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19 pages, 33241 KB  
Article
Integrated Multi-Omics Analysis Reveals Activation of the PPAR Signaling Pathway by Koumiss in Experimental Ulcerative Colitis
by Guanglin Guo, Pinjie Bao, Bolag Altan and Bateer Siqin
Int. J. Mol. Sci. 2026, 27(9), 3821; https://doi.org/10.3390/ijms27093821 (registering DOI) - 25 Apr 2026
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by persistent mucosal inflammation and dysregulated immune–metabolic responses. Koumiss, a traditional fermented mare’s milk, has long been used in ethnomedicine for gastrointestinal disorders; however, its molecular mechanisms in UC remain unclear. In this [...] Read more.
Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by persistent mucosal inflammation and dysregulated immune–metabolic responses. Koumiss, a traditional fermented mare’s milk, has long been used in ethnomedicine for gastrointestinal disorders; however, its molecular mechanisms in UC remain unclear. In this study, an integrated multi-omics approach combining network pharmacology, quantitative proteomics, and molecular docking was employed to elucidate the therapeutic mechanism of koumiss powder (KP) in a dextran sulfate sodium (DSS)-induced murine colitis model. Network pharmacology identified twelve bioactive compounds targeting fourteen UC-associated proteins, predominantly enriched in the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In vivo experiments demonstrated that high-dose KP significantly alleviated disease activity, improved colon shortening and histopathological injury, reduced serum TNF-α and IL-6 levels, and restored anti-inflammatory cytokines IL-4 and IL-10. Proteomic analysis further revealed activation of the PPAR signaling pathway, with significant upregulation of Plin4 and Sorbs1. Immunofluorescence staining further confirmed that KP restored the expression of PPARA and increased the levels of Plin4 and Sorbs1 in colonic tissues. Molecular docking confirmed strong binding affinities between key koumiss-derived lipid metabolites, including 13(S)-HOTrE and stearoyl ethanolamide, and PPAR-related target proteins. Collectively, these findings demonstrate that koumiss exerts protective effects against experimental UC primarily through activation of PPAR-mediated lipid metabolic and anti-inflammatory pathways. This study provides mechanistic insight into the biological activity of koumiss and highlights the value of multi-omics integration in natural product research. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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28 pages, 5518 KB  
Article
Low-Frequency Electrical Stimulation Optimizes Neurotrophic and Neuroimmune Signaling in Bisvinyl Sulfonemethyl-Based Nerve Guidance Conduits
by Ching-Feng Su, Chung-Chia Chen, Wei-Cheng Hsu, Ming-Hsuan Lu, Joanna Pi-Jung Lee, Yung-Hsiang Chen and Yueh-Sheng Chen
Int. J. Mol. Sci. 2026, 27(9), 3820; https://doi.org/10.3390/ijms27093820 (registering DOI) - 25 Apr 2026
Abstract
Peripheral nerve injuries involving critical-sized gaps remain a major clinical challenge. Although autologous nerve grafting is considered the gold standard for peripheral nerve repair, its clinical application is limited by the availability of donor nerve tissue and the risk of donor-site morbidity, including [...] Read more.
Peripheral nerve injuries involving critical-sized gaps remain a major clinical challenge. Although autologous nerve grafting is considered the gold standard for peripheral nerve repair, its clinical application is limited by the availability of donor nerve tissue and the risk of donor-site morbidity, including sensory deficits and functional impairment. Therefore, nerve guidance conduits (NGCs) have emerged as a promising alternative when combined with bioactive modulation strategies. In this study, we evaluated bisvinyl sulfonemethyl (BVSM)-crosslinked gelatin conduits integrated with electrical stimulation (ES) at different frequencies (0, 2, 20, and 200 Hz) in a rat sciatic nerve defect model over a 4-week recovery period (n = 10 per group). Structural regeneration was assessed by morphometric analysis, electrophysiology, macrophage infiltration, CGRP immunoreactivity, retrograde Fluorogold tracing, quantitative PCR of growth factors and inflammatory cytokines, and behavioral testing. Among all stimulation paradigms, low-frequency ES at 2 Hz produced the most pronounced regenerative effects. The 2 Hz group demonstrated significantly greater axon number, axonal density, and regenerated nerve area compared with control and high-frequency groups (p < 0.05). Electrophysiological assessments revealed improved nerve conduction velocity, higher MAP amplitudes, and shorter latencies. Enhanced macrophage recruitment and elevated CGRP expression were observed, suggesting coordinated neuroimmune and neurochemical activation. Gene expression analysis indicated upregulation of neurotrophic factors and balanced inflammatory cytokine responses under low-frequency stimulation. In contrast, high-frequency stimulation (200 Hz) failed to enhance overall regeneration and showed reduced axonal metrics, suggesting possible overstimulation-associated suppression. Collectively, these findings demonstrate that BVSM-crosslinked conduits provide a stable and biocompatible regenerative scaffold, and that appropriately tuned low-frequency electrical stimulation (2 Hz) optimally enhances structural, molecular, and functional recovery. The integration of material engineering with bioelectrical modulation represents a promising strategy for next-generation bioelectronic interfaces in peripheral nerve repair. Full article
(This article belongs to the Special Issue Advancements in Regenerative Medicine Research)
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20 pages, 1847 KB  
Article
Evaluation of the Potential Anti-Inflammatory Effect of a New Coumarin–Quinoline Hybrid in LPS-Induced Neuroinflammation
by Omnia Hamdy Mohamed Shehata, Eman Abdelaziz, Hadeer Ali, Elshaymaa I. Elmongy, Reem Binsuwaidan, Wafaa M. Ibrahim, Sabreen El-Gamasy and Ibrahim El Tantawy El Sayed
Pharmaceuticals 2026, 19(5), 673; https://doi.org/10.3390/ph19050673 (registering DOI) - 25 Apr 2026
Abstract
Background/Objectives: Neuroinflammation is characterized by the sustained activation of neuroglial cells, resulting in the production of cytokines and chemokines. It is associated with neurodegenerative processes. This study aims to assess the potential mitigating effect of a novel coumarin–quinoline hybrid by evaluating oxidative [...] Read more.
