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22 pages, 6391 KB  
Article
Differential Expression and Target Gene Analysis of PBMC-Derived microRNAs as Prognostic Biomarkers in Acute Lymphoblastic Leukemia
by Fatemah S. Basingab, Hadil Alahdal, Deemah Alwadaani, Ghaida Almuneef, Ahmed S. Barefah, Ali H. Algiraigri, Rawan Hammad, Mohamed Elnakeeb, Jehan S. Alrahimi, Kawther A. Zaher and Alia M. Aldahlawi
Int. J. Mol. Sci. 2026, 27(9), 3868; https://doi.org/10.3390/ijms27093868 (registering DOI) - 27 Apr 2026
Abstract
Acute lymphoblastic leukemia (ALL) is a clinically diverse cancer in which microRNA (miRNA)-mediated post-transcriptional regulation contributes to leukemogenesis and subtype heterogeneity. In this study, miRNA expression profiling by microarray was performed on ALL cases (B-ALL and T-ALL) and healthy controls. Data were normalized [...] Read more.
Acute lymphoblastic leukemia (ALL) is a clinically diverse cancer in which microRNA (miRNA)-mediated post-transcriptional regulation contributes to leukemogenesis and subtype heterogeneity. In this study, miRNA expression profiling by microarray was performed on ALL cases (B-ALL and T-ALL) and healthy controls. Data were normalized and analyzed for differential expression using false discovery rate (FDR)-adjusted p-values. Differentially expressed miRNAs were further examined using unsupervised visualization to assess overall disease-related expression patterns. To explore their biological significance, experimentally validated miRNA–target interactions were obtained using multiMiR, limited to validated databases (miRTarBase, TarBase, and miRecords) and summarized via target-burden ranking, miRNA–target network analysis, and Circos–style interaction mapping. A unique miRNA expression signature was identified in ALL. Upregulated miRNAs included miR-106a-5p, miR-106b-5p, miR-17-5p, miR-20a-5p, miR-20b-5p, miR-181b-5p, and miR-128-3p, while miR-127-3p, miR-139-5p, miR-433-3p, and miR-584-5p were downregulated. Validated targets concentrated on key leukemia-related genes like PTEN, BCL2L11, CDKN1A, CCND1, RB1, E2F1, and TGFBR2. KEGG pathway analysis highlighted pathways associated with leukemic cell survival and growth, including MAPK, cell cycle, autophagy, Hippo, ubiquitin-mediated proteolysis, and mTOR signaling pathways. These findings reveal a concise ALL-associated miRNA panel predominantly comprising the miR-17/20/106 family and provide a prioritized set of candidate regulatory networks for subtype-specific validation and functional follow-up studies. Full article
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25 pages, 4630 KB  
Article
Multi-Omics Integration Identifies a Six-Gene Diagnostic Signature for Ankylosing Spondylitis via Metabolic–Immune Crosstalk
by Xuejian Dan, Xiangyuan Guan, Hangjian Hu, Wei Liu, Zhourui Wu, Xiao Hu, Wei Xu, Yunfei Zhao and Bin Ma
Int. J. Mol. Sci. 2026, 27(9), 3860; https://doi.org/10.3390/ijms27093860 (registering DOI) - 27 Apr 2026
Abstract
Ankylosing spondylitis (AS) is a chronic immune-mediated inflammatory disease affecting the axial skeleton, characterized by progressive structural damage and functional impairment. Although biologic therapies targeting tumor necrosis factor and interleukin-17 have improved clinical outcomes, a substantial proportion of patients fail to achieve sustained [...] Read more.
