Search Results (732)

Despite major advances in lipid-lowering therapies, a significant unmet need remains, particularly for patients with homozygous familial hypercholesterolemia (HoFH), severe heterozygous familial hypercholesterolemia (HeFH), and those who fail to achieve guideline-recommended LDL-C targets. Nucleic acid-based therapeutics have emerged as a transformative approach for treating hypercholesterolemia. Antisense oligonucleotides and small interfering RNAs (siRNAs) have demonstrated durable hepatic gene silencing and have led to approved therapies, while gene replacement and in vivo genome-editing strategies offer the potential for long-lasting, and possibly one-time, interventions. In parallel, microRNAs (miRNAs) have attracted increasing interest because of their ability to coordinately regulate multiple genes involved in lipoprotein metabolism, cholesterol transport, and lipid homeostasis. Human genetic studies further support the importance of miRNA-mediated regulation, exemplified by a rare ~2.5 kb deletion in the distal LDLR 3′UTR (“del2.5”) that disrupts miRNA-binding sites and is associated with lifelong low LDL-C levels. This review summarizes recent advances, mechanisms of action, clinical progress, and remaining challenges across antisense oligonucleotides, siRNAs, gene therapy, genome editing, and emerging miRNA-based therapeutics for hypercholesterolemia. As an example of the latter approach, the liver-directed miR-30c analog C2 has demonstrated preclinical activity by coordinately reducing hepatic lipoprotein secretion and lipogenesis while enhancing cholesterol elimination, resulting in reduced LDL-C and atherosclerosis. However, it must be noted that these findings remain preclinical, and further optimization of delivery, pharmacokinetics, safety, and long-term efficacy will be required before clinical evaluation. Continued advances in RNA chemistry, targeted delivery, and genome engineering are expected to further expand the therapeutic landscape for dyslipidemia and cardiovascular disease. Full article

Grafting profoundly influences fruit tree performance, yet the molecular mechanisms underlying rootstock–scion interactions in mulberry (Morus multicaulis) remain poorly understood. To investigate the regulatory networks linking grafting to scion physiology, we performed an integrated analysis combining small RNA sequencing, transcriptome-based KEGG pathway assessment, and qRT-PCR validation of key target genes across five rootstock–scion combinations. High-throughput miRNA profiling of phloem tissues identified 71 conserved and 156 novel miRNAs, which exhibited distinct, genotype-dependent expression patterns. Recurrent activation of nutrient- and stress-responsive families (e.g., miR399, miR397, and miR395) was observed. Target prediction and functional enrichment analyses revealed that these miRNAs likely regulate pathways related to metabolic processes, hormone signaling, cell wall modification, and stress responses. The expression trends of their predicted target genes—including TCP4, Laccase-3, and ATP sulfurylase 1—were subsequently confirmed by qRT-PCR, revealing significant rootstock-specific regulation. Collectively, this study establishes a reference framework for elucidating the molecular mechanisms underlying scion biological processes in Morus species, which is of great significance for improving fruit quality, enhancing abiotic and biotic stress resistance, and boosting long-term planting productivity. Full article

