Search Results (4,578)

Sorghum seeds accumulate substantial amounts of condensed tannins (CTs), which are also referred to as proanthocyanidins (PAs), contributing to their characteristic astringent taste. Flavan-3-ol polymers, known as PAs, are sequestered within plant vacuoles and become catalytically activated via laccase enzymes. However, the biological roles and regulatory pathways of laccases in sorghum are still largely unclear. Here, integrated transcriptomic and metabolomic profiling of developing sorghum seeds identified 7942 differentially expressed genes between low- and high-CT lines, with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealing flavonoid biosynthesis as a key pathway; weighted gene co-expression network analysis (WGCNA) further pinpointed SbLAC14 as a hub gene within the module most strongly correlated with CT content. We then examined its regulation by microRNA397 (SbmiR397-5p). Dual-luciferase assays confirmed the binding of SbmiR397-5p to SbLAC14 in co-transformed tobacco leaves. Overexpressing SbLAC14 in transgenic Arabidopsis significantly increased CT accumulation while decreasing catechin and epicatechin levels. Furthermore, transgenic plants overexpressing miR397 (OEmiR397-5p) exhibited reduced CT content, accompanied by a lightening of seed color. Conversely, transgenic lines overexpressing a miR397-insensitive laccase transcript exhibited a reversed phenotypic outcome. Our findings indicate that SbmiR397-5p negatively regulates the expression of SbLAC14 in relation to CT biosynthesis, identifying it as a potential target for manipulating CT metabolism in sorghum. Those results provide a genetic entry point for metabolic engineering and breeding efforts aimed at modulating grain phenolic profiles. Full article

Estrogen receptor (ER)-positive breast cancer (BrCa) accounts for two-thirds of all BrCa cases worldwide. Therefore, ER-targeted endocrine therapy is the standard treatment for this disease. There has been a recent trend towards developing combination therapies using molecularly targeted drugs to improve outcomes. This study aimed to identify therapeutic targets demonstrating efficacy when combined with fulvestrant (a selective ER downregulator/degrader). We generated microRNA (miRNA) signatures from fulvestrant-treated MCF-7 cells by RNA sequencing. From the signature, we evaluated miR-374b-5p because its expression was elevated by fulvestrant treatment in MCF-7 cells. Also, in expression analysis by subtype of BrCa patients, miR-374b-5p expression was suppressed only in luminal BrCa. Ectopic expression assays revealed that miR-374b-5p attenuated the malignant phenotypes of MCF-7 cells. We searched for genes regulated by miR-374b-5p and discovered that 11 (NEK2, NUF2, HMMR, DEPDC1B, FOXM1, ELOVL6, KIF20A, NCAPH, CENPK, FAM83D, and KIAA0101) are closely involved in BrCa molecular pathogenesis. Among these target genes, we focused on forkhead box M1 (FOXM1), a transcription factor regulating cell cycle progression and division. Notably, combination therapy with fulvestrant and a FOXM1 inhibitor significantly suppressed MCF-7 cell proliferation. From the miRNA signature established in this study, we identified antitumor miR-374b-5p and its target genes and used these findings to explore candidate drugs with potential efficacy when combined with fulvestrant. Full article

Post-myocardial infarction (MI) remodeling is accompanied by metabolic stress, but the myocardial genes associated with copper handling are poorly defined. We sought to prioritize a tissue-derived candidate rather than establish a copper-dependent mechanism. Regional MI transcriptomes and an in-house left anterior descending coronary artery ligation mouse RNA-sequencing cohort were integrated with protein quantitative trait locus-based Mendelian randomization (MR). Follow-up comprised local and external tissue validation, cardiac single-cell RNA sequencing, Genotype-Tissue Expression co-expression, computational perturbation, and CRIP2 knockdown or overexpression in H9c2 cells exposed to hypoxia/reoxygenation (H/R). CRIP2 showed a nominal protective-direction MR association (odds ratio 0.831, 95% confidence interval 0.735–0.939; p = 0.0031), but did not pass the Bonferroni threshold. Crip2 was lower in the local MI model (p = 0.0168; n = 5 per group) and in an independent dataset. A prespecified lipoylated-tricarboxylic-acid module was negatively enriched after MI (normalized enrichment score −1.63; false discovery rate 0.012), whereas the broader copper-homeostasis set was not significant. Single-cell data localized Crip2 mainly to cardiomyocytes, but were not adequately replicated for condition-level inference. Under H/R, Atp7a was the only copper-handling transcript whose knockdown-by-oxygen interaction remained significant after adjustment (q = 0.0405). CRIP2 overexpression was associated with higher Cell Counting Kit-8 metabolic activity during H/R (interaction p = 0.00551), whereas the knockdown interaction was not significant. Copper abundance, mitochondrial function, and cuproptosis markers were not measured. The data prioritize CRIP2 for mechanistic study, but do not show that it regulates copper flux or post-MI remodeling. Full article

