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Search Results (448)

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Keywords = hsa-miR-20a-5p

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22 pages, 1409 KB  
Article
Integrated Plasma and Glial Cell Evidence Indicates a Functional Role for hsa-miR-342-5p in Spinocerebellar Ataxia Type 7 and Its Potential Use as a Biomarker
by Verónica M. Borgonio-Cuadra, Aranza Meza-Dorantes, José Manuel Rodríguez-Pérez, Ian A. García-Aguirre, Nadia Mireya Murillo-Melo, Nonanzit Pérez-Hernández, Oscar Hernández-Hernández, Marcela Hernández-Ortega, Zazil Herrera-Carrillo, Bulmaro Cisneros and Jonathan J. Magaña
Int. J. Mol. Sci. 2026, 27(2), 683; https://doi.org/10.3390/ijms27020683 - 9 Jan 2026
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease characterized by cerebellar ataxia and retinal degeneration, caused by an abnormal expansion of CAG repeats at the ATXN7 gene. Disease onset and progression vary among patients, underscoring the need for novel tools to improve [...] Read more.
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease characterized by cerebellar ataxia and retinal degeneration, caused by an abnormal expansion of CAG repeats at the ATXN7 gene. Disease onset and progression vary among patients, underscoring the need for novel tools to improve disease monitoring. Circulating miRNAs represent a promising prognostic tool, due to their minimally invasive sampling and high stability. The aim of this study was to assess the expression of twelve circulating miRNAs associated with neurodegeneration in plasma samples from SCA7 patients and in an inducible SCA7 glial cell model. A comparison of SCA7 patients and controls revealed that nine miRNAs exhibited significantly higher expression. Furthermore, comparison of patients with different SCA7 phenotypes to controls revealed that most miRNAs were overexpressed in plasma from early-onset patients corresponding to the clinically more severe phenotype. Regarding the cell model, we identified three miRNAs that were dysregulated; however, only hsa-miR-342-5p displayed a pattern consistent with that observed in the plasma of patient. Our findings indicate that hsa-miR-342-5p is differentially expressed in the plasma of patients and the SCA7 cellular model, implying that it can serve as a biomarker and facilitate the identification of novel processes involved in SCA7. Full article
(This article belongs to the Special Issue Molecular Research on Ataxia)
20 pages, 4347 KB  
Article
Integrated ceRNA Network Analysis in Silica-Induced Pulmonary Fibrosis and Discovery of miRNA Biomarkers
by Jia Wang, Yuting Jin, Qianwei Chen, Fenglin Zhu and Min Mu
Toxics 2026, 14(1), 63; https://doi.org/10.3390/toxics14010063 - 9 Jan 2026
Abstract
Silicosis is an irreversible and progressive pulmonary fibrotic disease caused by the long-term inhalation of silica dust. The precise molecular mechanisms underlying the disease remain incompletely understood, and effective early diagnostic biomarkers are still lacking. In this study, we used a silicosis mouse [...] Read more.
Silicosis is an irreversible and progressive pulmonary fibrotic disease caused by the long-term inhalation of silica dust. The precise molecular mechanisms underlying the disease remain incompletely understood, and effective early diagnostic biomarkers are still lacking. In this study, we used a silicosis mouse model and transcriptomic sequencing to identify 2950 mRNAs, 461 lncRNAs, 81 miRNAs, and 44 circRNAs that were differentially expressed in lung tissue. Enrichment analysis revealed that these differentially expressed genes were significantly enriched in the phosphatidylinositol 3-kinase (PI3K)–protein kinase B (Akt) signaling pathway, nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) signaling pathway, and tumor necrosis factor (TNF) signaling pathway. The constructed competing endogenous RNA (ceRNA) network highlighted extensive regulatory interactions among lncRNAs/circRNAs, miRNAs, and mRNAs. Human validation showed that the expression levels of hsa-miR-215-5p and hsa-miR-146b-5p were significantly upregulated in the peripheral blood of early-stage pneumoconiosis patients, while hsa-miR-485-5p was downregulated. Logistic regression analysis revealed that hsa-miR-215-5p (OR = 1.966, 95% CI: 1.6938–2.2796, p < 0.001) and hsa-miR-146b-5p (OR = 1.9367, 95% CI: 1.697–2.201, p < 0.001) were independent risk factors for pneumoconiosis (p < 0.001). ROC curve analysis showed that both miRNAs demonstrated good diagnostic efficacy for pneumoconiosis, with AUC values of 0.9563 and 0.8876, respectively. These results provide novel insights into the complex ceRNA regulatory network involved in silicosis pathogenesis and suggest potential early, non-invasive diagnostic biomarkers. Full article
(This article belongs to the Special Issue Effects of Air Pollutants on Cardiorespiratory Health)
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20 pages, 3144 KB  
Communication
miR-204 Negatively Regulates HIV-Tat-Mediated Inflammation in Cervical Epithelial Cells via the NF-κB Axis: Insights from an In Vitro Study
by Kadambari Akolkar and Vandana Saxena
Cells 2026, 15(2), 117; https://doi.org/10.3390/cells15020117 - 9 Jan 2026
Abstract
Despite antiretroviral therapy, HIV proteins, such as Tat, persist in tissues, driving chronic inflammation. Cervical inflammation in females not only accelerates HIV progression but also increases the risk of other STIs; hence, understanding the underlying factors/regulators is vital. However, Tat-induced cervical inflammation and [...] Read more.