Ankylosing spondylitis (AS) is a chronic immune-mediated inflammatory disease affecting the axial skeleton, characterized by progressive structural damage and functional impairment. Although biologic therapies targeting tumor necrosis factor and interleukin-17 have improved clinical outcomes, a substantial proportion of patients fail to achieve sustained disease control. Emerging evidence suggests that metabolic alterations may contribute to AS pathogenesis; however, systematic characterization of metabolism-related biomarkers and their regulatory networks remains limited, and the interplay between metabolic dysfunction and immune dysregulation in AS is poorly understood. Two whole-blood GEO datasets (GSE25101, GSE73754; n = 104) were integrated as the primary analytical cohort. A third dataset (GSE11886, n = 18; monocyte-derived macrophages) was included for exploratory cross-tissue analysis. Differential expression analysis identified 847 DEGs, which were refined to 16 metabolism-related genes through weighted gene co-expression network analysis (WGCNA) and GeneCards database filtering. Eleven machine learning algorithms with 5-fold cross-validation were applied to construct diagnostic models and identify hub genes. Validation analyses included immune cell infiltration estimation using CIBERSORT, metabolic pathway activity assessment via ssGSEA, single-cell transcriptomics from GSE268839, functional enrichment through GSEA/GSVA, and chromosomal localization analysis. A competing endogenous RNA (ceRNA) regulatory network was constructed to map post-transcriptional regulation. Natural compounds from 66 AS-treating traditional Chinese medicines were screened against hub genes using deep learning-based binding prediction. Multiple machine learning algorithms achieved comparable cross-validated performance (CV AUC range 0.741–0.836; top five models: 0.805–0.836) using the six hub genes (MFN2, SLC27A3, RHOB, SMG7, AKR1B1, LCOR) identified through SHAP-based feature importance analysis of the PLS model. Leave-one-dataset-out validation between the two whole-blood cohorts showed that all algorithms exceeded an AUC of 0.77 in Round 1 (validate: GSE73754, n = 72; best AUC 0.861), while Round 2 (validate: GSE25101, n = 32) yielded more modest performance (best AUC, 0.715) reflecting the smaller validation sample. Exploratory application to GSE11886 (macrophage-derived samples) showed near-chance performance, consistent with the tissue-source discrepancy. AS patients exhibited significant downregulation of oxidative phosphorylation, TCA cycle, and glycolysis pathways (p < 0.01), accompanied by elevated glutathione metabolism (p < 0.001). Immune cell deconvolution revealed reduced CD8+ T cell proportions correlating with MFN2 downregulation, and increased neutrophil frequencies correlating with SLC27A3 upregulation. Exploratory single-cell analysis indicated that RHOB expression was relatively enriched in border-associated macrophages and fibroblasts, while AKR1B1 was more prominently expressed in vascular endothelial cells and plasmacytoid dendritic cells. The ceRNA network identified 21 miRNAs and 65 lncRNAs forming 86 regulatory interactions, with four key regulatory axes (SATB1-AS1/miR-539-5p/LCOR, FAM95B1/miR-223-3p/RHOB, LINC01106/miR-106a-5p/MFN2, AATBC/miR-185-5p/SMG7) predicted to regulate hub gene expression. Compound screening identified betaine, pyruvic acid, citric acid, etc., as top-ranking candidates, with MFN2 showing the highest binding capacity among hub genes. This study provides an integrative framework linking metabolic reprogramming with immune dysfunction in AS. The six-gene diagnostic signature showed preliminary discriminatory ability in the available datasets, while the ceRNA regulatory network and natural compound screening results prioritize candidate regulatory pathways and compounds for future validation. These findings advance our understanding of AS pathogenesis and may guide future biomarker development and targeted intervention strategies. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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15 pages, 1616 KB  
Review
The Multifaceted Role of microRNA-10b (miR-10b) in Glioblastoma: From Oncogenic Driver to Therapeutic Target
by Ming Chen, Zdravka Medarova, Lisa R. Rogers and Anna Moore
Cells 2026, 15(9), 784; https://doi.org/10.3390/cells15090784 (registering DOI) - 26 Apr 2026
Viewed by 54
Abstract
Glioblastoma (GBM) remains one of the most lethal and treatment-resistant human malignancies, characterized by extreme molecular heterogeneity and a highly immunosuppressive tumor microenvironment (TME). MicroRNAs are a set of small endogenous non-coding RNA molecules which play critical roles in various biological processes including [...] Read more.