Background/Objectives: Neuroinflammation is characterized by the sustained activation of neuroglial cells, resulting in the production of cytokines and chemokines. It is associated with neurodegenerative processes. This study aims to assess the potential mitigating effect of a novel coumarin–quinoline hybrid by evaluating oxidative stress, apoptosis, and pyroptosis in an experimentally induced model of neuroinflammation. Methods: The study was conducted on 60 mice, allocated into six groups of ten: Group I served as the control; Group II received the new coumarin–quinoline hybrid; Group III received lipopolysaccharide (LPS); Group IV received LPS followed by the coumarin–quinoline hybrid; Group V received LPS followed by dexamethasone (DEX); and Group VI received LPS followed by the coumarin–quinoline hybrid and DEX. The model was validated by behavioral assessments, while oxidative stress was quantified via nitric oxide (NO), malondialdehyde (MDA) levels, superoxide dismutase (SOD) activity, apoptosis by caspase-3, and pyroptosis by NLRP3. Results: An anti-inflammatory effect of a new coumarin–quinoline hybrid, evidenced by decreased NLRP3 and NF-κB expression, reduced NO and MDA production, elevated SOD activity, and brought about suppression of caspase-3. Additionally, the newly formulated coumarin–quinoline hybrid demonstrated favorable ADMET characteristics, with in silico molecular studies indicating a stable energetic profile and dynamic equilibrium. Conclusions: Findings suggest that the new coumarin–quinoline hybrid holds significant potential as an adjuvant therapeutic option for neuroinflammation. Full article
(This article belongs to the Section Medicinal Chemistry)
25 pages, 654 KB  
Review
Refining Prognostic Stratification in Clear Cell Renal Cell Carcinoma: Genomic, Tissue-Based, Circulating Biomarkers and Integrated Models
by Mariana Bianca Chifu, Simona Eliza Giușcă, Andrei Daniel Timofte, Constantin Aleodor Costin, Andreea Rusu, Ana-Maria Ipatov and Irina Draga Căruntu
Cancers 2026, 18(9), 1371; https://doi.org/10.3390/cancers18091371 (registering DOI) - 25 Apr 2026
Abstract
Clear cell renal cell carcinoma (ccRCC) is characterized by marked biological heterogeneity, which limits the prognostic accuracy of conventional clinicopathological models. Increasing attention has therefore focused on identification of biomarkers that can enhance risk stratification throughout all stages of the disease. Starting from [...] Read more.