Despite antiretroviral therapy, HIV proteins, such as Tat, persist in tissues, driving chronic inflammation. Cervical inflammation in females not only accelerates HIV progression but also increases the risk of other STIs; hence, understanding the underlying factors/regulators is vital. However, Tat-induced cervical inflammation and its regulation are hitherto poorly understood, which we investigated using TZM-bl cells. Tat stimulation in these cervical epithelial cells significantly increased the expression of various inflammatory mediators, including cytokines (IL-1β, TNF-α, IL-6, IL-17a, GM-CSF), chemokines (MIP-1α, MIP-1β), adhesion molecules (ICAM-1, P-Selectin, E-Selectin), and ROS. Further upregulation of inflammatory mediators (NF-κB, IRAK-4) along with TLR7 was observed in Tat-stimulated cells. Interestingly, Tat stimulation decreased miR-204-5p expression in these cells, suggesting a role in regulating Tat-mediated inflammatory processes. Using a gain-of-function approach, we further observed that the overexpression of miR-204-5p reduced the expression of IL-1β, TNF-α, IL-6, MIP-1α, MIP-1β, ICAM-1, P-Selectin, and ROS in the Tat-stimulated TZM-bl cells, along with NF-κB, IRAK-1, and IRAK-4. Using Western blotting and luciferase assays, miR-204-5p was further shown to directly target NF-κB. Here, we report that HIV-1 Tat stimulation in cervical epithelial cells downregulates hsa-miR-204-5p, thereby activating the pro-inflammatory TLR7/NF-κB axis, highlighting its relevance to understanding mechanisms underlying cervical inflammation. Full article
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18 pages, 3327 KB  
Article
Non-Coding RNA Biomarkers in Prostate Cancer: Evidence Mapping and In Silico Characterization
by Lorena Albarracín-Navas, Nicolás I. Lara-Salas, Javier H. Alarcon-Roa, Maylin Almonte-Becerril, Enmanuel Guerrero and Ángela L. Riffo-Campos
Life 2026, 16(1), 95; https://doi.org/10.3390/life16010095 - 8 Jan 2026
Abstract
Non-coding RNAs (ncRNAs) have emerged as promising biomarkers for prostate cancer (PCa), yet evidence remains dispersed across heterogeneous studies and their regulatory context is seldom analyzed in an integrated manner. This study systematically maps ncRNAs reported as diagnostic biomarkers for PCa and characterizes [...] Read more.
Non-coding RNAs (ncRNAs) have emerged as promising biomarkers for prostate cancer (PCa), yet evidence remains dispersed across heterogeneous studies and their regulatory context is seldom analyzed in an integrated manner. This study systematically maps ncRNAs reported as diagnostic biomarkers for PCa and characterizes their molecular interactions through in silico analyses. A comprehensive evidence-mapping strategy across major bibliographic databases identified 693 studies, of which 58 met eligibility criteria. Differentially expressed ncRNAs were extracted and classified by RNA type. Subsequently, miRNA–target prediction, miRNA–protein interaction network construction, and functional enrichment analyses were performed to explore the regulatory landscape of miRNA-associated proteins. Results: The final dataset included 4500 participants (2871 PCa cases and 2093 controls) and reported 94 differentially expressed miRNAs, eight lncRNAs, and several circRNAs, snoRNAs, snRNAs, and piRNAs. In silico analyses predicted 13,493 miRNA–mRNA interactions converging on 4916 unique target genes, with an additional 2481 prostate tissue-specific targets. The miRNA–protein network comprised 845 nodes and 2335 edges, revealing highly connected miRNAs (e.g., hsa-miR-16-5p, hsa-miR-20a-5p) and protein hubs (QKI, YOD1, TBL1XR1; prostate-specific CDK6, ACVR2B). Enrichment analysis showed strong overrepresentation of metabolic process-related GO terms and cancer-associated KEGG pathways. Conclusions: These findings refine the list of promising ncRNA biomarkers and highlight candidates for future clinical validation. Full article
(This article belongs to the Special Issue Prostate Cancer: 4th Edition)
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18 pages, 3264 KB  
Article
The Role of the LINC01376/miR-15b-3p_R-1/FGF2 Axis in A549 and H1299 Cells EMT Induced by LMW-PAHs
by Jiali Qin, Yamin Huang, Yixuan Hu, Haitao Ma, Zhengyi Zhang, Yuanjie Li, Shiyao Jiang, Chengyun Li, Kaikai Li, Junling Wang and Xiaoping Liu
Toxics 2026, 14(1), 54; https://doi.org/10.3390/toxics14010054 - 6 Jan 2026
Viewed by 138
Abstract
Low-molecular-weight polycyclic aromatic hydrocarbons (LMW-PAHs), such as the 400 μM mixture of phenanthrene and fluorene used in this study, are prevalent environmental pollutants. Induction of epithelial–mesenchymal transition (EMT) by LMW-PAHs promote cell invasion and migration and contribute to disease pathogenesis. Long non-coding RNAs [...] Read more.
