Search Results (17,277)

Dysregulation of microRNA expression in breast cancer (BC) has been associated with molecular disturbances involved in cancer initiation, progression and metastasis. Specific microRNAs also act as endocrine modulators in BC, thereby influencing the biological behavior of the tumor and drug responses. Our objective was to employ bioinformatics tools to identify and characterize microRNAs acting as candidate players involved in epithelial–mesenchymal transition, migration, invasion, and/or hormonal regulation in BC. We systematically integrated microRNA profiling data from three different studies on BC cell lines with different invasive capabilities and from another study on lymph node metastases and matching primary BC, resulting in five microRNA hits—DE-microRNAs miR-146a-5p, miR-222-3p, miR-205-5p, miR-141-3p and miR-200c-3p. This set of microRNAs was evaluated for clinical significance in BC and subjected to target prediction, microRNA–mRNA network construction, functional enrichment analysis and quantification in BC cell lines by qPCR. An upregulated DE-microRNA, miR-222-3p, displayed distinctive pro-metastatic features, supported by its clinical relevance, as well as by the results of the functional enrichment analysis of its target genes. Downregulation of the members of the miR-200 family and miR-205-5p were significantly associated with negative clinical features, while their targets were enriched with genes that were relevant to cancer aggressiveness. These results are in line with the presumed functional relevance of the selected DE-microRNAs in BC. Full article

Saffron (Crocus sativus L.) is a high-value crop vulnerable to potyvirus infections threatening its yield and quality. In this study, we combined Oxford Nanopore long-read sequencing with exploratory transcriptomic profiling to characterize the saffron virome and to describe expression profiles associated with two distinct infection histories: (i) saffron plants experimentally inoculated with cucumber mosaic virus (CMV; Cucumovirus CMV) and turnip mosaic virus (TuMV; Potyvirus rapae) under controlled greenhouse conditions, and (ii) saffron plants naturally infected by diverse viruses. We identified six plant-infecting viral families in both conditions, including Potyviridae, Geminiviridae, Caulimoviridae, Tymoviridae, Aspiviridae, and Partitiviridae. Transcriptomic profiling revealed distinct expression profiles associated with each infection background. Given the limitations of the experimental design, gene expression differences are interpreted descriptively. We describe pathway enrichments associated with antiviral responses. Naturally infected plants exhibited a broad-spectrum, tolerance-based response characterized by the upregulation of photosynthesis-related genes, calcium-mediated signaling components, and stress-responsive transcription factors. In contrast, virus-inoculated plants activated a targeted antiviral program involving RNA silencing, autophagy, ubiquitin-mediated proteolysis, and hormonal regulation. Both GO and KEGG enrichment analyses supported these findings, highlighting photosynthesis and metabolic flexibility in naturally infected plants versus hypersensitive response, RNA surveillance, and lignin biosynthesis in virus-inoculated plants. This work provides a comprehensive view of the saffron virome and offers a hypothesis-generating overview of transcriptional responses associated with natural versus experimental virus infections. These findings advance the understanding of the saffron virome and provide a valuable resource for breeding virus-resistant cultivars. Full article

Chagas disease (CD) is a neglected tropical disease caused by the flagellate protozoan Trypanosoma cruzi, representing a major socioeconomic challenge. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression, and several pathogens, including T. cruzi, can modulate host miRNA networks. In this context, we hypothesized that host-derived miRNAs could serve as biomarkers in chronic CD. Given the intrinsic lability of RNA, we evaluated the efficacy of a 6 M guanidine-HCl/0.2 M EDTA solution, widely used in the molecular detection of T. cruzi DNA, in preserving mRNAs and miRNAs when mixed in a 1:1 ratio with human blood. Samples with or without guanidine were enriched with exogenous miRNAs (cel-miR-39 and cel-miR-54) and stored at 4 °C. RNase P expression was also evaluated in blood samples stored for up to 120 days and in samples from patients with CD, allowing direct comparison of mRNA stability over time. Samples preserved with guanidine-EDTA showed Ct values that were 4 to 5 cycles lower for all targets analyzed and demonstrated greater RNA stability over time. Taken together, these findings demonstrate that guanidine-EDTA robustly preserves mRNA and miRNAs in human blood, expanding the feasibility of molecular analyses in retrospective samples and corroborating its potential application in the studies of biomarkers of therapeutic response and prognosis in CD. Full article