Background: Childhood obesity is a growing health concern and added sugar intake has been associated with increased obesity risk. Emerging evidence suggests that miR-143-5p and miR-223-3p are involved in metabolic regulation. Therefore, this study evaluated their plasma expression according to added sugar intake and their association with cardiometabolic risk parameters. Methods: This cross-sectional study included 91 children aged 6–12 years, comprising 44 with normal weight and 47 with overweight/obesity. Anthropometric measurements, clinical characteristics, and dietary added sugar intake were assessed. Plasma expression of miR-143-5p and miR-223-3p was quantified by RT-qPCR. Results: Compared with low added sugar intake, high added sugar intake was associated with lower plasma miR-143-5p expression and higher miR-223-3p expression. Both miR-143-5p and miR-223-3p expression levels were higher in children with overweight/obesity and insulin resistance than in their respective counterparts. In adjusted analyses, neither miRNA was associated with cardiometabolic risk parameters. However, added sugar intake was positively associated with miR-223-3p expression (β = 0.188, 95% CI: 0.022, 0.354) and glucose levels (β = 1.944, 95% CI: 0.133, 3.755). Conclusions: These findings suggest that higher added sugar intake is associated with altered circulating miRNA expression and higher fasting glucose concentrations in school-aged children. Full article

Introduction: Cystinuria is an inherited disorder characterized by impaired proximal tubular reabsorption of cystine, resulting in recurrent cystine stone formation. Mutations in the SLC3A1 and SLC7A9 genes are the main genetic causes of the disease, while variants in PBX1 have also been associated with cystinuria in specific populations. Despite advances in understanding its molecular basis, cystinuria remains clinically heterogeneous, making disease progression and prognosis difficult to predict. This study aimed to investigate circulating microRNAs (miRNAs) as potential molecular biomarkers, characterize their expression profile in patients with cystinuria, and evaluate their association with clinical indicators of disease severity. Methods: The study group included 16 patients with a clinically established diagnosis of cystinuria, while the control group consisted of 11 healthy individuals without a history of nephrolithiasis. Candidate miRNAs were selected based on their predicted regulatory interactions with genes implicated in cystinuria pathogenesis. Eight microRNAs (miR-29a-3p, miR-29b-3p, miR-29c-3p, miR-1207-3p, miR-10a-3p, miR-3658, miR-141-3p, and miR-200a-3p) were analyzed by quantitative real-time PCR (qPCR). Results: Among the eight miRNAs evaluated, miR-10a, miR-141, miR-200a, and miR-3658 were significantly downregulated in patients with cystinuria compared with healthy controls. Higher expression levels of miR-10a, miR-141, and miR-200a were significantly associated with a greater number of previous surgical procedures (p < 0.05). Additionally, increased miR-10a expression was associated with impaired renal function, defined as serum creatinine levels above 1.2 mg/dL. Conclusions: miR-10a, miR-141, miR-200a, and miR-3658 were significantly downregulated in patients with cystinuria compared with healthy controls. Within the cystinuria cohort, higher expression of miR-10a was associated with impaired renal function, whereas increased expression of miR-10a, miR-141, and miR-200a correlated with a greater number of surgical interventions, suggesting a potential relationship with disease severity. Further studies in larger, genetically characterized cohorts are warranted to clarify the biological role and clinical utility of these miRNAs as biomarkers of cystinuria. Full article

