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Search Results (594)

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Keywords = micro and small RNA analysis

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22 pages, 3611 KB  
Article
Hypoxia-Associated Alternative Polyadenylation of CARM1 and Tumor Microenvironment Alterations in Non-Small Cell Lung Cancer
by Xinyu Qin, Chunlong Zhang, Sijia Wu, Jing Lu, Guohua Wang and Yang Li
Genes 2026, 17(5), 505; https://doi.org/10.3390/genes17050505 (registering DOI) - 24 Apr 2026
Abstract
Background: Tumor hypoxia in non-small cell lung cancer (NSCLC) promotes malignant progression and treatment resistance by enhancing abnormal vasculature, invasiveness, and metastasis. However, the molecular mechanisms underlying hypoxia-driven tumor progression remain incompletely understood. Methods: In this study, patient samples, cell lines, single-cell transcriptomic [...] Read more.
Background: Tumor hypoxia in non-small cell lung cancer (NSCLC) promotes malignant progression and treatment resistance by enhancing abnormal vasculature, invasiveness, and metastasis. However, the molecular mechanisms underlying hypoxia-driven tumor progression remain incompletely understood. Methods: In this study, patient samples, cell lines, single-cell transcriptomic data, and spatial transcriptomic data were comprehensively analyzed to investigate hypoxia-associated molecular alterations in NSCLC. Results: A global trend toward shortened 3’ untranslated regions (3’UTRs) was observed in hypoxic tumors. Analysis of hypoxia-related alternative polyadenylation (APA) events revealed preferential usage of proximal polyadenylation sites (poly(A) sites, PASs) in CARM1. Shortening of the CARM1 3’UTR was associated with hypoxia and may serve as a candidate biomarker. This APA event may reduce putative microRNA (miRNA) binding sites and contribute to increased CARM1 expression, while potentially influencing the expression of hypoxia-related genes such as SELENBP1. Drug sensitivity analysis further suggested that patients with shorter CARM1 3’UTRs may exhibit differential responses to cisplatin chemotherapy. Moreover, single-cell and spatial transcriptomic analyses demonstrated enhanced interactions between hypoxic tumor cells and fibroblasts, highlighting a potential role for APA in remodeling the hypoxic tumor microenvironment. Conclusions: Our findings identify hypoxia-related APA features and characterize hypoxia-associated alterations within the NSCLC tumor microenvironmen, providing new insights into the molecular landscape of hypoxia-associated tumor progression. Full article
(This article belongs to the Section Bioinformatics)
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16 pages, 1390 KB  
Article
Upregulation of miR-589-3p Contributes to Lung Adenocarcinoma Progression Through Inhibition of WWC2
by Sultan F. Kadasah
Cancers 2026, 18(9), 1349; https://doi.org/10.3390/cancers18091349 - 23 Apr 2026
Abstract
Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer and remains a leading cause of cancer-related mortality worldwide. MicroRNAs (miRNAs) are critical regulators of tumor progression; however, the biological role and molecular mechanisms of miR-589-3p in LUAD remain unclear. [...] Read more.
Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer and remains a leading cause of cancer-related mortality worldwide. MicroRNAs (miRNAs) are critical regulators of tumor progression; however, the biological role and molecular mechanisms of miR-589-3p in LUAD remain unclear. In this study, the expression levels of miR-589-3p and WWC2 were analyzed using The Cancer Genome Atlas lung adenocarcinoma (TCGA-LUAD) datasets via the UALCAN platform. Flow cytometric apoptosis analysis and functional assays including CCK-8, colony formation, AO/EB staining, and Transwell invasion assays were performed in LUAD cell lines. The interaction between miR-589-3p and WWC2 was validated using dual-luciferase reporter assays, Western blotting, and rescue experiments. miR-589-3p expression was significantly elevated in LUAD tissues compared with normal lung tissues (p < 0.05) and was positively associated with an advanced tumor stage and lymph node metastasis (p < 0.05). Inhibition of miR-589-3p significantly suppressed proliferation and colony formation (p < 0.05), reduced invasive capacity (p < 0.05), and markedly increased apoptosis (p < 0.01) in LUAD cells. Dual-luciferase reporter assays confirmed WWC2 as a direct target of miR-589-3p, with miR-589-3p mimics significantly reducing WWC2 wild-type reporter activity (p < 0.05). WWC2 expression was significantly downregulated in LUAD tissues (p < 0.05), and WWC2 knockdown reversed the anti-proliferative, pro-apoptotic, and anti-invasive effects induced by miR-589-3p inhibition (p < 0.01). These findings demonstrate that miR-589-3p promotes lung adenocarcinoma progression by directly suppressing WWC2. The miR-589-3p/WWC2 axis represents a novel molecular mechanism contributing to LUAD malignancy and may provide a foundation for future mechanistic and translational studies. Full article
(This article belongs to the Section Cancer Biomarkers)
17 pages, 28610 KB  
Article
Decoding Prognostic Signatures in Brain Metastatic Non-Small-Cell Lung Cancer via Integrated Multi-Omics and Network Analysis
by Prithvi Singh, Ravins Dohare, Tarique Sarwar, Hajed Obaid A. Alharbi and Arshad Husain Rahmani
Int. J. Mol. Sci. 2026, 27(8), 3598; https://doi.org/10.3390/ijms27083598 - 17 Apr 2026
Viewed by 200
Abstract
Non-small-cell lung cancer (NSCLC) constitutes approximately all lung cancers (LCs), and metastasis remains a major challenge in its treatment, thus necessitating the detection of novel molecular players involved in this process. In this study, we performed a comprehensive analysis of microarray and RNA-seq [...] Read more.