Glioblastoma (GBM) remains one of the most lethal and treatment-resistant human malignancies, characterized by extreme molecular heterogeneity and a highly immunosuppressive tumor microenvironment (TME). MicroRNAs are a set of small endogenous non-coding RNA molecules which play critical roles in various biological processes including carcinogenesis. Recent evidence identifies microRNA-10b (miR-10b) as a regulator of gliomagenesis, with glioblastoma exhibiting a unique state of “oncogene addiction” to this molecule. This review summarizes current research on the mechanistic roles of miR-10b in GBM tumor progression and immune evasion, evaluates innovative antisense oligonucleotide delivery systems, and explores the clinical potential of combining miR-10b inhibition with standard-of-care treatments. Full article
(This article belongs to the Special Issue Cell Death Mechanisms and Therapeutic Opportunities in Glioblastoma)
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17 pages, 17647 KB  
Article
CircPRKCA Promotes NSCLC Progression via miR-200b-3p/FRMD6/SNAI2 Axis
by He Zhong, Ning Wang, Hui Zhang, Min Chen, Xin Liao and Chao Huang
Int. J. Mol. Sci. 2026, 27(9), 3824; https://doi.org/10.3390/ijms27093824 (registering DOI) - 25 Apr 2026
Viewed by 125
Abstract
Circular RNAs (circRNAs) have been reported to be closely associated with tumor progression in multiple malignancies. However, the specific mechanism by which circPRKCA influences tumor progression has not been fully elucidated. CircPRKCA is highly expressed in non-small cell lung cancer (NSCLC) tissues and [...] Read more.
Circular RNAs (circRNAs) have been reported to be closely associated with tumor progression in multiple malignancies. However, the specific mechanism by which circPRKCA influences tumor progression has not been fully elucidated. CircPRKCA is highly expressed in non-small cell lung cancer (NSCLC) tissues and cells. Knockdown of circPRKCA inhibits the malignant behaviors of NSCLC cells. RNA sequencing results revealed that FRMD6 and SNAI2 mRNAs are positively correlated with circPRKCA. Subsequently, we proved that circPRKCA acts as a molecular sponge for miR-200b-3p. Additionally, miR-200b-3p binds to the 3′ untranslated regions (3′UTRs) of FRMD6 and SNAI2 mRNAs to promote their degradation. Overexpression of circPRKCA thereby suppresses this degradation process and coun-teracts the tumor-suppressive effects induced by miR-200b-3p. CircPRKCA functions as the sponge of miR-200b-3p, suppressing the SNAI2/FRMD6 mRNA degradation driven by miR-200b-3p and accelerating NSCLC progression. Full article
(This article belongs to the Section Molecular Biology)
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19 pages, 4578 KB  
Article
Exosomes Generated by Normal Peritoneal Cells Driven to Senescence by Carboplatin and Paclitaxel Awaken Dormant Ovarian Cancer Cells and Support Their Growth Reinitiation In Vitro
by Szymon Rutecki, Adrianna Krawiec, Agnieszka Leśniewska-Bocianowska, Julia Matuszewska, Eryk Naumowicz, Sebastian Szubert, Krzysztof Książek and Justyna Mikuła-Pietrasik
Cancers 2026, 18(9), 1346; https://doi.org/10.3390/cancers18091346 - 23 Apr 2026
Viewed by 295
Abstract
Background: Recurrence poses a major challenge in epithelial ovarian cancer (EOC), often occurring despite optimal first-line therapy. Dormant cancer cells are believed to play a key role, yet the mechanisms driving their reactivation remain unclear. This study examined whether exosomes released by [...] Read more.
Background: Recurrence poses a major challenge in epithelial ovarian cancer (EOC), often occurring despite optimal first-line therapy. Dormant cancer cells are believed to play a key role, yet the mechanisms driving their reactivation remain unclear. This study examined whether exosomes released by normal peritoneal mesothelial cells (PMCs) and fibroblasts (PFBs) undergoing iatrogenic senescence after carboplatin and paclitaxel exposure contribute to EOC recurrence. Methods and Results: Senescent PMCs and PFBs secreted markedly more exosomes, identified by CD9, CD63, and CD81, compared with young cells. Exosomes from both cell types more effectively reactivated dormant EOC cells (pEOCs, A2780, OVCAR-3, SKOV-3) than non-exosomal medium constituents. Importantly, senescent PMC-derived exosomes most strongly reactivated pEOCs and SKOV-3, whereas those from senescent PFBs exerted greater effects on pEOCs, OVCAR-3, and SKOV-3. Kinetic studies of exosome internalization revealed that this process was generally more efficient in the presence of exosomes derived from senescent cells compared with those from young donor cells. Compositional analysis revealed distinct profiles between young and senescent exosomes compared in two variants: young PMCs/senescent PMCs and young PFBs/senescent PFBS. Senescent PMC exosomes displayed reduced miR-210-3p, miR-409-3p, and miR-421, alongside elevated MMP1, MMP3, and VEGF, while senescent PFB exosomes showed increased amphiregulin and osteopontin but lower MMP1, MMP3, TIMP1, bFGF, VEGF, and HGF. Functionally, senescent PMC exosomes enhanced pEOC migration, invasion, and spheroid formation, and induced the expression of CCL11 and ABCB1. Senescent PFB exosomes promoted migration and upregulated CCL11, TGF-β1, BIRC5, and CHEK1. Conclusions: These findings suggest that therapy-induced senescence in peritoneal cells may contribute to EOC recurrence by reactivating dormant tumor cells through exosomal signaling. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Cancer Progression)
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23 pages, 4116 KB  
Article
Impact of DNA Extraction Strategies on Genomic and Bioinformatic Outcomes in Eight Selected Fungal Strains
by Cyrine Abid, Hela Zouari-Mechichi, Riadh Benmarzoug, Tahar Mechichi and Najla Kharrat
J. Fungi 2026, 12(5), 299; https://doi.org/10.3390/jof12050299 - 22 Apr 2026
Viewed by 450
Abstract
High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving [...] Read more.