Behçet’s disease (BD) is a chronic, multisystem vasculitis characterized by dysregulated immune responses and prominent Th1/Th17 polarization; however, the upstream epigenetic regulatory mechanisms driving this inflammatory imbalance remain incompletely understood. Here, we investigated the coordinated expression and diagnostic relevance of key long non-coding RNAs (lncRNAs; NEAT1 and MEG3) and microRNAs (miR-124 and miR-146a), and their association with IL-17/IL-6-mediated inflammation in BD. In a case–control study, serum levels of the selected non-coding RNAs were quantified by quantitative real-time PCR, while cytokine concentrations were measured using ELISA, complemented by bioinformatic interaction analysis and integrated statistical and machine learning approaches. Patients with BD exhibited marked downregulation of NEAT1, MEG3, miR-124, and miR-146a (p < 0.0001), accompanied by significantly elevated IL-17 and IL-6 levels. Individually, biomarkers demonstrated strong discriminatory capacity (AUC 0.83–0.92), while combined panels further improved classification performance. Multivariate modeling identified these non-coding RNAs as independent predictors of BD, and machine learning analysis identified miR-146a and IL-17 as the most influential contributors to disease classification. Notably, selected biomarkers showed associations with specific clinical manifestations, supporting their potential clinical relevance. Bioinformatic analyses identified putative interactions between NEAT1 and miR-124/miR-146a, while MEG3 demonstrated independent diagnostic value without evidence of direct interaction with the investigated miRNAs. Collectively, these findings provide a hypothesis-generating framework for future mechanistic investigations and support the potential diagnostic value of the investigated biomarker panel, although validation in larger multicenter cohorts and disease-control populations is warranted. Full article

MicroRNAs (miRNAs) are conserved post-transcriptional regulators that play essential roles in cellular development and differentiation. Although miRNAs involved in oligodendrocyte lineage cell (OLLC) differentiation have been extensively studied in rodent models, their functions in human oligodendrocyte (OL) development remain poorly understood. To address this, we used a human embryonic stem cell (hESC) reporter system and an optimized differentiation protocol to generate and isolate well-characterized OLLCs at defined developmental stages. Next-generation sequencing-based miRNA profiling identified stage-specific miRNAs associated with OL lineage specification and maturation. In addition to canonical OL-associated miRNAs, we identified several previously uncharacterized oligodendrocyte progenitor cell (OPC)/oligodendrocyte (OL)-enriched miRNAs, including miR-3943, miR-4286, miR-1296-5p, miR-488-3p, miR-675-5p, and miR-128-3p, as potential novel regulators and molecular markers for human OLLC development. Computational target analysis further identified candidate regulatory genes, including ZNF488, DLX1, CSNK2B, and KCNJ1, and predicted their association with AKT, SMAD2/3, estrogen-receptor, and insulin-signaling pathways. Together, these findings provide a comprehensive stage-specific miRNA resource for human OL lineage development and provide insight into potential miRNA-mediated regulatory networks governing human OL development. Full article

Testicular germ cell tumors (TGCTs) are highly curable malignancies, yet their clinical management still relies heavily on conventional serum tumor markers, including alpha-fetoprotein, beta-human chorionic gonadotropin, and lactate dehydrogenase, which have limited sensitivity and specificity in several clinically relevant settings. Circulating microRNAs, particularly miR-371a-3p, have emerged as promising liquid biopsy biomarkers with potential applications across the TGCT disease continuum. This narrative review summarizes the current evidence on the biological basis, diagnostic performance, clinical utility, and limitations of circulating microRNAs in TGCTs. MiR-371a-3p demonstrates high diagnostic accuracy for viable non-teratomatous TGCTs and consistently outperforms classical serum tumor markers in primary diagnosis. Its rapid decline after effective treatment and its association with tumor burden support potential roles in chemotherapy monitoring, early relapse detection during surveillance, and the assessment of selected post-chemotherapy residual masses. However, its inability to detect teratoma remains a major biological limitation, particularly in non-seminomatous residual disease and surveillance settings. Additional barriers to implementation include assay heterogeneity, the lack of universally accepted cutoffs, the variable use of serum versus plasma, and the absence of broad regulatory approval. Emerging translational data suggest that miR-371a-3p may also contribute to tumor–microenvironment communication and cisplatin resistance, although these findings remain preclinical. Overall, miR-371a-3p represents one of the most promising biomarkers in TGCT management, but its routine clinical integration will require standardized analytical protocols and prospective validation in marker-guided decision pathways. Full article

