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19 pages, 4255 KiB  
Article
Investigating the Genetic Links Between Immune Cell Profiles and Bladder Cancer: A Multidisciplinary Bioinformatics Approach
by Jin Zhang, Zhongji Jiang, Jiali Jin, Gaohaer Kadeerhan, Hong Guo and Dongwen Wang
Biomedicines 2025, 13(5), 1203; https://doi.org/10.3390/biomedicines13051203 - 15 May 2025
Viewed by 632
Abstract
Background: Bladder cancer (BC) is a common malignancy in the urinary system, with an increasing incidence rate. Immune cell infiltration within the tumor microenvironment (TME) plays a crucial role in BC progression and treatment response. However, the immune cell composition of the [...] Read more.
Background: Bladder cancer (BC) is a common malignancy in the urinary system, with an increasing incidence rate. Immune cell infiltration within the tumor microenvironment (TME) plays a crucial role in BC progression and treatment response. However, the immune cell composition of the TME presents a significant challenge to the effectiveness of current therapeutic strategies. Methods: We performed bidirectional Mendelian randomization (MR) analysis to investigate the impact of immune cells on BC risk. Single nucleotide polymorphisms (SNPs) related to immune cells were annotated, and candidate genes associated with BC risk were identified. Differential expression analysis identified immune-related differentially expressed genes (iDEGs), and a protein–protein interaction (PPI) network along with functional enrichment analysis were conducted to explore their roles in tumor development. Machine learning-based feature selection was applied to identify potential biomarkers and therapeutic targets. Results: MR analysis revealed eight immune cell subtypes significantly associated with BC. Using SNPs linked to these immune cells, 129 candidate genes were identified through the SNPense tool and cross-referenced with differentially expressed genes in BC, resulting in identification of 28 iDEGs. Machine learning identified five potential diagnostic biomarkers (COLEC12, TMCC1, CEP55, KLK3, COL4A1) with an AUC of 0.903, which are implicated in immune modulation and cancer progression. Conclusions: This study provides new insights into immune mechanisms in BC and identifies promising biomarkers for early diagnosis and therapeutic intervention. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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22 pages, 7330 KiB  
Article
Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer
by Sharda P. Singh, Chathurika S. Dhanasekara, Michael W. Melkus, Chhanda Bose, Sonia Y. Khan, Flavia Sardela de Miranda, Maria F. Mahecha, Prrishti J. Gukhool, Sahil S. Tonk, Se-Ran Jun, Sahra Uygun and Rakhshanda Layeequr Rahman
Biomedicines 2025, 13(5), 1058; https://doi.org/10.3390/biomedicines13051058 - 28 Apr 2025
Viewed by 786
Abstract
Background: Breast cancer is a complex and heterogeneous disease characterized by distinct molecular subtypes with varying prognoses and treatment responses. Multiple factors influence breast cancer outcomes including tumor biology, patient characteristics, and treatment modalities. Demographic factors such as age, race/ethnicity, menopausal status, and [...] Read more.
Background: Breast cancer is a complex and heterogeneous disease characterized by distinct molecular subtypes with varying prognoses and treatment responses. Multiple factors influence breast cancer outcomes including tumor biology, patient characteristics, and treatment modalities. Demographic factors such as age, race/ethnicity, menopausal status, and body mass index have been correlated with variations in incidence, mortality, and survival rates. Over the past decade, comprehensive genomic profiling has been widely used to identify molecular biomarkers and signatures to develop novel therapeutic strategies for patients. For instance, the FLEX registry (NCT03053193) enrolled stage I–III breast cancer patients across 90 institutions in the United States and stratified risk groups based on a 70-gene signature (MammaPrint®-MP) and molecular subtype based on an 80-gene signature (BluePrint®-BP). This study aimed to identify the gene expression patterns and biomarkers associated with breast cancer risk and progression by integrating transcriptomic and clinical data. Methods: Targeted 111 unique gene expression and clinical data points from 978 breast cancer samples, representing each BP subtype (26% Luminal A, 26% Luminal B, 25% Basal, 23% HER2), obtained from Agendia Inc. These genes were selected based on their involvement in the mercapturic acid pathway, white and brown adipose tissue markers, inflammation markers, tumor-associated genes, apoptosis, autophagy, and ER stress markers. All statistical analyses, including principal component analysis (PCA), were performed using R version [4.4.0]. Prognostic values and genetic alterations were investigated using various web-based programs as described in the Methods section. Results: PCA of gene expression data