Clear cell renal cell carcinoma (ccRCC) is characterized by marked biological heterogeneity, which limits the prognostic accuracy of conventional clinicopathological models. Increasing attention has therefore focused on identification of biomarkers that can enhance risk stratification throughout all stages of the disease. Starting from the current state of the art, this narrative review summarizes and critically appraises the evidence published over the past decade regarding prognostic biomarkers in ccRCC. The analysis is structured into four overarching domains: (i) genomic biomarkers, covering somatic alterations and transcriptomic signatures; (ii) tissue-based biomarkers, including immunohistochemical surrogates and immune microenvironment features; (iii) circulating biomarkers, such as systemic inflammation parameters and indices; and (iv) integrated predictive models, represented by emerging multi-omic approaches. Going through the broad framework of potential prognostic biomarkers, emphasis is placed on their individual and integrative value in relation to classic clinical-pathological factors and survival parameters. At the tissue level, chromosome 3p-related alterations constitute a central molecular feature of ccRCC. Among these, BAP1 loss has emerged as one of the most consistently validated indicators of aggressive tumor behavior. Disruption of the SETD2/H3K36me3 axis and immune-related biomarkers, including PD-L1 expression, have demonstrated prognostic associations in selected settings, although with variable and context-dependent performance. In the circulating compartment, plasma KIM-1 has shown prognostic relevance following nephrectomy, while postoperative detection of circulating tumor DNA (ctDNA) may identify patients at increased risk of recurrence. However, limited analytical sensitivity and methodological heterogeneity currently restrict the broader clinical applicability of ctDNA-based strategies. Systemic inflammatory indices, such as the neutrophil-to-lymphocyte ratio, show reproducible associations with outcomes but largely reflect host inflammatory status rather than tumor-specific biology. However, no single biomarker currently supports routine prognostic implementation in ccRCC. Future progress will likely depend on integrative models combining genomic, tissue-based, immune, and circulating parameters with established clinical variables. Prospective validation and clear demonstration of incremental clinical utility will be essential before such strategies can meaningfully inform therapeutic decision-making. Full article
(This article belongs to the Special Issue Advances in Renal Cell Carcinoma)
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25 pages, 3085 KB  
Article
Gestational and Lactational Atrazine Exposure Potentially Mediates Behavioral and Dopaminergic Alterations in Rat Offspring: Insights into Nurr1-Related ceRNA Regulation
by Yongjie Ma, Tianao Sun, Minglian Pan, Zhanyue Zheng, Jingxia Wei, Xinyu Yuan, Jinhao Wan, Yingjie Zhou and Yan Sun
Int. J. Mol. Sci. 2026, 27(9), 3818; https://doi.org/10.3390/ijms27093818 (registering DOI) - 25 Apr 2026
Abstract
This study aimed to investigate the molecular mechanisms underlying dopaminergic injury induced by gestational and lactational atrazine (ATR) exposure in rat offspring, with a particular focus on non-coding RNA-mediated regulation. Pregnant rats were exposed to ATR during gestation and lactation. Offspring underwent behavioral [...] Read more.
This study aimed to investigate the molecular mechanisms underlying dopaminergic injury induced by gestational and lactational atrazine (ATR) exposure in rat offspring, with a particular focus on non-coding RNA-mediated regulation. Pregnant rats were exposed to ATR during gestation and lactation. Offspring underwent behavioral testing at postnatal day 21 (PND21) and were sacrificed for midbrain tissue collection at PND28. Behavioral alterations, histopathological changes in the substantia nigra, and dopaminergic marker expression were assessed to evaluate ATR-induced neurotoxicity. Whole-transcriptome sequencing was then performed to identify differentially expressed mRNAs, miRNAs, and lncRNAs, followed by co-expression, protein–protein interaction, and competing endogenous RNA (ceRNA) network analyses. Key targets were validated by qRT-PCR. Candidate molecules identified from transcriptomic and ceRNA analyses were further examined in an ATR-induced neurotoxicity model established in RA-differentiated SK-N-SH cells. Dual-luciferase reporter, Ago2-RNA immunoprecipitation, and biotin-labeled RNA pull-down assays were used to examine putative binding relationships and molecular interactions. In addition, lentivirus-mediated Elavl4 overexpression was performed to further evaluate the role of this candidate regulator in ATR-induced Nurr1 downregulation. Gestational and lactational ATR exposure induced significant behavioral abnormalities in rat offspring. These changes were accompanied by histopathological alterations in the substantia nigra, including reduced TH immunoreactivity, as well as abnormal expression of dopaminergic markers, characterized by decreased TH and Nurr1 levels and increased α-syn expression. Together, these findings indicate the presence of dopaminergic injury. Whole-transcriptome analysis further revealed widespread dysregulation of mRNAs, miRNAs, and lncRNAs in ATR-exposed offspring. Subsequent integrative analysis suggested a potential ceRNA regulatory relationship among Elavl4, miR-301a-5p, and Nurr1, which was further supported by qRT-PCR. Dual-luciferase reporter, RIP, and RNA pull-down assays supported direct interactions between miR-301a-5p and both Elavl4 and Nurr1, as well as their association with the Ago2-containing silencing complex. Moreover, Elavl4 overexpression partially reversed ATR-induced Nurr1 downregulation in vitro. Gestational and lactational ATR exposure induced behavioral abnormalities and dopaminergic injury in rat offspring. Whole-transcriptome analysis combined with experimental validation suggests a potential association between the Elavl4/miR-301a-5p/Nurr1 ceRNA axis and ATR-induced dopaminergic injury, providing insight into the post-transcriptional mechanisms underlying developmental neurotoxicity. Full article
(This article belongs to the Section Molecular Biology)
17 pages, 10619 KB  
Article
Exosomal miR-373-3p Derived from Docetaxel-Resistant Lung Cancer Cells Targets PDCD4 to Promote Proliferation and Inhibit Apoptosis in Lung Cancer Cells
by Yuan Yuan, Buyi Zhu, Linfei Yang, Yumu Leng, Feifei Chen, Zhenhua Yang, Wei Gu and Kai Zhang
Biomedicines 2026, 14(5), 986; https://doi.org/10.3390/biomedicines14050986 (registering DOI) - 25 Apr 2026
Abstract
Background: Lung cancer ranks among the most common and deadly malignant tumors worldwide. Drug resistance is a critical factor hindering the effect of chemotherapy for lung cancer. Exosomes, as intercellular signaling molecule carriers, play an important role in carcinogenesis, metastasis and drug resistance. [...] Read more.
