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Search Results (185)

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Keywords = miR-518f-5p

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20 pages, 4428 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 (registering DOI) - 13 Nov 2025
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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15 pages, 22820 KB  
Article
circ_0000132 Regulates Chicken Granulosa Cell Proliferation Apoptosis and E2/P4 Synthesis via miR-206 E2F5 Signaling
by Huanqi Yang, Wei Li, Guanhua Fu, Sihan Liu and Tenghe Ma
Int. J. Mol. Sci. 2025, 26(21), 10779; https://doi.org/10.3390/ijms262110779 - 5 Nov 2025
Viewed by 205
Abstract
This study investigates the regulatory role of circFBN1 in chicken follicular granulosa cells (GCs) and its underlying molecular mechanisms through the miR-206/E2F5 pathway. circFBN1 was found to significantly enhance GC proliferation and inhibit apoptosis, as evidenced by increased expression of proliferation-related genes (PCNA, [...] Read more.
This study investigates the regulatory role of circFBN1 in chicken follicular granulosa cells (GCs) and its underlying molecular mechanisms through the miR-206/E2F5 pathway. circFBN1 was found to significantly enhance GC proliferation and inhibit apoptosis, as evidenced by increased expression of proliferation-related genes (PCNA, CDK1, and CCND1) and decreased expression of apoptosis-related genes (Caspase-3). Additionally, circFBN1 overexpression promoted the secretion of estradiol (E2) and progesterone (P4) by upregulating steroidogenesis-related genes (StAR and CYP11A1). Mechanistic studies revealed that circFBN1 functions as a molecular sponge for miR-206, thereby alleviating its inhibitory effect on the target gene E2F5. Dual-luciferase reporter assays confirmed the specific binding between circFBN1 and miR-206. Overexpression of miR-206 had the opposite effects, inhibiting GC proliferation, inducing apoptosis, and reducing E2 and P4 secretion by downregulating StAR and CYP11A1. Furthermore, E2F5 was identified as a direct target of miR-206, and its knockdown significantly reduced GC proliferation, increased apoptosis, and decreased steroid hormone secretion. These findings elucidate the regulatory mechanisms of the circFBN1/miR-206/E2F5 axis in avian follicle development and provide potential molecular targets for improving poultry reproductive performance. Future research should focus on exploring the upstream regulators of this axis and its interactions with other signaling pathways. Full article
(This article belongs to the Section Biochemistry)
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17 pages, 1275 KB  
Article
miRNA Signatures in Endometrial Cancer: Implications for Oncogenesis and Polymerase Epsilon (POLE) Mutation Status
by Alexandros Lazaridis, Nikolas Dovrolis, Hector Katifelis, Despoina Myoteri, Iakovos Vlahos, Nikos F. Vlahos and Maria Gazouli
Int. J. Mol. Sci. 2025, 26(21), 10438; https://doi.org/10.3390/ijms262110438 - 27 Oct 2025
Viewed by 567
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression with critical roles in oncogenic signaling. Endometrial cancer (EC) has been redefined with the identification of POLE-ultramutated tumors which, despite their hypermutated phenotype, show more favorable prognosis. We profiled miRNA expression in tumor tissues from [...] Read more.
MicroRNAs (miRNAs) are key regulators of gene expression with critical roles in oncogenic signaling. Endometrial cancer (EC) has been redefined with the identification of POLE-ultramutated tumors which, despite their hypermutated phenotype, show more favorable prognosis. We profiled miRNA expression in tumor tissues from forty (40) EC patients and twenty (20) healthy controls using qPCR panels. POLE exonuclease domain mutations (P286R, V411L) were genotyped, and subgroup analyses were conducted between POLE-mutated (n = 7) and POLE-wild-type (n = 33) tumors. Bioinformatic analyses included validated miRNA–mRNA interactions, target enrichment, and Gene Ontology (GO) pathway mapping. Comparison of EC versus healthy endometrium revealed 50 significantly dysregulated (∣log2 (FoldReg)∣ > 1 and BH FDR < 0.05) miRNAs, including up-regulation of the oncogenic hsa-miR-181a-5p, hsa-miR-23a-3p, hsa-miR-200c-3p, and down-regulation of tumor-suppressive let-7 family members. Target enrichment implicated canonical oncogenic regulators such as MYC, TP53, and VEGFA. POLE-mutated tumor analysis demonstrated a miRNA signature, with 19 miRNAs significantly down-regulated, including let-7f-5p and hsa-miR-200b-3p. Findings for the EC versus healthy endometrium comparison were validated against TCGA-UCEC sequencing data which confirmed concordant dysregulation of key miRNAs across platforms. Our findings reveal that EC is characterized by widespread miRNA deregulation, with a unique global down-regulation signature in POLE-mutated tumors. These results highlight the potential of miRNAs as complementary biomarkers for classification and potential targets in EC. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Oncology)
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26 pages, 3716 KB  
Article
Ligusticum chuanxiong Hort. Targets hsa-miR-10a-5p to Potentially Induce Apoptosis and Modulate Lipid Metabolism in Glioblastoma: A Natural-Product-Based Therapeutic Strategy
by Xiao-Xuan Cai, Hua-Li Zuo, Jing Li, Hsi-Yuan Huang, Li-Ping Li, Jie Ni, Pei-Sen Wu, Xiao-Yuan Xu, Dan Zhang, Yue-Yang Xie, Hsien-Da Huang and Yang-Chi-Dung Lin
Pharmaceuticals 2025, 18(10), 1553; https://doi.org/10.3390/ph18101553 - 15 Oct 2025
Viewed by 454
Abstract
Background/Objectives: Glioblastoma (GBM), the most aggressive primary malignant brain tumor, has a dismal prognosis and limited treatment options. The dried rhizome of Ligusticum chuanxiong Hort. (Chuanxiong, CX) is a traditional Chinese medicinal herb frequently prescribed in formulas intended to invigorate blood circulation. CX [...] Read more.