Low-molecular-weight polycyclic aromatic hydrocarbons (LMW-PAHs), such as the 400 μM mixture of phenanthrene and fluorene used in this study, are prevalent environmental pollutants. Induction of epithelial–mesenchymal transition (EMT) by LMW-PAHs promote cell invasion and migration and contribute to disease pathogenesis. Long non-coding RNAs (lncRNAs) regulate gene expression by acting as competing endogenous RNAs (ceRNAs) that sequester microRNAs (miRNAs), a mechanism important for modulating EMT. Previously, regulation of the PI3K/AKT pathway and EMT in A549 cells are shown to occur through the hsa_circ_0039929/miR-15b-3p_R-1/FGF2 axis. Here, the functional role of the related LINC01376/miR-15b-3p_R-1/FGF2 axis in LMW-PAH-induced EMT was examined in A549 and H1299 cells. The miR-15b-3p_R-1 was downregulated, whereas LINC01376 and FGF2 were upregulated following LMW-PAH exposure. LINC01376 overexpression enhanced EMT, migration, and invasion. Interactions between miR-15b-3p_R-1 and FGF2, as well as direct binding of LINC01376 to miR-15b-3p_R-1, were confirmed experimentally. The results indicate that, in LMW-PAH-treated cells, LINC01376 functions as a ceRNA to sponge miR-15b-3p_R-1, thereby elevating FGF2 expression and promoting EMT, migration, and invasion. Identification of the LINC01376/miR-15b-3p_R-1/FGF2 regulatory axis highlighted as a key mechanism in LMW-PAH-driven EMT and suggests its potential as a therapeutic target in PAH-related pathologies. Full article
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18 pages, 5869 KB  
Article
Identification of a Prognostic ceRNA Network Regulating TMBIM6 in Prostate Adenocarcinoma via Integrated Bioinformatic Analysis
by Mst Sahida Khatun, Mohammad Mamun Ur Rashid, Muhammad Kamal Hossain and Hyung-Ryong Kim
Int. J. Mol. Sci. 2026, 27(1), 213; https://doi.org/10.3390/ijms27010213 - 24 Dec 2025
Viewed by 266
Abstract
TMBIM6, a transmembrane BAX inhibitor motif containing six proteins, is correlated with tumor progression and metastasis. While its correlation in several malignancies has been shown, its expression in prostate adenocarcinoma (PRAD) is unclear. In this work, we explored, using integrated bioinformatics, a novel [...] Read more.
TMBIM6, a transmembrane BAX inhibitor motif containing six proteins, is correlated with tumor progression and metastasis. While its correlation in several malignancies has been shown, its expression in prostate adenocarcinoma (PRAD) is unclear. In this work, we explored, using integrated bioinformatics, a novel ceRNA network of TMBIM6 involved in PRAD prognosis. According to TCGA and GEO datasets, we proposed a new TMBIM6/hsa-miR-222-3p/DHRS4-AS1 ceRNA axis associated with PRAD prognosis. The network was estimated by differential expression, correlation, and survival analysis. Co-expression analysis was used to identify pathways involved in tumor progression, and immune infiltration analysis suggested that there is a correlation between the expression of TMBIM6 and the abundance of epithelial cells. Overall, these results indicate that the DHRS4-AS1/hsa-miR-222-3p/TMBIM6 axis is involved in the progression of PRAD and may act as a prognostic biomarker. Our results provide a foundation for further experimental validation and potential clinical translation. Full article
(This article belongs to the Section Molecular Informatics)
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17 pages, 1137 KB  
Article
MicroRNA Signatures and Machine Learning Models for Predicting Cardiotoxicity in HER2-Positive Breast Cancer Patients
by Maria Anastasiou, Evangelos Oikonomou, Panagiotis Theofilis, Maria Gazouli, George-Angelos Papamikroulis, Athina Goliopoulou, Vasiliki Tsigkou, Vasiliki Skandami, Angeliki Margoni, Kyriaki Cholidou, Amanda Psyrri, Konstantinos Tsioufis, Flora Zagouri, Gerasimos Siasos and Dimitris Tousoulis
Pharmaceuticals 2025, 18(12), 1908; https://doi.org/10.3390/ph18121908 - 18 Dec 2025
Viewed by 454
Abstract
Background: HER2-positive breast cancer patients receiving chemotherapy and targeted therapy (including anthracyclines and trastuzumab) face an elevated risk of cardiotoxicity, which can lead to long-term cardiovascular complications. Identifying predictive biomarkers is essential for early intervention. Circulating microRNAs (miRNAs), known regulators of gene expression [...] Read more.
