in incidence and mortality of CaP. This review examines the progress of understanding in CaP genetics and genomics and highlight the need to increase the representation from minority populations. Full article
(This article belongs to the Special Issue Molecular Research on Urology)
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16 pages, 822 KiB  
Review
Ca2+ Regulation of TRP Ion Channels
by Raquibul Hasan and Xuming Zhang
Int. J. Mol. Sci. 2018, 19(4), 1256; https://doi.org/10.3390/ijms19041256 - 23 Apr 2018
Cited by 65 | Viewed by 6860
Abstract
Ca2+ signaling influences nearly every aspect of cellular life. Transient receptor potential (TRP) ion channels have emerged as cellular sensors for thermal, chemical and mechanical stimuli and are major contributors to Ca2+ signaling, playing an important role in diverse physiological and [...] Read more.
Ca2+ signaling influences nearly every aspect of cellular life. Transient receptor potential (TRP) ion channels have emerged as cellular sensors for thermal, chemical and mechanical stimuli and are major contributors to Ca2+ signaling, playing an important role in diverse physiological and pathological processes. Notably, TRP ion channels are also one of the major downstream targets of Ca2+ signaling initiated either from TRP channels themselves or from various other sources, such as G-protein coupled receptors, giving rise to feedback regulation. TRP channels therefore function like integrators of Ca2+ signaling. A growing body of research has demonstrated different modes of Ca2+-dependent regulation of TRP ion channels and the underlying mechanisms. However, the precise actions of Ca2+ in the modulation of TRP ion channels remain elusive. Advances in Ca2+ regulation of TRP channels are critical to our understanding of the diversified functions of TRP channels and complex Ca2+ signaling. Full article
(This article belongs to the Special Issue Calcium Binding Proteins)
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17 pages, 2269 KiB  
Review
Clinicopathological Characteristics and Mutations Driving Development of Early Lung Adenocarcinoma: Tumor Initiation and Progression
by Kentaro Inamura
Int. J. Mol. Sci. 2018, 19(4), 1259; https://doi.org/10.3390/ijms19041259 - 23 Apr 2018
Cited by 101 | Viewed by 11801
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide, with lung adenocarcinoma representing the most common lung cancer subtype. Among all lung adenocarcinomas, the most prevalent subset develops via tumorigenesis and progression from atypical adenomatous hyperplasia (AAH) to adenocarcinoma in situ (AIS), [...] Read more.
Lung cancer is the leading cause of cancer-related deaths worldwide, with lung adenocarcinoma representing the most common lung cancer subtype. Among all lung adenocarcinomas, the most prevalent subset develops via tumorigenesis and progression from atypical adenomatous hyperplasia (AAH) to adenocarcinoma in situ (AIS), to minimally invasive adenocarcinoma (MIA), to overt invasive adenocarcinoma with a lepidic pattern. This stepwise development is supported by the clinicopathological and molecular characteristics of these tumors. In the 2015 World Health Organization classification, AAH and AIS are both defined as preinvasive lesions, whereas MIA is identified as an early invasive adenocarcinoma that is not expected to recur if removed completely. Recent studies have examined the molecular features of lung adenocarcinoma tumorigenesis and progression. EGFR-mutated adenocarcinoma frequently develops via the multistep progression. Oncogene-induced senescence appears to decrease the frequency of the multistep progression in KRAS- or BRAF-mutated adenocarcinoma, whose tumor evolution may be associated with epigenetic alterations and kinase-inactive mutations. This review summarizes the current knowledge of tumorigenesis and tumor progression in early lung adenocarcinoma, with special focus on its clinicopathological characteristics and their associations with driver mutations (EGFR, KRAS, and BRAF) as well as on its molecular pathogenesis and progression. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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17 pages, 7774 KiB  
Review
The Role of PPAR and Its Cross-Talk with CAR and LXR in Obesity and Atherosclerosis
by Pengfei Xu, Yonggong Zhai and Jing Wang
Int. J. Mol. Sci. 2018, 19(4), 1260; https://doi.org/10.3390/ijms19041260 - 23 Apr 2018
Cited by 82 | Viewed by 13434
Abstract
The prevalence of obesity and atherosclerosis has substantially increased worldwide over the past several decades. Peroxisome proliferator-activated receptors (PPARs), as fatty acids sensors, have been therapeutic targets in several human lipid metabolic diseases, such as obesity, atherosclerosis, diabetes, hyperlipidaemia, and non-alcoholic fatty liver [...] Read more.