Non-small-cell lung cancer (NSCLC) constitutes approximately all lung cancers (LCs), and metastasis remains a major challenge in its treatment, thus necessitating the detection of novel molecular players involved in this process. In this study, we performed a comprehensive analysis of microarray and RNA-seq cohorts extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) and associated them with metastasis-related genes involved in brain metastasis (BM) in NSCLC. We thus identified differentially expressed metastatic genes (DEMGs) and constructed a protein–protein interaction network (PPIN) using these DEMGs. These DEMGs were further analyzed for associations with patient age, gender, and tumor stage, and the significant impact of specific genes on overall survival (OS) was assessed to determine the prognostic significance of the identified targets. We finally constructed a three-node microRNA (miRNA) feed-forward loop (FFL) involving miR-23b-3p, CD44, and five transcription factors (TFs) [EOMES, FOS, FOSL1, GLIS3, TP63] specific to NSCLC metastasis. Further mutational analysis of these FFL elements revealed that all were altered in the patient samples analyzed. Thus, our study identified potential genomic drivers that may play crucial roles in NSCLC BM. Overall, it provides valuable insights for the discovery of novel therapeutic targets in the management of NSCLC metastasis. However, further in vitro and in vivo experimentations are needed to justify the prognostic role of NSCLC biomarkers in BM pathogenesis. Full article
(This article belongs to the Special Issue Advances in Multi-Omics in Cancer: Second Edition)
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13 pages, 818 KB  
Article
Comparative Circulating microRNA Profiling in Dogs with Pyometra and Other Inflammatory Diseases
by Myeong-Seon Jeong, Gyo-Bin Choo, Bum-Kyu Choi, Mun-Ik Lee and Ju-Hyun An
Vet. Sci. 2026, 13(4), 387; https://doi.org/10.3390/vetsci13040387 - 16 Apr 2026
Viewed by 199
Abstract
Circulating microRNAs (miRNAs) regulate inflammatory responses and have emerged as potential minimally invasive biomarkers of disease. However, comprehensive profiling of circulating miRNAs in naturally occurring inflammatory conditions in dogs remains limited. This study aimed to characterize circulating miRNA expression profiles using small RNA [...] Read more.
Circulating microRNAs (miRNAs) regulate inflammatory responses and have emerged as potential minimally invasive biomarkers of disease. However, comprehensive profiling of circulating miRNAs in naturally occurring inflammatory conditions in dogs remains limited. This study aimed to characterize circulating miRNA expression profiles using small RNA sequencing in plasma samples from dogs with pyometra, non-reproductive inflammatory diseases, and healthy controls to identify shared and disease-related miRNA alterations. Global expression patterns, including heatmap and principal component analysis (PCA), demonstrated separation between healthy controls and diseased dogs. Based on DESeq2 analysis (adjusted p-value < 0.05), 39 circulating miRNAs were commonly altered in both pyometra and non-reproductive inflammatory diseases compared with healthy controls. A total of 83 miRNAs were differentially expressed in the pyometra group, whereas 4 miRNAs were differentially expressed in the non-reproductive inflammatory disease group. Direct comparison between the two disease groups further identified three circulating miRNAs—cfa-miR-885, cfa-miR-599, and cfa-miR-122—as significantly differentially expressed. These findings suggest that circulating miRNA profiles in dogs with pyometra reflect both systemic inflammation and condition-related molecular variation. Further studies with larger cohorts are warranted to validate the clinical relevance of these candidate circulating miRNAs. Full article
(This article belongs to the Section Veterinary Reproduction and Obstetrics)
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19 pages, 1451 KB  
Article
Circadian Phase Shapes Muscle-Derived Extracellular Vesicle microRNA Profiles with Context-Dependent Modulation by Exercise in High-Fat-Diet-Fed Mice
by Shuo Wang, Noriaki Kawanishi, Cong Wu, Haruki Kobori and Katsuhiko Suzuki
Nutrients 2026, 18(7), 1076; https://doi.org/10.3390/nu18071076 - 27 Mar 2026
Viewed by 452
Abstract
Background: Extracellular vesicles (EVs) released from skeletal muscle mediate metabolic communication via microRNAs (miRNAs). While both circadian rhythms and exercise influence metabolism, the joint modulation of the muscle-derived EV miRNA landscape by circadian rhythms and chronic exercise remains undefined, particularly under the metabolic [...] Read more.