High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)
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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 229
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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20 pages, 1922 KB  
Article
Cellular, Molecular, and Behavioural Sequelae of Early-Life Continuous Low-Dose-Rate Irradiation in Mice
by Feng Ru Tang, Hong Wang, Salihah Lau and Amanda Tan
Cells 2026, 15(8), 711; https://doi.org/10.3390/cells15080711 - 17 Apr 2026
Viewed by 172
Abstract
The Fukushima nuclear accident highlighted that evacuation-related psychosocial harm can outweigh direct radiation risks, underscoring the need to define the health impacts of chronic low-dose-rate (LDR) radiation and evidence-based thresholds for intervention. This study investigated the effects of continuous, postnatal LDR gamma irradiation [...] Read more.
The Fukushima nuclear accident highlighted that evacuation-related psychosocial harm can outweigh direct radiation risks, underscoring the need to define the health impacts of chronic low-dose-rate (LDR) radiation and evidence-based thresholds for intervention. This study investigated the effects of continuous, postnatal LDR gamma irradiation (1.2 mGy/h, cumulative dose: 5 Gy) in male mice. While no changes in body weight, hippocampal neurogenesis, or major glial and neuronal populations were observed, persistent DNA damage (γ-H2AX foci) in dentate gyrus granule cells occurred in both irradiated male and female mice. Irradiated male mice developed anxiety-like behaviour, a phenotype not observed in a previously published study of female mice subjected to an identical irradiation protocol. Molecular profiling revealed two novel, dysregulated miRNA/mRNA axes in the hippocampus linking DNA damage to behaviour: a maladaptive miR-466i-5p/Tfcp2l1 pathway associated with genomic instability, and a potentially adaptive miR-101a-5p/BMP6 pathway promoting neuronal survival. Venn analysis further identified miR-124b-3p and novel-miR489-3p as conserved exposure biomarkers, altered in both the hippocampus and blood of irradiated animals. Our results show that a high cumulative dose of chronic LDR induces markedly less severe hippocampal pathology than has been reported for equivalent acute doses. These findings support the concept of dose-rate-dependent threshold dose and contribute to the evidence base for developing countermeasures following nuclear incidents or other radiation exposures. Full article
(This article belongs to the Section Cellular Neuroscience)
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16 pages, 949 KB  
Review
From Integrated Analysis to Clinical Insight: ncRNA-Mediated Ferroptosis in Glioblastoma
by Venkata N. Seerapu, Rajalakshmi Amaresan and Udhayakumar Gopal
Cancers 2026, 18(8), 1238; https://doi.org/10.3390/cancers18081238 - 14 Apr 2026
Viewed by 412
Abstract
Glioblastoma (GBM) is the most lethal and aggressive primary brain tumor in adults. Despite a standard-of-care regimen involving surgical resection, radiotherapy and temozolomide (TMZ), median overall survival typically hovers between 12 and 15 months. This poor prognosis is driven by profound intratumoral heterogeneity, [...] Read more.