The prevalence of obesity and atherosclerosis has substantially increased worldwide over the past several decades. Peroxisome proliferator-activated receptors (PPARs), as fatty acids sensors, have been therapeutic targets in several human lipid metabolic diseases, such as obesity, atherosclerosis, diabetes, hyperlipidaemia, and non-alcoholic fatty liver disease. Constitutive androstane receptor (CAR) and liver X receptors (LXRs) were also reported as potential therapeutic targets for the treatment of obesity and atherosclerosis, respectively. Further clarification of the internal relationships between these three lipid metabolic nuclear receptors is necessary to enable drug discovery. In this review, we mainly summarized the cross-talk of PPARs-CAR in obesity and PPARs-LXRs in atherosclerosis. Full article
(This article belongs to the Special Issue PPARs in Cellular and Whole Body Energy Metabolism)
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18 pages, 797 KiB  
Review
ROS-Activated Ion Channels in Plants: Biophysical Characteristics, Physiological Functions and Molecular Nature
by Vadim Demidchik
Int. J. Mol. Sci. 2018, 19(4), 1263; https://doi.org/10.3390/ijms19041263 - 23 Apr 2018
Cited by 110 | Viewed by 8620
Abstract
Ion channels activated by reactive oxygen species (ROS) have been found in the plasma membrane of charophyte Nitella flixilis, dicotyledon Arabidopsis thaliana, Pyrus pyrifolia and Pisum sativum, and the monocotyledon Lilium longiflorum. Their activities have been reported in charophyte [...] Read more.
Ion channels activated by reactive oxygen species (ROS) have been found in the plasma membrane of charophyte Nitella flixilis, dicotyledon Arabidopsis thaliana, Pyrus pyrifolia and Pisum sativum, and the monocotyledon Lilium longiflorum. Their activities have been reported in charophyte giant internodes, root trichoblasts and atrichoblasts, pollen tubes, and guard cells. Hydrogen peroxide and hydroxyl radicals are major activating species for these channels. Plant ROS-activated ion channels include inwardly-rectifying, outwardly-rectifying, and voltage-independent groups. The inwardly-rectifying ROS-activated ion channels mediate Ca2+-influx for growth and development in roots and pollen tubes. The outwardly-rectifying group facilitates K+ efflux for the regulation of osmotic pressure in guard cells, induction of programmed cell death, and autophagy in roots. The voltage-independent group mediates both Ca2+ influx and K+ efflux. Most studies suggest that ROS-activated channels are non-selective cation channels. Single-channel studies revealed activation of 14.5-pS Ca2+ influx and 16-pS K+ efflux unitary conductances in response to ROS. The molecular nature of ROS-activated Ca2+ influx channels remains poorly understood, although annexins and cyclic nucleotide-gated channels have been proposed for this role. The ROS-activated K+ channels have recently been identified as products of Stellar K+ Outward Rectifier (SKOR) and Guard cell Outwardly Rectifying K+ channel (GORK) genes. Full article
(This article belongs to the Special Issue Plasma-Membrane Transport)
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27 pages, 3196 KiB  
Review
Molecular Pharmacology of VEGF-A Isoforms: Binding and Signalling at VEGFR2
by Chloe J. Peach, Viviane W. Mignone, Maria Augusta Arruda, Diana C. Alcobia, Stephen J. Hill, Laura E. Kilpatrick and Jeanette Woolard
Int. J. Mol. Sci. 2018, 19(4), 1264; https://doi.org/10.3390/ijms19041264 - 23 Apr 2018
Cited by 314 | Viewed by 29533
Abstract
Vascular endothelial growth factor-A (VEGF-A) is a key mediator of angiogenesis, signalling via the class IV tyrosine kinase receptor family of VEGF Receptors (VEGFRs). Although VEGF-A ligands bind to both VEGFR1 and VEGFR2, they primarily signal via VEGFR2 leading to endothelial cell proliferation, [...] Read more.