Background: Extracellular vesicles (EVs) released from skeletal muscle mediate metabolic communication via microRNAs (miRNAs). While both circadian rhythms and exercise influence metabolism, the joint modulation of the muscle-derived EV miRNA landscape by circadian rhythms and chronic exercise remains undefined, particularly under the metabolic stress of obesity. Methods: Employing a 2 × 2 factorial design (Phase: ZT3 vs. ZT15; Condition: sedentary vs. exercise; ZT, Zeitgeber Time), EV-enriched fractions were isolated from ex vivo quadriceps muscle (QUA) cultures of high-fat diet-fed mice following an 8-week treadmill training regimen using polymer-based precipitation, and comprehensive miRNA profiling was performed by small RNA sequencing. Results: Principal component analysis (PCA) revealed that circadian phase accounted for a greater proportion of global variance in EV miRNA profiles than exercise. Differential expression analysis identified miR-1a-3p and miR-1b-5p as upregulated across both composite phase and exercise contrasts; however, condition-specific analyses indicated that this signal was primarily driven by the sedentary-phase comparison (ZT15-sed vs. ZT3-sed), in which the miR-29 family was also prominently co-upregulated, rather than constituting independent phase and exercise effects; this phase-associated signature was absent in the corresponding exercise-condition comparison. Exploratory functional enrichment of experimentally validated targets revealed phase-preferential association with metabolic and iron–heme pathways, whereas exercise-associated miRNAs mapped to signaling, inflammatory, and transcription-related networks. Conclusions: Circadian phase was the dominant contributor to global variance in muscle-derived EV-enriched miRNA profiles in obesity, as reflected by the phase-associated separation along principal component 1 (PC1, 33.47% of total variance), with exercise introducing context-dependent adaptive modulation. This study provides a foundational basis for investigating the temporal regulation of muscle secretome dynamics under high-fat diet conditions, highlighting temporal specificity as a key dimension in EV-mediated exercise physiology research. Full article
(This article belongs to the Special Issue Gene–Diet Interactions and Obesity)
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16 pages, 1749 KB  
Article
Integrated Genomic Analysis Unveils MicroRNA Roles in Glioma Development
by Sevan Omer Majed, Gaylany H. Abdullah, Kazhal Muhammad Sulaiman, Shawnim M. Maaruf, Raya Kh. Yashooa, Saman S. Abdulla, Chiara Villa and Suhad A. Mustafa
Biology 2026, 15(7), 533; https://doi.org/10.3390/biology15070533 - 27 Mar 2026
Viewed by 717
Abstract
Gliomas are the most common type of primary brain tumors in adults, with a high level of recurrence and mortality. Their complex biology and adaptive resistance mechanisms pose major obstacles to existing treatment strategies. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), are crucial in [...] Read more.
Gliomas are the most common type of primary brain tumors in adults, with a high level of recurrence and mortality. Their complex biology and adaptive resistance mechanisms pose major obstacles to existing treatment strategies. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), are crucial in tumor development and progression. Small RNA sequencing technology was performed in 25 patients with high-grade gliomas (HGGs) to analyze ncRNA expression in gliomas compared to normal adjacent tissues (NATs) aiming to elucidate their possible roles in these malignancies. Samples from patients with gliomas were examined, revealing an overall upregulation of ncRNAs. Specific ncRNA classes, including miRNAs, transfer RNAs (tRNAs), Piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs) showed notable shifts in abundance between tumor and normal samples. Among the upregulated miRNAs, a set of top five, such as miR-21, miR-221, miR-1321, miR-1306-5p, and miR-374a-5p, were validated by real-time quantitative PCR (RT-qPCR) in a cohort of 17 low-grade gliomas (LGGs) and 52 HGGs. These miRNAs are associated with critical oncogenic pathways and correlated with a worse prognosis. This study expanded the understanding of glioma biology and further confirmed the role of ncRNAs in the pathogenesis, supporting their potential use as novel possible biomarkers or therapeutic targets. Moreover, it provided an integrated analysis of multiple ncRNA classes, offering validation across both LGG and HGG, and uniquely incorporating a Kurdish cohort. Full article
(This article belongs to the Section Cancer Biology)
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45 pages, 2437 KB  
Review
Radiation-Responsive Promoters: Molecular Mechanisms, Screening Strategies, and Translational Applications as Radiation Biomarkers
by Nanxin Xu, Xin Huang and Pingkun Zhou
Curr. Issues Mol. Biol. 2026, 48(4), 348; https://doi.org/10.3390/cimb48040348 - 26 Mar 2026
Viewed by 514
Abstract
Radiation-responsive promoters represent a functionally distinct class of transcriptional regulatory elements that translate genotoxic stress signals into quantifiable gene expression outputs. These promoters occupy a unique mechanistic position within the broader radiation biomarker landscape: rather than directly measuring molecular damage products, they report [...] Read more.