Glioblastoma (GBM) is the most lethal and aggressive primary brain tumor in adults. Despite a standard-of-care regimen involving surgical resection, radiotherapy and temozolomide (TMZ), median overall survival typically hovers between 12 and 15 months. This poor prognosis is driven by profound intratumoral heterogeneity, glioma stem cell populations, and an immunosuppressive microenvironment that collectively fuel resistance to traditional apoptosis-centric therapies. Ferroptosis—a form of regulated cell death driven by iron-dependent phospholipid peroxidation and the collapse of antioxidant defenses—has emerged as a compelling alternative for eliminating therapy-refractory GBM cells. This review examines the molecular machinery of ferroptosis in glioma and explores how an additional regulatory layer, noncoding RNAs (ncRNAs), modulates this process. We highlight key experimentally validated axes where microRNAs, long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) orchestrate iron handling and antioxidant thresholds. These include sensitizers like miR-147a and circLRFN5, which promote iron overload, and resistors like circCDK14 and TMEM161B-AS1, which act as “ferroptosis brakes”. Furthermore, we discuss how integrative analyses of TCGA and CGGA cohorts have yielded ferroptosis-related lncRNA signatures that robustly predict patient survival. Finally, we outline the clinical potential of these ncRNAs as biomarkers and therapeutic targets while addressing the delivery challenges, such as the blood–brain barrier, that must be overcome to achieve precision, ferroptosis-oriented GBM therapy. Full article
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16 pages, 2623 KB  
Article
lncRNA-803 Suppresses Apoptosis in DF-1 Cells via the miR-6555-3p/MDM4/p53 Axis
by Shuo Han, Jingyi Yang, Yunqiao Qiu, Shuang Zhao, Yingxue Jiang, Liping Han and Limei Han
Genes 2026, 17(4), 440; https://doi.org/10.3390/genes17040440 - 12 Apr 2026
Viewed by 460
Abstract
Background/Objectives: Long non-coding RNAs (lncRNAs) are integral to the regulation of viral tumorigenesis. We have previously identified that the chicken lncRNA-803, which responds to Marek’s disease virus (MDV), inhibits apoptosis in the chicken embryonic fibroblast cell line DF-1, accompanied by changes in the [...] Read more.
Background/Objectives: Long non-coding RNAs (lncRNAs) are integral to the regulation of viral tumorigenesis. We have previously identified that the chicken lncRNA-803, which responds to Marek’s disease virus (MDV), inhibits apoptosis in the chicken embryonic fibroblast cell line DF-1, accompanied by changes in the expression of the p53 protein. Nonetheless, the molecular mechanism of lncRNA-803 in apoptosis has yet to be elucidated. Methods: In this study, through lentivirus-mediated overexpression and knockdown experiments, we determined that the overexpression of lncRNA-803 induces elevated expression levels of murine double minute 2 (MDM2), murine double minute 4 (MDM4), tumor protein p53 (p53), and tumor protein p53 binding protein 1 (TP53BP1) within the p53 signaling pathway. Results: This modulation subsequently leads to an upregulation of B-cell lymphoma-2 (Bcl-2) expression, while concurrently resulting in the downregulation of cysteinyl aspartate specific proteinase 8 (Caspase-8), cysteinyl aspartate specific proteinase 9 (Caspase-9), Bcl-2 associated protein X (Bax), and cysteinyl aspartate specific proteinase 9 (Caspase-3) in the apoptosis pathway. In terms of its mechanism, lncRNA-803 functions as a molecular sponge for miR-6555-3p. lncRNA-803 engages in competitive binding with miR-6555-3p, thereby diminishing its inhibitory effect on MDM4. Conclusions: These results elucidate that lncRNA-803 modulates apoptosis in DF-1 cells through a novel competing endogenous RNA mechanism involving the miR-6555-3p/MDM4/p53 axis. These findings provide new insights into the molecular pathogenesis of MDV. Full article
(This article belongs to the Section RNA)
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19 pages, 1539 KB  
Article
Assessment of miR-1-3p, miR-let-7b-5p, miR-21-5p, and miR-26b-5p in Children with Cardiovascular Diseases
by Marta Pasławska-Zyskowska, Piotr Majewski, Anetta Sulewska, Paweł Muszyński, Miłosz Nesterowicz, Filip Bossowski, Joanna Gościk, Beata Sawicka, Justyna Dunaj-Małyszko, Anna Moniuszko-Malinowska, Jacek Nikliński and Artur Tadeusz Bossowski
Cells 2026, 15(8), 674; https://doi.org/10.3390/cells15080674 - 10 Apr 2026
Viewed by 381
Abstract
Background: Cardiovascular diseases remain important causes of morbidity and potential premature mortality in children. Although clinical imaging and electrophysiologic testing have advanced, early, minimally invasive biomarkers that can both detect myocardial injury and help differentiate among overlapping pediatric phenotypes are still limited. Circulating [...] Read more.