Background/Objectives: Glioblastoma (GBM), the most aggressive primary malignant brain tumor, has a dismal prognosis and limited treatment options. The dried rhizome of Ligusticum chuanxiong Hort. (Chuanxiong, CX) is a traditional Chinese medicinal herb frequently prescribed in formulas intended to invigorate blood circulation. CX also exhibits anti-glioma activity, but its molecular mechanisms remain incompletely understood. Methods: In this study, we combined transcriptomics and Raman spectroscopy to investigate the effects of reconstituted CX-dispensing granules (hereafter referred to as CXG solution) on U87MG cells, suggesting their dual role in promoting cell death and modulating collagen deposition and lipid metabolism. Results: Mechanistically, we demonstrated that the CXG solution downregulates hsa-miR-10a-5p, which directly targets BCL2L11, known to induce pro-apoptotic effects, as validated by qPCR and dual-luciferase reporter assays. Furthermore, the CXG solution and hsa-miR-10a-5p suppress lipid metabolism through a coherent feed-forward loop via targeting transcription factors SREBF1 and E2F1. An electrophoretic mobility shift assay (EMSA) confirmed E2F1 binds to the hsa-miR-29a promoter, leading to the synergistic repression of hsa-miR-29a-3p by SREBF1 and E2F1. Network pharmacology analysis combined with molecular docking suggested that the ferulic acid and adenosine in CX potentially modulate EGFR-the E2F1-hsa-miR-10a-5p axis. Conclusions: These findings elucidate CX’s multi-target anti-GBM mechanisms and propose a novel therapeutic strategy combining metabolic intervention with miRNA-targeted therapy, providing novel insights into feed-forward loop regulation in miRNA networks. Full article
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20 pages, 1631 KB  
Article
Effects of a Bacillus licheniformis Fermentation Extract and Monensin on the Rumen and Hindgut Microbiota Composition of Lactating Dairy Cows
by Phoebe Hartoonian, Lucille C. Jonas, Shedrack Omale, Sydney Rigert, Catherine Bradley, Erin Horst, Donald Beitz, Stephan Schmitz-Esser and Ranga Appuhamy
Animals 2025, 15(20), 2980; https://doi.org/10.3390/ani15202980 - 15 Oct 2025
Viewed by 490
Abstract
This research reports ruminal and fecal microbiota composition of lactating dairy cows enrolled in a study aimed at investigating the effects of a fermentation extract derived from Bacillus licheniformis (BLFE), monensin (Rumensin®; R), and their interactions on feed efficiency (FE, FE [...] Read more.
This research reports ruminal and fecal microbiota composition of lactating dairy cows enrolled in a study aimed at investigating the effects of a fermentation extract derived from Bacillus licheniformis (BLFE), monensin (Rumensin®; R), and their interactions on feed efficiency (FE, FE = milk yield/DMI). In a completely randomized design, 48 Holstein cows at 108 ± 35 days in milk were matched for parity and assigned to monensin (0 or 17.6 g/kg of DM) and BLFE (0 or 166 mg/kg of DM) in a 2 × 2 factorial arrangement. Treatments were fed daily for 63 d, including a 21 d adaptation period followed by a 42 d measurement period (P2). On d 38 and d 39 of P2, rumen-fluid (RF) and fecal samples were collected. DNA from RF and feces was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq platform. Fecal and RF volatile fatty acid (VFA) concentrations were analyzed, and propionate/acetate (P: A) was determined. The BLFE increased milk yield (3.3 kg/d) and FE (1.20 to 1.28), when fed alone rather than with monensin, while monensin increased energy-corrected milk yield (2.5 kg/d, p < 0.05), regardless of the BLFE in the diet. The BLFE tended to increase ruminal Firmicutes/Bacteroidetes (F: B) when fed alone, while alpha and beta diversities remained unmodified. The BLFE increased the abundances of Bifidobacterium (p = 0.02) and Erysipelotrichaceae_UCG-002 (p = 0.01) in RF, whereas monensin increased and decreased the abundances of Oscillospirales_ge (p = 0.02) and an unclassified Clostridia genus (p = 0.03), respectively. The monensin-suppressed Clostridia were negatively associated with ruminal P: A (r = −0.66; p < 0.01) and feed efficiency (r = −0.30; p = 0.04). The BLFE and monensin interactively affected several fecal genera (p < 0.05), but they had negligible or weak correlations with fecal P: A and FE. Overall, the results showed the ability of dietary supplementations of monensin and BLFE to increase milk production performance and FE by modulating ruminal rather than lower-gut microbiota composition, this is predominantly attributed to the ratio between the Firmicutes and Bacteroidetes abundances in lactating dairy cows. Full article
