International Journal of Molecular Sciences

20 pages, 5060 KiB

Open AccessArticle

Lidocaine Enhanced Antitumor Efficacy and Relieved Chemotherapy-Induced Hyperalgesia in Mice with Metastatic Gastric Cancer

by Peiwen Gao, Fei Peng, Jing Liu, Weiwei Wu, Guoyan Zhao, Congyan Liu, Hangxue Cao, Yuncheng Li, Feng Qiu and Wensheng Zhang

Int. J. Mol. Sci. 2025, 26(2), 828; https://doi.org/10.3390/ijms26020828 (registering DOI) - 19 Jan 2025

Abstract

With the widespread use of lidocaine for pain control in cancer therapy, its antitumor activity has attracted considerable attention in recent years. This paper provides a simple strategy of combining lidocaine with chemotherapy drugs for cancer therapy, aiming to relieve chemotherapy-induced pain and [...] Read more.

With the widespread use of lidocaine for pain control in cancer therapy, its antitumor activity has attracted considerable attention in recent years. This paper provides a simple strategy of combining lidocaine with chemotherapy drugs for cancer therapy, aiming to relieve chemotherapy-induced pain and achieve stronger antitumor efficacy. However, there is still a lack of substantial pre-clinical evidence for the efficacy and related mechanisms of such combinations, obstructing their potential clinical application. In this study, we propose intraperitoneal chemotherapy (IPC) against gastric cancer (GC) as an ideal scenario to evaluate the efficacy of a lidocaine/paclitaxel combination. Firstly, we used human GC cells MKN-45-luc to investigate the antitumor activity and related mechanisms of the lidocaine/paclitaxel combination in vitro. Then, we used C57BL/6 mice with intraperitoneal drug suffusion to evaluate the efficacy of lidocaine to suppress paclitaxel-induced hyperalgesia and related mechanisms. Lastly, in BALB/c tumor-bearing nude mice we evaluated the synergistic antitumor activity and pain-relieving effect of the lidocaine/paclitaxel combination. Our results showed enhanced antitumor activity for the lidocaine/paclitaxel combination, which induced apoptosis, inhibited migration, and the invasion of GC cells in a synergistic manner. In animal models, the lidocaine/paclitaxel combination effectively inhibited growth and peritoneal metastasis of the tumor, resulting in prolonged survival time. Meanwhile, lidocaine showed considerable anti-inflammatory activity alongside its anesthetic effect, which, in combination, effectively relieved hyperalgesia induced by paclitaxel. These results suggested that intraperitoneal suffusion with lidocaine/paclitaxel could be a pain-free IPC formulation with enhanced antitumor activity, which could provide a promising treatment for GC with peritoneal metastasis. Full article

(This article belongs to the Section Molecular Oncology)

27 pages, 1874 KiB

Open AccessReview

The Importance of Edible Medicinal Mushrooms and Their Potential Use as Therapeutic Agents Against Insulin Resistance

by Zsuzsanna Németh, Mariann Paulinné Bukovics, Liza Dalma Sümegi, Gábor Sturm, István Takács and Laura Simon-Szabó

Int. J. Mol. Sci. 2025, 26(2), 827; https://doi.org/10.3390/ijms26020827 (registering DOI) - 19 Jan 2025

Abstract

In addition to conventional treatments, there is growing interest in preventive and complementary therapies. Proper nutrition can prevent the manifestation of several chronic diseases such as obesity, diabetes, cardiovascular disease, and cancer, and can attenuate the severity of these diseases. Edible mushrooms have [...] Read more.

In addition to conventional treatments, there is growing interest in preventive and complementary therapies. Proper nutrition can prevent the manifestation of several chronic diseases such as obesity, diabetes, cardiovascular disease, and cancer, and can attenuate the severity of these diseases. Edible mushrooms have been used as nutrition and medicine for thousands of years. The spectrum and quantity of their medicinal compounds made them a widely investigated target both in basic research and clinical trials. The most abundant and medically important components are polysaccharides, terpenoids, phenols, and heterocyclic amines, but bioactive proteins, vitamins, including vitamin D, polyunsaturated fatty acids, and essential minerals are also important ingredients with noteworthy health benefits. Mushroom extracts have anti-diabetic, anti-hyperlipidemic, anti-inflammatory, antioxidant, cardioprotective, anti-osteoporotic, and anti-tumor effects and are well tolerated, even by cancer patients. In our previous review we detailed the molecular aspects of the development of type 2 diabetes, discussing the role of physical activity and diet, but we did not detail the role of medicinal mushrooms as part of nutrition. In this review, we aimed to summarize the most important medical mushrooms, along with their natural habitats, growing conditions, and components, that are presumably sufficient for the prevention and treatment of insulin resistance. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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12 pages, 616 KiB

Open AccessArticle

Biomarkers of Intrathecal Synthesis May Be Associated with Cognitive Impairment at MS Diagnosis

by Eleonora Virgilio, Valentina Ciampana, Chiara Puricelli, Paola Naldi, Angelo Bianchi, Umberto Dianzani, Domizia Vecchio and Cristoforo Comi

Int. J. Mol. Sci. 2025, 26(2), 826; https://doi.org/10.3390/ijms26020826 (registering DOI) - 19 Jan 2025

Abstract

The pathophysiology of cognitive impairment (CI) in multiple sclerosis (MS) remains unclear. Meningeal B cell aggregates may contribute to cortical grey matter pathology. Cerebrospinal fluid (CSF), kappa free light chains (KFLC), and KFLCs-Index (kappa-Index) are reliable quantitative markers of intrathecal synthesis, but few [...] Read more.