Background: Cardiovascular diseases remain important causes of morbidity and potential premature mortality in children. Although clinical imaging and electrophysiologic testing have advanced, early, minimally invasive biomarkers that can both detect myocardial injury and help differentiate among overlapping pediatric phenotypes are still limited. Circulating microRNAs (miRNAs; miRs) are becoming attractive biomarker candidates because many are abundant in the heart, actively released into the circulation, and remarkably stable in plasma. The study aimed to assess the expression of miR-1-3p, miR-let-7b-5p, miR-21-5p, and miR-26b-5p in children with cardiovascular disease. Methods: Children aged 10–18 years with cardiac arrhythmias, myocarditis, or cardio-myopathies were recruited. The control group consisted of healthy age- and sex-matched children. For each participant, peripheral venous blood was collected for plasma isolation and miRNA profiling. The expression of miR-1-3p, miR-let-7b-5p, miR-21-5p, miR-26b-5p, and UniSp6 molecules was analyzed using the comparative cycle threshold delta Ct (ΔCt) method. A p-value ≤ 0.05 was considered statistically significant. Results: miR-26b-5p was significantly downregulated in patients with cardiac disease compared with healthy controls. miR-21-5p and miR-26b-5p were downregulated in patients with ventricular arrhythmia. Moreover, miR-26b-5p was downregulated in arrhythmia in general. We found no significant difference in the expression of miR-1-3p, miR-let-7b-5p, miR-21b-5p, and miR-26b-5p between patients with and without myocarditis, as well as with and without hypertrophic cardiomyopathy. Conclusions: miR-26b-5p may distinguish young patients with cardiovascular disease and those with arrhythmias from healthy individuals. miR-21-5p and miR-26b-5p may also be seen as potential biomarkers of ventricular arrhythmia. Further studies involving a larger sample size are required to obtain sufficient data and validate these findings. Full article
(This article belongs to the Special Issue MicroRNAs: Regulators of Cellular Fate)
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19 pages, 13469 KB  
Article
Omic Profiling of Extracellular Vesicles from Two Cord-Related Sources Reveals Divergent Effects on Melanogenesis
by Chia-Ni Hsiung, Wen-Yu Lien, Martin Sieber and Wen-Hsien Lin
Curr. Issues Mol. Biol. 2026, 48(4), 391; https://doi.org/10.3390/cimb48040391 - 10 Apr 2026
Viewed by 626
Abstract
Extracellular vesicles (EVs) mediate intercellular communication by delivering proteins and RNAs, with their molecular cargo often reflecting the biological context of their source. Perinatal tissues are promising sources of EV-related biomaterials with potential dermatologic applications. In this study, we compared EV-related molecular cargo [...] Read more.