(This article belongs to the Section Animal Nutrition)
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14 pages, 1530 KB  
Article
miR-129 as a Molecular Biomarker in Gastric Cancer and Its Association with Neurodegenerative and Vascular Pathology
by Sabrina Birsan, Adrian-Gheorghe Boicean, Paula Anderco, Cristian Ichim, Samuel Bogdan Todor, Roman Iulian, Blanca Grama, Anca-Rafila Stîngaciu, Olga Brusnic, Tiberia Ilias and Corina Roman-Filip
Life 2025, 15(10), 1603; https://doi.org/10.3390/life15101603 - 14 Oct 2025
Viewed by 487
Abstract
Background: MicroRNA-129 (miR-129) is a tumor suppressor involved in regulating oncogenic pathways, but its role in gastric adenocarcinoma and its potential connections to vascular and neurological dysfunction remain insufficiently defined. Objectives: To assess gastric juice-derived miR-129 as a diagnostic and prognostic biomarker for [...] Read more.
Background: MicroRNA-129 (miR-129) is a tumor suppressor involved in regulating oncogenic pathways, but its role in gastric adenocarcinoma and its potential connections to vascular and neurological dysfunction remain insufficiently defined. Objectives: To assess gastric juice-derived miR-129 as a diagnostic and prognostic biomarker for gastric cancer and to explore its associations with systemic inflammation, vascular impairment, and neurodegenerative changes. Methods: A prospective study was conducted in 38 patients undergoing upper gastrointestinal endoscopy (22 with histologically confirmed gastric adenocarcinoma, 16 controls). Gastric juice was aspirated prior to biopsy, and miR-129-2-3p expression was quantified by means of RT-qPCR normalized to U6 RNA. Tumor stage, serum biomarkers (CEA, CA 19-9, LDH, and CRP), carotid index (Doppler ultrasound), and neuroimaging (MRI) were recorded. Statistical analyses included ANOVA, Mann–Whitney U, ROC curve analysis, and correlation testing. Results: miR-129 expression was significantly reduced in gastric cancer compared with controls (ANOVA: F(3,34) = 3.70, p = 0.021, η2 = 0.25). ΔCt values increased progressively from controls to T2–T4 tumors, indicating stage-dependent downregulation. ROC analysis demonstrated moderate diagnostic performance (AUC = 0.75, 95% CI 0.54–0.92). Lower miR-129 levels correlated inversely with serum tumor markers (CEA, CA 19-9), LDH, and CRP. Patients with elevated carotid index (>1.3) and abnormal brain imaging findings exhibited significantly lower miR-129 expression (both p < 0.05). Conclusion: Gastric juice-derived miR-129 is downregulated in gastric adenocarcinoma, with progressive decline across tumor stages. Its inverse association with systemic tumor and inflammatory markers, as well as vascular and neurological impairment, suggests that miR-129 may function as a minimally invasive, multi-system biomarker for integrated cancer and vascular–neurological risk assessment. Full article
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18 pages, 6821 KB  
Article
Multi-Omics Integration Reveals PBDE-47 as an Environmental Risk Factor for Intracranial Aneurysm via F2R-Mediated Metabolic and Epigenetic Pathways
by Hongjun Liu, Jinliang You, Junsheng Bai, Dilaware Khan and Sajjad Muhammad
Brain Sci. 2025, 15(10), 1091; https://doi.org/10.3390/brainsci15101091 - 9 Oct 2025
Viewed by 554
Abstract
Background: Intracranial aneurysm (IA) rupture is a life-threatening cerebrovascular event with a mortality rate of up to 40%, affecting approximately 500,000 people globally each year. Although environmental pollutants such as 2,2′,4,4′-tetrabromodiphenyl ether (PBDE-47) have been implicated in the pathogenesis of IA, the causal [...] Read more.