revealed distinct clustering patterns associated with risk categories and molecular subtypes, particularly with principal component 4 (PC4). Genes related to oxidative stress, autophagy, apoptosis, and histone modification showed altered expression across risk categories and molecular subtypes. Key differentially expressed genes included SOD2, KLK5, KLK7, IL8, GSTM1/2, GLI1, CBS, and IGF1. Pathway analysis highlighted the enrichment of processes related to autophagy, cellular stress response, apoptosis, glutathione metabolism, deacetylation, and oxidative stress in high-risk and basal-like tumors compared with Ultralow and Luminal A tumors, respectively. Conclusions: This study identified gene expression signatures associated with breast cancer risk and molecular subtypes. These findings provide insights into the biological processes that may drive breast cancer progression and could inform the development of prognostic biomarkers and personalized therapeutic strategies. Full article
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25 pages, 28238 KiB  
Article
Analysis of Kallikrein 6, Acetyl-α-Tubulin, and Aquaporin 1 and 2 Expression Patterns During Normal Human Nephrogenesis and in Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)
by Nela Kelam, Marin Ogorevc, Ivona Gotovac, Ivana Kuzmić Prusac, Katarina Vukojević, Mirna Saraga-Babić and Snježana Mardešić
Genes 2025, 16(5), 499; https://doi.org/10.3390/genes16050499 - 27 Apr 2025
Viewed by 498
Abstract
Background/Objectives: The human kallikrein-related peptidase 6 (KLK6), a serine protease with trypsin-like properties, belongs to the 15-member kallikrein (KLK) gene family and is predominantly recognized for its role in oncogenesis, neurodegenerative disorders, and skin conditions. Aquaporins (AQPs) are integral membrane [...] Read more.
Background/Objectives: The human kallikrein-related peptidase 6 (KLK6), a serine protease with trypsin-like properties, belongs to the 15-member kallikrein (KLK) gene family and is predominantly recognized for its role in oncogenesis, neurodegenerative disorders, and skin conditions. Aquaporins (AQPs) are integral membrane proteins that facilitate water transport across cell membranes. AQP1 is constitutively active in the kidneys and plays a crucial role in reabsorbing filtered water, while AQP2 is regulated by vasopressin and is essential for maintaining body fluid homeostasis. The primary objective of the present study is to investigate the spatio-temporal expression patterns of KLK6, AQP1, and AQP2 throughout normal human nephrogenesis and congenital kidney and urinary tract (CAKUT) abnormalities: duplex kidneys, horseshoe kidneys, and dysplastic kidneys. Methods: An immunofluorescence analysis of KLK6, AQP1, and AQP2 was performed on 37 paraffin-embedded fetal kidney samples. The area percentage of KLK6 in the kidney cortex was calculated in normal developing samples during developmental phases 2, 3, and 4 and compared with CAKUT samples. Results: KLK6 exhibits distinct spatiotemporal expression patterns during human kidney development, with consistent localization in proximal tubules. Its subcellular positioning shifts from the basolateral cytoplasm in early phases to the apical cytoplasm in later stages, which may be strategically positioned to act on its substrate in either the peritubular space or the tubular fluid. KLK6 expression followed a quadratic trajectory, peaking at Ph4. This marked increase in the final developmental phase aligns with its strong expression in mature kidneys, suggesting a potential role in proximal tubule differentiation and functional maturation through facilitating extracellular matrix remodeling and activating proteinase-activated receptors, modulating the signaling pathways that are essential for tubular development. In duplex kidneys, structural abnormalities such as ureteral obstruction and hydronephrosis may upregulate KLK6 as part of a reparative response, while its downregulation could impair epithelial remodeling and cytoskeletal integrity, exacerbating dysplastic phenotypes. Conclusions: These findings highlight the potential of KLK6 involvement in normal kidney development and the pathology of CAKUT. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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26 pages, 8277 KiB  
Article
Kallikrein-Related Peptidase 6 Contributes to Murine Intestinal Tumorigenesis Driven by a Mutant Adenomatous polyposis coli Gene
by Teodora G. Georgieva, Dalila Darmoul, Hwudaurw Chen, Haiyan Cui, Photini F. S. Rice, Jennifer K. Barton, David G. Besselsen and Natalia A. Ignatenko
Cancers 2024, 16(22), 3842; https://doi.org/10.3390/cancers16223842 - 15 Nov 2024
Viewed by 1388
Abstract
Background/Objectives: The objective of this study was to assess the role of a secreted serine protease, kallikrein-related peptidase 6 (KLK6), during colorectal tumorigenesis driven by a mutant Adenomatous polyposis coli (APC) tumor suppressor gene. A first analysis of KLK6 expression in the intestinal [...] Read more.