Background: Camel husbandry underpins food security in drylands, and dromedary (Camelus dromedarius) milk is valued as a functional food whose composition is thought to be shaped by the desert forage that camels browse. Dietary plant microRNAs (miRNAs) have been proposed as one molecular route linking diet to mammalian physiology, and two interactions are widely cited from experimental reports: rice miR168a repressing LDLRAP1 and plant miR159 repressing TCF7. The hypothesis remains contested, however, and it has not been tested for camel forage against camel transcripts. Methods: We generated de novo, hairpin-based miRNA repertoires for three arid-zone forage plants relevant to camel feeding (Moringa oleifera, Ziziphus jujuba, Medicago sativa) and screened the mature miRNAs against 48,746 reconstructed C. dromedarius 3′-UTRs under stringent thresholds, retaining one transcript per gene, weighting interactions by read abundance, normalising scores for 3′-UTR length, and testing over-representation against a matched background. The two previously reported cross-kingdom pairs served as internal positive controls and seed-level grouping as a sensitivity control. Results: The three forages yielded 170 hairpin-validated miRNA loci (81 M. sativa, 49 Z. jujuba, 40 M. oleifera) peaking at 21 nt, collapsing to 116 mature sequences and 104 seed groups. The pooled read set was strongly concentrated: five mature sequences shared by all three species carried 51% of reads, miR159 alone 31%, and 19 sequences assignable to conserved miRBase families carried 64%. The pipeline recovered the reported miR168a–LDLRAP1 pairing in the camel; the miR159–TCF7 pairing, by contrast, was not recovered, although TCF7 was among the genes targeted by other plant miRNAs. Genome-wide, predicted targeting was sparse (median 2 miRNAs per gene) and no GO, KEGG or Hallmark category was enriched at either threshold (best FDR 0.56); the nominal p-value distribution was approximately uniform, giving no evidence of systematic enrichment under the tested framework. Targeting multiplicity scaled with 3′-UTR length (Pearson r = 0.63; Spearman ρ = 0.58), so apparent “hub” genes are largely long-3′-UTR genes. Of 19, 12 curated milk-fat and lactation genes were among predicted targets, without over-representation (Fisher p = 0.36). Conclusions: A sensitive, species-matched analysis recovered a previously reported cross-kingdom pairing yet found no coordinated enrichment of dietary plant miRNAs on the dromedary transcriptome, and showed that an individual cross-kingdom pairing cannot be assumed to transfer between mammalian species. The work provides a first forage miRNA resource in the context of camel nutrition, sets out a reusable, species-matched analytical framework for cross-kingdom claims, and narrows future experimental work to five abundant forage-derived sequences and a short list of candidate genes (LDLRAP1, TCF7/TCF7L2, PRLR, INSR). Full article

Background/Objectives: Preoperative discrimination of benign from malignant adnexal masses remains a major clinical challenge, and circulating microRNAs (miRNAs) are candidate non-invasive biomarkers. This exploratory, hypothesis-generating study—not a diagnostic validation study—evaluated serum hsa-miR-200c-3p as a candidate diagnostic biomarker for ovarian malignancy. Methods: Serum from 39 women with an adnexal mass and a surgical indication (20 benign, 19 malignant), all with histological confirmation, was analysed. Of 179 assayed miRNAs, 178 were tested for differential expression (miR-103a-3p as endogenous reference) using the Mann–Whitney U test with Benjamini–Hochberg false-discovery-rate (FDR) correction; hsa-miR-200c-3p, a pre-specified miR-200 family candidate, was evaluated by ROC analysis and compared with, and adjusted for, CA 125, HE4 and age. Results: The malignant group was substantially older and more frequently postmenopausal. Thirty-eight miRNAs were significant after FDR correction; hsa-miR-200c-3p was up-regulated in malignancy. In the complete-case analysis restricted to the 35 participants with a detectable marker (20 benign, 15 malignant), the AUC was 0.893 (95% CI 0.76–0.99); however, four high-grade serous carcinomas showed undetectable serum hsa-miR-200c-3p, and when these were included and imputed as low expression (all-case analysis, n = 39) the AUC fell to 0.705 (95% CI 0.51–0.88). hsa-miR-200c-3p did not demonstrate statistically superior performance to HE4 (AUC 0.93) or CA 125 (0.89), with overlapping confidence intervals; any incremental value beyond established markers and age was modest and exploratory. Conclusions: Serum hsa-miR-200c-3p is a preliminary candidate that requires prospective, age-matched, adequately powered validation with pre-specified assays and analysis plans. Full article