Inflammatory joint diseases, including osteoarthritis, are multifactorial disorders in which dysregulated innate immune signaling and non-coding RNA (ncRNA)-mediated regulation of gene expression play essential roles. MicroRNA-155 (miR-155), its host gene MIR155HG, and Toll-like receptor 4 (TLR4) form a tightly linked inflammatory signaling axis, yet their combined genetic variability in chronic joint inflammation remains insufficiently characterized. The aim of this study was to investigate genetic variants in MIR155HG exon 3, mature miR-155, and TLR4 exon 3 and assess their potential synergistic role in chronic inflammatory joint disease. A case–control study was conducted with 100 cases (50 osteoarthritis patients and 50 matched healthy controls). Genomic DNA was analysed using polymerase chain reaction (PCR) and Sanger sequencing. Variant alleles and genotypes were identified, and their allele frequencies and genotypes were calculated using Mutation Surveyor. Detected variants were compared with public databases, and in silico tools were used to estimate the structural impact of TLR4 missense mutations. Sixteen heterozygous variants were identified in MIR155HG exon 3, most of them novel and population-specific. Interestingly, the highest variant frequencies for MIR155HG exon 3 were observed at positions 12448G>GC and 12481T>TA (both 64.3%), followed by 12442T>TC (57.1%). Additionally, two novel variants were detected in the miR-155 gene (chr21:29,694,314 G>A and chr21:29,646,351 T>C), each present at an allele frequency of 7.1% and absent from current external variant databases. Moreover, two rare TLR4 exon-3 variants were identified; a synonymous variant, c.147C>A (Pro49Pro; rs375037549), and a missense mutation, c.148G>A (Asp50Asn; rs776561489). Notably, in silico analyses and molecular dynamic simulations indicated that the Asp50Asn (D50N) substitution destabilizes the TLR4 protein. Conclusion: Concurrent variants in MIR155HG, miR-155, and TLR4 suggest a convergent regulatory molecular axis that may contribute to disease susceptibility and inflammatory progression. Full article

Skin aging and wound healing are the result of intricate and interconnected processes involving chronic inflammation, oxidative stress, cellular senescence and extracellular matrix degradation. Mesenchymal stem cell (MSC)-derived exosomes are rich in bioactive components, particularly microRNAs (miRNAs), which play a crucial role in regulating gene expression and key signaling pathways critical for maintaining skin homeostasis. This article reviews the current evidence regarding the roles of MSC-derived exosomal miRNAs (MSC-Exo-miRNAs) in cutaneous repair and rejuvenation. Specific exosomal miRNAs are analyzed for their ability to modulate inflammatory responses, promote fibroblast proliferation and collagen synthesis, enhance angiogenesis, and facilitate keratinocyte migration and re-epithelialization. Their roles in regulating key signaling pathways are discussed in the context of skin regeneration and aging, including nuclear factor-κB (NF-κB), PI3K/Akt, TGF-β/Smad, Wnt/β-catenin, and nuclear factor erythroid 2-related factor 2 (Nrf2). Additionally, emerging engineering strategies aimed at optimizing miRNA cargo loading, improving delivery efficiency, and advancing clinical translation are highlighted. Overall, MSC-Exo-miRNAs represent a promising cell-free therapeutic strategy for skin repair and rejuvenation; however, further mechanistic investigations and rigorous clinical studies are necessary to fully realize their translational potential. Full article