Background/Objectives: The objective of this study was to assess the role of a secreted serine protease, kallikrein-related peptidase 6 (KLK6), during colorectal tumorigenesis driven by a mutant Adenomatous polyposis coli (APC) tumor suppressor gene. A first analysis of KLK6 expression in the intestinal tract of Apc-mutant multiple intestinal neoplasia (ApcMin/+) mice revealed up to four-fold induction of Klk6 mRNA levels in adenomas relative to its level in the adjacent mucosa. Methods and Results: The presence of KLK6 protein in the adenomatous areas was confirmed by immunohistochemistry and optical coherence tomography/laser-induced fluorescence (OCT/LIF) imaging. To assess the contribution of the KLK6 expression on the Apc-mutant intestinal and colon tumorigenesis, we engineered a mouse with floxed alleles of the Klk6 gene (Klk6lox/lox) and crossed it with a mouse expressing the truncated APC protein under control of the intestinal tract-specific human CDX2P9.5-NLS Cre transgene (CPC;Apcfl/fl;Klk6+/+). We found that CPC;Apcfl/fl mice with disrupted Klk6 gene expression (CPC;Apcfl/fl;Klk6fl/fl) had a significantly smaller average size of the small intestinal and colon crypts (p < 0.001 and p = 0.04, respectively) and developed a significantly fewer adenomas (p = 0.01). Moreover, a decrease in high-grade adenomas (p = 0.03) and adenomas with a diameter above 2 mm (p < 0.0001) was noted in CPC;Apcfl/fl;Klk6fl/fl mice. Further molecular analysis showed that Klk6 gene inactivation in the small intestine and colon tissues of CPC;Apcfl/fl;Klk6fl/fl mice resulted in a significant suppression of transforming growth factor β2 (TGF-β2) protein (p ≤ 0.02) and mitogen-activated protein kinase (MAPK) phosphorylation (p ≤ 0.01). Conclusions: These findings demonstrate the oncogenic role of KLK6 in the mutant Apc-mediated intestinal tumorigenesis and suggest the utility of KLK6 for early diagnosis of colorectal tumors. Full article
(This article belongs to the Section Cancer Biomarkers)
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20 pages, 3630 KiB  
Article
Tissue Kallikrein-1 Suppresses Type I Interferon Responses and Reduces Depressive-Like Behavior in the MRL/lpr Lupus-Prone Mouse Model
by Priyanka S. Bhoj, Cassandra Nocito, Namdev S. Togre, Malika Winfield, Cody Lubinsky, Sabeeya Khan, Nikhita Mogadala, Alecia Seliga, Ellen M. Unterwald, Yuri Persidsky and Uma Sriram
Int. J. Mol. Sci. 2024, 25(18), 10080; https://doi.org/10.3390/ijms251810080 - 19 Sep 2024
Cited by 1 | Viewed by 2085
Abstract
Excessive production and response to Type I interferons (IFNs) is a hallmark of systemic lupus erythematosus (SLE). Neuropsychiatric lupus (NPSLE) is a common manifestation of human SLE, with major depression as the most common presentation. Clinical studies have demonstrated that IFNα can cause [...] Read more.