Radiation-responsive promoters represent a functionally distinct class of transcriptional regulatory elements that translate genotoxic stress signals into quantifiable gene expression outputs. These promoters occupy a unique mechanistic position within the broader radiation biomarker landscape: rather than directly measuring molecular damage products, they report the cellular interpretation of radiation-induced stress through coordinated gene regulatory networks. This review provides a systematic analysis of five major classes of radiation-responsive promoters—microRNA (miRNA) promoters, tRNA-derived small RNA (tsRNA) promoters, acute-phase protein gene promoters, DNA repair gene promoters, and long non-coding RNA (lncRNA) promoters—with emphasis on their regulatory logic, dose-response characteristics, and current evidence for clinical deployment. We further describe four complementary screening strategies: homology-based conservation analysis, functional genomics and transcriptomics, epigenetic modification profiling, and synthetic biology promoter engineering. Applications spanning biosensor development, biological dosimetry, treatment response prediction, and radiation-guided gene therapy are evaluated within a two-track framework that distinguishes biomarker-oriented applications (Track A) from tool-oriented reporter gene systems (Track B). Critical appraisal of current limitations—including insufficient clinical-grade validation, absence of standardized dose-response curves, and reproducibility deficits—is integrated throughout. Future priorities include multi-center prospective validation studies, FAIR-compliant data infrastructure, AI-driven multi-omics integration, and point-of-care detection platforms. Radiation-responsive promoter biology holds significant potential for advancing precision radiotherapy and nuclear emergency medical response, contingent upon systematic closure of the current evidence gap relative to established gold-standard cytogenetic methods. Full article
(This article belongs to the Special Issue Radiation-Induced Cellular and Molecular Responses)
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26 pages, 2548 KB  
Systematic Review
MicroRNAs as Diagnostic and Therapeutic Biomarkers in Childhood Asthma: A Systematic Review with Bioinformatics Analysis
by Ahmed I. Alrefaey, Elena V. Vorobeva, Jamil Jubrail, Ibemusu Michael Otele, Mikaela Lee, Tilman Sanchez-Elsner, Syed Hasan Arshad, Ramesh J. Kurukulaaratchy and Mohammed Aref Kyyaly
J. Pers. Med. 2026, 16(4), 179; https://doi.org/10.3390/jpm16040179 - 25 Mar 2026
Viewed by 889
Abstract
Background: MicroRNAs (miRNAs) are stable, small non-coding RNAs involved in asthma-related pathways and are promising diagnostic biomarkers and therapeutic targets in childhood asthma. Objective: To identify miRNAs differentially expressed in preschool wheezing and childhood asthma, evaluate their association with asthma diagnosis and severity-related [...] Read more.
Background: MicroRNAs (miRNAs) are stable, small non-coding RNAs involved in asthma-related pathways and are promising diagnostic biomarkers and therapeutic targets in childhood asthma. Objective: To identify miRNAs differentially expressed in preschool wheezing and childhood asthma, evaluate their association with asthma diagnosis and severity-related phenotypes, and explore their potential translational relevance through exploratory bioinformatic analyses. Methods: A systematic search of Medline, Embase, SCOPUS, PubMed, CINAHL, and Web of Science was conducted for English-language articles published up to March 19, 2025. Eligible human studies reported that miRNAs were differentially expressed in children with wheeze or asthma versus healthy controls (p < 0.05, fold change ≥ 1.5). Bioinformatic analysis identified hub genes, constructed protein–protein interaction networks, and predicted drug–gene interactions. Results: Forty-seven studies met the inclusion criteria, yielding 58 differentially expressed miRNAs (31 up, 27 down). Recurrently reported miRNAs included miR-497, let-7e, miR-98, miR-21, miR-126a, miR-196a2, miR-1, miR-146a-5p, miR-210-3p, miR-145-5p, and miR-200c-3p across blood, nasal swabs, BALF, and exhaled breath condensate. miR-26a showed strong diagnostic performance (sensitivity 83%, specificity 93%; p < 0.002, 95% CI 0.831–0.987). Functional enrichment implicated 56 differentially expressed genes in metabolic and immune processes. Ten hub genes (including TNF, IL5, IL13, TLR4) were linked to 339 potential therapeutic agents; the exploratory network analysis highlighted overlap between predicted miRNA-regulated hub genes and existing asthma-relevant drug targets, including approved biologics. Conclusions: Our review findings suggest that several miRNAs are promising candidate biomarkers for childhood asthma phenotyping and severity assessment; however, their diagnostic utility remains exploratory and requires rigorous external validation and standardisation before clinical application. Full article
(This article belongs to the Special Issue Pathogenesis and Personalized Management of Asthma)
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25 pages, 7983 KB  
Article
Integrative Multi-Omics Analysis Identifies NUP205 as a Candidate Prognostic Biomarker in Liver Hepatocellular Carcinoma
by Eun-A Jeong, Jae-Ho Lee and Jongwan Kim
Int. J. Mol. Sci. 2026, 27(6), 2860; https://doi.org/10.3390/ijms27062860 - 21 Mar 2026
Viewed by 452
Abstract
Patients with Liver Hepatocellular carcinoma (LIHC) have a poor prognosis due to late-stage diagnosis and the limited efficacy of drug treatments. Dysregulation of nuclear pore complex (NPC) components, particularly nucleoporins (NUPs), may play a role in tumor progression. However, the specific role of [...] Read more.