Background: HER2-positive breast cancer patients receiving chemotherapy and targeted therapy (including anthracyclines and trastuzumab) face an elevated risk of cardiotoxicity, which can lead to long-term cardiovascular complications. Identifying predictive biomarkers is essential for early intervention. Circulating microRNAs (miRNAs), known regulators of gene expression and cardiovascular function, have emerged as potential indicators of cardiotoxicity. This study aims to evaluate the differential expression of circulating miRNAs in HER2-positive breast cancer patients undergoing chemotherapy and to assess their prognostic ability for therapy-induced cardiotoxicity using machine learning models. Methods: Forty-seven patients were assessed for cardiac toxicity at baseline and every 3 months, up to 15 months. Blood samples were collected at baseline. MiRNA expression profiling for 84 microRNAs was performed using the miRCURY LNA miRNA PCR Panel. Differential expression was calculated via the 2−∆∆Ct method. The five most upregulated and five most downregulated miRNAs were further assessed using univariate logistic regression and receiver operating characteristic (ROC) analysis. Five machine learning models (Decision Tree, Random Forest (RF), Support Vector Machine (SVM), Gradient Boosting Machine (GBM), k-Nearest Neighbors (KNN)) were developed to classify cardiotoxicity based on miRNA expression. Results: Forty-five miRNAs showed significant differential expression between cardiac toxic and non-toxic groups. ROC analysis identified hsa-miR-155-5p (AUC 0.76, p = 0.006) and hsa-miR-124-3p (AUC 0.75, p = 0.007) as the strongest predictors. kNN, SVM, and RF models demonstrated high prognostic accuracy. The decision tree model identified hsa-miR-17-5p and hsa-miR-185-5p as key classifiers. SVM and RF highlighted additional miRNAs associated with cardiotoxicity (SVM: hsa-miR-143-3p, hsa-miR-133b, hsa-miR-145-5p, hsa-miR-185-5p, hsa-miR-199a-5p, RF: hsa-miR-185-5p, hsa-miR-145-5p, hsa-miR-17-5p, hsa-miR-144-3p, and hsa-miR-133a-3p). Performance metrics revealed that SVM, kNN, and RF models outperformed the decision tree in overall prognostic accuracy. Pathway enrichment analysis of top-ranked miRNAs demonstrated significant involvement in apoptosis, p53, MAPK, and focal adhesion pathways, all known to be implicated in chemotherapy-induced cardiac stress and remodeling. Conclusions: Circulating miRNAs show promise as biomarkers for predicting cardiotoxicity in breast cancer patients. Machine learning approaches may enhance miRNA-based risk stratification, enabling personalized monitoring and early cardioprotective interventions. Full article
(This article belongs to the Special Issue Chemotherapeutic and Targeted Drugs in Antitumor Therapy)
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16 pages, 1133 KB  
Article
Expression Alterations and Correlative Analysis of TPH1/hsa-miR-194-5p/NEAT1 and MAOA/hsa-miR-1276/NEAT1 Axes in Pediatric Inflammatory Bowel Disease
by Mehmet Tughan Kiziltug, Mehmet Emin Erdal, Bahar Tasdelen, Ferah Tuncel and Yusuf Usta
Int. J. Mol. Sci. 2025, 26(24), 11923; https://doi.org/10.3390/ijms262411923 - 10 Dec 2025
Viewed by 337
Abstract
Pediatric inflammatory bowel disease (pIBD), comprising ulcerative colitis (UC) and Crohn’s disease (CD), involves complex mechanisms that include non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), alongside enzymes regulating serotonin metabolism. Tryptophan hydroxylase 1 (TPH1) and monoamine oxidase A [...] Read more.