Triple-negative breast cancer (TNBC) remains a major therapeutic challenge due to pronounced molecular heterogeneity, transcriptional plasticity, and frequent treatment resistance. MicroRNA (miRNA)-based strategies have emerged as potential approaches for modulating dysregulated gene expression networks in TNBC; however, the contribution of understudied miRNA families to TNBC-associated regulatory programs remains incompletely understood. This study aimed to investigate the tumor-suppressive role of miR-548f-3p in TNBC and to identify candidate downstream effectors, with particular focus on ANP32E. An integrative analysis combining public transcriptomic datasets, clinical expression profiling, computational target prediction, network-based prioritization, pathway analysis, and single-cell transcriptomic assessment identified miR-548f-3p as consistently downregulated in TNBC. Among candidate downstream targets, ANP32E, a chromatin-associated regulator involved in H2A.Z histone variant dynamics, was identified as a potential effector exhibiting increased expression in TNBC and enrichment within malignant epithelial cell populations. An inverse association between miR-548f-3p and ANP32E expression was observed in patient-derived samples. In breast cancer cell models, miR-548f-3p mimic restoration increased apoptosis, promoted G₀/G₁ accumulation, and reduced migration- and invasion-associated readouts, although measurable effects were also observed in non-tumorigenic MCF-10A cells. These phenotypic changes were accompanied by reduced ANP32E expression at the protein level, indicating that ANP32E expression is responsive to miR-548f-3p restoration. This study supports miR-548f-3p as a candidate tumor-suppressive miRNA in TNBC. The reduction in ANP32E protein expression following miR-548f-3p restoration, together with computational, single-cell, and clinical expression evidence, supports ANP32E as an expression-responsive candidate downstream effector of miR-548f-3p. Further reporter-based and rescue experiments are required to confirm direct 3′UTR-mediated targeting and to define the mechanistic contribution of ANP32E within the broader miR-548f-3p regulatory network. Full article

Chronic hepatitis B virus (CHB) infection remains a major cause of hepatocellular carcinoma (HCC), yet the premalignant microenvironment that links to HBV-associated HCC (HBV-HCC) is still poorly defined. This review synthesizes evidence that HBV-infected hepatocytes function as signaling hubs that, through microRNA (miRNA)-regulated crosstalk with Kupffer cells, liver sinusoidal endothelial cells, hepatic stellate cells and cancer-associated fibroblasts (CAFs), progressively remodel the liver from an antiviral tissue into a premalignant and early tumor microenvironment. Across the HBV-HCC continuum, a core set of dysregulated miRNAs, including miR-21, miR-29a/b, miR-122, miR-146a, miR-155, miR-200a, miR-126, miR-210 and the miR-130/301 family, coordinates transition from innate antiviral responses to HSC activation, extracellular matrix deposition, mechanotransduction, angiogenesis, chronic inflammation and cancer-associated CAF programing. By mapping these stage-specific miRNA networks onto acute infection, CHB, early fibrogenesis, advanced fibrosis and CAF-rich dysplastic states, the review reframes HBV-HCC pathogenesis as a sequence of miRNA-guided hepatocyte–stromal states rather than a purely hepatocyte-intrinsic process. This perspective suggests that composite, cell-type-resolved miRNA signatures in serum or liver tissue could serve as biomarkers for identifying CHB patients who are entering a premalignant microenvironment before conventional surveillance markers become abnormal. It further highlights miRNA hubs that couple antiviral, fibrogenic, angiogenic and CAF-associated signaling as potential therapeutic targets for reprograming the HBV-driven premalignant microenvironment, with the long-term goal of intercepting HBV-HCC development at earlier, microenvironmentally defined stages. Full article

Background/Objectives: Carotid intima–media thickness (CIMT) is widely recognized as an established biomarker of systemic atherosclerosis and coronary artery disease (CAD). Nevertheless, the connection between circulating miR-29 family members, CIMT and CAD severity has not yet been determined. The aim of this study was to investigate the association of plasma miR-29a and miR-29c with CIMT and CAD severity. Methods: A total of 628 patients scheduled for elective coronary angiography were included in the study. CAD severity was estimated using the Gensini scoring system and was classified into mild, moderate, and severe categories. Additionally, CIMT was evaluated using high-resolution B-mode ultrasonography, while plasma miR-29a and miR-29c levels were detected using qRT-PCR. Results: CIMT increased significantly with CAD severity (0.76 ± 0.15, 0.94 ± 0.18, and 1.12 ± 0.22 mm for mild, moderate, and severe CAD, respectively; p < 0.001). MiR-29a expression progressively increased, whereas miR-29c expression decreased with advancing CAD (both p < 0.001). MiR-29a correlated positively with CIMT (r = 0.612) and Gensini score (r = 0.658), while miR-29c showed negative correlations (r = −0.527 and −0.584, respectively; all p < 0.001). CIMT, miR-29a, and miR-29c were found to be independently associated with CAD severity. Their combined model demonstrated a powerful association with severe CAD (AUC = 0.927; sensitivity 88.6%; specificity 84.1%). Conclusions: Plasma miR-29a and miR-29c are independent biomarkers of CIMT and CAD severity. Their combination with CIMT can improve diagnosis of severe CAD and may enhance cardiovascular risk stratification. Full article