Vascular endothelial growth factor-A (VEGF-A) is a key mediator of angiogenesis, signalling via the class IV tyrosine kinase receptor family of VEGF Receptors (VEGFRs). Although VEGF-A ligands bind to both VEGFR1 and VEGFR2, they primarily signal via VEGFR2 leading to endothelial cell proliferation, survival, migration and vascular permeability. Distinct VEGF-A isoforms result from alternative splicing of the Vegfa gene at exon 8, resulting in VEGFxxxa or VEGFxxxb isoforms. Alternative splicing events at exons 5–7, in addition to recently identified posttranslational read-through events, produce VEGF-A isoforms that differ in their bioavailability and interaction with the co-receptor Neuropilin-1. This review explores the molecular pharmacology of VEGF-A isoforms at VEGFR2 in respect to ligand binding and downstream signalling. To understand how VEGF-A isoforms have distinct signalling despite similar affinities for VEGFR2, this review re-evaluates the typical classification of these isoforms relative to the prototypical, “pro-angiogenic” VEGF165a. We also examine the molecular mechanisms underpinning the regulation of VEGF-A isoform signalling and the importance of interactions with other membrane and extracellular matrix proteins. As approved therapeutics targeting the VEGF-A/VEGFR signalling axis largely lack long-term efficacy, understanding these isoform-specific mechanisms could aid future drug discovery efforts targeting VEGF receptor pharmacology. Full article
(This article belongs to the Special Issue Vascular Endothelial Growth Factor)
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11 pages, 10785 KiB  
Case Report
A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis
by Giovanni Luca Scaglione, Paola Concolino, Maria De Bonis, Elisa De Paolis, Angelo Minucci, Gabriella Ferrandina, Giovanni Scambia and Ettore Capoluongo
Int. J. Mol. Sci. 2018, 19(4), 961; https://doi.org/10.3390/ijms19040961 - 23 Mar 2018
Cited by 14 | Viewed by 5288
Abstract
BRCA1/2 screening in Hereditary Breast and Ovarian Syndrome (HBOC) is an essential step for effective patients’ management. Next-Generation Sequencing (NGS) can rapidly provide high throughput and reliable information about the qualitative and quantitative status of tumor-associated genes. Straightforwardly, bioinformatics methods play a key [...] Read more.
BRCA1/2 screening in Hereditary Breast and Ovarian Syndrome (HBOC) is an essential step for effective patients’ management. Next-Generation Sequencing (NGS) can rapidly provide high throughput and reliable information about the qualitative and quantitative status of tumor-associated genes. Straightforwardly, bioinformatics methods play a key role in molecular diagnostics pipelines. BRCA1/2 genes were evaluated with our NGS workflow, coupled with Multiplex Amplicon Quantification (MAQ) and Multiplex Ligation-dependent Probe Amplification (MLPA) assays. Variant calling was performed on Amplicon Suite, while Copy Number Variant (CNV) prediction by in house and commercial CNV tools, before confirmatory MAQ/MLPA testing. The germline profile of BRCA genes revealed a unique HBOC pattern. Although variant calling analysis pinpointed heterozygote and homozygote polymorphisms on BRCA1 and BRCA2, respectively, the CNV predicted by our script suggested two conflicting interpretations: BRCA1 duplication and/or BRCA2 deletion. Our commercial software reported a BRCA1 duplication, in contrast with variant calling results. Finally, the MAQ/MLPA assays assessed a whole BRCA2 copy loss. In silico CNV analysis is a time and cost-saving procedure to powerfully identify possible Large Rearrangements using robust and efficient NGS pipelines. Our layout shows as bioinformatics algorithms alone cannot completely and correctly identify whole BRCA1/2 deletions/duplications. In particular, the complete deletion of an entire gene, like in our case, cannot be solved without alternative strategies as MLPA/MAQ. These findings support the crucial role of bioinformatics in deciphering pitfalls within NGS data analysis. Full article
(This article belongs to the Special Issue Ovarian Cancer: Pathogenesis, Diagnosis, and Treatment)
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7 pages, 20189 KiB  
Case Report
Lynch Syndrome-Related Clear Cell Carcinoma of the Cervix: A Case Report
by Kohei Nakamura, Kentaro Nakayama, Toshiko Minamoto, Tomoka Ishibashi, Kaori Ohnishi, Hitomi Yamashita, Ruriko Ono, Hiroki Sasamori, Sultana Razia, Mohammad Mahmud Hossain, Shanta Kamrunnahar, Masako Ishikawa, Noriyoshi Ishikawa and Satoru Kyo
Int. J. Mol. Sci. 2018, 19(4), 979; https://doi.org/10.3390/ijms19040979 - 25 Mar 2018
Cited by 8 | Viewed by 4657
Abstract
Lynch syndrome, a hereditary cancer syndrome, occurs because of germline mutations in at least one of four DNA mismatch repair genes (MutL Homolog 1 (MLH1), MutS Homolog 2 (MSH2), MutS Homolog 6 (MSH6), and PMS1 Homolog 2 [...] Read more.