Pediatric inflammatory bowel disease (pIBD), comprising ulcerative colitis (UC) and Crohn’s disease (CD), involves complex mechanisms that include non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), alongside enzymes regulating serotonin metabolism. Tryptophan hydroxylase 1 (TPH1) and monoamine oxidase A (MAOA) play critical roles in serotonin turnover and may contribute to intestinal inflammation. We investigated the expression of TPH1, MAOA, hsa-miR-194-5p, hsa-miR-1276, and the lncRNA Nuclear Enriched Abundant Transcript 1 (NEAT1) in intestinal tissue biopsies and peripheral blood from pIBD patients and controls. TPH1 was significantly elevated in the inflamed transverse colon (p = 0.034), whereas MAOA was reduced in the ileum (p = 0.041) and descending colon (p = 0.001), with further decreases in inflamed ileum (p < 0.001), ascending (p = 0.008), and descending colon (p = 0.001). Subgroup analysis revealed decreased MAOA in the ascending colon of UC patients (p = 0.011). hsa-miR-194-5p was upregulated in the transverse colon (p = 0.015), inflamed transverse (p = 0.013) and descending colon (p = 0.015), and in blood of UC patients (p = 0.01). NEAT1 expression increased in the ascending colon (p = 0.042) but decreased in the ileum (p = 0.006). Correlation analysis showed strong positive associations between TPH1 and NEAT1 in the ileum (r = 0.945, p < 0.01) and transverse colon (r = 0.609, p < 0.01). These results highlight region-specific dysregulation of serotonin-related genes and ncRNAs in pIBD, with the TPH1/miR-194-5p/NEAT1 axis potentially contributing to disease pathophysiology and warranting further mechanistic investigation. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 2253 KB  
Article
Personalizing Clozapine in Treatment-Resistant Schizophrenia: The Role of MicroRNA Biomarkers—A Pilot Study
by Dmitry N. Sosin, Aiperi K. Khasanova, Roman A. Illarionov, Anastasia K. Popova, Karin B. Mirzaev, Andrey S. Glotov, Sergey N. Mosolov and Dmitry A. Sychev
Curr. Issues Mol. Biol. 2025, 47(12), 1020; https://doi.org/10.3390/cimb47121020 - 7 Dec 2025
Viewed by 328
Abstract
Background: Clozapine remains the only antipsychotic with proven efficacy in treatment-resistant schizophrenia (TRS). However, it is effective in only about 40% of patients and is associated with numerous adverse drug reactions. Personalization of clozapine therapy is therefore of critical importance in clinical psychiatry. [...] Read more.
Background: Clozapine remains the only antipsychotic with proven efficacy in treatment-resistant schizophrenia (TRS). However, it is effective in only about 40% of patients and is associated with numerous adverse drug reactions. Personalization of clozapine therapy is therefore of critical importance in clinical psychiatry. MiRNA expression may serve as a promising exploratory marker for understanding individual variability in clozapine efficacy and safety. Methods: In this study, we determined the complete miRNA expression profile in TRS patients before initiation of clozapine and after four weeks of treatment. Results: In 15 inpatients with TRS receiving 4-week clozapine monotherapy, PANSS total decreased from 98.8 ± 13.19 to 80.47 ± 14.63 (p = 0.001). The most frequent adverse drug reactions were hypersalivation (n = 13), drowsiness/sedation (n = 12), and prolonged sleep (n = 12). We detected 24 differentially expressed miRNAs after clozapine. Changes in hsa-miR-129-5p, hsa-miR-6068, and hsa-miR-6814-5p correlated with improvements in positive symptoms; hsa-miR-128-1-5p tracked general psychopathology; and hsa-miR-6814-5p aligned with global improvement (lower PANSS total, higher PSP). Safety signals included associations of hsa-miR-4472 with asthenia/fatigue and prolonged sleep, hsa-miR-4510 with prolonged sleep, hsa-miR-615-3p and hsa-miR-4715-3p with tachycardia, and hsa-miR-329-1-5p with weight gain. Conclusions: Because miRNAs regulate the expression of a wide range of genes, including those involved in clozapine’s efficacy and safety, these findings underscore the need for further studies integrating pharmacoepigenetic and pharmacogenetic biomarkers. Our preliminary findings suggest that specific miRNAs could be candidate biomarkers associated with clozapine response in TRS, although these results require validation in larger and controlled studies. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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22 pages, 4657 KB  
Article
Multi-Transcriptome-Informed Network Pharmacology Reveals Novel Biomarkers and Therapeutic Candidates for Parkinson’s Disease
by Md. Al Amin Pappu, Md. Alamin, Md Al Noman, Most. Humaira Sultana, Md. Foysal Ahmed, Md. Sanoar Hossain, Md. Abdul Latif, Md. Fahim Faysal, AKM Azad, Salem A. Alyami, Naif Alotaibi and Md. Nurul Haque Mollah
Genes 2025, 16(12), 1459; https://doi.org/10.3390/genes16121459 - 7 Dec 2025
Viewed by 801
Abstract
Background: Parkinson’s disease (PD) is a complex neurodegenerative disorder in aged people with multifaceted molecular underpinnings. It poses a severe threat to millions of older adults worldwide. The understanding of the molecular mechanisms of PD development and the performance of its therapeutic strategies [...] Read more.