The present work was designed to investigate the impacts of tartary buckwheat flavonoids (TBF) on the growth performance and physiological metabolism of Liangshan Yanying chickens. A total of 144 healthy 4-week-old Liangshan Yanying chickens of uniform body weight were randomly divided into four groups. Each group consisted of six replicates with six chickens per replicate. The control group was fed a basal diet, whereas the treatment groups received the same basal formulation supplemented with TBF at concentrations of 20, 40, and 60 mg/kg, respectively. The entire feeding trial lasted for 10 consecutive weeks. Growth performance, serum parameters, bone quality, slaughter traits, and hepatic lipid metabolism were determined and statistically analyzed. Results showed that dietary TBF supplementation had no significant impact on the overall growth performance (p > 0.05); however, final body weight and average daily weight gain displayed a positive linear trend in response to increasing TBF levels (0.05 < p < 0.1). For serum parameters, TBF supplementation significantly increased total antioxidant capacity (p < 0.05) and decreased malondialdehyde content (p < 0.05) in a linear manner. Specifically, compared with the control group, the 60 mg/kg TBF group increased T-AOC by approximately 64.6% and reduced MDA by approximately 67.9%, demonstrating a robust antioxidant effect. A linear increase in high-density lipoprotein cholesterol levels approaching significance (p = 0.055) was also observed. A significant quadratic regulatory effect of TBF was observed on serum glucose concentrations (p < 0.05), whereby the 60 mg/kg TBF dose reduced serum glucose by 15.6% relative to the control (p < 0.05), reflecting a robust hypoglycemic effect. Regarding bone quality, supplementation with 20 and 60 mg/kg TBF significantly elevated tibial phosphorus content relative to the 0 mg/kg TBF group (p < 0.05). Regression analysis showed that increasing dietary TBF levels linearly elevated tibial calcium content (p < 0.05) and resulted in linear increasing trends in tibial ash content, tibial phosphorus content, femur ash content, and femur calcium content (0.05 < p < 0.1). Concerning slaughter performance, dietary TBF inclusion resulted in a significant linear rise in breast muscle percentage (p < 0.05). At the molecular level, TBF upregulated the mRNA expression of hepatic AMPKα1 and CPT1, while concurrently downregulating the expression of FAS and ACC (p < 0.05). Collectively, dietary TBF supplementation in Liangshan Yanying chickens effectively improved antioxidant capacity, promoted tibial calcium and phosphorus deposition, regulated hepatic fatty acid oxidation and synthesis via AMPK-related genes, and enhanced lean meat deposition, with no adverse effects on growth performance under the experimental conditions. Full article

Cardiovascular diseases remain a leading cause of morbidity and mortality worldwide, underscoring the need to better understand cardiovascular physiology. A key aspect involves identifying regulatory molecules that govern metabolic shifts. Forkhead box protein O1 (FoxO1) has emerged as a potential regulator; however, its role and underlying mechanisms remain unclear. This study investigated FoxO1 in metabolic adaptation using Wistar rats divided into age groups (fetal, postnatal day 1, postnatal day 7, adult) and treatment groups (control, hypoxia, FoxO1 inhibitor, combination). Hypoxia (12–14% O₂) and FoxO1 inhibitor (AS1842856, 10 mg/kgBW/day) were administered accordingly. Parameters assessed included hypoxia inducible factor 1 α (HIF-1α), FoxO1 mRNA and protein, glucose transporter type 1 (GLUT1), glucose transporter type 4 (GLUT4), cluster of differentiation 36 (CD36), hexokinase, pyruvate dehydrogenase kinase isoform 4 (PDK4), phosphoenolpyruvate carboxykinase (PEPCK), lactic acid, malonyl-CoA, carnitine palmitoyltransferase 1 (CPT1), citrate synthase, cytochrome c, and adenosine triphosphate (ATP). ATP production increased with age, associated with higher FoxO1 expression and metabolic shifts. Hypoxia in fetal hearts reduced HIF-1α and FoxO1. FoxO1 inhibition elevated glycolytic and oxidative markers. In conclusion, FoxO1 regulates glycolysis and lipid metabolism, offering insights into cardiac adaptation to hypoxia and potential therapeutic strategies. Full article