Fibrosis emerges when normally self-limiting tissue repair fails to resolve and overlapping phases of injury, stromal activation, extracellular matrix (ECM) deposition and remodelling become sustained. MicroRNAs (miRNAs) shape this transition by coordinating signalling, cell-state and matrix programmes. Functionally, pro-fibrotic fibro-miRs amplify fibrogenic pathways, whereas anti-fibrotic miRNAs restrain fibroblast activation and ECM production; the miR-29 family is a principal member of the latter group. This review examines miR-29 family organisation, the regulation of miR-29b by transforming growth factor-β (TGF-β)/Smad and additional transcriptional and inflammatory inputs, and the molecular targets through which miR-29b controls collagen synthesis, processing and crosslinking. Direct canonical targets are distinguished from experimentally supported, predicted and indirect pathway components. Evidence is evaluated across fibroblasts and myofibroblasts, epithelial and endothelial cells, and pulmonary, hepatic, renal, cardiac, dermal and ocular fibrosis models. Therapeutic translation is considered in relation to miR-29b mimics and agomirs, local and tissue-targeted delivery, pharmacokinetics, dose control, off-target repression, immune activation and long-term safety. Overall, miR-29b remains a credible network-level anti-fibrotic candidate, but successful translation requires cell- and disease-specific target validation, selective delivery and preservation of physiological wound repair. Full article

Background: Autophagy is a process that diversely impacts the stages of both tumor initiation and progression. Elucidating the molecular mechanisms underlying autophagy and its role in tumorigenesis is a key component of anticancer strategies in both prostate cancer and other malignancies. Because advanced prostate cancer frequently exploits enhanced autophagy as a defense mechanism against therapy-induced stress (e.g., from abiraterone), the pharmacological modulation of miRNA levels presents a tremendous opportunity to block the tumor’s escape route and overcome drug resistance. Methods: A comprehensive literature review was conducted to evaluate the molecular pathways determining cancer cell survival and death. The analysis focused on the dual nature of autophagy (functioning as a ‘double-edged sword’) within the tumor microenvironment, microRNA (miRNA) regulatory networks, and the efficacy of synergistic therapeutic strategies in overcoming treatment resistance. Results: The primary focus of this paper is the dual and complex role of autophagy, which serves, on the one hand, as a cellular protective shield against metabolic stress—thereby facilitating metastasis—and, on the other hand, as a potential pathway leading to autophagic cell death. The progression of this crucial process is regulated by intricate interactions (crosstalk) with apoptotic pathways, mediated by Bcl-2 family proteins, key kinases (such as mTOR, JNK, and DAPK), and transcription factors, such as p53. Furthermore, the autophagic machinery is precisely regulated by specific miRNA molecules (e.g., miR-21, miR-141, and miR-375). These not only act as crucial intracellular modulators of autophagy but also serve as promising circulating biomarkers, enabling the monitoring of this process’s activity throughout disease progression. Conclusions: Autophagy, and in particular its modulation via miRNA signaling networks, represents a major and highly promising translational target. By directly impairing this autophagic survival mechanism, ‘double-hit’ combination therapies—integrating autophagy inhibitors (such as hydroxychloroquine or VPS34 inhibitors) with standard antiandrogen or cytotoxic agents—demonstrate promising preclinical potential in overcoming treatment resistance and favorably modulating the immune microenvironment in advanced prostate cancer. Full article