Background: Parkinson’s disease (PD) is a complex neurodegenerative disorder in aged people with multifaceted molecular underpinnings. It poses a severe threat to millions of older adults worldwide. The understanding of the molecular mechanisms of PD development and the performance of its therapeutic strategies has not yet reached a satisfactory level. Methods: This study integrated six transcriptomic datasets to uncover key genes (KGs) and their underlying pathogenic mechanisms, providing insights into potential therapeutic strategies for PD. We designed a comprehensive computational pipeline using various bioinformatics tools and databases to investigate PD-causing KGs, focusing on their functions, pathways, regulatory mechanisms, and potential therapeutic drug molecules. Results: In order to explore PD-causing KGs, we initially identified 303 differentially expressed genes (DEGs) between PD and control samples with 204 upregulated and 99 downregulated DEGs using the LIMMA approach with threshold values at Adj. p-value < 0.05 and abs (log2FC) ≥ 1.0. Then, protein–protein interaction (PPI) network analysis pinpointed seven top-ranked DEGs (GAPDH, PTEN, CCND1, APOE, ESR1, MAPK3/ERK1, and SNCA) as KGs or central modulators of PD pathogenesis. Regulatory network analysis of KGs identified 3 top-ranked transcription factors (FOXC1, NFKB1, and TFAP2A) and 6 microRNAs (hsa-let-7b-5p, hsa-mir-16-5p, and others) as the pivotal regulators of KGs. Gene Ontology (GO) terms and KEGG pathway enrichment analyses with KGs revealed several crucial biological processes, molecular functions, cellular components, and neurodegenerative pathways associated with the development of PD. Finally, the top five molecules guided by KGs (Nilotinib, Bromocriptine, Withaferin-A, Celastrol, and Donepezil) were identified as promising drug candidates against PD and validated computationally through ADME/T analysis and molecular dynamics simulation studies. Conclusions: The findings of this study may serve as valuable resources for developing effective treatment strategies for PD patients. Full article
(This article belongs to the Special Issue Novel Biomarkers of Neurodegenerative Diseases)
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22 pages, 8429 KB  
Article
SOX18 and SOX30 in NSCLC: The Epigenetic Landscape of Methylation, miRNA Regulation, and Network Crosstalk in Tumor Progression
by Mateusz Olbromski, Aleksandra Piotrowska, Monika Mrozowska, Alicja Kmiecik, Natalia Glatzel-Plucinska, Agnieszka Gomulkiewicz, Aleksandra Stepien, Klaudia Krawczynska, Piotr Blasiak, Marzenna Podhorska-Okolow and Piotr Dziegiel
Int. J. Mol. Sci. 2025, 26(23), 11669; https://doi.org/10.3390/ijms262311669 - 2 Dec 2025
Viewed by 595
Abstract
SOX (SRY-related HMG-box) transcription factors are key regulators of embryogenesis and vascular development, with emerging roles in cancer biology. In non-small-cell lung cancer (NSCLC), the contributions of SOX18 and SOX30 remain insufficiently understood, particularly regarding their epigenetic regulation and network interactions with angiogenic [...] Read more.
SOX (SRY-related HMG-box) transcription factors are key regulators of embryogenesis and vascular development, with emerging roles in cancer biology. In non-small-cell lung cancer (NSCLC), the contributions of SOX18 and SOX30 remain insufficiently understood, particularly regarding their epigenetic regulation and network interactions with angiogenic and immune-modulatory pathways. We examined 800 NSCLC specimens (400 lung adenocarcinomas, 400 squamous cell carcinomas) using immunohistochemistry, RT-qPCR, Western blotting, and spatial transcriptomics to profile SOX18, SOX30, and related signaling partners (SOX7, SOX17, MEF2C—Myocyte Enhancer Factor 2C, VCAM1—Vascular Cell Adhesion Molecule 1, p-STAT3—Signal Transducer and Activator of Transcription 3). Epigenetic regulation was assessed via droplet digital methylation-specific PCR of promoter CpG islands, while functional validation employed adenoviral delivery of hsa-miR-24-3p in NSCLC cell lines and 3D spheroid cultures. SOX18 protein was markedly overexpressed in both NSCLC subtypes, despite reduced transcript levels and consistent promoter hypermethylation, suggesting post-transcriptional regulation. In contrast, SOX30 expression was uniformly downregulated at both mRNA and protein levels, frequently linked to promoter hypermethylation, especially in squamous carcinoma. Spatial transcriptomics revealed SOX18 enrichment at tumor cores and invasive borders, co-localizing with MEF2C, VCAM1, and p-STAT3 in vascular and stromal niches, while SOX30 expression remained low across all tumor regions. Functional assays demonstrated that hsa-miR-24-3p suppressed SOX18 expression and partially modulated SOX30 and MEF2C, reinforcing a miRNA-driven regulatory axis. In summary, SOX18 and SOX30 play divergent roles in NSCLC progression: SOX18 functions as a pro-oncogenic factor driving angiogenesis and tumor–stroma interactions, while SOX30 acts as an epigenetically silenced tumor suppressor. Regulation of SOX18 by miR-24-3p highlights a potential therapeutic vulnerability. These findings underscore the significance of SOX transcription factors as biomarkers and potential targets for novel treatment strategies in NSCLC. Full article
(This article belongs to the Special Issue Advancements in Cancer Biomarkers)
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17 pages, 6149 KB  
Article
Divergent Tissue and Circulatory Expression of miR-10a in Canine Hepatocellular Carcinoma: Comparative Insights from Human HCC
by Most Shumi Akhter Shathi, Mohammad Arif, Nobuhiro Nozaki, Yutaro Ide, Yoshiyuki Akiyama, Shaohsu Wang, Masashi Takahashi and Naoki Miura
Curr. Issues Mol. Biol. 2025, 47(11), 950; https://doi.org/10.3390/cimb47110950 - 15 Nov 2025
Viewed by 642
Abstract
Canine hepatocellular carcinoma (HCC), the most common primary liver malignancy in dogs, shares many clinicopathological and molecular similarities with human HCC. However, its molecular characteristics remain insufficiently defined, and reliable diagnostic biomarkers are lacking. Elucidating dysregulated microRNAs (miRNAs) may aid in both disease [...] Read more.