Cardiac rhythm and pumping function are essential outputs of cardiac homeostasis and depend on precise molecular regulation. The histone acetyltransferases CBP/p300 have been implicated in cardiac remodeling and functional regulation. nej, the Drosophila homolog of CBP/p300, may therefore represent an important regulator of cardiac function. However, the relationship between miR-276a and nej in the heart, as well as the potential involvement of the fat body in this regulatory relationship, remains unclear. Using Drosophila as a model, we first examined the effects of cardiac-specific nej overexpression and knockdown on cardiac function and tested the interaction between miR-276a and the nej 3′ untranslated region using a dual-luciferase reporter assay. We subsequently manipulated miR-276a using Hand-Gal4 and Cg-Gal4 and assessed miR-276a and nej expression in cardiac samples, cardiac function, and climbing ability. Finally, we investigated the effects of an exercise intervention on cardiac miR-276a/nej expression and functional outcomes. Both cardiac-specific overexpression and knockdown of nej impaired cardiac rhythm, reduced pumping function, and decreased climbing ability. The reporter assay supported a functional interaction between miR-276a and the nej 3′ untranslated region, while cardiac-specific miR-276a manipulation was accompanied by inverse changes in nej mRNA expression and by cardiac and climbing abnormalities. Cg-Gal4-mediated miR-276a upregulation or downregulation was associated with altered miR-276a and nej expression in cardiac samples and with cardiac and climbing impairments. Exercise improved cardiac and climbing ability in both cardiac miR-276a knockdown and overexpression groups. It increased cardiac miR-276a expression and decreased nej expression in the cardiac knockdown group but did not significantly alter either transcript in the cardiac overexpression group. Exercise also improved cardiac function in both Cg-Gal4-mediated miR-276a knockdown and overexpression groups. In the Cg-Gal4-mediated knockdown group, this improvement was accompanied by increased miR-276a and decreased nej expression in cardiac samples. These findings indicate that exercise modulates cardiac function and miR-276a/nej expression in a context-dependent manner and suggests a possible contribution of the fat body. 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

Grape pomace (GP) is being explored as a sustainable feed ingredient for ruminants due to its fiber and polyphenol content; however, its systemic effects under farming conditions remain unclear. This study tested whether 5% dried grape pomace (GP5) modulates serum circulating miRNAs (cmiRNAs) in dairy sheep. Twelve Sarda ewes were enrolled in a 30-day trial and assigned to a control (CTRL) or GP5 diet. Small RNA sequencing was initially performed in GP5 animals (paired T30 vs. T0 comparison); after quality filtering, five paired animals were included in the sequencing analyses. The differentially expressed (DE) cmiRNAs were validated by RT-qPCR in GP5 and CTRL groups. RT-qPCR confirmed the NGS-derived miRNA signature, identifying miR-143, miR-382-5p, miR-409-3p, and miR-194 as significantly downregulated (p < 0.05) in GP5 animals. Ingenuity Pathway Analysis (IPA) showed that DE miRNAs target shared hubs, with PPAR signaling among the most enriched pathways (BH-adjusted p = 1.35 × 10⁻⁹), predicted to be inhibited (Z = −2.646). Cholecystokinin/gastrin-mediated and S100 signaling were also enriched (BH-adjusted p = 7.08 × 10⁻¹¹ and 3.21 × 10⁻⁸) and predicted to be activated (Z = 2.828 and 3.162). Overall, GP5 supplementation was associated with a selective cmiRNA signature consistent with targeted post-transcriptional regulation. Full article