The pathophysiology of cognitive impairment (CI) in multiple sclerosis (MS) remains unclear. Meningeal B cell aggregates may contribute to cortical grey matter pathology. Cerebrospinal fluid (CSF), kappa free light chains (KFLC), and KFLCs-Index (kappa-Index) are reliable quantitative markers of intrathecal synthesis, but few data have been presented exploring the association with CI, and no data are present for lambda FLC (LFLC) in MS. We evaluated cognition using the Brief International Cognitive Assessment for MS (BICAMS) battery and collected serum and CSF at diagnosis in newly diagnosed drug-naïve MS patients. We observed that patients with impaired verbal memory and overall CI showed increased CSF KFLCs (respectively p: 0.0003 and p: 0.003) and kappa-Index (respectively p: 0.01 and p: 0.02) compared to those with normal verbal memory and no CI. Patients with CI also displayed lower CSF LFLCs (p: 0.04) and lambda-Index (p: 0.001); however, only CSF KFLC negatively correlated with normalized results of verbal memory (for age, sex, and educational levels), even after correction for EDSS (r: −0.27 p: 0.01). Finally, CSF FKLC and kappa-Index were significant predictors of verbal memory in a multivariate analysis. Our results, suggest that intrathecal B cell activity might contribute to CI development in MS patients. Full article

(This article belongs to the Special Issue Multiple Sclerosis: The Latest Developments in Immunology and Therapy)

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32 pages, 4595 KiB

Open AccessReview

Repetitive Transcranial Magnetic Stimulation for the Treatment of Spinal Cord Injury: Current Status and Perspective

by Shu Fan, Wei Wang and Xiaolong Zheng

Int. J. Mol. Sci. 2025, 26(2), 825; https://doi.org/10.3390/ijms26020825 (registering DOI) - 19 Jan 2025

Abstract

Spinal cord injury (SCI) can lead to devastating dysfunctions and complications, significantly impacting patients’ quality of life and aggravating the burden of disease. Since the main pathological mechanism of SCI is the disruption of neuronal circuits, the primary therapeutic strategy for SCI involves [...] Read more.

Spinal cord injury (SCI) can lead to devastating dysfunctions and complications, significantly impacting patients’ quality of life and aggravating the burden of disease. Since the main pathological mechanism of SCI is the disruption of neuronal circuits, the primary therapeutic strategy for SCI involves reconstructing and activating circuits to restore neural signal transmission. Repetitive transcranial magnetic stimulation (rTMS), a noninvasive brain stimulation technique, can modulate the function or state of the nervous system by pulsed magnetic fields. Here, we discuss the basic principles and potential mechanisms of rTMS for treating SCI, including promoting the reconstruction of damaged circuits in the spinal cord, activating reorganization of the cerebral cortex and circuits, modulating the balance of inputs to motoneurons, improving the microenvironment and intrinsic regeneration ability in SCI. Based on these mechanisms, we provide an overview of the therapeutic effects of rTMS in SCI patients with motor dysfunction, spasticity and neuropathic pain. We also discuss the challenges and prospectives of rTMS, especially the potential of combination therapy of rTMS and neural progenitor cell transplantation, and the synergistic effects on promoting regeneration, relay formation and functional connectivity. This review is expected to offer a relatively comprehensive understanding and new perspectives of rTMS for SCI treatment. Full article

(This article belongs to the Special Issue Comprehensive Insights into Molecular Mechanisms and Pathophysiology of Spinal Cord Injury)

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16 pages, 12939 KiB

Open AccessArticle

A High-Resolution Crystallographic Study of Cytochrome c6: Structural Basis for Electron Transfer in Cyanobacterial Photosynthesis

by Botao Zhang, Yuancong Xu, Shuwen Liu, Sixu Chen, Wencong Zhao, Zhaoyang Li, Junshuai Wang, Weijian Zhao, Heng Zhang, Yuhui Dong, Yong Gong, Wang Sheng and Peng Cao

Int. J. Mol. Sci. 2025, 26(2), 824; https://doi.org/10.3390/ijms26020824 (registering DOI) - 19 Jan 2025

Abstract

Cyanobacterial cytochrome c6 (Cyt c6) is crucial for electron transfer between the cytochrome b6f complex and photosystem I (PSI), playing a key role in photosynthesis and enhancing adaptation to extreme environments. This study investigates the high-resolution crystal structures of Cyt c6 from Synechococcus [...] Read more.

Cyanobacterial cytochrome c6 (Cyt c6) is crucial for electron transfer between the cytochrome b6f complex and photosystem I (PSI), playing a key role in photosynthesis and enhancing adaptation to extreme environments. This study investigates the high-resolution crystal structures of Cyt c6 from Synechococcus elongatus PCC 7942 and Synechocystis PCC 6803, focusing on its dimerization mechanisms and functional implications for photosynthesis. Cyt c6 was expressed in Escherichia coli using a dual-plasmid co-expression system and characterized in both oxidized and reduced states. X-ray crystallography revealed three distinct crystal forms, with asymmetric units containing 2, 4, or 12 molecules, all of which consist of repeating dimeric structures. Structural comparisons across species indicated that dimerization predominantly occurs through hydrophobic interactions within a conserved motif around the heme crevice, despite notable variations in dimer positioning. We propose that the dimerization of Cyt c6 enhances structural stability, optimizes electron transfer kinetics, and protects the protein from oxidative damage. Furthermore, we used AlphaFold3 to predict the structure of the PSI-Cyt c6 complex, revealing specific interactions that may facilitate efficient electron transfer. These findings provide new insights into the functional role of Cyt c6 dimerization and its contribution to improving cyanobacterial photosynthetic electron transport. Full article

(This article belongs to the Special Issue Molecular Enzymology and Biotechnology for Extreme Environments)

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18 pages, 4917 KiB

Open AccessArticle

Proteomics Reveals the Response Mechanism of Embryonic Bovine Lung Cells to Mycoplasma bovis Infection

by Li Wang, Qing Wang, Yudong Liu, Yunxia Chen, Shijun Bao, Xiaoli Zhang and Chuan Wang

Int. J. Mol. Sci. 2025, 26(2), 823; https://doi.org/10.3390/ijms26020823 (registering DOI) - 19 Jan 2025

Abstract

Mycoplasma bovis (M. bovis) has caused huge economic losses to the cattle industry. The interaction between M. bovis and host cells is elucidated by screening and identifying the target protein of M. bovis adhesin on the surface of the host cell [...] Read more.