Patients with Liver Hepatocellular carcinoma (LIHC) have a poor prognosis due to late-stage diagnosis and the limited efficacy of drug treatments. Dysregulation of nuclear pore complex (NPC) components, particularly nucleoporins (NUPs), may play a role in tumor progression. However, the specific role of NUP205 in LIHC has not been comprehensively investigated. We evaluated the expression, prognostic significance, epigenetic regulation, microRNA(miRNA) interactions, drug sensitivity, and biological functions of NUP205 in LIHC. Comprehensive bioinformatics analyses were performed using publicly available databases and web-based analysis platforms, including The Cancer Genome Atlas (TCGA), UALCAN, and the Kaplan–Meier Plotter (KM Plotter), among others. In vitro validation was performed using small interfering RNA (siRNA)-mediated knockdown of NUP205 in HepG2 cells, followed by quantitative reverse transcription PCR (RT-qPCR), apoptosis assay and wound-healing assay. NUP205 expression was significantly elevated in patients with LIHC and was associated with advanced clinicopathological features and poor prognosis. Promoter hypomethylation and miRNAs were identified as regulatory mechanisms influencing NUP205 expression. Increased NUP205 levels were associated with resistance to multiple chemotherapeutic agents. NUP205 knockdown significantly reduced messenger RNA (mRNA) expression in HepG2 and PLC/PRF/5 cells, and also reduced the expression of Transmembrane protein 209 (TMEM209) in HepG2 cells and improved sensitivity to doxorubicin. NUP205 expression was consistently associated with adverse clinicopathological features, poor prognosis, and altered drug sensitivity in LIHC. Integrative analyses suggest that NUP205 dysregulation may be linked to epigenetic and miRNA-associated regulatory mechanisms. These findings support NUP205 as a candidate prognostic biomarker and a potential regulatory factor in LIHC, warranting further mechanistic and protein-level validation. Further research is necessary to fully elucidate its underlying mechanisms and potential clinical applications. Full article
(This article belongs to the Special Issue Advancements in Cancer Biomarkers)
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27 pages, 3750 KB  
Article
SMR Peptide Modulates Tumor-Derived Extracellular Vesicles microRNA and Inflammatory Transcript Signatures in TNBC
by Ming-Bo Huang, Fengxia Yan, Uswa Jadoon, Jennifer Y. Wu, Dara Brena, Erica L. Johnson, Jonathan Stiles, Lily Yang, Brian M. Rivers and Vincent C. Bond
Cells 2026, 15(6), 550; https://doi.org/10.3390/cells15060550 - 19 Mar 2026
Viewed by 602
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype lacking targeted therapies and characterized by pronounced heterogeneity and widespread dysregulation of microRNAs (miRNAs) that influence epithelial-to-mesenchymal transition (EMT) and metastasis. Tumor-derived extracellular vesicles (tEVs) further contribute to TNBC progression by transporting oncogenic cargo that [...] Read more.