Excessive production and response to Type I interferons (IFNs) is a hallmark of systemic lupus erythematosus (SLE). Neuropsychiatric lupus (NPSLE) is a common manifestation of human SLE, with major depression as the most common presentation. Clinical studies have demonstrated that IFNα can cause depressive symptoms. We have shown that the kallikrein–kinin system (KKS) [comprised of kallikreins (Klks) and bradykinins] and angiotensin-converting enzyme inhibitors suppressed Type I IFN responses in dendritic cells from lupus-prone mice and human peripheral blood mononuclear cells. Tissue Klk genes are decreased in patients with lupus, and giving exogenous Klk1 ameliorated kidney pathology in mice. We retro-orbitally administered mouse klk1 gene-carrying adenovirus in the Murphy Roths Large lymphoproliferative (MRL/lpr) lupus-prone mice at early disease onset and analyzed immune responses and depressive-like behavior. Klk1 improved depressive-like behavior, suppressed interferon-responsive genes and neuroinflammation, and reduced plasma IFNα levels and proinflammatory cytokines. Klk1 also reduced IFNAR1 and JAK1 protein expression, important upstream molecules in Type I IFN signaling. Klk1 reduced bradykinin B1 receptor expression, which is known to induce proinflammatory response. Together, these findings suggest that Klk1 may be a potential therapeutic candidate to control IFNα production/responses and other inflammatory responses in SLE and NPSLE. Full article
(This article belongs to the Topic Inflammation: The Cause of all Diseases 2.0)
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12 pages, 3745 KiB  
Article
Placental Transcriptome Analysis in Connection with Low Litter Birth Weight Phenotype (LBWP) Sows
by Julia Linck Moroni, Stephen Tsoi, Irene I. Wenger, Graham S. Plastow and Michael K. Dyck
Genes 2024, 15(6), 703; https://doi.org/10.3390/genes15060703 - 28 May 2024
Viewed by 1478
Abstract
It is possible to identify sub-populations of sows in every pig herd that consistently give birth to low birth weight (BW) piglets, irrespective of the litter size. A previous study from our group demonstrated that placental development is a main factor affecting the [...] Read more.
It is possible to identify sub-populations of sows in every pig herd that consistently give birth to low birth weight (BW) piglets, irrespective of the litter size. A previous study from our group demonstrated that placental development is a main factor affecting the litter birth weight phenotype (LBWP) in sows, thereby impacting the BW of entire litters, but the biological and molecular pathways behind this phenomenon are largely unknown. The aim of this study was to investigate the differential gene expression in placental tissues at day 30 of gestation between low LBWP (LLBWP) vs. high LBWP (HLBWP) sows from a purebred Large White maternal line. Using mRNA sequencing, we found 45 differentially expressed genes (DEGs) in placental tissues of LLBWP and HLBWP sows. Furthermore, (GO) enrichment of upregulated DEGs predicted that there were two biological processes significantly related to cornification and regulation of cell population proliferation. To better understand the molecular interaction between cell proliferation and cornification, we conducted transcriptional factor binding site (TFBS) prediction analysis. The results indicated that a highly significant TFBS was located at the 5′ upstream of all four upregulated genes (CDSN, DSG3, KLK14, KRT17), recognized by transcription factors EGR4 and FOSL1. Our findings provide novel insight into how transcriptional regulation of two different biological processes interact in placental tissues of LLBWP sows. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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14 pages, 9810 KiB  
Article
Unveiling the Genomic Landscape of Intraductal Carcinoma of the Prostate Using Spatial Gene Expression Analysis
by Ryuta Watanabe, Noriyoshi Miura, Mie Kurata, Riko Kitazawa, Tadahiko Kikugawa and Takashi Saika
Int. J. Mol. Sci. 2024, 25(9), 4818; https://doi.org/10.3390/ijms25094818 - 28 Apr 2024
Cited by 6 | Viewed by 2226
Abstract
Intraductal carcinoma of the prostate (IDCP) has recently attracted increasing interest owing to its unfavorable prognoses. To effectively identify the IDCP-specific gene expression profile, we took a novel approach of characterizing a typical IDCP case using spatial gene expression analysis. A formalin-fixed, paraffin-embedded [...] Read more.
Intraductal carcinoma of the prostate (IDCP) has recently attracted increasing interest owing to its unfavorable prognoses. To effectively identify the IDCP-specific gene expression profile, we took a novel approach of characterizing a typical IDCP case using spatial gene expression analysis. A formalin-fixed, paraffin-embedded sample was subjected to Visium CytAssist Spatial Gene Expression analysis. IDCP within invasive prostate cancer sites was recognized as a distinct cluster separate from other invasive cancer clusters. Highly expressed genes defining the IDCP cluster, such as MUC6, MYO16, NPY, and KLK12, reflected the aggressive nature of high-grade prostate cancer. IDCP sites also showed increased hypoxia markers HIF1A, BNIP3L, PDK1, and POGLUT1; decreased fibroblast markers COL1A2, DCN, and LUM; and decreased immune cell markers CCR5 and FCGR3A. Overall, these findings indicate that the hypoxic tumor microenvironment and reduced recruitment of fibroblasts and immune cells, which reflect morphological features of IDCP, may influence the aggressiveness of high-grade prostate cancer. Full article
(This article belongs to the Special Issue Molecular Mechanisms Underlying the Progression of Prostate Cancer)
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14 pages, 3564 KiB  
Article
Genomic and Immunologic Correlates in Prostate Cancer with High Expression of KLK2
by Lucía Paniagua-Herranz, Irene Moreno, Cristina Nieto-Jiménez, Esther Garcia-Lorenzo, Cristina Díaz-Tejeiro, Adrián Sanvicente, Bernard Doger, Manuel Pedregal, Jorge Ramón, Jorge Bartolomé, Arancha Manzano, Balázs Gyorffy, Álvaro Gutierrez-Uzquiza, Pedro Pérez Segura, Emiliano Calvo, Víctor Moreno and Alberto Ocana
Int. J. Mol. Sci. 2024, 25(4), 2222; https://doi.org/10.3390/ijms25042222 - 13 Feb 2024
Cited by 2 | Viewed by 3311
Abstract
The identification of surfaceome proteins is a main goal in cancer research to design antibody-based therapeutic strategies. T cell engagers based on KLK2, a kallikrein specifically expressed in prostate cancer (PRAD), are currently in early clinical development. Using genomic information from different sources, [...] Read more.