Background: Lung cancer ranks among the most common and deadly malignant tumors worldwide. Drug resistance is a critical factor hindering the effect of chemotherapy for lung cancer. Exosomes, as intercellular signaling molecule carriers, play an important role in carcinogenesis, metastasis and drug resistance. Our study was aimed at exploring the impact of exosomes derived from docetaxel (DTX)-resistant lung cancer cells on regulating biological behaviors of DTX-sensitive cells, further investigating the molecular mechanisms regarding exosome-mediated intercellular communication. Methods: We extracted and identified the exosomes derived from A549, A549/DTX, H1299 and H1299/DTX cells, and then analyzed the expression of exosomal miR-373-3p between DTX-sensitive and DTX-resistant cells. Cell proliferation and apoptosis experiments were verified using a CCK-8 assay, a colony formation assay, a TUNEL assay and flow cytometry. The molecular interaction between miR-373-3p and PDCD4 was evaluated using a dual-luciferase reporter assay. The function of miR-373-3p was further assessed using an in vivo mouse xenograft model. Results: We found that the exosomal miR-373-3p level from DTX-resistant A549/DTX or H1299/DTX cells significantly exceeded that from DTX-sensitive A549 or H1299 cells. In addition, both exosomes derived from DTX-resistant lung cancer cells and miR-373-3p mimics could promote the proliferation of DTX-sensitive cells and inhibit their apoptosis. Moreover, we identified PDCD4 as a key target gene of miR-373-3p, which could induce the malignant behaviors of DTX-sensitive cells by reducing PDCD4 expression. Conclusions: Our results demonstrated that DTX-resistant lung cancer cells could transfer miR-373-3p to DTX-sensitive cells through exosomes, where miR-373-3p could exert its carcinogenic effect via targeting PDCD4. Full article
(This article belongs to the Special Issue RNA Therapy in Cancer Treatment: From Design to Clinical Translation)
16 pages, 20185 KB  
Article
Molecular Signatures of Maladaptive Plasticity in the Amygdala in a Rat Model of Chronic Neuropathic Pain
by Peyton Presto, Julian Cardenas, Christian Bustamante, Brent R. Kisby, Guangchen Ji, Olga Ponomareva, Volker Neugebauer and Igor Ponomarev
Cells 2026, 15(9), 775; https://doi.org/10.3390/cells15090775 (registering DOI) - 25 Apr 2026
Abstract
Chronic pain, a complex multidimensional disorder, remains a major healthcare issue and a therapeutic challenge. Neuropathic pain is a chronic pain condition that results from damage or dysfunction in the nervous system. While mechanisms of neuropathic pain at the peripheral and spinal cord [...] Read more.
Chronic pain, a complex multidimensional disorder, remains a major healthcare issue and a therapeutic challenge. Neuropathic pain is a chronic pain condition that results from damage or dysfunction in the nervous system. While mechanisms of neuropathic pain at the peripheral and spinal cord level have been extensively studied, pain mechanisms in the brain remain underexplored. The amygdala, a limbic brain region, has emerged as a critical brain area for the emotional–affective dimension of pain and pain modulation. Amygdala neuroplasticity has been associated with pain states, but the exact molecular and cellular mechanisms underlying these states and the transition from acute to chronic pain are not well understood. Here, we used the spinal nerve ligation (SNL) model of neuropathic pain in male rats to investigate changes in gene expression in the amygdala at the chronic pain stage using RNA sequencing (RNA-Seq). Two amygdala nuclei, the basolateral (BLA) and central (CeA), were investigated in a hemisphere-dependent manner. We used an integrative approach that focuses on functional significance and cell-type specificity of differentially expressed genes (DEGs) to nominate mechanistic targets for central regulation of chronic pain. Our integrative transcriptomic and bioinformatic analyses identified individual genes (e.g., Cxcl10, Cxcl12, Mbp, Plp1, Mag, Mog, Slc17a6, Gad1, and Sst), molecular pathways (e.g., cytokine-mediated signaling pathway), biological processes (e.g., myelination, synaptic transmission), and specific cell types (e.g., oligodendrocytes, glutamatergic, and GABAergic neurons) affected by chronic pain. Our results also provide some evidence for the emerging concept of hemispheric lateralization of pain processing in the amygdala. Overall, our study proposes oligodendrocyte dysfunction in the amygdala, neuroimmune signaling in the CeA, and glutamatergic neurotransmission in the BLA as key processes and potential therapeutic targets for the management of chronic neuropathic pain. Full article
(This article belongs to the Section Cellular Neuroscience)
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32 pages, 875 KB  
Systematic Review
Genetic Determinants of Stress Reactivity in Pregnancy: A Systematic Review and Meta-Analysis: Implications for Maternal and Fetal Health
by Socol Ioana Denisa, Socol Flavius George, Farcaș Simona Sorina, Dumitriu Bogdan-Ionel, Dumitriu Alina-Iasmina, Antal Andreea, Boarta Aris, Iacob Daniela and Andreescu Nicoleta Ioana
Genes 2026, 17(5), 509; https://doi.org/10.3390/genes17050509 (registering DOI) - 25 Apr 2026
Abstract
Background: Gestation is a period of significant biological plasticity where the intrauterine environment influences fetal development via “fetal programming”. This study systematically reviews and meta-analyzes the association between genetic determinants—specifically the NR3C1, FKBP5, and CRHR1 genes, chosen for their pivotal [...] Read more.