Fruit branch length in cotton is a key trait influencing plant architecture and suitability for mechanisation; elucidating its molecular regulatory mechanisms is crucial for breeding varieties with desirable plant architecture. In this study, an F₂ segregating population was established using the long-fruit-branch upland cotton line L16 and the short-fruit-branch line S14 as parents. By integrating morphological, cytological, and omics approaches, we systematically analysed the underlying mechanisms of variation in fruit branch length. Phenotypic analysis indicated that the inter-node elongation rate of the first fruit branch in L16 was significantly higher than that in S14. Tissue section observations revealed that the length of cortical parenchyma cells in L16 was significantly greater than that in S14, suggesting that the difference in fruit branch length primarily stems from variations in the extent of cortical parenchyma cell elongation. BSA-Seq analysis identified five QTL regions significantly associated with fruit branch length, encompassing 82 coding genes. Further RNA-Seq analysis of the fruit branch initiation stage (T0) and rapid elongation stage (T1) identified 3106 differentially expressed genes common to both stages. GO and KEGG enrichment analyses revealed that these genes were significantly enriched in pathways related to plant hormone signalling, the cytoskeleton, and microtubule organisation. By integrating BSA-Seq and RNA-Seq data, three candidate genes were screened that simultaneously harboured non-synonymous mutations and were significantly highly expressed in the short fruit branch line S14. Combined with bioinformatics analysis, GH_D02G0744 was predicted to be the most likely key candidate gene regulating cotton fruit branch length. This study provides important genetic resources to elucidate the molecular regulatory mechanisms of cotton fruit branch length and lays a theoretical foundation for molecular breeding to improve cotton plant architecture. Full article

Non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression and cellular homeostasis, and their dysregulation is now recognized as a hallmark of cancer. Over the past decades, extensive research has demonstrated that diverse ncRNA classes, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and other small ncRNA species, participate in complex regulatory networks that influence tumor initiation, progression, metastasis, and therapy response. Through mechanisms such as transcriptional regulation, post-transcriptional gene silencing, epigenetic modulation, and competitive endogenous RNA interactions, ncRNAs shape the molecular circuitry underlying cancer development. In addition to their functional roles in tumor biology, many ncRNAs are released into biological fluids and can be detected as circulating molecules in blood, urine, saliva, and other biofluids. Their remarkable stability in extracellular environments has generated considerable interest in their use as minimally invasive biomarkers in liquid biopsy applications. Emerging evidence has shown that circulating ncRNAs (c-ncRNAs) can support cancer detection, disease stratification, and treatment monitoring. This narrative review provides an integrated view that links ncRNA-mediated regulatory networks with their application as liquid biopsy biomarkers, positioning ncRNAs as comprehensive indicators of tumor conditions. Particular emphasis is placed on c-ncRNA biomarkers, the integration of multiple ncRNA classes, and multi-analyte biomarker strategies that combine ncRNAs with complementary circulating molecules such as cell-free DNA and protein markers. Finally, we discuss the technical and clinical challenges that currently limit the translation of ncRNA-based diagnostics into clinical practice and highlight future directions for advancing ncRNA-guided liquid biopsy approaches in precision oncology. Full article

Small noncoding RNAs play critical regulatory roles in development across organisms. This study profiled microRNAs (miRNAs) and tRNA-derived fragments (tRFs) during bovine conceptus elongation. Elongating conceptuses were obtained via superovulation of eight Angus heifers. Twenty samples from ovoid (OV, n = 6; 0.5–3 mm), tubular (TUB, n = 7; 5–15 mm), and filamentous (FIL, n = 7; 20–34 mm) stages underwent small RNA sequencing. Differential expression of miRNAs and tRFs was analyzed using DESeq2, accounting for donor-sire effects. No tRFs showed differential abundance across any pairwise comparisons. For miRNAs, the expressions of six miRNAs were upregulated in OV versus TUB conceptuses (padj < 0.05), including four let-7 family members (bta-let-7g, bta-let-7f, bta-let-7a-5p, and bta-let-7c) and two additional miRNAs (bta-miR-224 and bta-miR-449a). Furthermore, there were 3 miRNAs differently abundant between the ovoid and filamentous transition (padj < 0.04), including two members of the let7 family (bta-let-7g and bta-let-7f) and bta-miR-449a. Predicted targets of these differentially abundant miRNAs were identified using miRanda. Enrichment analyses of the targeted genes included pathways regulating cellular proliferation, pathways in cancer, and immune-related pathways. The let-7 family, along with miR-449a and miR-224, are candidate regulators of the balance between cellular proliferation and differentiation during elongation, based on their differential abundance and in silico target predictions. Full article