Mycoplasma bovis (M. bovis) has caused huge economic losses to the cattle industry. The interaction between M. bovis and host cells is elucidated by screening and identifying the target protein of M. bovis adhesin on the surface of the host cell membrane. However, the response mechanism of embryonic bovine lung (EBL) cells to M. bovis infection is not yet fully understood. Additionally, it is necessary to further explore whether infection with M. bovis induces oxidative stress and mitochondrial damage in EBL cells. In this study, oxidation reaction, mitochondrial membrane potential, mitochondrial structure, and apoptosis ability of EBL cells infected with M. bovis were assessed at different times (12, 24, 48 h post-infection; hpi). Then, the differential proteomic analysis of M. bovis-infected EBL cells at 12 h and 24 h was performed with uninfected cells as the control. The results showed that M. bovis infection reduced the antioxidant capacity of EBL cells, increased ROS levels, and decreased mitochondrial membrane potential. The mitochondrial membrane of EBL cells was damaged, and the ridge arrangement was disordered after infection by transmission electron microscopy. With the increase in infection time, the mitochondrial matrix partially dissolved and spilled. The apoptosis rate of EBL cells increased with the increase in infection time of M. bovis. Furthermore, proteomic analysis identified 268 and 2061 differentially expressed proteins (DEPs) at 12 hpi and 24 hpi, respectively, compared with the uninfected cells. According to GO analysis, these DEPs were involved in the mitosis and negative regulation of cell growth. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated the following pathways were linked to mitochondrial damage or cell growth regulation, including glycolysis/gluconeogenesis, pentose phosphate pathway, oxidative phosphorylation, AMPK, cGMP-PKG, cAMP, calcium, Wnt, Phospholipase D, apoptosis, MAPK, cell cycle, Ras, PI3K-Akt, mTOR, HIF-1. PPI results indicated that YWHAZ, PIK3CA, HSP90AB1, RAP1A, TXN, RAF1, MAPK1, PKM, PGK1, and GAPDH might be involved in mitochondrial pathway apoptosis induced by M. bovis infection. This study offers helpful data toward understanding the response of mitochondria of EBL cells to M. bovis infection. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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15 pages, 608 KiB

Open AccessArticle

Comparative Analysis of Iodine Levels, Biochemical Responses, and Thyroid Gene Expression in Rats Fed Diets with Kale Biofortified with 5,7-Diiodo-8-Quinolinol

by Justyna Waśniowska, Ewa Piątkowska, Piotr Pawlicki, Sylwester Smoleń, Aneta Kopeć, Agnieszka Dyląg, Joanna Krzemińska and Aneta Koronowicz

Int. J. Mol. Sci. 2025, 26(2), 822; https://doi.org/10.3390/ijms26020822 (registering DOI) - 19 Jan 2025

Abstract

Iodine is a key micronutrient essential for the synthesis of thyroid hormone, which regulates metabolic processes and maintains overall health. Despite its importance, iodine deficiency is a global health issue, leading to disorders such as goiter, hypothyroidism, and developmental abnormalities. Biofortification of crops [...] Read more.

Iodine is a key micronutrient essential for the synthesis of thyroid hormone, which regulates metabolic processes and maintains overall health. Despite its importance, iodine deficiency is a global health issue, leading to disorders such as goiter, hypothyroidism, and developmental abnormalities. Biofortification of crops with iodine is a promising strategy to enhance the dietary iodine intake, providing an alternative to iodized salt. Curly kale (Brassica oleracea var. sabellica) is a nutrient-rich vegetable high in vitamins A, C, K; minerals; fiber; and bioactive compounds with antioxidant, anti-inflammatory, and detoxifying properties. This study evaluates the effects of diets containing iodine-biofortified curly kale (‘Oldenbor F₁’ and ‘Redbor F₁’) on iodine content, tissue iodine levels, and various biochemical parameters in laboratory rats. The biofortified curly kale was enriched with 5,7-diiodo-8-quinolinol. The iodine content in the AIN-93G (control) diet and the non-biofortified curly kale diets did not differ significantly. However, diets with 5,7-diiodo-8-quinolinol biofortified kale showed significantly higher iodine levels compared with the control diets. Tissue analysis revealed the highest iodine concentrations in the liver and kidneys of rats fed diets with biofortified curly kale, indicating better iodine bioavailability. Biochemical analysis showed that rats fed the biofortified kale diet had lower total cholesterol (TC) and triglyceride (TG) levels compared with rats fed the control diet. Additionally, the biofortified diet improved the liver function markers (ALAT, ASAT) and reduced oxidative stress markers (TBARS). The study also investigated the expression of thyroid-related genes (Slc5A5, Tpo, Dio1, Dio2) in response to diets containing biofortified kale. The results demonstrated significant changes in gene expression, indicating adaptive mechanisms to dietary iodine levels and the presence of bioactive compounds in the biofortified kale. The study also observed variations in uric acid levels, with lower concentrations in rats fed a diet with biofortified curly kale. Biofortified curly kale supports thyroid function and improves liver and kidney health by reducing oxidative stress and modulating key biochemical and genetic markers. These findings suggest that biofortified curly kale can effectively increase dietary iodine intake as a nutritional intervention to address iodine deficiency and promote overall health. Full article