Background: Gestation is a period of significant biological plasticity where the intrauterine environment influences fetal development via “fetal programming”. This study systematically reviews and meta-analyzes the association between genetic determinants—specifically the NR3C1, FKBP5, and CRHR1 genes, chosen for their pivotal role in the functional regulation and feedback sensitivity of the hypothalamic–pituitary–adrenal (HPA) axis—and stress reactivity during pregnancy. Methods: Following PRISMA guidelines, a systematic search was conducted across PubMed, Scopus, and Web of Science, yielding an initial total of 1430 records. After removing duplicates and screening 669 studies, a total of 34 primary observational studies were included in the systematic review and qualitative synthesis. For the quantitative synthesis, 27 articles provided sufficient data, resulting in k = 39 independent effect sizes analyzed via a mixed-effects model to account for tissue-specific and cohort-specific outcomes. Results: Systematic analysis reveals that maternal psychosocial stress significantly correlates with NR3C1 hypermethylation, acting as a biological mediator for neonatal cortisol dysregulation and hippocampal volume reduction. The FKBP5 rs1360780 polymorphism emerged as a key moderator of structural vulnerability, showing a “double-hit” effect when combined with epigenetic alterations. Furthermore, the study identifies sex-specific susceptibility, with divergent placental trajectories for male and female fetuses. Meta-analytic estimates confirmed the robustness of these associations (Rosenthal Fail-Safe N = 431,000), despite a general trend toward statistical significance (p = 0.079) in heterogeneous cohorts. Conclusions: The findings underscore a stable link between genetic determinants and prenatal stress reactivity. The interaction between molecular predisposition and environmental factors defines the health of the mother–infant dyad. These results advocate for a transition toward Precision Prenatal Medicine, integrating polygenic risk scores and epigenetic monitoring to implement early, targeted preventive interventions. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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14 pages, 1862 KB  
Article
Discovery of Structurally Distinct Covalent KRAS G12C Inhibitor Scaffolds Through Large-Scale In Silico Screening and Experimental Validation
by Glen J. Weiss, Joseph C. Loftus, David W. Mallery and Nhan L. Tran
Cancers 2026, 18(9), 1367; https://doi.org/10.3390/cancers18091367 (registering DOI) - 25 Apr 2026
Abstract
Background/Objectives: KRAS G12C mutations define a clinically actionable subset of solid tumors, particularly non–small cell lung cancer. Clinical responses to approved covalent inhibitors remain limited by intrinsic and acquired resistance, highlighting the need for structurally distinct inhibitor scaffolds to expand therapeutic options. The [...] Read more.