PBU (N-phenyl-N′-thiazolylurea) promotes callus induction and adventitious bud differentiation in eucalyptus, but the miRNA-mediated regulatory mechanisms underlying these effects remain unclear. In this study, calli of Eucalyptus urophylla × E. grandis clone DH32-29 with distinct phenotypes were cultured at four PBU concentrations (0, 0.1, 1 and 5 mg L⁻¹) and analyzed by small-RNA sequencing, targeted metabolomics, and qRT-PCR validation. A total of 114 common differentially expressed miRNAs were identified, targeting 610 mRNAs. Functional enrichment analysis revealed that these targets were predominantly associated with lignin metabolism, phenylpropanoid metabolism, biotin metabolism, tryptophan metabolism, protein processing in the endoplasmic reticulum, and galactose metabolism. Metabolomic profiling detected 3029 metabolites, with differential metabolites enriched in the ABC transporter pathway, galloyl sugar biosynthesis, and cofactor biosynthesis. Key miRNA families, including miR164, miR165/166, and miR396, exhibited PBU concentration-dependent expression patterns and were predicted, based on in silico target prediction and qRT-PCR co-expression, to be potentially associated with target genes involved in lignin biosynthesis, ROS-related metabolism, and cytokinin homeostasis; these regulatory relationships remain to be experimentally validated. Among the tested concentrations, 1 mg L⁻¹ PBU was the dosage associated with the strongest reprogramming of secondary metabolism and with metabolic signatures suggestive of better preserved redox homeostasis; future work will build on this reference dataset with quantitative regeneration phenotyping and direct redox measurements to confirm this candidate optimum. These findings provide new insights into PBU-mediated in vitro regeneration in eucalyptus and offer a molecular basis for optimizing regeneration systems in E. urophylla × E. grandis. These findings provide new insights into the miRNA-metabolite regulatory network underlying phenylurea-mediated callus differentiation in woody plants. Full article

Cancer stem cells (CSCs) drive therapeutic resistance, metastasis, and tumor recurrence through reversible transitions among stem-like, differentiated, epithelial, and mesenchymal states, which are sustained by interconnected epigenetic mechanisms. To our knowledge, this is the first review to integrate curcumin-mediated regulation of DNA methylation, chromatin remodeling, and non-coding RNAs within a single CSC plasticity framework and to propose the concept of an “epigenetic collapse of CSC plasticity” as a mechanistic explanation for how curcumin may weaken stemness, state switching, and adaptive treatment resistance. Evidence was critically evaluated through structured searches of PubMed/MEDLINE, Scopus, Web of Science Core Collection, Google Scholar, and citation tracking, while direct curcumin–epigenetic evidence was distinguished from independent CSC evidence and inferential mechanistic links. Curcumin has been reported to modulate DNMT1 and locus-specific DNA methylation; regulate HDACs, p300/CBP, EZH2, H3K27me3, and BMI1; and alter selected microRNA, long non-coding RNA, and circular RNA pathways, with comparatively stronger evidence involving the miR-34 family, miR-200c, miR-21, H19, and circHN1. However, current evidence is constrained by the predominance of bulk cancer-cell models, heterogeneous formulations and exposure conditions, and the scarcity of epigenetic rescue experiments combined with rigorous functional CSC assays. By unifying previously fragmented epigenetic evidence, this review advances a new evidence-weighted model in which curcumin may suppress CSC persistence not through a single molecular target, but by destabilizing the multilayer epigenetic circuitry that enables plasticity. Curcumin should therefore be regarded as a context-dependent, multilayer epigenetic modulator rather than an established CSC-eradicating therapy, and its translational relevance requires validation in prospectively defined CSC models with pharmacologically justified delivery and exposure conditions. Full article