Canine hepatocellular carcinoma (HCC), the most common primary liver malignancy in dogs, shares many clinicopathological and molecular similarities with human HCC. However, its molecular characteristics remain insufficiently defined, and reliable diagnostic biomarkers are lacking. Elucidating dysregulated microRNAs (miRNAs) may aid in both disease characterization and comparative oncology research. Small RNA sequencing datasets from canine HCC were analyzed to identify significantly dysregulated miRNAs with high expression and biomarker potential. The top candidate was validated in clinical tissues, cell lines, patient’s plasma and plasma exosomes using RT-qPCR. Comparative analyses were conducted using human HCC datasets (TCGA and GEO), followed by target prediction and functional enrichment to identify conserved molecular pathways. Among the 59 differentially expressed miRNAs, cfa-miR-10a showed the highest average expression level and yet was significantly downregulated in canine HCC tissues. RT-qPCR confirmed reduced expression of cfa-miR-10a in canine HCC tissues, whereas plasma exosomes showed significant enrichment, demonstrating excellent diagnostic performance (AUC = 0.94). The mature sequence of cfa-miR-10a is highly conserved with hsa-miR-10a-5p. TCGA datasets confirmed downregulation of hsa-miR-10a-5p in HCC tissues, whereas a GEO dataset showed no significant change in serum exosome levels. Target prediction and functional annotation identified 59 overlapping genes, with the Proteoglycans in cancer pathways being conserved in both species, mediated by ACTG1, SDC1, FRS2, and WNT9B. Collectively, these findings demonstrate distinct intra-tumoral and exosomal expression pattern of miR-10a in canine HCC and support its potential as a non-invasive biomarker with translational relevance. Full article
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20 pages, 5455 KB  
Article
Neuronal Enriched Extracellular Vesicle miR-122-5p as a Potential Biomarker for Alzheimer’s Disease
by Kumudu Subasinghe, Courtney Hall, Megan Rowe, Zhengyang Zhou, Robert Barber and Nicole Phillips
Cells 2025, 14(22), 1784; https://doi.org/10.3390/cells14221784 - 13 Nov 2025
Viewed by 944
Abstract
Alzheimer’s disease (AD) is the leading cause of dementia and is often prefaced by mild cognitive impairment (MCI). Detection of AD-related changes via blood-based biomarkers would enable critical therapeutic interventions early in disease progression. Neuronal enriched extracellular vesicle (NEEV) miRNAs regulate peripheral genes [...] Read more.
Alzheimer’s disease (AD) is the leading cause of dementia and is often prefaced by mild cognitive impairment (MCI). Detection of AD-related changes via blood-based biomarkers would enable critical therapeutic interventions early in disease progression. Neuronal enriched extracellular vesicle (NEEV) miRNAs regulate peripheral genes as a response to early AD brain changes and hence may have biomarker potential. Plasma NEEVs were captured from plasma samples of Mexican Americans (MAs) and Non-Hispanic Whites (NHWs) using an antibody against the neuronal surface marker CD171. miRNAs isolated from NEEVs were sequenced and analyzed using miRDeep2/DEseq2 and QIAGEN RNA-seq portal for differential expression between cognitively impaired (CI) and cognitively unimpaired controls. hsa-miR-122-5p was significantly underrepresented in the CI group in both MAs and NHWs compared to the healthy control. Other population-specific miRNAs (MAs: hsa-miR-26a-5p, hsa-let-7f-5p, and hsa-miR-139-5p, NHWs: hsa-miR-133a-3p, hsa-miR-125b-5p, and hsa-miR-100-5p) identified may have biomarker potential in AD precision medicine. Some of these differentially expressed miRNAs were associated with key AD-related comorbidities such as APOE genotype, age, and metabolic burden and were predicted to target genes within NF-κB -regulated inflammatory pathways. Together, these findings suggest that dysregulated miRNA networks may serve as a mechanistic link between comorbidity burden and AD-related neuroinflammation and neurodegeneration. Full article
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12 pages, 2619 KB  
Article
Elucidating Circular Ribonucleic Acid Mechanisms Associated with Splicing Factor 3 Inhibition in Cervical Cancer
by Amahle Nyalambisa, Babatunde Adebola Alabi, Zodwa Dlamini and Rahaba Marima
Int. J. Mol. Sci. 2025, 26(22), 10883; https://doi.org/10.3390/ijms262210883 - 10 Nov 2025
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Abstract
Cervical cancer (CCa) is the fourth leading cause of cancer-related deaths among women worldwide, with nearly 90% of cases in low- and middle-income countries, especially in Sub-Saharan Africa. This study explores the roles of circular ribonucleic acids (circRNAs), hsa_circ_0001038 and circRNA_400029, and [...] Read more.