Background: Intracranial aneurysm (IA) rupture is a life-threatening cerebrovascular event with a mortality rate of up to 40%, affecting approximately 500,000 people globally each year. Although environmental pollutants such as 2,2′,4,4′-tetrabromodiphenyl ether (PBDE-47) have been implicated in the pathogenesis of IA, the causal relationship and underlying mechanisms remain unclear. This study aims to systematically explore the potential causal role of PBDE-47 in the development of IA by integrating multi-omics approaches. Methods: We utilized the UK Biobank Drug Proteomics Project (UKB-PPP) genome-wide association study (GWAS) data, including 2940 plasma proteins and 1400 metabolites, along with IA genetic data from 456,348 individuals, to perform a two-sample Mendelian randomization (MR) analysis. Instrumental variables were selected based on genome-wide significance (p < 5 × 10−8) or suggestive thresholds (p < 5 × 10−5). Analytical methods included inverse variance weighting (IVW), MR-Egger, weighted median, MR-PRESSO, and Steiger filtering for sensitivity analysis. Molecular docking and 100-nanosecond molecular dynamics simulations were used to evaluate interactions between PBDE-47 and proteins. Mediation analysis assessed the roles of plasma metabolites and miRNAs, and SMR-HEIDI tests were used to verify causal relationships. Results: MR analysis identified 93 plasma proteins potentially causally associated with IA, including 53 protective factors and 40 risk factors. By integrating PBDE-47 targets, IA-related genes, and metabolite-related genes, we identified 15 hub genes. Molecular docking revealed potential binding between PBDE-47 and F2R (binding energy: −5.516 kcal/mol), and SMR-HEIDI testing supported F2R as a potential causal risk factor for IA. Molecular dynamics simulations indicated the stability of the complex structure. Mediation analysis suggested that F2R may influence IA risk through eight plasma metabolites, and miR-130b-3p may indirectly promote IA development by upregulating F2R. Conclusions: Our findings suggest that exposure to PBDE-47 may have a potential causal relationship with IA risk, potentially mediated through the “PBDE–47–F2R–metabolite–miRNA” regulatory axis. These results provide preliminary evidence for early diagnostic biomarkers and targeted interventions for IA. The multi-omics analytical framework established in this study offers new insights into environmental determinants of neurovascular diseases, although further validation is needed to address potential limitations. Full article
(This article belongs to the Section Environmental Neuroscience)
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17 pages, 1488 KB  
Communication
Significant Association Between Abundance of Gut Microbiota and Plasma Levels of microRNAs in Individuals with Metabolic Syndrome and Their Potential as Biomarkers for Metabolic Syndrome: A Pilot Study
by Sanghoo Lee, Jeonghoon Hong, Yiseul Kim, Hee-Ji Choi, Jinhee Park, Jihye Yun, Yun-Tae Kim, Kyeonghwan Choi, SaeYun Baik, Mi-Kyeong Lee and Kyoung-Ryul Lee
Genes 2025, 16(10), 1161; https://doi.org/10.3390/genes16101161 - 30 Sep 2025
Viewed by 413
Abstract
Background/Objectives: The relationship between gut microbiota (GM) and microRNAs (miRs) related to lipid metabolism in individuals with metabolic syndrome (MetS) remains unclear. This pilot study examined the relationship between Bacteroidetes and Firmicutes abundance at the phylum level and the plasma levels of miR-122 [...] Read more.
Background/Objectives: The relationship between gut microbiota (GM) and microRNAs (miRs) related to lipid metabolism in individuals with metabolic syndrome (MetS) remains unclear. This pilot study examined the relationship between Bacteroidetes and Firmicutes abundance at the phylum level and the plasma levels of miR-122 and miR-370, both of which are associated with lipid metabolism, in Korean individuals with MetS and in healthy controls. We also evaluated the potential of these miRs as biomarkers for MetS. Methods: This study enrolled 7 individuals with MetS and 8 controls. The abundance of GM was analyzed by 16S rRNA amplicon sequencing. To evaluate the relationship between the dominant phyla in the 2 groups, the log ratio of Firmicutes to Bacteroidetes (F/B) was calculated using a centered log-ratio (CLR) transformation. The abundance of the 2 plasma miRs was also quantified by real-time quantitative PCR (RT-qPCR). Pearson’s and Spearman’s correlation analyses were then performed to evaluate the relationship between Bacteroidetes and Firmicutes abundance, the clinical parameters, and plasma levels of the 2 miRs. Additionally, the area under the curve (AUC) value of the receiver operating characteristic (ROC) curve was calculated to evaluate the potential of the 2 miRs as MetS biomarkers. Results: The 2 most abundant phyla were Bacteroidetes and Firmicutes. Bacteroidetes made up an average of 24.7% in the MetS group and 69.7% in the control group. Meanwhile, the average abundance of Firmicutes was 69.8% in the MetS group and 26.5% in the control group. The log F/B ratios in the MetS and control groups were 0.7 ± 0.5 and −0.4 ± 0.1 (p < 0.001), respectively. FDR analysis revealed significant correlations between Bacteroidetes abundance and BMI, DBP, FBG, total