(This article belongs to the Special Issue Plant-Derived Food Products in the Prevention of Chronic Non-Communicable Diseases)

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17 pages, 2774 KiB

Open AccessReview

The Role of E3 Ubiquitin Ligase Gene FBK in Ubiquitination Modification of Protein and Its Potential Function in Plant Growth, Development, Secondary Metabolism, and Stress Response

by Yuting Wu, Yankang Zhang, Wanlin Ni, Qinghuang Li, Min Zhou and Zhou Li

Int. J. Mol. Sci. 2025, 26(2), 821; https://doi.org/10.3390/ijms26020821 (registering DOI) - 19 Jan 2025

Abstract

As a crucial post-translational modification (PTM), protein ubiquitination mediates the breakdown of particular proteins, which plays a pivotal role in a large number of biological processes including plant growth, development, and stress response. The ubiquitin-proteasome system (UPS) consists of ubiquitin (Ub), ubiquitinase, deubiquitinating [...] Read more.

As a crucial post-translational modification (PTM), protein ubiquitination mediates the breakdown of particular proteins, which plays a pivotal role in a large number of biological processes including plant growth, development, and stress response. The ubiquitin-proteasome system (UPS) consists of ubiquitin (Ub), ubiquitinase, deubiquitinating enzyme (DUB), and 26S proteasome mediates more than 80% of protein degradation for protein turnover in plants. For the ubiquitinases, including ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3), the FBK (F-box Kelch repeat protein) is an essential component of multi-subunit E3 ligase SCF (Skp1-Cullin 1-F-box) involved in the specific recognition of target proteins in the UPS. Many FBK genes have been identified in different plant species, which regulates plant growth and development through affecting endogenous phytohormones as well as plant tolerance to various biotic and abiotic stresses associated with changes in secondary metabolites such as phenylpropanoid, phenolic acid, flavonoid, lignin, wax, etc. The review summarizes the significance of the ubiquitination modification of protein, the role of UPS in protein degradation, and the possible function of FBK genes involved in plant growth, development, secondary metabolism, and stress response, which provides a systematic and comprehensive understanding of the mechanism of ubiquitination and potential function of FBKs in plant species. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

17 pages, 3136 KiB

Open AccessArticle

Two-Step Cell Death Induction by the New 2-Arachidonoyl Glycerol Analog and Its Modulation by Lysophosphatidylinositol in Human Breast Cancer Cells

by Mikhail G. Akimov, Natalia M. Gretskaya, Evgenia I. Gorbacheva, Nisreen Khadour, Galina D. Sherstyanykh and Vladimir V. Bezuglov

Int. J. Mol. Sci. 2025, 26(2), 820; https://doi.org/10.3390/ijms26020820 (registering DOI) - 19 Jan 2025

Abstract

2-arachnadoyl glycerol (2-AG) is one of the most common endocannabinoid molecules with anti-proliferative, cytotoxic, and pro-proliferative effects on different types of tumors. Typically, it induces cell death via cannabinoid receptor 1/2 (CB1/CB2)-linked ceramide production. In breast cancer, ceramide is counterbalanced by the sphingosine-1-phosphate, [...] Read more.

2-arachnadoyl glycerol (2-AG) is one of the most common endocannabinoid molecules with anti-proliferative, cytotoxic, and pro-proliferative effects on different types of tumors. Typically, it induces cell death via cannabinoid receptor 1/2 (CB1/CB2)-linked ceramide production. In breast cancer, ceramide is counterbalanced by the sphingosine-1-phosphate, and thus the mechanisms of 2-AG influence on proliferation are poorly understood. We evaluated the mechanism of the anti-proliferative action by 2-AG and the influence of lysophaosphatidylinositol (LPI) on it in six human breast cancer cell lines of different tumor degree (MCF-10A, MCF-7, BT-474, BT-20, SK-BR-3, and MDA-MB-231) using resazurin test, inhibitor, blocker, and anti-oxidant analysis, and siRNA interference. To avoid acyl migration in 2-AG, we replaced it with the analog 2-arachidonoyl-1,3-difluoropropanol (2-ADFP) newly synthesized by us. Using a molecular docking approach, we showed that at the CB2 receptor, 2-ADFP and 2-AG were very close to each other. However, 2-ADFP demonstrated a stronger affinity towards CB1 in the antagonist-bound conformation. 2-ADFP was anti-proliferative in all the cell lines tested. The toxicity of 2-ADFP was enhanced by LPI. 2-ADFP activity was reduced or prevented by the CB2 and vanilloid receptor 1 (TRPV1) blockers, inositol triphosphate receptor, CREB, and cyclooxygenase 2 inhibitor, and by anti-oxidant addition. Together with the literature data, these results indicate CB2- and TRPV1-dependent COX-2 induction with concomitant cell death induction by the oxidized molecule’s metabolites. Full article

(This article belongs to the Special Issue Breast Cancers: From Molecular Basis to Therapy)

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22 pages, 15910 KiB

Open AccessArticle

A Study on Potential Sources of Perineuronal Net-Associated Sema3A in Cerebellar Nuclei Reveals Toxicity of Non-Invasive AAV-Mediated Cre Expression in the Central Nervous System

by Geoffrey-Alexander Gimenez, Maurits Romijn, Joëlle van den Herik, Wouter Meijer, Ruben Eggers, Barbara Hobo, Chris I. De Zeeuw, Cathrin B. Canto, Joost Verhaagen and Daniela Carulli

Int. J. Mol. Sci. 2025, 26(2), 819; https://doi.org/10.3390/ijms26020819 (registering DOI) - 19 Jan 2025

Abstract

Semaphorin 3A (Sema3A) is an axon guidance molecule, which is also abundant in the adult central nervous system (CNS), particularly in perineuronal nets (PNNs). PNNs are extracellular matrix structures that restrict plasticity. The cellular sources of Sema3A in PNNs are unknown. Most Sema3A-bearing [...] Read more.