Background/Objectives: KRAS G12C mutations define a clinically actionable subset of solid tumors, particularly non–small cell lung cancer. Clinical responses to approved covalent inhibitors remain limited by intrinsic and acquired resistance, highlighting the need for structurally distinct inhibitor scaffolds to expand therapeutic options. The objective of this study was to identify novel covalent binders targeting the KRAS G12C switch-II pocket through large-scale in silico screening and experimental validation. Methods: More than 1.9 million small molecules from diverse commercial libraries were screened using covalent docking, followed by multi-stage refinement incorporating molecular dynamics simulations, MM/GBSA free-energy estimation, and cancer-focused QSAR modeling. Results: This integrated workflow yielded 50 prioritized compounds spanning several chemically distinct scaffold classes. These candidates displayed favorable predicted binding energetics, stable ligand-protein interactions over extended simulation timescales, and low structural similarity to clinically approved KRAS G12C inhibitors sotorasib and adagrasib. Benchmarking against these clinical agents, using identical computational parameters, yielded comparable predicted binding energies for several candidate molecules. In cellular NanoBRET target-engagement assays, selected scaffolds, including K788-7251 and AN-989/14669131, exhibited sub-micromolar engagement of KRAS G12C with minimal endothelial cytotoxicity. Conclusions: Collectively, these findings identify structurally distinct, KRAS G12C inhibitor chemotypes and provide tractable starting points for the development of next-generation targeted therapies. Full article
(This article belongs to the Section Cancer Drug Development)
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25 pages, 28621 KB  
Article
Empagliflozin Ameliorates Diabetic Cardiomyopathy by Inhibiting Ferroptosis via SIRT3: Mechanisms and Therapeutic Implications
by Taoshan Feng, Meilian Liu, Dan Zhong, Xusan Xu, Zhengqiang Luo, Wensen Zhang, Yajun Wang, Riling Chen, Xiaoming Chen and Guoda Ma
Antioxidants 2026, 15(5), 543; https://doi.org/10.3390/antiox15050543 (registering DOI) - 24 Apr 2026
Abstract
Empagliflozin (EMPA), a sodium-glucose cotransporter 2 inhibitor, has garnered attention for its cardiovascular benefits beyond glycemic control. Ferroptosis, a novel form of regulated cell death, contributes to the pathogenesis of diabetic cardiomyopathy (DCM). However, whether EMPA mitigates DCM by suppressing ferroptosis remains unclear. [...] Read more.
Empagliflozin (EMPA), a sodium-glucose cotransporter 2 inhibitor, has garnered attention for its cardiovascular benefits beyond glycemic control. Ferroptosis, a novel form of regulated cell death, contributes to the pathogenesis of diabetic cardiomyopathy (DCM). However, whether EMPA mitigates DCM by suppressing ferroptosis remains unclear. Here, Type 2 diabetic db/db mice were used to establish a DCM model and treated with EMPA (10 mg/kg/day) for 12 weeks. EMPA significantly improved cardiac function, reduced myocardial fibrosis, and attenuated ferroptosis, concomitant with upregulated silent information regulator 3 (SIRT3) expression. In the rat cardiomyocytes (H9c2 cells) exposed to high glucose and palmitic acid, EMPA treatment or SIRT3 overexpression alleviated oxidative stress, mitochondrial dysfunction, and ferroptosis. Mechanistically, molecular docking, molecular dynamics simulation, cellular thermal shift assay and drug affinity responsive target stability assay confirmed that SIRT3 is the drug target of EMPA, stabilizing its protein levels and reducing acetylated p53 expression. Notably, SIRT3 silencing abolished EMPA’s beneficial effects on oxidative stress and ferroptosis. Our findings demonstrate that EMPA exerts cardioprotective effects by inhibiting oxidative stress and ferroptosis in cardiomyocytes, which is mediated by SIRT3. This study provides novel insights into the mechanisms underlying EMPA’s therapeutic effects in DCM. Full article
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22 pages, 11126 KB  
Article
Cell Type-Specific Downregulation of Dnmt3a in Nucleus Accumbens Oligodendrocytes Prevents Myelin Damage and Reduces Susceptibility to Social Stress in Male Mice
by Yifan Niu, Kaiwei Li, Kaiyuan Zhan, Mingshan Pi, Qi Xiong, Ji Wang, Xiaochuan Wang, Xiji Shu, Yiyuan Xia and Mengbing Huang
Biomolecules 2026, 16(5), 639; https://doi.org/10.3390/biom16050639 - 24 Apr 2026
Abstract
Background: Chronic stress is a major contributing factor to mood disorders, including depression and anxiety; however, the molecular mechanisms underlying individual differences in susceptibility to such disorders remain poorly understood. DNA methyltransferase 3a (Dnmt3a), a key epigenetic regulator, has been increasingly implicated in [...] Read more.