Background/Objectives: Oral squamous cell carcinoma (OSCC) commonly arises from oral potentially malignant disorders (OPMDs), yet reliable molecular biomarkers that predict malignant transformation remain scarce. Because epithelial carcinogenesis follows similar multistep trajectories across multiple organs, pan-cancer transcriptional analyses may reveal conserved pathways relevant to early oral tumorigenesis. This study aimed to identify shared transcriptional signatures across carcinomas and evaluate their applicability to precancerous-to-carcinoma progression. Methods: Bulk RNA-seq data from five carcinomas (lung, colon, breast, prostate, and head and neck squamous cell carcinoma, HNSCC) were obtained from TCGA to identify shared differentially expressed genes (DEGs) (|log₂FC| ≥ 2; FDR < 0.05). Functional enrichment, clustering, and gene–pathway network analyses characterized conserved biological processes. Independent GEO datasets containing premalignant and malignant samples, including OPMD and OSCC cohorts, were examined to assess early-stage relevance. Results: A conserved 45-gene signature was identified, enriched for transcriptional regulation, chromatin organization, and RNA polymerase II-mediated processes. Regulatory hubs, including ZIC5, MYBL2, ONECUT2, POU4F1, and PDX1, and strong upregulation of cancer-testis antigens (MAGEA3, MAGEA6, MAGEC2) were notable. Integration with premalignant datasets revealed 13 genes consistently dysregulated across early lesions, involving pathways such as cell differentiation, apoptosis, and lipid transport. Several genes remained altered from normal tissue through OPMD to OSCC, supporting their potential as stable biomarkers. Conclusions: This study identifies conserved transcriptional programs shared across epithelial cancers and detectable in OPMDs. These findings highlight promising biomarker and regulatory candidates for improving early detection and risk stratification of oral precancer, addressing a critical unmet need in OSCC prevention and clinical management. Full article

With the rapid development of cancer treatment, immunotherapy has revolutionized renal cell carcinoma (RCC) treatment, yet patient responses remain heterogeneous. Here, a computational pipeline was constructed by integrating single-cell and bulk RNA sequencing data to identify immune-related candidate driver genes and characterize their impact on RCC immunotherapy. Based on gene regulatory networks (GRN), 25 immune-related candidate driver genes were identified, leading to the stratification of patients into three clusters (C1–C3). Compared to the C2/C3 cluster, the C1 cluster exhibited elevated immune infiltration, tumor mutation burden and checkpoint expression, which may represent immunotherapy responders. Dynamic analysis of GRNs revealed the critical role of candidate driver genes in predicting the efficacy of immunotherapy. IRF1, IRF9 and STAT1 in lymphoid cells of C1 participated in anti-tumor immune response by impacting target genes CD8A, HLA-A/E, TAP1 and PD-1. JUN, FOS, STAT3, JUND and NR2F1 were up-regulated in clusters C2 and C3, leading to tumor progression and immune evasion by influencing target genes HSPA1A, CXCL9 and PDGFR. In conclusion, integration of the transcriptome with molecular networks provided a network-based framework to uncover immune-related candidate driver genes for stratifying RCC patients, thereby serving as potential therapeutic targets to improve the outcome of RCC immunotherapy. Full article

Hypercholesterolemia is a major modifiable risk factor for cardiovascular disease. Although germinated brown rice (GBR) is rich in bioactive constituents and has shown preliminary lipid-regulating potential, the active compounds and underlying mechanisms remain unclear. Therefore, this study comparatively investigated extracts from four GBR cultivars and evaluated their cholesterol-regulating activity using untargeted metabolomics in combination with a cholesterol-induced HepG2 cell model. After 36 h of germination, the extracts showed significantly increased total phenolic content, total flavonoid content, and antioxidant activities (p < 0.05), with cultivar Q showing the strongest response. In the in vitro cholesterol-induced HepG2 cell model, GBR extract at 150 μg/mL significantly reduced intracellular total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) levels by approximately 69%, 73%, and 46%, respectively, while increasing high-density lipoprotein cholesterol (HDL-C) levels by approximately 125% (all p < 0.05). Untargeted metabolomics and subsequent validation suggested that p-coumaric acid is a candidate bioactive compound contributing to the cholesterol-lowering effect of GBR. Further analysis indicated that this effect may be associated with modulation of the mRNA expression levels of SREBP2, HMGCR, and LDLR. These findings indicate that germination enhances the bioactivity of brown rice in a cultivar-dependent manner and provides supporting evidence for the potential application of GBR as a functional food ingredient for lipid management. Full article