The identification of surfaceome proteins is a main goal in cancer research to design antibody-based therapeutic strategies. T cell engagers based on KLK2, a kallikrein specifically expressed in prostate cancer (PRAD), are currently in early clinical development. Using genomic information from different sources, we evaluated the immune microenvironment and genomic profile of prostate tumors with high expression of KLK2. KLK2 was specifically expressed in PRAD but it was not significant associated with Gleason score. Additionally, KLK2 expression did not associate with the presence of any immune cell population and T cell activating markers. A mild correlation between the high expression of KLK2 and the deletion of TMPRSS2 was identified. KLK2 expression associated with high levels of surface proteins linked with a detrimental response to immune checkpoint inhibitors (ICIs) including CHRNA2, FAM174B, OR51E2, TSPAN1, PTPRN2, and the non-surface protein TRPM4. However, no association of these genes with an outcome in PRAD was observed. Finally, the expression of these genes in PRAD did not associate with an outcome in PRAD and any immune populations. We describe the immunologic microenvironment on PRAD tumors with a high expression of KLK2, including a gene signature linked with an inert immune microenvironment, that predicts the response to ICIs in other tumor types. Strategies targeting KLK2 with T cell engagers or antibody–drug conjugates will define whether T cell mobilization or antigen release and stimulation of immune cell death are sufficient effects to induce clinical activity. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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28 pages, 5678 KiB  
Article
Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes
by Jason G. Randall, John Gatesy, Michael R. McGowen and Mark S. Springer
Genes 2024, 15(2), 228; https://doi.org/10.3390/genes15020228 - 10 Feb 2024
Cited by 2 | Viewed by 2450
Abstract
Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with [...] Read more.
Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman’s rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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19 pages, 5428 KiB  
Article
Gene Signature Associated with Nervous System in an Experimental Radiation- and Estrogen-Induced Breast Cancer Model
by Gloria M. Calaf, Debasish Roy, Lilian Jara, Francisco Aguayo and Leodan A. Crispin
Biomedicines 2023, 11(12), 3111; https://doi.org/10.3390/biomedicines11123111 - 22 Nov 2023
Cited by 1 | Viewed by 1902
Abstract
Breast cancer is frequently the most diagnosed female cancer in the world. The experimental studies on cancer seldom focus on the relationship between the central nervous system and cancer. Despite extensive research into the treatment of breast cancer, chemotherapy resistance is an important [...] Read more.