chol, insulin and HOMA-IR (FDR-adjusted p < 0.05), as well as between Firmicutes abundance and BMI, FBG, total chol, insulin and HOMA-IR (FDR-adjusted p < 0.05). Plasma levels of the 2 miRs differed significantly between the MetS and control groups: miR-122 (1.43 vs. 0.73; p = 0.0065) and miR-370 (1.39 vs. 0.83; p = 0.0089). The AUC values for miR-122 and miR-370 were 0.946 (p < 0.001) and 0.964 (p < 0.001), respectively. Pearson’s and Spearman’s correlation analyses revealed significant negative correlations between Bacteroidetes abundance and levels of miR-122 (p = 0.0048 and p = 0.0045, respectively) and miR-370 (p = 0.0003 and p < 0.0001, respectively), as well as significant positive correlations between Firmicutes abundance and levels of miR-122 (p = 0.0038 and p = 0.0027, respectively) and miR-370 (p = 0.0004 and p < 0.0001, respectively). However, as our exploratory findings were based on a small sample size, the high correlation results may partly reflect the separation between the MetS and control groups. Conclusions: Our exploratory findings suggest that the GM abundances of individuals with MetS may be significantly associated with plasma levels of miR-122 and miR-370, which are related to lipid metabolism. These miRs may therefore serve as potential MetS biomarkers. Full article
(This article belongs to the Section RNA)
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29 pages, 1843 KB  
Article
QMR® and Patient Blood-Derived Secretome Modulate RPE microRNA Networks Under Oxidative Stress
by Simona Alibrandi, Domenico Mordà, Concetta Scimone, Angela D’ascola, Federica Aliquò, Alessandro Pozzato, Sergio Zaccaria Scalinci, Rosalia D’Angelo, Antonina Sidoti and Luigi Donato
Int. J. Mol. Sci. 2025, 26(17), 8614; https://doi.org/10.3390/ijms26178614 - 4 Sep 2025
Viewed by 812
Abstract
Oxidative stress destabilizes microRNA homeostasis in the retinal pigment epithelium (RPE), driving apoptosis and the epithelial-to-mesenchymal transition, which contribute to age-related macular degeneration. We investigated whether Quantum Molecular Resonance (QMR®) electrostimulation, alone or combined with Patient Blood-Derived (PBD) secretoma, can reprogram [...] Read more.
Oxidative stress destabilizes microRNA homeostasis in the retinal pigment epithelium (RPE), driving apoptosis and the epithelial-to-mesenchymal transition, which contribute to age-related macular degeneration. We investigated whether Quantum Molecular Resonance (QMR®) electrostimulation, alone or combined with Patient Blood-Derived (PBD) secretoma, can reprogram the RPE miRNome and mitigate stress-induced damage. Human ARPE-19 cells were exposed to tert-butyl-hydroperoxide and treated with QMR®, PBD secretome, or their combination. The deep sequencing of small RNAs at 24 h and 72 h, followed by differential expression and pathway enrichment analyses, delineated treatment-driven miRNA signatures. Oxidative stress deregulated > 50 miRNAs, enriching pro-apoptotic, fibrotic, and inflammatory pathways. QMR® restored roughly 40% of these miRNAs and upregulated additional cytoprotective species such as miR-590-3p, a known regulator of the NF-κB and NLRP3 pathways according to validated target databases. While these observations suggest the potential involvement of inflammatory and stress-related cascades, functional assays will be required to directly confirm such effects. Secretome treatment preferentially increased anti-inflammatory miR-146a-5p and regenerative miR-204-5p while suppressing pro-fibrotic let-7f-5p. Combined QMR® + secretome triggered the broadest miRNA response, normalizing over two-thirds of stress-altered miRNAs. These changes are predicted to influence antioxidant, anti-apoptotic, and anti-fibrotic pathways, although they did not translate into additional short-term cytoprotection compared with QMR® alone. These data indicate that QMR® and PBD secretome modulate complementary miRNA programs that converge on stress response networks. This broader molecular reprogramming may reflect regulatory complementarity, but functional validation is needed to determine whether it provides benefits beyond those observed with QMR® alone. These findings offer molecular insights into potential non-invasive, cell-free strategies for retinal degeneration, although in vivo validation will be required before any clinical translation to Age-Related Macular Degeneration (AMD) therapy. Full article
(This article belongs to the Special Issue Unravelling Functional Biology in Retinal Dystrophies and Eye Disease)
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15 pages, 1834 KB  
Article
Serum Levels of miR-34a-5p, miR-30b-5p, and miR-140-5p Are Associated with Disease Activity and Brain Atrophy in Early Multiple Sclerosis
by Riccardo Orlandi, Leopoldo Torresan, Francesca Gobbin, Elisa Orlandi, Macarena Gomez Lira and Alberto Gajofatto
Int. J. Mol. Sci. 2025, 26(17), 8597; https://doi.org/10.3390/ijms26178597 - 4 Sep 2025
Viewed by 763
Abstract
In recent years, research has focused on biomarkers as key tools to predict clinical outcomes and guide therapeutic decisions in Multiple Sclerosis (MS). MicroRNAs (miRs)—small non-coding RNA molecules that regulate gene expression at the post-transcriptional level—have emerged as promising biomarkers in MS due [...] Read more.