Exogenously induced RNA interference (exoRNAi) is a powerful biotechnology tool for precise gene regulation. The plant chalcone synthase (CHS) gene serves as a valuable model for molecular biology due to its central role in flavonoid biosynthesis. However, there are currently very few studies addressing the advantages and disadvantages of in vitro (enzymatic) or in vivo (bacterial) methods for producing double-stranded RNA (dsRNA) for exogenous application. This study aims to optimize and compare the two methods for producing dsRNAs targeting the Arabidopsis thaliana CHS gene: enzymatic synthesis in vitro using a commercial kit and bacterial synthesis in vivo using an engineered E. coli HT115 (DE3) system. Bacterial synthesis conditions were optimized with respect to IPTG concentration and cultivation time, and the resulting dsRNA preparations were purified and quality-controlled. Their biological activities were assessed by treating A. thaliana plants and analyzing the effects on AtCHS gene expression and flavonoid production using qRT-PCR and HPLC-MS. The results demonstrated that purified AtCHS-dsRNA from both methods effectively suppressed AtCHS expression and downstream flavonoid biosynthetic gene expression, leading to significant reductions in anthocyanins and flavanols. This study confirmed the efficacy of exogenous dsRNAs in regulating plant metabolic pathways and provided a comparative analysis of dsRNA synthesis methods, highlighting their benefits and limitations for practical applications in plant biology and protection. Full article

Background: Chronic kidney disease (CKD) associated vascular calcification (VC) is a leading cause of cardiovascular mortality, partially driven by osteogenic transdifferentiation of vascular smooth muscle cells (VSMCs). Chaperone-mediated autophagy (CMA) is a selective lysosomal degradation cellular process. However, the precise role and mechanism of CMA in CKD-associated vascular calcification remain unknown. Methods: We studied calcified arteries from CKD patients and rats fed on a high-phosphate diet using histological and ultrastructural methods. VSMCs' calcification was induced by a calcification medium containing high phosphate and calcium. CMA activity was measured by a KFERQ reporter and lysosomal staining. The expression of LAMP2a and HSP90AA1 was knocked down by siRNA, overexpressed by plasmid, and activated by QX77.1. Bioinformatic analysis, protein interaction studies, immunofluorescence and co-immunoprecipitation were performed to investigate the potential mechanism of CMA in VC. Results: The expression of LAMP2a was increased in human calcified radial artery tissues (n = 3, p < 0.05) and rats' calcified aortic tissues (n = 3, p < 0.01), accompanied by lysosomal abnormalities. The activity of CMA was increased during the osteogenic transdifferentiation of VSMCs, as indicated by increased expression of RUNX2 and reduced expression of SM22α (p < 0.05). LAMP2a knockdown attenuated VSMCs’ calcification (p < 0.05), whereas pharmacological activation of CMA aggravated calcification in VSMCs (p < 0.01). Bioinformatic screening identified HSP90AA1 as a candidate involved in CMA in vascular calcification. Elevated HSP90AA1 expression was observed in human calcified radial artery tissues (n = 3, p < 0.01) and rat calcified aortic tissues (n = 3, p < 0.01), which promoted osteogenic transdifferentiation of VSMCs (p < 0.05). HSP90AA1 interacted with LAMP2a and positively regulated its expression (p < 0.01). Conclusions: These findings support an association between CMA activation and CKD vascular calcification. It suggests that HSP90AA1 facilitates vascular calcification in chronic kidney disease involving chaperone-mediated autophagy. Full article