Semaphorin 3A (Sema3A) is an axon guidance molecule, which is also abundant in the adult central nervous system (CNS), particularly in perineuronal nets (PNNs). PNNs are extracellular matrix structures that restrict plasticity. The cellular sources of Sema3A in PNNs are unknown. Most Sema3A-bearing neurons do not express Sema3A mRNA, suggesting that Sema3A may be released from other neurons. Another potential source of Sema3A is the choroid plexus. To identify sources of PNN-associated Sema3A, we focused on the cerebellar nuclei, which contain Sema3A⁺ PNNs. Cerebellar nuclei neurons receive prominent input from Purkinje cells (PCs), which express high levels of Sema3A mRNA. By using a non-invasive viral vector approach, we overexpressed Cre in PCs, the choroid plexus, or throughout the CNS of Sema3A^fl/fl mice. Knocking out Sema3A in PCs or the choroid plexus was not sufficient to decrease the amount of PNN-associated Sema3A. Alternatively, knocking out Sema3A throughout the CNS induced a decrease in PNN-associated Sema3A. However, motor deficits, microgliosis, and neurodegeneration were observed, which were due to Cre toxicity. Our study represents the first attempt to unravel cellular sources of PNN-associated Sema3A and shows that non-invasive viral-mediated Cre expression throughout the CNS could lead to toxicity, complicating the interpretation of Cre-mediated Sema3A knock-out. Full article

(This article belongs to the Section Molecular Neurobiology)

21 pages, 4336 KiB

Open AccessArticle

Genome-Wide Characterization of Extrachromosomal Circular DNA in the Midgut of BmCPV-Infected Silkworms and Its Potential Role in Antiviral Responses

by Xinyu Tong, Chao Lei, Yilin Liu, Mei Yin, Huan Peng, Qunnan Qiu, Yongjie Feng, Xiaolong Hu, Chengliang Gong and Min Zhu

Int. J. Mol. Sci. 2025, 26(2), 818; https://doi.org/10.3390/ijms26020818 (registering DOI) - 19 Jan 2025

Abstract

Extrachromosomal circular DNAs (eccDNAs) has been found to be widespread and functional in various organisms. However, comparative analyses of pre- and post-infection of virus are rarely known. Herein, we investigated the changes in expression patterns of eccDNA following infection with Bombyx mori cytoplasmic [...] Read more.

Extrachromosomal circular DNAs (eccDNAs) has been found to be widespread and functional in various organisms. However, comparative analyses of pre- and post-infection of virus are rarely known. Herein, we investigated the changes in expression patterns of eccDNA following infection with Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) and explore the role of eccDNA in viral infection. Circle-seq was used to analyze eccDNAs in the midgut of BmCPV-infected and BmCPV-uninfected silkworms. A total of 5508 eccDNAs were identified, with sizes varying from 72 bp to 17 kb. Most of eccDNAs are between 100 to 1000 bp in size. EccDNA abundance in BmCPV-infected silkworms was significantly higher than in BmCPV-uninfected silkworms. GO and KEGG analysis of genes carried by eccDNAs reveals that most are involved in microtubule motor activity, phosphatidic acid binding, cAMP signaling pathway, and pancreatic secretion signaling pathways. Several eccDNAs contain sequences of the transcription factor SOX6, sem-2, sp8b, or Foxa2. Association analysis of eccDNA-mRNA/miRNA/circRNA revealed that some highly expressed genes are transcribed from relevant sequences of eccDNA and the transcription of protein coding genes influenced the frequency of eccDNA. BmCPV infection resulted in changes in the expression levels of six miRNAs, but no known miRNAs with altered expression levels due to changes in eccDNA abundance were identified. Moreover, it was found that 1287 and 924 sequences representing back-spliced junctions of circRNAs were shared by the junctions of eccDNAs in the BmCPV-infected and uninfected silkworms, respectively, and some eccDNAs loci were shared by circRNAs on Chromosomes 2, 7, 11, 14, and 24, suggesting some eccDNAs may exert its function by being transcribed into circRNAs. These findings suggest that BmCPV infection alter the expression pattern of eccDNAs, leading to changes in RNA transcription levels, which may play roles in regulating BmCPV replication. In the future, further experiments are needed to verify the association between eccDNA-mRNA/miRNA/circRNA and its function in BmCPV infection. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

13 pages, 246 KiB

Open AccessArticle

A Haplotype GWAS in Syndromic Familial Colorectal Cancer

by Litika Vermani, Johanna Samola Winnberg, Wen Liu, Veronika Soller, Tilde Sjödin, Mats Lindblad and Annika Lindblom

Int. J. Mol. Sci. 2025, 26(2), 817; https://doi.org/10.3390/ijms26020817 (registering DOI) - 19 Jan 2025

Abstract

A previous genome-wide association study (GWAS) in colorectal cancer (CRC) patients with gastric and/or prostate cancer in their families suggested genetic loci with a shared risk for these three cancers. A second haplotype GWAS was undertaken in the same colorectal cancer patients and [...] Read more.