Breast cancer is frequently the most diagnosed female cancer in the world. The experimental studies on cancer seldom focus on the relationship between the central nervous system and cancer. Despite extensive research into the treatment of breast cancer, chemotherapy resistance is an important issue limiting the efficacy of treatment. Novel biomarkers to predict prognosis or sensitivity to chemotherapy are urgently needed. This study examined nervous-system-related genes. The profiling of differentially expressed genes indicated that high-LET radiation, such as that emitted by radon progeny, in the presence of estrogen, induced a cascade of events indicative of tumorigenicity in human breast epithelial cells. Bioinformatic tools allowed us to analyze the genes involved in breast cancer and associated with the nervous system. The results indicated that the gene expression of the Ephrin A1 gene (EFNA1), the roundabout guidance receptor 1 (ROBO1), and the kallikrein-related peptidase 6 (KLK6) was greater in T2 and A5 than in the A3 cell line; the LIM domain kinase 2 gene (LIMK2) was greater in T2 than A3 and A5; the kallikrein-related peptidase 7 (KLK7), the neuroligin 4 X-linked gene (NLGN4X), and myelin basic protein (MBP) were greater than A3 only in T2; and the neural precursor cell expressed, developmentally down-regulated 9 gene (NEDD9) was greater in A5 than in the A3 and E cell lines. Concerning the correlation, it was found a positive correlation between ESR1 and EFNA1 in BRCA-LumA patients; with ROBO1 in BRCA-Basal patients, but this correlation was negative with the kallikrein-related peptidase 6 (KLK6) in BRCA-LumA and –LumB, as well as with LIMK2 and ROBO1 in all BRCA. It was also positive with neuroligin 4 X-linked (NLGN4X) in BRCA-Her2 and BRCA-LumB, and with MBP in BRCA-LumA and –LumB, but negative with KLK7 in all BRCA and BRCA-LumA and NEDD9 in BRCA-Her2. The differential gene expression levels between the tumor and adjacent tissue indicated that the ROBO1, KLK6, LIMK2, KLK7, NLGN4X, MBP, and NEDD9 gene expression levels were higher in normal tissues than in tumors; however, EFNA1 was higher in the tumor than the normal ones. EFNA1, LIMK2, ROBO1, KLK6, KLK7, and MBP gene expression had a negative ER status, whereas NEDD9 and NLGN4X were not significant concerning ER status. In conclusion, important markers have been analyzed concerning genes related to the nervous system, opening up a new avenue of studies in breast cancer therapy. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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17 pages, 4315 KiB  
Article
Screening and Identification of Saline-Tolerant Germplasm in Melon
by Wenli Yang, Yueming Ling, Meihua Li, Xuejun Zhang and Bin Liu
Agriculture 2023, 13(11), 2051; https://doi.org/10.3390/agriculture13112051 - 26 Oct 2023
Cited by 2 | Viewed by 2027
Abstract
Melon (Cucumis melo L.) holds significant importance as a horticultural crop, but it faces several yield-limiting factors, including salinity stress. While salinity traditionally hampers the vegetative growth of melon and detrimentally impacts fruit development and quality, certain melon cultivars exhibit the ability [...] Read more.
Melon (Cucumis melo L.) holds significant importance as a horticultural crop, but it faces several yield-limiting factors, including salinity stress. While salinity traditionally hampers the vegetative growth of melon and detrimentally impacts fruit development and quality, certain melon cultivars exhibit the ability to flourish in conditions of relatively high soil salinity. However, truly salt-tolerant melon varieties are quite rare. In this article, we conducted seedling indoor tests, assessed morphological, physiological and biochemical indices, and explored different salt tolerance types among five melon varieties. As a result, we identified three salt-tolerant varieties, with ‘kuizilike’ (KLK) demonstrating the most impressive performance under salt stress. ‘KLK’ exhibited minimal growth and development constraints during salt stress, with the lowest Na+ content, the highest K+ content, and the highest K+/Na+ ratio. Moreover, it displayed the lowest content of malondialdehyde, the highest concentrations of osmoregulation substances, and the highest activity of antioxidant enzymes. Real-time fluorescence quantitation PCR results revealed significantly elevated gene expression levels of TPK, NHX2, LTP, POD, SuSy, HK, PRP and P5CR in ‘KLK’ compared to other varieties. These newly identified salt-tolerant melon germplasms will serve as valuable genetic resources for future studies on the mechanisms underlying melon salt tolerance, and provide insights into melon improvement and molecular breeding. Full article
(This article belongs to the Section Ecosystem, Environment and Climate Change in Agriculture)
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14 pages, 1615 KiB  
Article
Antioxidant Profile of Origanum dictamnus L. Exhibits Antiaging Properties against UVA Irradiation
by Sophia Letsiou, Maria Trapali, Despina Vougiouklaki, Aliki Tsakni, Dionysis Antonopoulos and Dimitra Houhoula
Cosmetics 2023, 10(5), 124; https://doi.org/10.3390/cosmetics10050124 - 6 Sep 2023
Cited by 3 | Viewed by 3333
Abstract
Skin aging mainly occurs due to intrinsic and extrinsic factors. Extrinsic aging is a consequence of exposure to ultraviolet radiation. Meanwhile, natural products exhibit protective properties against skin aging as well as photoaging. In this context, the research on natural anti-aging agents is [...] Read more.