Triple-negative breast cancer (TNBC) is an aggressive subtype lacking targeted therapies and characterized by pronounced heterogeneity and widespread dysregulation of microRNAs (miRNAs) that influence epithelial-to-mesenchymal transition (EMT) and metastasis. Tumor-derived extracellular vesicles (tEVs) further contribute to TNBC progression by transporting oncogenic cargo that can enhance pro-inflammatory signaling. The synthetic SMRwt peptide has been suggested to modulate oncogenic pathways; however, its effects on EV miRNA composition and inflammatory transcript profiles in TNBC remain unclear. Here, we investigated whether SMRwt alters tEV-associated miRNAs and cytokine transcript signatures relevant to EMT and inflammasome-linked pathways. Extracellular vesicles were isolated from SMR-treated and untreated MDA-MB-231 cells, followed by nanoparticle tracking analysis and small RNA sequencing. SMRwt treatment enriched 11 tumor-suppressive miRNAs (including Let-7a-5p, Let-7b-5p, miR-24-3p, miR-26b-5p, miR-92a-3p, miR-93-5p, and miR-496) previously associated with the regulation of proliferation, EMT, migration, and metastasis. We also observed modest, non-significant decreases (1.01–1.27-fold) in oncogenic miR-1200, miR-374a-5p, and miR-937-3p, which have been implicated in the progression of breast, lung, and bone malignancies. Complementary transcriptomic profiling using the NanoString nCounter Breast Cancer 360 Gene Expression Panel (NanoString Technologies, Inc., Seattle, CA, USA) demonstrated reduced expression of inflammasome-associated cytokines in TNBC cells relative to non-tumorigenic controls, including a log2 fold change of −1.15 for IL 1β (MDA-MB-231 vs. MCF10A). These transcript-level changes suggest potential modulation. Additionally, SMRwt suppresses ASC-mediated caspase-1 activation and reduces IL-1β secretion, thereby inhibiting NLRP3 inflammasome signaling. Therefore, we infer that SMRwt simultaneously restores tumor-suppressive miRNA networks and suppresses inflammasome-driven inflammation, supporting its potential as a dual-target therapeutic strategy for TNBC. Full article
(This article belongs to the Special Issue Research on Extracellular Vesicles in Health and Disease)
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19 pages, 1193 KB  
Article
Circulating EV miRNA Cargo in Glioblastoma Patients Is Associated with Distinct Gene Expression Signatures in Peripheral Immune Cells, Suggesting an Early, Compartment-Specific Immune Priming State
by Marija Popovic-Vukovic, Ivana Kolic, Aleksandra Stankovic, Maja Zivkovic, Mihailo Milicevic, Ivan Bogdanovic, Ivana Srbljak, Nina Petrovic, Tatjana Stanojkovic, Marina Nikitovic and Ivan Jovanovic
Biomedicines 2026, 14(3), 703; https://doi.org/10.3390/biomedicines14030703 - 18 Mar 2026
Viewed by 495
Abstract
Background: Glioblastoma is the most lethal primary brain tumor, being characterized not only by marked intratumoral heterogeneity but also by strong systemic immunosuppression. Circulating extracellular vesicles (EVs) have gained growing recognition during the past decade as important mediators of intercellular communication, particularly [...] Read more.
Background: Glioblastoma is the most lethal primary brain tumor, being characterized not only by marked intratumoral heterogeneity but also by strong systemic immunosuppression. Circulating extracellular vesicles (EVs) have gained growing recognition during the past decade as important mediators of intercellular communication, particularly through their microRNA (miRNA) cargo. However, the global EV miRNA landscape of circulating EV-associated miRNAs in glioblastoma patients and their relation with gene expression patterns in peripheral immune cells remain incompletely defined. Methods: To investigate these systemic associations, we profiled EV-associated miRNA expression in plasma samples from glioblastoma patients and matched healthy controls using the small RNA sequencing method, followed by differential expression and pathway analyses. Based on these findings and literature evidence, identified changes in selected EV miRNA levels were validated by qPCR in an extended cohort. In parallel, expression of their predicted immune-related mRNA targets was analyzed in peripheral blood mononuclear cells (PBMCs) obtained from the same individuals, allowing for the assessment of EV miRNA–PBMC mRNA correlation patterns. Results: Small RNA sequencing revealed a distinct circulating EV-associated miRNA profile in glioblastoma patients compared to controls. The validation analysis of relative expression of the identified DEmiRNAs has shown a statistically significant upregulation of hsa-miR-142-3p, hsa-miR-19b-3p, and hsa-miR-98-5p in circulating EVs of glioblastoma patients compared to controls. PBMCs from glioblastoma patients exhibited increased expression of the regulatory genes SOCS1, SOCS3, and PTEN, while CCND1 was downregulated. Correlation analyses suggested that certain EV miRNA changes parallel with alterations in PBMC gene expression in glioblastoma patients, suggesting early immune priming in the circulation. Conclusions: Our findings indicate that circulating EV miRNAs in glioblastoma patients are associated with specific gene expression patterns in peripheral immune cells, suggesting a complex regulatory balance between pro-inflammatory and anti-inflammatory cues, potentially preceding full tumor-associated macrophage polarization. These molecular interactions may offer opportunities for developing early biomarkers or new therapeutic approaches. Full article
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20 pages, 1179 KB  
Review
The Architecture of Deep Phenotyping in Asthma: Integrating Molecular, Metabolic, and Neuro-Hormonal Endotypes
by Nicolae Demenciuc, Corina Ureche, Corina Eugenia Budin, Mircea Stoian, Teodora Nicola-Varo, Edith Simona Ianosi, Dariana-Elena Pătrîntașu, Anca Goman, Lavinia Davidescu and Diana Deleanu
Int. J. Mol. Sci. 2026, 27(6), 2545; https://doi.org/10.3390/ijms27062545 - 10 Mar 2026
Viewed by 575
Abstract
Asthma is increasingly recognized as a heterogeneous syndrome where traditional management fails, particularly given spirometry’s limitations in assessing small airway dysfunction. This review synthesizes the transition from clinical phenotyping to deep molecular endotyping, establishing a framework for precision medicine. We highlight the insufficiency [...] Read more.