In recent years, research has focused on biomarkers as key tools to predict clinical outcomes and guide therapeutic decisions in Multiple Sclerosis (MS). MicroRNAs (miRs)—small non-coding RNA molecules that regulate gene expression at the post-transcriptional level—have emerged as promising biomarkers in MS due to their accessibility in biological fluids. This study investigates the role of specific serum miRs mainly involved in immune response regulation as potential prognostic biomarkers in MS, focusing on young patients with recent diagnosis. The study had a prospective design, involving a cohort of patients followed in the Hub and Spoke MS network of Verona province. Fifty-one patients (33F) aged 18–40 years with recent MS diagnosis (≤2 years; 45 relapsing-remitting, 6 primary progressive) were consecutively enrolled. At baseline, serum samples were collected for miR analysis alongside clinical-demographic and MRI data, including T2 lesion volume, normalized brain volume (NBV), gray matter volume, white matter volume (WMV) calculated at baseline and annual percentage brain volume change (PBVC) and occurrence of new T2 or gadolinium-enhancing (Gd+) lesions on follow-up scans. Candidate miRs were chosen based on their potential biological role in MS pathogenesis reported in the literature. miRs assays were done using real-time PCR and expressed as a ratio relative to a normalizer (i.e., miR-425-5p). Levels of miR-34a-5p were significantly higher in patients with Gd+ lesions (p < 0.001) and correlated to lower NBV (rho = −0.454, p = 0.001) and WMV (rho = −0.494, p < 0.001). Conversely, miR-140-5p exhibited a protective effect against occurrence of new T2 or Gd+ lesions over time (HR 0.43; IC 95% 0.19–0.99; p = 0.048). Additionally, miR-30b-5p correlated directly with PBVC (adjusted rho = −0.646; p < 0.001). These findings support the potential of serum miR-34a-5p, miR-140-5p, and miR-30b-5p as markers of disease activity and progression in patients with recently diagnosed MS. Full article
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16 pages, 1298 KB  
Article
Genetic Effects of Chicken Pre-miR-3528 SNP on Growth Performance, Meat Quality Traits, and Serum Enzyme Activities
by Jianzhou Shi, Jinbing Zhao, Bingxue Dong, Na Li, Lunguang Yao and Guirong Sun
Animals 2025, 15(15), 2300; https://doi.org/10.3390/ani15152300 - 6 Aug 2025
Viewed by 582
Abstract
The aim was to investigate the genetic effects of a SNP located in the precursor region of gga-miR-3528. (1) Single-nucleotide polymorphisms within precursor regions of microRNAs play crucial biological roles. (2) Utilizing a Gushi–Anka F2 resource population (n = 860), [...] Read more.
The aim was to investigate the genetic effects of a SNP located in the precursor region of gga-miR-3528. (1) Single-nucleotide polymorphisms within precursor regions of microRNAs play crucial biological roles. (2) Utilizing a Gushi–Anka F2 resource population (n = 860), we screened and validated miRNA SNPs. A SNP mutation in the miR-3528 precursor region was identified. Specific primers were designed to amplify the polymorphic fragment. Genotyping was performed for this individual SNP across the population, using the MassArray system. Association analyses were conducted between this SNP and chicken growth and body measurement traits, carcass traits, meat quality traits, and serum enzyme activities. (3) The rs14098602 (+12 bp A > G) was identified within the precursor region of gga-miR-3528. Significant associations (p < 0.05) were observed between this SNP and chicken growth traits (body weight at the age of 0 day, body weight at the age of 2 weeks, and body weight at the age of 4 weeks), carcass traits (evisceration weight), meat quality traits (subcutaneous fat rate and pectoral muscle density), and serum enzyme activities (total protein, albumin, globulin, cholinesterase, and lactate dehydrogenase). (4) These findings suggest that the polymorphism at rs14098602 may influence chicken growth, meat quality, and serum biochemical indices, through specific mechanisms. The gga-miR-3528 gene likely plays an important role in chicken development. Therefore, this SNP can serve as a molecular marker for genetic breeding and auxiliary selection of growth-related traits, facilitating the rapid establishment of elite chicken populations with superior genetic resources. Full article
(This article belongs to the Section Poultry)
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24 pages, 4372 KB  
Article
PavSPL Expression Dynamics in Fruits and Seeds and in Relation to Endocarp Lignification Status During the Transition from Development to Ripening in Sweet Cherry
by Matías Zavala, Marcela Menares, Orlando Acevedo, Mirna Melo, Carlos Nuñez, Camila Arancibia, Romina Pedreschi, José Manuel Donoso, Lee A. Meisel, Jonathan E. Maldonado and Nathalie Kuhn
Horticulturae 2025, 11(6), 706; https://doi.org/10.3390/horticulturae11060706 - 19 Jun 2025
Cited by 1 | Viewed by 981
Abstract
The transition to ripening in non-climacteric species is governed by several signals, including hormones that enhance or counteract the abscisic acid (ABA)-promoting effect. The SQUAMOSA Promoter-binding protein-Like (SPL) transcription factors are involved in ripening through the modulation of anthocyanin biosynthesis. In sweet cherry [...] Read more.