The prognostic relevance of IDH1 mutations remains unclear in acute myeloid leukemia (AML). This study, representing the first Turkish AML cohort characterized for IDH1 mutations, aimed to determine the frequency of IDH1, FLT3 and NPM1 mutations and to describe the associated clinical characteristics. We retrospectively analyzed clinical, cytogenetic, and molecular data for 57 AML patients. Bone marrow aspirates were evaluated cytogenetically using G-banding, and molecular mutations were assessed by PCR or NGS (MiSeq-Illumina). IDH1 mutations were detected in 7% of patients; FLT3 and NPM1 mutations were detected in 38.6% and 19.3% of patients, respectively. A significant positive correlation existed between IDH1 and NPM1 mutations (r = 0.388, p = 0.003). Overall mortality was 56.1% and remission was achieved in 43.9%. Older age (p = 0.029) and comorbidities (p = 0.009) were significantly linked to mortality. Mortality was 100% in the four IDH1-mutant patients and significantly higher in NPM1-mutant patients. Overall survival was shorter in IDH1-mutants, although the difference did not reach statistical significance (log-rank p = 0.057). Relapse occurred in 26.3%, rising to 50% in the IDH1-mutated subgroup. In this limited cohort, IDH1-mutant cases were associated with shorter overall survival and higher mortality; however, the small number of IDH1-mutant patients (n = 4) precludes definitive prognostic conclusions. Outcomes in NPM1-mutated patients were also less favorable than typically expected, possibly related to co-occurring IDH1 mutations. These descriptive findings characterize the molecular landscape of AML in an underrepresented Turkish population and may provide a foundation for larger, multicenter studies rather than confirming a prognostic role for these mutations. Full article

Background/Objectives: Prostate cancer (PCa) remains a leading cause of cancer-related mortality in men. While localized PCa carries a favorable prognosis, progression to locally advanced disease substantially worsens outcomes. There is an unmet need for molecular markers that reliably distinguish indolent from aggressive tumors. MicroRNAs (miRNAs), small non-coding RNAs that post-transcriptionally regulate gene expression, are implicated in cancer development and progression, and their expression profiles may serve as putative biomarkers of disease stage. Methods: We performed small RNA sequencing on formalin-fixed paraffin-embedded (FFPE) prostate tumor tissues from nine patients (five localized, four locally advanced-stage). Differentially expressed miRNAs were identified using a bioinformatics pipeline (fold-change ≥ 2, p < 0.05). Target gene prediction, KEGG pathway enrichment, and miRNA–mRNA interaction network analyses were conducted, followed by in silico validation using two independent public mRNA datasets (GSE46602 and GSE21034, a subseries of GSE21032). Results: Seven unique mature miRNAs were differentially expressed between localized and locally advanced PCa. Five miRNAs (miR-145-5p, miR-205-5p, miR-206, miR-24-1-5p, and hsa-miR-3648) were downregulated in locally advanced tumors, while hsa-miR-625-3p and miR-324-5p were upregulated. Network analysis identified CLTC and CDK6 as putative downstream targets co-targeted by multiple downregulated miRNAs. Independent validation using GSE46602 and GSE21034 consistently demonstrated significantly higher expression of CLTC and CDK6 in locally advanced prostate cancer following Benjamini–Hochberg correction. Conclusions: This exploratory pilot analysis identified several miRNAs that differ between localized (pT2) and locally advanced (pT3–T4/N+) prostate cancer. Independent validation across two publicly available mRNA cohorts supports CLTC and CDK6 as candidate stage-associated genes. However, these findings remain hypothesis-generating and require validation in larger prospective cohorts together with functional confirmation before biomarker or therapeutic claims can be made. Full article

The increasing demand for plant-based beverages as alternatives to dairy milk requires rapid and reliable methods to assess their composition and authenticity. This study investigated the feasibility of mid-infrared (MIR) and near-infrared (NIR) spectroscopy for classifying plant-based beverages and predicting their nutritional profile. A total of 57 commercial beverages from five categories (oat, almond, soybean, rice, and coconut) were analyzed. Canonical discriminant analysis was used to discriminate among beverage categories, and modified partial least-squares regression models were developed using reference chemical analyses and spectral data to predict protein, fat, sugars, ash, acidity traits, minerals, and amino acid composition. Both MIR and NIR successfully discriminated among the five beverage categories. Quantitative prediction models were generally more accurate with MIR than with NIR. The most robust MIR models were obtained for protein, fat, glucose, ash, and selected minerals (P and K), reaching accuracy levels suitable for quality-control applications. Protein was predicted with excellent accuracy by both technologies. The most robust prediction models were achieved for amino acid composition, with all amino acids except phenylalanine showing satisfactory predictive performance, particularly with MIR spectroscopy. In conclusion, these results demonstrate the feasibility of infrared spectroscopy for the authentication and compositional assessment of plant-based beverages. In particular, MIR spectroscopy showed considerable potential for integration into routine quality-control workflows, similar to those currently implemented for dairy milk analysis. 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