Skin aging mainly occurs due to intrinsic and extrinsic factors. Extrinsic aging is a consequence of exposure to ultraviolet radiation. Meanwhile, natural products exhibit protective properties against skin aging as well as photoaging. In this context, the research on natural anti-aging agents is greatly advanced, and in recent years, numerous plant-based products have been investigated. The aim of this study was to assess the antioxidant profile of Origanum dictamnus L. extract as well as its antiaging effects on 2D cultures of fibroblasts and keratinocytes under UVA irradiation to unravel the potential role of Origanum dictamnus L. in cosmetology. In an attempt to explore the antioxidant profile of the extract, we employed well-established enzymatic assays (DPPH, FRAP, ABTS, and TPC) and a phytochemical screening by LC/MS. According to our findings, the Origanum dictamnus L. extract possesses high scavenging activity (DPPH, ABTS), high phenolic content (TPC), and high Fe(III)-reduction activity (FRAP). Moreover, the LC/MS analysis revealed that the extract was rich in flavonoids, holding a high content of curcumin, kampferol, silymarin, cyanidin-3-glucoside, deosmin, rutin, and quercetin. To gain insight into the bioactivity of Origanum dictamnus L. extract in cell aging, the expression of various genes that are implicated in the skin aging process in keratinocytes and fibroblasts was studied. The gene expression analysis revealed that the extract increases cell proliferation in the cells exposed to UVA irradiation and concomitantly modulates the expression of genes related to the aging process in keratinocytes (KLK7, OCLN, GBA1) and fibroblasts (SIRT2, FOXO3, COL3A1) under the same conditions. Full article
(This article belongs to the Special Issue Bioactive Compounds From Natural Resources Against Skin Aging)
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13 pages, 2998 KiB  
Article
Kallikrein-Related Peptidase 12 (KLK12) in Breast Cancer as a Favorable Prognostic Marker
by Ai Sato, Kiyoshi Takagi, Ayano Yoshimura, Wakana Tsukamoto, Mio Yamaguchi-Tanaka, Yasuhiro Miki, Akiko Ebata, Minoru Miyashita and Takashi Suzuki
Int. J. Mol. Sci. 2023, 24(9), 8419; https://doi.org/10.3390/ijms24098419 - 8 May 2023
Cited by 8 | Viewed by 2224
Abstract
Kallikrein-related peptides (KLKs) form an evolutionally conserved subgroup of secreted serine proteases that consists of 15 members (KLK1-15). Previous studies have shown that KLKs regulate diverse biological processes, but the clinical significance of KLKs remains largely unclear in human breast cancers. We examined [...] Read more.
Kallikrein-related peptides (KLKs) form an evolutionally conserved subgroup of secreted serine proteases that consists of 15 members (KLK1-15). Previous studies have shown that KLKs regulate diverse biological processes, but the clinical significance of KLKs remains largely unclear in human breast cancers. We examined the expression profile of 15 KLK genes in breast carcinomas using microarray data. Next, we immunolocalized KLK12 in 140 breast carcinomas and evaluated its clinical significance. Subsequently, we examined the effects of KLK12 on proliferation and migration in breast cancer cell lines. From microarray analyses, it turned out that KLK12 was the most strongly associated with low-grade malignancy in breast carcinomas among the 15 KLK members. Immunohistochemical KLK12 status was positively associated with ER and PR status, while it was inversely associated with stage, pathological T factor, lymph node metastasis, and distant metastasis. Prognostic analyses demonstrated that KLK12 was a favorable prognostic factor for both disease-free and breast cancer-specific survival of the patients. Furthermore, the knockdown of KLK12 significantly increased cell proliferation activity and cell migration of breast cancer cells. These results suggest that KLK12 has antitumorigenic effects associated with proliferation and migration and immunohistochemical KLK12 status as a potent favorable prognostic factor in breast carcinoma patients. Full article
(This article belongs to the Section Molecular Oncology)
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20 pages, 25838 KiB  
Article
Epigenetic and Tumor Microenvironment for Prognosis of Patients with Gastric Cancer
by Zenghong Wu, Weijun Wang, Kun Zhang, Mengke Fan and Rong Lin
Biomolecules 2023, 13(5), 736; https://doi.org/10.3390/biom13050736 - 25 Apr 2023
Cited by 16 | Viewed by 4215
Abstract
Background: Epigenetics studies heritable or inheritable mechanisms that regulate gene expression rather than altering the DNA sequence. However, no research has investigated the link between TME-related genes (TRGs) and epigenetic-related genes (ERGs) in GC. Methods: A complete review of genomic data was performed [...] Read more.