Asthma is increasingly recognized as a heterogeneous syndrome where traditional management fails, particularly given spirometry’s limitations in assessing small airway dysfunction. This review synthesizes the transition from clinical phenotyping to deep molecular endotyping, establishing a framework for precision medicine. We highlight the insufficiency of absolute eosinophil counts, proposing eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) as superior activation metrics. Furthermore, we explore Type 2 drivers (IL-4/IL-13, periostin) and epithelial alarmins like TSLP. Beyond classical immunology, the text describes metabolic dysregulation, specifically asymmetric dimethylarginine (ADMA) in obese-asthma phenotypes where nitric oxide synthase uncoupling promotes oxidative stress. We also analyze YKL-40 and surfactant protein D (SP-D) as markers of remodeling and barrier permeability, alongside microRNAs—specifically miR-21—in corticosteroid resistance. We conclude that managing refractory asthma requires shifting from reactive symptom control to an integrated analysis of multi-omic biomarkers. Establishing this comprehensive molecular profile via specialized centers is fundamental for addressing current diagnostic limitations, selecting biological therapies, and modifying the disease trajectory through an endotype-driven strategy addressing inflammatory, metabolic, and structural pathologies. Full article
(This article belongs to the Special Issue Advances in Molecular Approaches to Asthma Management)
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13 pages, 922 KB  
Article
EBV BART microRNA Profiles and Host Gene Links in Gastric Cancer
by Esra Dirimtekin, D. Alwyn Dart and Pinar Uysal-Onganer
Viruses 2026, 18(3), 329; https://doi.org/10.3390/v18030329 - 7 Mar 2026
Cited by 1 | Viewed by 844
Abstract
Epstein–Barr virus (EBV), a ubiquitous human herpesvirus infecting over 90% of the adult population, is causally associated with a distinct molecular subtype of gastric cancer (GC). A key mechanism by which EBV influences tumour biology is the expression of viral microRNAs (miR/miRNA) encoded [...] Read more.
Epstein–Barr virus (EBV), a ubiquitous human herpesvirus infecting over 90% of the adult population, is causally associated with a distinct molecular subtype of gastric cancer (GC). A key mechanism by which EBV influences tumour biology is the expression of viral microRNAs (miR/miRNA) encoded within the BamHI-A rightward transcript (BART) region, although inter-patient variability in EBV-miRNA expression and its molecular significance remain incompletely defined. In this study, small RNA sequencing was performed on 11 primary gastric tumour samples to characterise EBV-derived miRNA expression, followed by quantitative RT-PCR analysis in an extended cohort of 21 tumours for targeted validation. EBV-miRNAs were detected in a subset of tumours and showed marked inter-tumour heterogeneity in abundance. EBV-miRNA-positive tumours were dominated by a conserved set of BART miRNAs, including miR-BART19-3p, miR-BART1-5p, miR-BART10-3p, miR-BART6-3p, miR-BART13-5p, and miR-BART22. These BART miRNAs displayed correlated expression patterns, characterised by concurrent elevation of multiple viral miRNA species within the same tumour samples. To link viral miRNA expression with host molecular responses, in silico virus–host interaction analysis was conducted using ViRBase to prioritise host genes associated with the detected BART miRNAs. PTEN, BCL2L11, FOXO3, and CDKN1A were identified as high-confidence targets and selected for experimental assessment. RT-qPCR analysis demonstrated differential expression of these host genes across tumours stratified by EBV BART miRNA abundance. Together, these findings identify a consistent BART miRNA pattern within this cohort. This study provides patient-level molecular evidence linking EBV-miRNA regulatory output to host gene expression states in GC. Full article
(This article belongs to the Special Issue EBV and Disease: New Perspectives in the Post COVID-19 Era)
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14 pages, 1711 KB  
Article
Pathway-Level Convergence Between Dynamic Plasma miRNAs and Endometrial Biological Processes During the Human Peri-Implantation Window
by Chun-I Lee, An Hsu, Yu-Jen Lee, En-Hui Cheng, Chi-Ying Lee, Pin-Yao Lin, Maw-Sheng Lee, Chung-I Chen, Tzu-Ning Yu, Tiffany Wang, Cai-Yun Wang, Shi-Ting Lin, Jung-Hsuan Yang, Hui-Ling Hsu, Eric Pok Yang and Tsung-Hsien Lee
Int. J. Mol. Sci. 2026, 27(5), 2414; https://doi.org/10.3390/ijms27052414 - 5 Mar 2026
Viewed by 470
Abstract
The peri-implantation window is a tightly regulated temporal phase during which the human endometrium undergoes coordinated molecular remodeling to establish receptivity. MicroRNAs (miRNAs) contribute to implantation-related processes; however, whether dynamic endometrial regulatory signals are functionally reflected in circulation within a defined temporal framework [...] Read more.