Extracellular vesicles (EVs) mediate intercellular communication by delivering proteins and RNAs, with their molecular cargo often reflecting the biological context of their source. Perinatal tissues are promising sources of EV-related biomaterials with potential dermatologic applications. In this study, we compared EV-related molecular cargo from two umbilical cord-associated sources, umbilical cord mesenchymal stem cell (UCMSC)-derived EVs and cord blood plasma (CBP), to investigate whether these materials exhibit distinct functional effects on melanogenesis. UCMSC-derived EVs were isolated from conditioned culture medium and characterized using nanoparticle tracking analysis (NTA), cryo-electron microscopy (cryo-EM), and canonical EV marker detection, while cord blood samples were processed to obtain plasma following centrifugation and filtration, containing EVs together with soluble plasma components. Functional assays in the murine melanocyte cell line B16F10 demonstrated that UCMSC-derived EVs suppressed melanin production, whereas CBP treatment enhanced melanogenesis. Integrative omics analyses combining microRNAs (miRNAs) microarray profiling and proteomic characterization revealed distinct molecular signatures between UCMSC-derived EVs and CBP samples. Functional validation using miRNA mimic assays showed that selected miRNAs, including miR-6862-5p, miR-3622b-5p, miR-7847-3p, miR-6774-5p, and miR-4685-5p, reduced melanin production, whereas others, including miR-203a-3p, miR-126-3p, miR-139-5p, and miR-15b-5p, increased melanin levels. Pathway analysis using Ingenuity Pathway Analysis (IPA) (QIAGEN Inc.) associated these miRNA subsets with signaling pathways involved in melanogenesis. Together, these findings indicate that UCMSC-derived EVs and CBP exhibit opposite functional effects on melanogenesis and possess distinct miRNA and protein cargo profiles, providing potential molecular targets for modulating pigmentation and supporting the development of EV-related therapeutic strategies for pigmentation disorders. Full article
(This article belongs to the Special Issue Omics Analysis for Personalized Medicine)
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18 pages, 4271 KB  
Article
Bioinformatics Analysis of Ferroptosis-Related Driver Genes in Stanford Type A Aortic Dissection
by Ruizhi Nie, Weiqing Han and Jianjun Xu
Curr. Issues Mol. Biol. 2026, 48(4), 382; https://doi.org/10.3390/cimb48040382 - 7 Apr 2026
Viewed by 304
Abstract
Stanford type A aortic dissection (TAAD) is a life-threatening cardiovascular condition associated with high mortality. Ferroptosis has been implicated in TAAD pathogenesis, but comprehensive analyses and experimental validation of ferroptosis-related driver genes (FRDGs) remain limited. This study systematically investigated FRDGs in TAAD using [...] Read more.
Stanford type A aortic dissection (TAAD) is a life-threatening cardiovascular condition associated with high mortality. Ferroptosis has been implicated in TAAD pathogenesis, but comprehensive analyses and experimental validation of ferroptosis-related driver genes (FRDGs) remain limited. This study systematically investigated FRDGs in TAAD using bioinformatics and experimental approaches. Differentially expressed ferroptosis-related driver genes (DEFRDGs) were identified by integrating the GSE153434 dataset with the FerrDb database. Functional enrichment analysis was subsequently performed, followed by the construction of a protein–protein interaction (PPI) network, assessment of immune cell infiltration, and prediction of potential miRNA interactions. Candidate hub genes were then validated using an independent cohort (GSE52093) and clinical tissue samples, with their diagnostic value evaluated via receiver operating characteristic (ROC) curve analysis and their protein expression confirmed by immunohistochemistry. We identified 25 DEFRDGs (17 upregulated, 8 downregulated) enriched in oxidative stress, iron binding, and ferroptosis/HIF-1 signaling pathways. Six hub genes (HIF1A, IL6, TIMP1, SAT1, HMOX1, LPCAT3) were significantly upregulated in validation cohorts, five genes (HIF1A, TIMP1, SAT1, HMOX1, LPCAT3) achieved an area under the curve (AUC) of 1.000, while IL6 also exhibited high diagnostic accuracy (AUC = 0.914). Fibroblast infiltration was elevated in TAAD tissues. Further miRNA interaction prediction revealed the potential involvement of miRNAs, such as miR-138-5p, miR-18b-5p, miR-199a-5p, miR-185-5p, miR-506-3p and miR-4644. Immunohistochemistry confirmed increased protein expression of HIF1A, SAT1, and LPCAT3. These three genes emerge as key ferroptosis-related drivers in TAAD. Their consistent upregulation and strong diagnostic performance support ferroptosis as a potential therapeutic target and provide a basis for mechanism-focused interventions. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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14 pages, 948 KB  
Article
Urinary miRNA Analysis for Clear Cell Renal Cell Carcinoma: miR-20a as a Key Endogenous Normalizer
by Giovanni Cochetti, Giacomo Vannuccini, Matteo Mearini, Alessio Paladini, Francesca Cocci, Raffaele La Mura, Daniele Mirra, Giuseppe Giardino and Ettore Mearini
Int. J. Mol. Sci. 2026, 27(7), 3323; https://doi.org/10.3390/ijms27073323 - 7 Apr 2026
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Abstract
Urinary microRNAs (miRNAs) are promising noninvasive biomarkers for cancer detection, but their clinical utility is reduced by inconsistent normalization strategies, reducing reproducibility and comparability across studies. In this study, we assessed the stability of miR-20a as an endogenous normalizer for urinary miRNA profiling [...] Read more.