Cervical cancer (CCa) is the fourth leading cause of cancer-related deaths among women worldwide, with nearly 90% of cases in low- and middle-income countries, especially in Sub-Saharan Africa. This study explores the roles of circular ribonucleic acids (circRNAs), hsa_circ_0001038 and circRNA_400029, and the impact of the serine/arginine-rich splicing factor 3 (SRSF3) inhibitor, theophylline, in CCa cell lines. We utilized cell cycle fluorescence-activated cell sorting (FACS) and Annexin V/propidium iodide (PI) assays to evaluate theophylline’s effects on SiHa and C33A cell lines. Results showed S-phase arrest in SiHa and G2/M arrest in C33A, with significant cytotoxic effects indicated by apoptosis analysis. Using CircAtlas, we identified micro ribonucleic acids (miRNAs) binding to hsa_circ_0001038, particularly miR-205-5p, which has a tumour-suppressive role. miRTarBase identified miR-16-5p as a key interacting miRNA for circRNA_400029. We constructed a competing endogenous ribonucleic acid (ceRNA) network, revealing multiple miRNA targets. Pathway analysis via the Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted critical signalling pathways involved in CCa oncogenesis. In conclusion, theophylline demonstrates cytotoxicity in CCa cells, suggesting its potential for repurposing in CCa theranostics, though further optimization is necessary. Full article
(This article belongs to the Section Molecular Oncology)
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21 pages, 7362 KB  
Article
Integrative Bioinformatics Analysis Reveals Key Regulatory Genes and Therapeutic Targets in Ulcerative Colitis Pathogenesis
by Sheikh Atikur Rahman, Mst. Tania Khatun, Mahendra Singh, Viplov Kumar Biswas, Forkanul Hoque, Nurun Nesa Zaman, Anzana Parvin, Mohammad Khaja Mafij Uddin, Md. Mominul Islam Sheikh, Most Morium Begum, Rakesh Arya and Hossain Md. Faruquee
Genes 2025, 16(11), 1296; https://doi.org/10.3390/genes16111296 - 1 Nov 2025
Viewed by 1268
Abstract
Background: Ulcerative colitis (UC), a chronic and relapsing form of inflammatory bowel disease (IBD), arises from a multifactorial interplay of genetic predisposition, immune dysregulation, and environmental triggers. Despite advances in understanding UC pathogenesis, the identification of reliable biomarkers and key regulatory genes remains [...] Read more.
Background: Ulcerative colitis (UC), a chronic and relapsing form of inflammatory bowel disease (IBD), arises from a multifactorial interplay of genetic predisposition, immune dysregulation, and environmental triggers. Despite advances in understanding UC pathogenesis, the identification of reliable biomarkers and key regulatory genes remains essential for unraveling disease mechanisms. Such insights are crucial for improving diagnostic precision and developing personalized therapeutic strategies. Methods: In this study, gene expression profiles from publicly available microarray and RNA-sequencing datasets were systematically analyzed using advanced bioinformatics tools. Differentially expressed genes (DEGs) were identified through statistical comparisons, and functional enrichment analyses were performed to explore their biological relevance. A total of 141 overlapping DEGs were extracted from three GEO datasets, and 20 key DEGs were further prioritized via protein–protein interaction (PPI) network construction. Hub genes, relevant signaling pathways, associated transcription factors (TFs), and microRNAs (miRNAs) linked to disease progression were identified. Potential therapeutic compounds were also predicted through computational drug–gene interaction analysis. Results: The analysis revealed a panel of novel biomarkers-TLR2, IFNG, CD163, CXCL9, CCL4, PRF1, TLR8, ARG1, LILRB2, FPR2, and PPARG-that function as key hub genes implicated in ulcerative colitis (UC) pathogenesis. These genes were associated with critical biological processes including signal transduction, inflammatory and immune responses, proteolysis, lipid transport, and cholesterol/triglyceride homeostasis. Furthermore, transcription factors (FOXC1, GABPA, GATA2, SUPT5H) and microRNAs (hsa-miR-34a-5p, hsa-miR-335-5p, hsa-miR-24-3p, hsa-miR-23a-5p, hsa-miR-26a-5p) revealed key regulatory networks influencing post-transcriptional gene regulation. Molecular docking analysis predicted Apremilast and Golotimod as promising therapeutic candidates for UC intervention. Conclusions: In conclusion, this study enhances our understanding of ulcerative colitis pathogenesis by identifying key biomarkers and therapeutic targets, paving the way for future advancements in personalized diagnosis and treatment strategies. Full article
(This article belongs to the Special Issue Computational Genomics and Bioinformatics of Cancer)
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