Background: Epigenetics studies heritable or inheritable mechanisms that regulate gene expression rather than altering the DNA sequence. However, no research has investigated the link between TME-related genes (TRGs) and epigenetic-related genes (ERGs) in GC. Methods: A complete review of genomic data was performed to investigate the relationship between the epigenesis tumor microenvironment (TME) and machine learning algorithms in GC. Results: Firstly, TME-related differential expression of genes (DEGs) performed non-negative matrix factorization (NMF) clustering analysis and determined two clusters (C1 and C2). Then, Kaplan–Meier curves for overall survival (OS) and progression-free survival (PFS) rates suggested that cluster C1 predicted a poorer prognosis. The Cox–LASSO regression analysis identified eight hub genes (SRMS, MET, OLFML2B, KIF24, CLDN9, RNF43, NETO2, and PRSS21) to build the TRG prognostic model and nine hub genes (TMPO, SLC25A15, SCRG1, ISL1, SOD3, GAD1, LOXL4, AKR1C2, and MAGEA3) to build the ERG prognostic model. Additionally, the signature’s area under curve (AUC) values, survival rates, C-index scores, and mean squared error (RMS) curves were evaluated against those of previously published signatures, which revealed that the signature identified in this study performed comparably. Meanwhile, based on the IMvigor210 cohort, a statistically significant difference in OS between immunotherapy and risk scores was observed. It was followed by LASSO regression analysis which identified 17 key DEGs and a support vector machine (SVM) model identified 40 significant DEGs, and based on the Venn diagram, eight co-expression genes (ENPP6, VMP1, LY6E, SHISA6, TMEM158, SYT4, IL11, and KLK8) were discovered. Conclusion: The study identified some hub genes that could be useful in predicting prognosis and management in GC. Full article
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18 pages, 2023 KiB  
Article
Gene-Transcript Expression in Urine Supernatant and Urine Cell-Sediment Are Different but Equally Useful for Detecting Prostate Cancer
by Marcelino Yazbek Hanna, Mark Winterbone, Shea P. O’Connell, Mireia Olivan, Rachel Hurst, Rob Mills, Colin S. Cooper, Daniel S. Brewer and Jeremy Clark
Cancers 2023, 15(3), 789; https://doi.org/10.3390/cancers15030789 - 27 Jan 2023
Cited by 6 | Viewed by 3744
Abstract
There is considerable interest in urine as a non-invasive liquid biopsy to detect prostate cancer (PCa). PCa-specific transcripts such as the TMPRSS2:ERG fusion gene can be found in both urine extracellular vesicles (EVs) and urine cell-sediment (Cell) but the relative usefulness of these [...] Read more.
There is considerable interest in urine as a non-invasive liquid biopsy to detect prostate cancer (PCa). PCa-specific transcripts such as the TMPRSS2:ERG fusion gene can be found in both urine extracellular vesicles (EVs) and urine cell-sediment (Cell) but the relative usefulness of these and other genes in each fraction in PCa detection has not been fully elucidated. Urine samples from 76 men (PCa n = 40, non-cancer n = 36) were analysed by NanoString for 154 PCa-associated genes-probes, 11 tissue-specific, and six housekeeping. Comparison to qRT-PCR data for four genes (PCA3, OR51E2, FOLH1, and RPLP2) was strong (r = 0.51–0.95, Spearman p < 0.00001). Comparing EV to Cells, differential gene expression analysis found 57 gene-probes significantly more highly expressed in 100 ng of amplified cDNA products from the EV fraction, and 26 in Cells (p < 0.05; edgeR). Expression levels of prostate-specific genes (KLK2, KLK3) measured were ~20× higher in EVs, while PTPRC (white-blood Cells) was ~1000× higher in Cells. Boruta analysis identified 11 gene-probes as useful in detecting PCa: two were useful in both fractions (PCA3, HOXC6), five in EVs alone (GJB1, RPS10, TMPRSS2:ERG, ERG_Exons_4-5, HPN) and four from Cell (ERG_Exons_6-7, OR51E2, SPINK1, IMPDH2), suggesting that it is beneficial to fractionate whole urine prior to analysis. The five housekeeping genes were not significantly differentially expressed between PCa and non-cancer samples. Expression signatures from Cell, EV and combined data did not show evidence for one fraction providing superior information over the other. Full article
(This article belongs to the Collection Urological Cancer 2023-2025)
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