Urinary microRNAs (miRNAs) are promising noninvasive biomarkers for cancer detection, but their clinical utility is reduced by inconsistent normalization strategies, reducing reproducibility and comparability across studies. In this study, we assessed the stability of miR-20a as an endogenous normalizer for urinary miRNA profiling in clear cell renal cell carcinoma (ccRCC) while standardizing the pre-analytical phase using a urine stabilizing solution. Ninety-nine urine samples were analyzed: 47 from healthy individuals, 30 from ccRCC patients pre-surgery, and 22 post-operative patients. Six candidate miRNAs—miR-20a, miR-15b, miR-16, miR-15a, miR-210-3p, and miR-let-7b—were quantified via RT-qPCR. Stability analysis with RefFinder, integrating multiple algorithms (geNorm, normFinder, BestKeeper, and ΔCt methods), identified miR-20a as the most stable among the six candidates. Raw Ct values of miR-20a were normally distributed (Shapiro–Wilk test, p > 0.05), with no significant intergroup differences (one-way ANOVA, F(2.96) = 2.324, p = 0.103) and minimal intragroup variability (CV% 4.98–6.38). MiR-20a expression remained stable across different tumor staging, grading, and urine storage durations. These findings confirm miR-20a as a robust endogenous normalizer for urinary miRNA analyses and support the feasibility of developing reproducible urinary liquid biopsy workflows for ccRCC, even in settings where immediate sample processing is not feasible. Full article
(This article belongs to the Special Issue Roles of Non-Coding RNAs in Cancer)
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15 pages, 3735 KB  
Article
miRNA Profiling Reveals the Role of Gibberellin Signaling Pathway in Low-Nitrogen Stress Adaptation of Xinjiang Spring Wheat
by Xin Gao, Chunsheng Wang, Yumei Su, Hongzhi Zhang, Zhun Zhao, Lihong Wang, Zhong Wang, Junjie Han, Jianfeng Li and Yueqiang Zhang
Plants 2026, 15(7), 1095; https://doi.org/10.3390/plants15071095 - 2 Apr 2026
Viewed by 395
Abstract
Understanding the molecular mechanisms of low-nitrogen (LN) tolerance in common wheat (Triticum aestivum L.) is crucial for developing cultivars with improved nitrogen-use efficiency (NUE). In this study, a LN-tolerant cultivar (‘Xin Chun 29’, XC29) and a LN-sensitive cultivar (‘Xin Chun 11’, XC11) [...] Read more.
Understanding the molecular mechanisms of low-nitrogen (LN) tolerance in common wheat (Triticum aestivum L.) is crucial for developing cultivars with improved nitrogen-use efficiency (NUE). In this study, a LN-tolerant cultivar (‘Xin Chun 29’, XC29) and a LN-sensitive cultivar (‘Xin Chun 11’, XC11) were used to investigate miRNA-mediated post-transcriptional regulation under LN stress. A total of 822 miRNAs were identified across root and grain tissues, including 104 known miRNAs and several tissue-specific candidates. In roots, tae-miR395a and tae-miR444a were significantly upregulated in XC29 under LN stress, putatively targeting an F-box ubiquitin ligase gene and glutathione reductase gene, respectively. In grains, the tae-miR156/SBP module was upregulated in XC29, whereas tae-miR1118 and tae-miR9778 were downregulated in XC11, potentially suppressing a receptor kinase gene and calmodulin gene. KEGG analysis revealed that target genes of differentially expressed miRNAs were significantly enriched in plant hormone signal transduction, ubiquitin-mediated proteolysis, and nitrogen metabolism. Notably, within the hormone signaling category, the gibberellin (GA) branch was highlighted by the co-targeting of DELLA genes by tae-miR1130b-3p and tae-miR1120c-3p. To elucidate this regulatory hub, a putative miRNA-target network centered on DELLA proteins was constructed, further underscoring the centrality of gibberellin signaling in the LN adaptation process. These findings suggest potential key miRNA-target modules contributing to LN adaptive responses and may provide useful genetic resources for molecular design breeding of nitrogen-efficient wheat. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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