The transition to ripening in non-climacteric species is governed by several signals, including hormones that enhance or counteract the abscisic acid (ABA)-promoting effect. The SQUAMOSA Promoter-binding protein-Like (SPL) transcription factors are involved in ripening through the modulation of anthocyanin biosynthesis. In sweet cherry fruits, several miR156-targeted PavSPLs are expressed before and during ripening. Recently, some PavSPLs were found in the transition from development to ripening in cultivars contrasting in maturity time. Additionally, several forms of miR156 were expressed in sweet cherry seeds of an early-season cultivar. In this work, we addressed the relevance of endocarp lignification and PavSPLs expression for the transition to ripening. First, we characterized early- and late-season sweet cherry cultivars, ‘Celeste’ and ‘Regina’, focusing on fruit and seed development, endocarp lignification, and PavSPL expression profile. Fruit growth dynamics revealed an earlier onset of color development and lignification in ‘Celeste’, while ‘Regina’ exhibited a prolonged lag phase and delayed embryo development. Transcript profiling at the light green stage showed a higher expression of PavSPL genes in fruits and identified cultivar-specific expressions, especially between ‘Regina’ and ‘Celeste’ seeds. Co-expression networks linked PavSPLs to genes involved in lignin and anthocyanin biosynthesis. We focused on PavSPL2 and PavSPL9, which were targeted by mtr-miR156a and gma-miR156f. Both PavSPLs and miRNAs were expressed in fruits and seeds at the yellow stage, an advanced point in the transition to ripening in sweet cherry. Exogenous application of auxin-related compounds in the mid-season cultivar ‘Lapins’ modulated endocarp lignification and pigmentation. Notably, p-IBA treatment, which enzymatically targets the lignin pathway, transiently increased anthocyanin accumulation and reduced lignin deposition, effects that correlated with the downregulation of PavSPL gene expression. These findings highlight the interplay between lignification, color evolution, and pigment biosynthesis during the transition from development to ripening in sweet cherry fruits, and suggest a role for PavSPL genes in this transition. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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29 pages, 539 KB  
Review
Exosomal Communication Between Cumulus–Oocyte Complexes and Granulosa Cells: A New Molecular Axis for Oocyte Competence in Human-Assisted Reproduction
by Charalampos Voros, Diamantis Athanasiou, Despoina Mavrogianni, Antonia Varthaliti, Kyriakos Bananis, Antonia Athanasiou, Aikaterini Athanasiou, Georgios Papadimas, Athanasios Gkirgkinoudis, Ioannis Papapanagiotou, Kyriaki Migklis, Dimitrios Vaitsis, Aristotelis-Marios Koulakmanidis, Dimitris Mazis Kourakos, Sofia Ivanidou, Maria Anastasia Daskalaki, Marianna Theodora, Panagiotis Antsaklis, Dimitrios Loutradis and Georgios Daskalakis
Int. J. Mol. Sci. 2025, 26(11), 5363; https://doi.org/10.3390/ijms26115363 - 3 Jun 2025
Cited by 5 | Viewed by 2318
Abstract
Exosomal microRNAs (ex-miRs), encapsulated in extracellular vesicles (EVs), play a vital role in facilitating paracrine communication among granulosa cells (GCs), cumulus cells (CCs), and the oocyte inside follicular fluid (FF). These small non-coding RNAs are crucial for regulating folliculogenesis, oocyte maturation, and early [...] Read more.
Exosomal microRNAs (ex-miRs), encapsulated in extracellular vesicles (EVs), play a vital role in facilitating paracrine communication among granulosa cells (GCs), cumulus cells (CCs), and the oocyte inside follicular fluid (FF). These small non-coding RNAs are crucial for regulating folliculogenesis, oocyte maturation, and early embryonic development via modulating intracellular signaling networks. Dysregulation o has been associated with reproductive disorders such as polycystic ovarian syndrome (PCOS), diminished ovarian reserve (DOR), and inadequate ovarian response (POR), impacting oocyte quality and fertility outcomes. This narrative review consolidates molecular data from current human and animal studies regarding ex-miR expression patterns, functional targets, and pathway involvement within the context of assisted reproductive technologies (ARTs). A literature-based analysis was undertaken, focusing on signaling pathways, pathogenic processes, and clinical implications. Specifically, ex-miRs—such as miR-21, miR-34c, miR-143-3p, miR-155-5p, miR-339-5p, and miR-424-5p—were identified as regulators of critical pathways including phosphoinositide 3-kinase (PI3K)–AKT, ERK1/2, TGF-β/SMAD, and Rb–E2F1. These ex-miRs regulate apoptosis, glycolysis, mitochondrial function, and cell cycle expansion to influence oocyte competence. Pathological patterns in PCOS and POR are associated with altered ex-miR expression that disrupts metabolic and developmental signaling. Research utilizing animal models confirmed that modifications in EV-associated miRNA influence in vitro maturation (IVM) efficiency and blastocyst quality. Ex-miRs serve as intriguing non-invasive biomarkers and potential therapeutic targets for ARTs. Their mechanical involvement in oocyte and follicular physiology positions them for integration into forthcoming precision-based infertility therapies. For its implementation in reproductive medicine, EV profiling requires standardization and further functional validation in clinical environments. Full article
(This article belongs to the Special Issue Molecular Advances in Obstetrical and Gynaecological Disorders)
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18 pages, 2590 KB  
Article
Circulating miR-10b-5p, miR-193a-3p, and miR-1-3p Are Deregulated in Patients with Heart Failure and Correlate with Hormonal Deficiencies
by Anna Maria Grimaldi, Roberta D’Assante, Francesco Fiore, Simone Marcella, Stefania Paolillo, Francesco Cacciatore, Valentina Mercurio, Eduardo Bossone, Antonio Cittadini, Carlo Gabriele Tocchetti and Mariarosaria Incoronato
Int. J. Mol. Sci. 2025, 26(11), 5225; https://doi.org/10.3390/ijms26115225 - 29 May 2025
Cited by 1 | Viewed by 900
Abstract
Heart failure (HF) is among the most important causes of worldwide morbidity, hospitalisation, and mortality. A reduction in anabolic hormonal axes seems to potentially play an important role in chronic HF progression and prognosis. Several lines of evidence support the critical roles of [...] Read more.