A previous genome-wide association study (GWAS) in colorectal cancer (CRC) patients with gastric and/or prostate cancer in their families suggested genetic loci with a shared risk for these three cancers. A second haplotype GWAS was undertaken in the same colorectal cancer patients and different controls with the aim of confirming the result and finding novel loci. The haplotype GWAS analysis involved 685 patients with colorectal cancer cases and 1642 healthy controls from Sweden. A logistic regression model was used with a sliding window haplotype approach. Whole-genome and exome sequencing datawere used to find candidate SNPs to be tested in a nested case-control study. In the analysis of 685 colorectal cancer cases and 1642 controls, all ten candidate loci from the previous study were confirmed. Fifty candidate loci were suggested with a p-value < 5 × 10⁻⁶ and odds ratios between 1.35–6.52. Two of the 50 loci, on 13q33.3 and 16q23.3, were the same as in the previous study. Whole-genome or exome data from 122 colorectal cancer patients was used to search for candidate variants in these 50 loci. A nested case-control study was performed to test genetic variants at 11 loci in a cohort of 827 familial colorectal cancer and a sub-cohort of 293 familial CRC cases with colorectal, gastric, and/or prostate cancer within their families and 1530 healthy controls. One SNP, rs115943733 on 10q11.21, reached statistical significance (OR = 3.26, p = 0.009). Seven SNPs in 4 loci had a higher OR in the smaller cohort compared to the larger study CRC cases. The results in this GWAS gave support for suggested loci with an increased shared risk of CRC, gastric, and/or prostate cancer. Further studies are needed to confirm the shared risk to be able to use this information in cancer prevention. Full article

(This article belongs to the Special Issue Molecular Targeted Therapies and Precision Medicine for Malignant Diseases)

23 pages, 1058 KiB

Open AccessReview

Challenges in Humoral Immune Response to Adeno-Associated Viruses Determination

by Daria A. Naumova, Tatyana Krokunova, Denis Maksimov, Olga N. Mityaeva, Ekaterina A. Astakhova and Pavel Yu Volchkov

Int. J. Mol. Sci. 2025, 26(2), 816; https://doi.org/10.3390/ijms26020816 (registering DOI) - 19 Jan 2025

Abstract

Adeno-associated viruses (AAVs) are non-pathogenic, replication-deficient viruses that have gained widespread attention for their application as gene therapy vectors. While these vectors offer high transduction efficiency and long-term gene expression, the host immune response poses a significant challenge to their clinical success. This [...] Read more.

Adeno-associated viruses (AAVs) are non-pathogenic, replication-deficient viruses that have gained widespread attention for their application as gene therapy vectors. While these vectors offer high transduction efficiency and long-term gene expression, the host immune response poses a significant challenge to their clinical success. This review focuses on the obstacles to evaluating the humoral response to AAVs. We discuss the problems with the validation of in vitro tests and the possible approaches to overcome them. Using published data on neutralizing titers of AAV serotypes, we built the first antigenic maps of AAVs in order to visualize the antigenic relationships between varying serotypes. Full article

(This article belongs to the Special Issue Latest Review Papers in Molecular Immunology 2024)

20 pages, 2238 KiB

Open AccessArticle

Somatic DNA Variants in Epilepsy Surgery Brain Samples from Patients with Lesional Epilepsy

by Jana Marie Schwarz, Lena-Luise Becker, Monika Wahle, Jessica Faßbender, Ulrich-Wilhelm Thomale, Anna Tietze, Susanne Morales-Gonzalez, Ellen Knierim, Markus Schuelke and Angela M. Kaindl

Int. J. Mol. Sci. 2025, 26(2), 815; https://doi.org/10.3390/ijms26020815 (registering DOI) - 19 Jan 2025

Abstract

Epilepsy affects 50 million people worldwide and is drug-resistant in approximately one-third of cases. Even when a structural lesion is identified as the epileptogenic focus, understanding the underlying genetic causes is crucial to guide both counseling and treatment decisions. Both somatic and germline [...] Read more.

Epilepsy affects 50 million people worldwide and is drug-resistant in approximately one-third of cases. Even when a structural lesion is identified as the epileptogenic focus, understanding the underlying genetic causes is crucial to guide both counseling and treatment decisions. Both somatic and germline DNA variants may contribute to the lesion itself and/or influence the severity of symptoms. We therefore used whole exome sequencing (WES) to search for potentially pathogenic somatic DNA variants in brain samples from children with lesional epilepsy who underwent epilepsy surgery. WES was performed on 20 paired DNA samples extracted from both lesional brain tissue and reference tissue from the same patient, such as leukocytes or fibroblasts. The paired WES data were jointly analyzed using GATK Mutect2 to identify somatic single nucleotide variants (SNVs) or insertions/deletions (InDels), which were subsequently evaluated in silico for their disease-causing potential using MutationTaster2021. We identified known pathogenic somatic variants in five patients (25%) with variant allele frequencies (VAF) ranging from 3–35% in the genes MTOR, TSC2, PIK3CA, FGFR1, and PIK3R1 as potential causes of cortical malformations or central nervous system (CNS) tumors. Depending on the VAF, we used different methods such as Sanger sequencing, allele-specific qPCR, or targeted ultra-deep sequencing (amplicon sequencing) to confirm the variant. In contrast to the usually straightforward confirmation of germline variants, the validation of somatic variants is more challenging because current methods have limitations in sensitivity, specificity, and cost-effectiveness. In our study, WES identified additional somatic variant candidates in additional genes with VAFs ranging from 0.7–7.0% that could not be validated by an orthogonal method. This highlights the importance of variant validation, especially for those with very low allele frequencies. Full article