Background: Chronic stress is a major contributing factor to mood disorders, including depression and anxiety; however, the molecular mechanisms underlying individual differences in susceptibility to such disorders remain poorly understood. DNA methyltransferase 3a (Dnmt3a), a key epigenetic regulator, has been increasingly implicated in stress-related neurobiological adaptations. In this study, we employed a well-established mouse model of chronic social defeat stress (CSDS) to investigate the functional role of Dnmt3a in modulating individual susceptibility to social stress. Methods: Male C57BL/6J mice were exposed to chronic/submaximal social defeat stress (CSDS/SSDS). AAV vectors were used to achieve Dnmt3a overexpression or global and oligodendrocyte-specific knockdown in the nucleus accumbens (NAc). Behavioral tests, including social interaction, open field, and elevated zero maze, were conducted alongside Western blotting and immunofluorescence assays. Results: CSDS selectively increased Dnmt3a expression in NAc oligodendrocytes of stress-susceptible mice. Overexpression of Dnmt3a in the NAc enhanced susceptibility to stress, whereas its knockdown conferred resilience, without affecting baseline behaviors. Dnmt3a negatively regulated myelin basic protein (MBP) and dopamine D1 receptor expression. Stress-susceptible mice exhibited shortened myelinated segments and reduced D1 receptor levels, while D2 receptor expression remained unchanged. Conclusions: Dnmt3a in NAc oligodendrocytes modulates susceptibility to social stress through a Dnmt3a-MBP/D1 receptor-NAc pathway, highlighting a critical glia-neuron interaction. This mechanism extends our understanding of the neurobiological basis of stress-related disorders and positions Dnmt3a as a promising therapeutic target for developing precision interventions or biomarkers. Full article
(This article belongs to the Section Molecular Medicine)
20 pages, 4142 KB  
Article
Integrated Molecular Docking and Network-Based Analysis Reveals Multitarget Interaction Patterns of Nutraceutical Compounds in Intervertebral Disc Degeneration
by Ersin Guner, Omer Faruk Yilmaz, Muharrem Furkan Yuzbasi, Mehmet Albayrak, Fatih Ugur and Ibrahim Yilmaz
Biomedicines 2026, 14(5), 983; https://doi.org/10.3390/biomedicines14050983 - 24 Apr 2026
Abstract
Background: Intervertebral disc degeneration (IVDD) is driven by the interplay between inflammatory signaling, extracellular matrix (ECM) degradation, and impaired cellular adaptation. Although several nutraceutical compounds have been reported to exert protective effects in IVDD-related models, their multitarget mechanisms within integrated molecular networks [...] Read more.
Background: Intervertebral disc degeneration (IVDD) is driven by the interplay between inflammatory signaling, extracellular matrix (ECM) degradation, and impaired cellular adaptation. Although several nutraceutical compounds have been reported to exert protective effects in IVDD-related models, their multitarget mechanisms within integrated molecular networks remain incompletely characterized. Methods: An in silico framework integrating molecular docking with network-based analyses was employed to evaluate resveratrol, quercetin, melatonin, curcumin, and baicalein against a predefined panel of IVDD-associated targets, within an exploratory in silico framework. Binding affinities and interaction profiles were assessed using molecular docking, followed by protein–protein interaction (PPI) network construction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and hub gene identification. Results: Docking analyses revealed binding energies ranging from −4.59 to −13.25 kcal/mol, with curcumin and quercetin showing plausible docking poses across a subset of selected targets under the applied protocol. Network analysis showed a highly interconnected structure centered on key inflammatory regulators, including NFKB1, IL6, TNF, IL1B, STAT3, and NLRP3, together with ECM-associated components such as ACAN, COL2A1, SOX9, MMP13, and ADAMTS5. Enrichment analyses further suggested significant associations with inflammatory signaling pathways, cytokine regulation, and ECM organization. Conclusions: These findings are compatible with a distributed, multitarget interaction pattern of nutraceutical compounds within IVDD-associated molecular networks. By integrating molecular docking with network-based analyses, this study offers a system-level framework for interpreting previously reported effects within a disease-specific context. Docking-derived interaction patterns should be interpreted as qualitative and exploratory observations, as docking scores represent model-dependent estimates and do not establish comparable pharmacological effects across heterogeneous targets. The results should be considered hypothesis-generating and require experimental validation. Full article
(This article belongs to the Section Drug Discovery, Development and Delivery)
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22 pages, 7939 KB  
Article
Machine Learning-Based Identification of Hub Genes and Temporal Regulation Mechanisms in Zebrafish Fin Regeneration
by Xiaoying Jiang, Junli Zheng, Yuqin Shu, Yinjun Jiang and Cheng Guo
Genes 2026, 17(5), 503; https://doi.org/10.3390/genes17050503 (registering DOI) - 24 Apr 2026
Abstract
Background/Objectives: Zebrafish fin regeneration serves as a classic model for investigating vertebrate tissue regeneration, yet the core regulatory networks and their crosstalk with the immune microenvironment remain incompletely characterized. This study aimed to identify hub genes, and elucidate the underlying molecular mechanisms [...] Read more.