The peri-implantation window is a tightly regulated temporal phase during which the human endometrium undergoes coordinated molecular remodeling to establish receptivity. MicroRNAs (miRNAs) contribute to implantation-related processes; however, whether dynamic endometrial regulatory signals are functionally reflected in circulation within a defined temporal framework remains unclear. We hypothesized that although individual miRNA identities differ between endometrial tissue and plasma, temporally regulated miRNAs in both compartments may exhibit overlap at the level of enriched biological pathways during the peri-implantation window. To test this hypothesis, we performed time-resolved small RNA sequencing on paired endometrial and plasma samples collected from 62 participants across progesterone exposure days P+3 to P+7 in hormonally controlled cycles. Temporal modeling identified 27 dynamic miRNAs in endometrial tissue and 17 in plasma (FDR < 0.05). Despite limited overlap at the individual miRNA level, functional enrichment analysis revealed recurrent overlap in apoptosis-, cell cycle-, aging-, inflammatory-, and metabolic-related pathways across compartments. Four miRNAs exhibited concordant directional temporal trends between tissue and plasma with moderate correlation coefficients. These findings suggest that dynamic miRNA-associated enrichment patterns during the peri-implantation window may exhibit pathway-level overlap despite divergence in specific molecular identities. This temporally aligned integrative framework provides a pathway-centric perspective for interpreting cross-compartment miRNA-associated temporal patterns and supports a hypothesis-generating systems-level view of human implantation biology. Full article
(This article belongs to the Section Molecular Endocrinology and Metabolism)
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29 pages, 12902 KB  
Article
Estradiol Reverses Ovariectomy-Induced Small RNA–mRNA Stress Signatures to Restore Neuroendocrine, Synaptic, and Immune Homeostasis in the Hypothalamus
by Muhammad Mubashir, Huan Yang, Xiaohuan Chao, Chunlei Zhang, Jiahao Chen, Yuan Ding, Hongwei Bi, Ziming Wang, Wen Guo, Junhong Fan, Mengjun Zhou and Bo Zhou
Biomolecules 2026, 16(3), 354; https://doi.org/10.3390/biom16030354 - 26 Feb 2026
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Abstract
Loss of ovarian hormones following menopause or ovariectomy is associated with increased anxiety, cognitive impairment, and dysregulation of hypothalamic neuroendocrine pathways. MicroRNAs (miRNAs) and tRNA-derived fragments (tRFs) are emerging classes of small non-coding RNAs that act as post-transcriptional regulators of stress, inflammation, and [...] Read more.
Loss of ovarian hormones following menopause or ovariectomy is associated with increased anxiety, cognitive impairment, and dysregulation of hypothalamic neuroendocrine pathways. MicroRNAs (miRNAs) and tRNA-derived fragments (tRFs) are emerging classes of small non-coding RNAs that act as post-transcriptional regulators of stress, inflammation, and synaptic function; however, their coordinated involvement in estradiol-mediated hypothalamic regulation remains poorly understood. In this study, adult female mice were assigned to control, estradiol-treated, ovariectomized (OVX), or OVX plus estradiol groups. Anxiety- and cognition-related behaviors were assessed using the open field, Y-maze, and elevated plus maze tests. Circulating estradiol levels and hypothalamic gonadotropin-releasing hormone (GnRH) expression were quantified by ELISA. Hypothalamic mRNA, miRNA, and tRF expression profiles were analyzed by RNA sequencing, followed by differential expression analysis, functional enrichment, integrative network construction, and quantitative real-time PCR validation. Ovariectomy induced anxiety-like behaviors, impaired working memory, reduced estradiol levels, and increased hypothalamic GnRH expression, all of which were reversed by estradiol treatment. Transcriptomic analysis identified 376 differentially expressed miRNAs, 182 differentially expressed tRFs, and 439 differentially expressed mRNAs, enriched in pathways related to stress responses, neuroendocrine regulation, synaptic signaling, metabolic homeostasis, and neuroinflammation. Integrated miRNA–mRNA and tRF–mRNA network analyses revealed several estradiol-responsive miRNAs (including miR-200a-5p, miR-182/183-5p, miR-381-3p, miR-148a-3p, and miR-10 family members) predicting key hub genes such as Gcg, Wnt4, Prkacb, Sgk1, Fpr2, and Aldoa, and key tRFs like tRFdb-1003, tRFdb-1013, tRFdb-1026, tRFdb-3001a and tRFdb-5020a, targeting hub genes such as Wnt4, Prkacb, Sh3rf2, Hpse, Cxcr2 and Zbtb16 respectively. Collectively, these findings demonstrate that estradiol ameliorates OVX-induced behavioral and endocrine dysfunction by reorganizing hypothalamic miRNA- and tRF-mediated regulatory networks involved in stress adaptation, synaptic homeostasis, and neuroimmune signaling. Full article
(This article belongs to the Section Molecular Reproduction)
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