(This article belongs to the Special Issue Epilepsy: From Molecular Basis to Therapy)

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30 pages, 1803 KiB

Open AccessArticle

Environmental Exposure to Bisphenol A Enhances Invasiveness in Papillary Thyroid Cancer

by Chien-Yu Huang, Ren-Hao Xie, Pin-Hsuan Li, Chong-You Chen, Bo-Hong You, Yuan-Chin Sun, Chen-Kai Chou, Yen-Hsiang Chang, Wei-Che Lin and Guan-Yu Chen

Int. J. Mol. Sci. 2025, 26(2), 814; https://doi.org/10.3390/ijms26020814 (registering DOI) - 19 Jan 2025

Abstract

Bisphenol A (BPA) is a prevalent environmental contaminant found in plastics and known for its endocrine-disrupting properties, posing risks to both human health and the environment. Despite its widespread presence, the impact of BPA on papillary thyroid cancer (PTC) progression, especially under realistic [...] Read more.

Bisphenol A (BPA) is a prevalent environmental contaminant found in plastics and known for its endocrine-disrupting properties, posing risks to both human health and the environment. Despite its widespread presence, the impact of BPA on papillary thyroid cancer (PTC) progression, especially under realistic environmental conditions, is not well understood. This study examined the effects of BPA on PTC using a 3D thyroid papillary tumor spheroid model, which better mimicked the complex interactions within human tissues compared to traditional 2D models. Our findings demonstrated that BPA, at environmentally relevant concentrations, could induce significant changes in PTC cells, including a decrease in E-cadherin expression, an increase in vimentin expression, and reduced thyroglobulin (TG) secretion. These changes suggest that BPA exposure may promote epithelial–mesenchymal transition (EMT), enhance invasiveness, and reduce cell differentiation, potentially complicating treatment, including by increasing resistance to radioiodine therapy. This research highlights BPA’s hazardous nature as an environmental contaminant and emphasizes the need for advanced in vitro models, like 3D tumor spheroids, to better assess the risks posed by such chemicals. It provides valuable insights into the environmental implications of BPA and its role in thyroid cancer progression, enhancing our understanding of endocrine-disrupting chemicals. Full article

(This article belongs to the Special Issue Design, Synthesis, and Bioapplications of Multifunctional Materials)

16 pages, 7030 KiB

Open AccessArticle

Methylglyoxal-Stimulated Mesothelial Cells Prompted Fibroblast-to-Proto-Myofibroblast Transition

by Yu-Syuan Wei, Su-Yi Tsai, Shuei-Liong Lin, Yi-Ting Chen and Pei-Shiue Tsai

Int. J. Mol. Sci. 2025, 26(2), 813; https://doi.org/10.3390/ijms26020813 (registering DOI) - 19 Jan 2025

Abstract

During long-term peritoneal dialysis, peritoneal fibrosis (PF) often happens and results in ultrafiltration failure, which directly leads to the termination of dialysis. The accumulation of extracellular matrix produced from an increasing number of myofibroblasts was a hallmark characteristic of PF. To date, glucose [...] Read more.

During long-term peritoneal dialysis, peritoneal fibrosis (PF) often happens and results in ultrafiltration failure, which directly leads to the termination of dialysis. The accumulation of extracellular matrix produced from an increasing number of myofibroblasts was a hallmark characteristic of PF. To date, glucose degradation products (GDPs, i.e., methylglyoxal (MGO)) that appeared during the heating and storage of the dialysate are considered to be key components to initiating PF, but how GDPs lead to the activation of myofibroblast in fibrotic peritoneum has not yet been fully elucidated. In this study, mesothelial cell line (MeT-5A) and fibroblast cell line (MRC-5) were used to investigate the transcriptomic and proteomic changes to unveil the underlying mechanism of MGO-induced PF. Our transcriptomic data from the MGO-stimulated mesothelial cells showed upregulation of genes involved in pro-inflammatory, apoptotic, and fibrotic pathways. While no phenotypic changes were noted on fibroblasts after direct MGO, supernatant from MGO-stimulated mesothelial cells promoted fibroblasts to change into proto-myofibroblasts, activated fibroblasts in the first stage toward myofibroblasts. In conclusion, this study showed that MGO-stimulated mesothelial cells promoted fibroblast-to-proto-myofibroblast transition; however, additional involvement of other factors or cells (e.g., macrophages) may be needed to complete the transformation into myofibroblasts. Full article

(This article belongs to the Section Molecular Biology)

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21 pages, 3450 KiB

Open AccessArticle

Subacute PM2.5 Exposure Induces Hepatic Insulin Resistance Through Inflammation and Oxidative Stress

by Yao Lu, Wenke Qiu, Ruiwei Liao, Wenjuan Cao, Feifei Huang, Xinyuan Wang, Ming Li and Yan Li

Int. J. Mol. Sci. 2025, 26(2), 812; https://doi.org/10.3390/ijms26020812 (registering DOI) - 19 Jan 2025

Abstract

Epidemiological studies prove that type II diabetes, characterized by insulin resistance (IR), may be caused by fine particulate matter 2.5 (PM2.5). However, underlying mechanisms whereby PM2.5, particularly during short-term exposure, induces liver dysfunction leading to IR remains poorly understood. In the present study, [...] Read more.