Background/Objectives: Zebrafish fin regeneration serves as a classic model for investigating vertebrate tissue regeneration, yet the core regulatory networks and their crosstalk with the immune microenvironment remain incompletely characterized. This study aimed to identify hub genes, and elucidate the underlying molecular mechanisms and immune microenvironment dynamics during zebrafish fin regeneration. Methods: We integrated multiple bulk RNA-seq datasets of zebrafish fin regeneration from the GEO database, followed by data standardization with batch effect removal. Hub genes were screened via differential expression analysis, weighted gene co-expression network analysis (WGCNA), and predictive models constructed with 13 classic machine learning algorithms. Functional enrichment, time-ordered gene co-expression network (TO-GCN) method, immune infiltration analyses and RT-qPCR validation were further performed. Results: We identified upregulated differentially expressed genes, regeneration-correlated gene modules and their overlapping genes, including 82 candidate genes and 10 hub genes enriched in cytoskeleton remodeling, extracellular matrix organization, and focal adhesion. Temporal analysis uncovered hierarchical gene regulation and functional switching during regeneration. Hub gene expression was significantly correlated with the infiltration of B cells, M1/M2 macrophages and CD8+ T cells, revealing a stage-specific immune microenvironment. RT-qPCR validation showed high consistency with the multi-omics data. Conclusions: This study provides potential gene targets for understanding zebrafish fin regeneration, and offers a valuable reference for investigating the crosstalk between regulatory networks and the immune microenvironment in vertebrate tissue regeneration. Full article
(This article belongs to the Section Bioinformatics)
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15 pages, 1307 KB  
Article
Sustainable Production of Chitosan from Mussel Shells with Upcycling of Demineralization Effluent into Calcium Formate
by Chaowared Seangarun, Banjong Boonchom, Somkiat Seesanong, Wimonmat Boonmee, Sirichet Punthipayanon, Nongnuch Laohavisuti and Pesak Rungrojchaipon
Int. J. Mol. Sci. 2026, 27(9), 3809; https://doi.org/10.3390/ijms27093809 - 24 Apr 2026
Abstract
This study proposes a sustainable, integrated biorefinery approach to valorize mussel shell waste into high-value products, including chitin, chitosan, and calcium formate. Formic acid was employed as an effective demineralizing agent, enabling not only efficient mineral removal but also the direct conversion of [...] Read more.
This study proposes a sustainable, integrated biorefinery approach to valorize mussel shell waste into high-value products, including chitin, chitosan, and calcium formate. Formic acid was employed as an effective demineralizing agent, enabling not only efficient mineral removal but also the direct conversion of the demineralization effluent into value-added calcium formate. The sequential extraction processes, demineralization, deproteinization, and decolorization, successfully yielded purified chitin (PCH), which was subsequently deacetylated to produce chitosan (CTS) with a degree of deacetylation of 85% and a molecular weight of 75 kDa. The physicochemical properties of all products were characterized using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM). FTIR and XRD analyses confirmed the successful extraction of chitin and chitosan, demonstrating the feasibility of mussel shells as an alternative biopolymer source. In parallel, calcium formate (CCF) was obtained from the demineralization effluent with a yield of 94.19%, and its formation was verified by FTIR and XRD. Elemental analysis by XRF exhibited 98.3% CaO with minimal non-toxic impurities. The TGA/DTG profiles of CCF exhibited a well-defined two-step thermal decomposition, confirming its anhydrous form. Overall, this environmentally benign process enables the simultaneous production of multiple value-added products while significantly improving resource utilization and reducing waste generation. The proposed integrated biorefinery model offers a promising, economically viable pathway for marine biomass valorization, aligned with the Bio-Circular-Green (BCG) economy concept. Full article
(This article belongs to the Section Materials Science)
20 pages, 651 KB  
Review
A Serotoninomic Framework for Reproductive and Integrative Toxicology: Molecular, Neurochemical, and Behavioural Perspectives on Permethrin Exposure
by Francisco Jiménez-Trejo, Liliana Carmona-Aparicio, Elvia Coballase-Urrutia, Katia L. Jiménez-García, Cristian Arriaga-Canon and Luis A. Herrera
Toxics 2026, 14(5), 365; https://doi.org/10.3390/toxics14050365 - 24 Apr 2026
Abstract
Serotoninomics, a nascent emerging discipline within the field of omics, provides a transdisciplinary framework for understanding reproductive toxicology via serotonergic signalling. This research investigates the neuroendocrine effects of permethrin, a commonly used pyrethroid insecticide often considered to pose a low risk to humans, [...] Read more.
Serotoninomics, a nascent emerging discipline within the field of omics, provides a transdisciplinary framework for understanding reproductive toxicology via serotonergic signalling. This research investigates the neuroendocrine effects of permethrin, a commonly used pyrethroid insecticide often considered to pose a low risk to humans, and positions it as a model compound for evaluating reproductive susceptibility beyond conventional endocrine endpoints. It is hypothesized that serotonin, traditionally examined in neuropsychiatric contexts, plays an essential role in gonadal function, hormonal regulation, and emotional resilience. Although permethrins are generally regarded as safe, acute exposure may subtly interfere with serotonergic pathways, potentially resulting in molecular, biochemical, behavioural, and reproductive alterations. These effects could extend beyond immediate exposure, including during gestation, considering permethrins’ ability to cross the placental barrier and influence foetal development. By synthesizing evidence across molecular, organismal, and environmental domains, we advocate for a serotonergic approach to facilitate a more comprehensive assessment of risk and resilience. We emphasize the importance of fostering a transdisciplinary dialogue to redefine reproductive health through the perspectives of serotonergic vulnerability and systemic resilience. Full article
(This article belongs to the Special Issue Neuronal Injury and Disease Induced by Environmental Toxicants)
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