Heart failure (HF) is among the most important causes of worldwide morbidity, hospitalisation, and mortality. A reduction in anabolic hormonal axes seems to potentially play an important role in chronic HF progression and prognosis. Several lines of evidence support the critical roles of miRNAs in the endocrine system, and differentially expressed miRNA patterns were found to be able to detect HF. To date, the ability of miRNAs to detect HF patients affected by hormonal deficiencies has yet to be addressed. The aim of this study was to explore the association between circulating miRNA profiles and multiple hormonal deficiencies in HF patients to provide new insights into HF pathophysiology. The study cohort included 129 subjects (94 HF patients and 35 controls). Circulating miRNAs assayed in plasma samples were miR-1-3p, miR-10b-5p, miR-24-3p, miR-193a-5p, miR-454-3p, miR-503-5p, miR-551b-3p, and miR-598-3p. NT-proBNP, IGF-1, fT3, DHEA-S, testosterone, HF subtypes, and NYHA class were also evaluated. A multiple hormonal deficiency syndrome (MHDS) was defined as the presence of ≥two hormone deficiencies. We found that miR-10b-5p, miR-193a-5p, and miR-1-3p could distinguish chronic HF patients from controls. The identified miRNAs were downregulated in HF patients, particularly those with NYHA I-II classifications and pathological values of NT-proBNP. In addition, these three circulating miRNAs correlated with each other, and their deregulation seems to be influenced by hormone deficiencies, especially in patients with reduced ejection fraction. Among the three miRNAs, miR-10b-5p was the best able to diagnose chronic HF-MHDS patients (AUC = 0.8). These results support the clinical utility of miR-10b-5p, miR-193a-5p, and miR-1-3p in detecting HF patients, especially those with hormone deficiencies. Full article
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11 pages, 2145 KB  
Article
One-Pot Detection of miRNA by Dual Rolling Circle Amplification at Ambient Temperature with High Specificity and Sensitivity
by Wenhua Sun, Kunling Hu, Ziting Song, Ran An and Xingguo Liang
Biosensors 2025, 15(5), 317; https://doi.org/10.3390/bios15050317 - 15 May 2025
Viewed by 981
Abstract
Rolling circle amplification (RCA) at ambient temperature is prone to false positive signals during nucleic acid detection, which makes it challenging to establish an efficient RCA detection method. The false positive signals are primarily caused by binding of non-target nucleic acids to the [...] Read more.
Rolling circle amplification (RCA) at ambient temperature is prone to false positive signals during nucleic acid detection, which makes it challenging to establish an efficient RCA detection method. The false positive signals are primarily caused by binding of non-target nucleic acids to the circular single-stranded template, leading to non-specific amplification. Here, we present an RCA method for miRNA detection at 37 °C using two circular ssDNAs, each of which is formed by ligating the intramolecularly formed nick (without any splint) in a secondary structure. The specific target recognition is realized by utilizing low concentrations (0.1 nM) of circular ssDNA1 (C1). A phosphorothioate modification is present at G*AATTC on C1 to generate a nick for primer extension during the primer self-generated rolling circle amplification (PG-RCA). The fragmented amplification products are used as primers for the following RCA that serves as signal amplification using circular ssDNA2 (C2). Notably, the absence of splints and the low concentration of C1 significantly inhibits non-target binding, thus minimizing false positive signals. A high concentration (10 nM) of C2 is used to carry out linear rolling circle amplification (LRCA), which is highly specific. This strategy demonstrates a good linear response to 0.01–100 pM of miRNA with a detection limit of 7.76 fM (miR-155). Moreover, it can distinguish single-nucleotide mismatch in the target miRNA, enabling the rapid one-pot detection of miRNA at 37 °C. Accordingly, this method performs with high specificity and sensitivity. This approach is suitable for clinical serum sample analysis and offers a strategy for developing specific biosensors and diagnostic tools. Full article
(This article belongs to the Section Biosensors and Healthcare)
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