Epidemiological studies prove that type II diabetes, characterized by insulin resistance (IR), may be caused by fine particulate matter 2.5 (PM2.5). However, underlying mechanisms whereby PM2.5, particularly during short-term exposure, induces liver dysfunction leading to IR remains poorly understood. In the present study, HepG2 cells and the BALB/c mouse model were used to explore how PM2.5 affects insulin sensitivity. The effects of subacute PM2.5 exposure on glucose metabolism were examined using commercial kits. Oxidative stress and inflammation were detected by fluorescent staining and RT-qPCR. The phosphorylation of PI3K/AKT was examined by Western blot. Subacute PM2.5 exposure induced IR, as reflected by increased glucose levels in cell supernatants, elevated insulin levels, and the impaired intraperitoneal glucose tolerance test in mice. PM2.5 induced oxidative stress, as evidenced by increased reactive oxygen species, cytochrome P450 2E1, and malondialdehyde, along with reduced superoxide dismutase 1/2 and silent information regulator 1. IL-6 and TNF-α were found to be upregulated using RT-qPCR. Western blot showed that PM2.5 inhibited the PI3K-AKT signaling pathway, indicated by the decreased phosphorylation of PI3K/AKT in HepG2 cells. Additionally, H&E staining showed only mild hepatic injury in mice liver. These results firmly suggest that subacute PM2.5 exposure induces insulin resistance through oxidative stress, inflammation, and the inhibition of the PI3K-AKT signaling pathway. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

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24 pages, 7359 KiB

Open AccessArticle

Integrative Single-Cell and Bulk RNA Sequencing Identifies a Macrophage-Related Prognostic Signature for Predicting Prognosis and Therapy Responses in Colorectal Cancer

by Shaozhuo Xie, Siyu Hou, Jiajia Chen and Xin Qi

Int. J. Mol. Sci. 2025, 26(2), 811; https://doi.org/10.3390/ijms26020811 (registering DOI) - 19 Jan 2025

Abstract

Colorectal cancer (CRC) is one of the most common malignant tumors, characterized by a high incidence and mortality rate. Macrophages, as a key immune cell type within the tumor microenvironment (TME), play a key role in tumor immune evasion and the progression of [...] Read more.

Colorectal cancer (CRC) is one of the most common malignant tumors, characterized by a high incidence and mortality rate. Macrophages, as a key immune cell type within the tumor microenvironment (TME), play a key role in tumor immune evasion and the progression of CRC. Therefore, identifying macrophage biomarkers is of great significance for predicting the prognosis of CRC patients. This study integrates scRNA-seq and bulk RNA-seq data to identify macrophage-related genes in CRC. By applying a comprehensive machine learning framework, the macrophage-related prognostic signature (MRPS) was constructed by 15 macrophage-related genes with prognostic values. The MRPS demonstrated strong predictive performance across multiple datasets, effectively stratifying high-risk and low-risk patients in terms of overall survival (OS) and disease-specific survival (DSS). Furthermore, immune analysis revealed significant differences between the high-risk and low-risk groups in immune cell infiltration levels and immune checkpoint gene expression patterns. Drug screening identified several small molecules, including Bortezomib and Mitoxantrone, as potential therapeutic options for high-risk patients. Pseudotime trajectory analysis further highlighted the potential role of genes comprising the MRPS in macrophage differentiation. This study provides a powerful tool for personalized prognosis prediction in CRC patients, offering new insights into macrophage-driven mechanisms in tumor progression and potential therapeutic strategies. Full article

(This article belongs to the Special Issue Machine Learning in Disease Diagnosis and Treatment)

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17 pages, 3202 KiB

Open AccessArticle

Quantitative Trait Loci Identification and Candidate Genes Characterization for Indole-3-Carbinol Content in Seedlings of Brassica napus

by Yiyi Xiong, Huaixin Li, Shipeng Fan, Yiran Ding, Mingli Wu, Jianjie He, Shuxiang Yan, Haibo Jia and Maoteng Li

Int. J. Mol. Sci. 2025, 26(2), 810; https://doi.org/10.3390/ijms26020810 (registering DOI) - 19 Jan 2025

Abstract

Brassica napus is a member of the cruciferous family with rich glucosinolate (GSL) content, particularly glucobrassicin (3-indolylmethyl glucosinolate, I3M), that can be metabolized into indole-3-carbinol (I3C), a compound with promising anticancer properties. To unravel the genetic mechanism influencing I3C content in rapeseed seedlings, [...] Read more.

Brassica napus is a member of the cruciferous family with rich glucosinolate (GSL) content, particularly glucobrassicin (3-indolylmethyl glucosinolate, I3M), that can be metabolized into indole-3-carbinol (I3C), a compound with promising anticancer properties. To unravel the genetic mechanism influencing I3C content in rapeseed seedlings, a comprehensive study was undertaken with a doubled haploid (DH) population. By quantitative trait loci (QTL) mapping, seven QTL that were located on A01, A07, and C04 were identified, with the most significant contribution to phenotypic variation observed on chromosome A07 (11.78%). The genes within the QTL confidence intervals (CIs) include transcription factors (TFs) and glycosyltransferases. After co-expression analysis, GSL-related regulatory network of TFs-targets was constructed and two TFs, BnaA07.ERF019 and BnaA07.NAC92, were identified as possible regulators in GSL biosynthesis. Three IGMT (glucosinolate methyltransferases) genes were found within the CIs that expressed higher in seedlings with more I3C, indicating their roles in I3C synthesis regulation. Molecular docking studies validated the binding capability of I3M to IGMTs, and those within the I3C QTL CIs have the strongest binding energy. These new discoveries offer critical insights into the genetic regulation of I3C content in rapeseed seedlings and establish a foundation for breeding high-I3C rapeseed varieties with potential health-promoting properties. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants (2nd Edition))

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