Field cancerization describes molecular alterations occurring in histologically normal tissues surrounding tumors that may contribute to cancer initiation and progression. In prostate cancer (PCa), the molecular characteristics of peritumoral tissue (PTT) remain incompletely understood. Because microRNAs (miRNAs) play key roles in gene regulation, tumor progression, and microenvironmental remodeling, we investigated miRNA expression patterns and regulatory networks across benign tissue (BT), PTT, and tumor tissue (TT). Small RNA sequencing was performed on matched formalin-fixed paraffin-embedded samples from 40 patients with PCa. Differential expression analysis was conducted using DESeq2, adjusting for age and Gleason grade, while functional enrichment analysis and weighted gene co-expression network analysis (WGCNA) were used to identify dysregulated pathways and conserved miRNA modules. PTT exhibited a molecular profile intermediate between BT and TT, consistent with a field cancerization effect. Compared with BT, 102 miRNAs were differentially expressed in TT and 57 in PTT, with 39 miRNAs (68% of the PTT-associated miRNAs) overlapping the tumor signature. Shared dysregulated pathways included PI3K–Akt, p53, and HIF-1 signaling; whereas, PTT showed additional enrichment in pathways related to epigenetic regulation (Polycomb Repressive Complex) and cellular stress responses (mitophagy, protein processing in ER) exclusively through up-regulated miRNAs; no pathways were uniquely enriched from down-regulated miRNAs in PTT. WGCNA identified conserved miRNA modules enriched for members of the let-7, miR-200, miR-103/107, and miR-106a~363 families, which have established roles in epithelial–mesenchymal transition, tumor progression, and microenvironmental remodeling. Collectively, these findings demonstrate that histologically benign peritumoral tissues harbor tumor-associated miRNA programs and regulatory networks that closely resemble those observed in prostate tumors, providing molecular evidence of field cancerization in PCa and identifying potential miRNA-mediated mechanisms relevant to disease progression and biomarker development. Full article

Background: MicroRNAs are key post-transcriptional regulators of gene expression and contribute to cancer progression, tumor heterogeneity, and context-dependent regulatory rewiring. However, most computational approaches rely on sequence-based target prediction or bulk expression association and are not designed to jointly model regulatory priors, expression context, and heterogeneous cancer states, particularly when matched single-cell microRNA/mRNA co-profiling data are scarce. Methods: We developed a context-aware graph transformer framework for microRNA–gene regulatory analysis across biological resolutions. The framework represents microRNAs, genes, and biological contexts as a heterogeneous graph, where contexts correspond to individual cells in single-cell data and tumor samples or subtype-defined profiles in bulk cohorts. Heterogeneous graph transformer learning generated regulatory embeddings, Bayesian topology optimization refined candidate microRNA–gene interactions, and a dominance-based competition layer with Dominance Share scoring identified master regulators and cooperative target modules. Results: We applied miR-CellMap to matched single-cell miRNA/mRNA co-sequencing data from K562 leukemia cells and paired bulk cancer datasets spanning pan-cancer and subtype-specific cohorts, including breast, colon, glioblastoma, lower-grade glioma, and ovarian cancer. The framework identified recurrent and dataset-specific miRNA regulatory programs, including regulators such as miR-186-5p, miR-214-3p, miR-27a-3p, and let-7 family members. Embedding-derived context analysis showed that predicted miRNA target programs were consistently closer to observed context-specific gene programs than random matched gene programs across all seven datasets. Dominance Share analysis further identified cooperative target modules and co-repressed target programs, supporting the use of miR-CellMap for interpretable cancer-focused miRNA regulatory discovery. Conclusions: This framework provides an interpretable strategy for mapping conserved, cancer-specific, and context-dependent microRNA–gene regulatory programs across single-cell and bulk cancer datasets. Full article