Lynch syndrome, a hereditary cancer syndrome, occurs because of germline mutations in at least one of four DNA mismatch repair genes (MutL Homolog 1 (MLH1), MutS Homolog 2 (MSH2), MutS Homolog 6 (MSH6), and PMS1 Homolog 2 (PMS2)). The disorder is associated with colorectal, endometrial, and other epithelial malignancies, but not cervical cancer. We report a woman with Lynch syndrome with synchronous cervical cancer. This is the first report of Lynch syndrome-related clear cell carcinoma of the cervix, which indicates the possibility of an association between cervical cancer and Lynch syndrome. Suitable genetic tests are required to determine whether common genetics can account for synchronous or subsequent malignancies in Lynch syndrome patients and their families. Such knowledge will also enhance our understanding of the genetic mechanisms governing the development of apparently unrelated cancers. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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1 pages, 160 KiB  
Correction
Lee, J.E. et al. Ethanol Extract of Oldenlandia diffusa Herba Attenuates Scopolamine-Induced Cognitive Impairments in Mice via Activation of BDNF, P-CREB and Inhibition of Acetylcholinesterase
by Jung Eun Lee, Hyo-Sook Song, Moon Nyeo Park, Sung-Hoon Kim, Bum-Sang Shim and Bonglee Kim
Int. J. Mol. Sci. 2018, 19(4), 996; https://doi.org/10.3390/ijms19040996 - 27 Mar 2018
Cited by 1 | Viewed by 2843
Abstract
The authors wish to make the following corrections to this paper [1].[...] Full article
(This article belongs to the Special Issue Traditional Medicine – Unraveling Its Molecular Mechanism)
7 pages, 13407 KiB  
Case Report
Dabrafenib Treatment in a Patient with an Epithelioid Glioblastoma and BRAF V600E Mutation
by Garry Ceccon, Jan-Michael Werner, Veronika Dunkl, Caroline Tscherpel, Gabriele Stoffels, Anna Brunn, Martina Deckert, Gereon R. Fink and Norbert Galldiks
Int. J. Mol. Sci. 2018, 19(4), 1090; https://doi.org/10.3390/ijms19041090 - 5 Apr 2018
Cited by 29 | Viewed by 4789
Abstract
Novel therapeutic targets in malignant glioma patients are urgently needed. Point mutations of the v-Raf murine sarcoma viral oncogene homolog B (BRAF) gene occur predominantly in melanoma patients, but may also occur in gliomas. Thus, this is a target of great [...] Read more.
Novel therapeutic targets in malignant glioma patients are urgently needed. Point mutations of the v-Raf murine sarcoma viral oncogene homolog B (BRAF) gene occur predominantly in melanoma patients, but may also occur in gliomas. Thus, this is a target of great interest for this group of patients. In a nine-year-old male patient, an anaplastic astrocytoma in the left temporoparietal region was diagnosed histologically. After first- and second-line treatment, a malignant progression to a secondary glioblastoma was observed ten years after the initial diagnosis. Within the following seven years, all other conventional treatment options were exhausted. At this time point, recurrent tumor histology revealed an epithelioid glioblastoma, without a mutation in the isocitrate dehydrogenase gene (IDH wild-type). In order to identify a potential target for an experimental salvage therapy, mutational tumor analysis showed a BRAF V600E mutation. Consecutively, dabrafenib treatment was initiated. The patient remained clinically stable, and follow-up magnetic resonance images (MRI) were consistent with “Stable Disease” according to the Response Assessment in Neuro-Oncology Working Group (RANO) criteria for the following ten months until tumor progression was detected. The patient died 16 months after dabrafenib treatment initiation. Particularly in younger glioma patients as well as in patients with an epithelioid glioblastoma, screening for a V600E BRAF mutation is promising since, in these cases, targeted therapy with BRAF inhibitors seems to be a useful salvage treatment option. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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