Background: Thoracic aortic aneurysm (TAA) is a potentially life-threatening degenerative disease whose principal danger arises from progressive aortic dilation with the attendant risk of rupture and dissection and which is characterized by extracellular matrix breakdown, smooth muscle loss, and endothelial dysfunction. Caveolae, plasma membrane microdomains built from caveolins (CAV1-3) and cavins (CAVIN1-4), govern nitric oxide (NO) signaling, endocytosis, and mechanotransduction. We hypothesized that downregulation of caveolae-associated genes, driven in part by microRNAs, contributes to endothelial failure and vascular remodeling in TAA. Methods: Normalized transcriptomic expression values for five caveolae-associated genes were retrieved from the GSE26155 dataset (43 TAA and 43 control aortas) using GEO2R. Differential expression was assessed for CAV1, CAV2, CAV3, CAVIN1, and CAVIN2, and Spearman correlation with Deming regression explored inter-gene relationships. Functional enrichment (Enrichr) and experimentally validated microRNA-target interactions (miRTarBase) were used to infer regulatory and mechanistic networks. CpG island mapping and gene-gene interactome construction (GeneMANIA) complemented the analyses. Results: CAV1 and CAV2 were downregulated in TAA at nominal significance (CAV1, p = 0.0225; CAV2, p = 0.0361); after Benjamini–Hochberg correction across the five candidate genes both differences attenuated to a consistent trend (q approximately 0.09), while the two caveolins were strongly co-expressed (Spearman r = 0.527, p < 0.001; Deming CAV2 = 1.881 × CAV1-0.892), indicating coordinated transcriptional regulation. Network analysis linked both genes to NOS3, NOSTRIN, EGFR, HRAS, and RAC1, consistent with impaired endothelial nitric oxide and GTPase signaling. Gene Ontology enrichment highlighted endothelial proliferation, nitric oxide metabolism, calcium homeostasis, vesicle organization, and MAPK regulation. Database-supported analysis (miRTarBase) identified miR-93-5p, miR-199a-3p, miR-203a-3p, and the miR-29 family as experimentally validated candidate repressors of CAV1/CAV2. Conclusions: This integrative transcriptomic and microRNA analysis identifies coordinated CAV1 and CAV2 downregulation as a candidate molecular event in thoracic aortic aneurysm, associated with caveolar loss, endothelial dysfunction, and disrupted nitric oxide homeostasis. The CAV1/CAV2-microRNA axis represents a candidate mechanistic signature warranting further investigation as a potential therapeutic target in aortic disease. Full article

Objective: Exercise training helps preserve skeletal muscle health during aging. However, the molecular responses to different exercise modalities in older adults remain unclear. This study reanalyzed human skeletal muscle transcriptomes to compare signatures associated with combined training, resistance training, and high-intensity interval training. Method: We analyzed the older adult subset of GSE97084. This subset included 46 skeletal muscle RNA-seq samples from 23 participants with paired biopsies before and after training. The dataset included seven paired participants in the combined group, eight in the resistance training (RT) group, and eight in the high-intensity interval training (HIIT) group. We performed paired differential expression analysis, GO/KEGG enrichment analysis, GSEA, WGCNA, PPI analysis, regulatory network analysis, and transcriptome-inferred microenvironment signature analysis. Results: The within-modality paired comparisons identified 264 DEGs in the combined group, 297 DEGs in the RT group, and 1098 DEGs in the HIIT group. A total of 62 DEGs were shared across all three modalities. Combined training was mainly linked to extracellular matrix (ECM) organization, vascular regulation, and mitochondrial oxidative metabolism. RT showed prominent collagen, ECM, integrin, focal adhesion, and structural remodeling signatures. HIIT showed the broadest DEG profile under the current threshold. HIIT was characterized by vascular endothelial, angiogenic, ECM/adhesion, oxidative phosphorylation, and immune-related microenvironment signatures. WGCNA and PPI analyses identified candidate hub gene patterns. ECM and basement membrane genes were more prominent after combined training and RT. Vascular endothelial genes were more evident after HIIT. Regulatory network analysis highlighted miR-29 family members as database-supported candidate regulators of ECM-related hub genes. Transcriptome-inferred microenvironment analysis suggested increased endothelial-related signatures across all modalities. This analysis also suggested increased fibroblast/stromal signatures after RT and HIIT and increased macrophage-related signatures after HIIT. Conclusions: Different exercise modalities were associated with partially overlapping but distinct transcriptomic signatures in aged human skeletal muscle. Combined training and RT were mainly related to ECM, stromal, and structural remodeling signatures. HIIT showed broader vascular endothelial and microenvironment-related signatures. These findings should be interpreted as exploratory because this reanalysis used a modest older adult subset from a single public bulk RNA-seq dataset and lacked an independent validation cohort. Larger studies and complementary experimental validation are needed before drawing definitive conclusions about exercise-modality-specific responses in aged human skeletal muscle. Full article