Search Results (4,581)

This study aimed to measure mRNA and miRNA expression profile in corneal impression cytology (IC) samples from patients with congenital aniridia (CA) and healthy controls, and to elucidate the key genes and signaling pathways involved in aniridia-associated keratopathy (AAK). Corneal IC samples were collected from 14 patients with CA and 14 healthy controls. RNA sequencing was performed to identify differentially expressed genes (DEGs) and miRNAs. Correlations with age and AAK grade were analyzed, selected miRNAs were validated by RT-qPCR, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to characterize biological functions and pathways. A total of 695 DEGs and 19 differentially expressed miRNAs were identified. KRT24 expression was negatively associated with age, whereas LY6D expression positively correlated with AAK grade. Several miRNAs were linked to disease severity, including positive correlations for miR-224-5p, miR-224-3p, and miR-452-5p, and negative correlations for miR-204-3p, miR-181b-5p, and miR-181a-5p. RT-qPCR confirmed significant downregulation of miR-204-5p and miR-138-5p in aniridia samples. Functional enrichment analyses showed that DEGs were mainly involved in cell adhesion, extracellular matrix remodeling, inflammatory and immune responses, and neural-related processes. Target genes of dysregulated miRNAs were enriched in transcriptional regulation, cell proliferation, apoptosis, and migration, with significant involvement of PI3K-Akt, AGE-RAGE, and EGFR signaling pathways. Corneal epithelial cells from patients with CA exhibit coordinated mRNA and miRNA dysregulation associated with extracellular matrix disruption, inflammation, and altered signaling pathways. These findings improve understanding of AAK pathogenesis and identify potential biomarkers and therapeutic targets. Full article

Systemic sclerosis (SSc) is a severe autoimmune rheumatic disease with high mortality. Epigenetic factors, particularly micro-RNAs (miRNAs), may contribute to its pathogenesis by regulating gene expression. In this cross-sectional study, we assessed altered miRNA–mRNA regulatory networks in SSc and associated them with disease-related biological processes. We analyzed the miRNA profiles and differentially expressed genes (DEGs) of peripheral blood mononuclear cells (PBMCs) from 52 SSc patients (42 women and 10 men; mean age: 59.1 years) and 24 age- and gender-matched healthy controls. Total RNA was isolated and subjected to high-throughput next-generation sequencing for both miRNA and mRNA profiling. We identified 58 differentially expressed miRNAs (DEMs), 33 upregulated and 25 downregulated in SSc. In parallel, 6610 DEGs were detected (Mann–Whitney U-test, p < 0.05); 31 remained upregulated and nine downregulated after false discovery rate (FDR) correction. Integration of miRNA and mRNA data revealed 180 validated inverse miRNA–mRNA interactions. Notably, 22 of 31 upregulated DEGs corresponded to targets of downregulated miRNAs, indicating coordinated derepression. Functional enrichment analyses highlighted pathways related to extracellular matrix (ECM) remodeling, immune responses, fibrosis, and transcriptional regulation. Our findings suggest that altered miRNA expression contributes to widespread transcriptional dysregulation in SSc, promoting pro-fibrotic and immune-activated molecular pathways through coordinated miRNA–mRNA interactions. Full article

RNA N⁶-methyladenosine (m⁶A) modification is a pivotal post-transcriptional regulator of diverse biological processes. Despite the growing interest in insect epitranscriptomics, a systematic evaluation of research trends and hotspots remains lacking. Here, we conducted a bibliometric analysis to map the global landscape of METTL3 and m⁶A research in entomology over the past decade. Our results reveal a steady increase in publications, signaling a phase of rapid expansion in this field. Notably, the number of studies on METTL3 is significantly lower than that of general m⁶A research, suggesting that current efforts prioritize phenotypic over the mechanistic roles of core regulatory components. Keyword co-occurrence analysis identifies Bombyx mori, Locusta migratoria, and Drosophila melanogaster as the primary model systems. Research hotspots predominantly center on METTL3-mediated regulation of development, behavioral plasticity, immunity, and host–pathogen interactions. These findings highlight insect METTL3 as a burgeoning research frontier. Future studies should emphasize cross-species comparisons and the systematic dissection of regulatory networks to provide novel theoretical frameworks and molecular targets for sustainable pest management and resource insect utilization. Full article

Age-related changes in neurotransmitter systems contribute to declines in cognitive, emotional, and motor function, yet the biological mechanisms linking these changes to aging are not completely understood. Epigenetic regulation offers a promising framework to bridge this gap. DNA methylation-based biomarkers of biological aging (i.e., epigenetic clocks) capture cumulative and dynamic aspects of biological aging that may reflect vulnerability in neural systems beyond chronological age. However, whether these indices track with the integrity of neurotransmitter systems has not been systematically examined. This scoping review synthesizes evidence across human studies to evaluate how epigenetic aging processes influence neurotransmitter gene regulation and system function across the lifespan. We included 109 studies spanning 2005–2026. GABAergic genes (GAD1, GABRA2) showed the most consistent and reproducible age-related promoter hypermethylation across the cortex, inversely correlated with mRNA expression and corroborated by MRS evidence of cortical GABA decline. Dopaminergic and serotonergic evidence during normative aging was sparse; most epigenetic data in these systems came from disease cohorts. Histone modifications converged on neurotransmission and synaptic-plasticity loci, predominantly in Alzheimer’s disease tissue. Subcortical and brainstem nuclei central to monoaminergic and cholinergic systems remain under-investigated for normative aging epigenetic processes. Environmental and social determinants, socioeconomic status, childhood adversity, and chronic stress, were consistently associated with accelerated peripheral epigenetic aging, but brain-specific data are scarce. Full article

Background: Impaired insulin secretion by pancreatic beta cells drives chronic hyperglycemia, which characterizes type 2 diabetes mellitus. The mechanosensitive ion channel Piezo2 has been implicated in various physiological processes. However, its expression and functional role in pancreatic endocrine cells remain poorly understood. Methods: We investigated the expression, cellular localization, and potential functional significance of Piezo2 in the pancreatic islets of mice fed normal- and high-fat diets (HFD) using molecular, immunohistochemical, and immunofluorescence approaches. Results: Piezo2 mRNA and protein expression were detected in rat pancreatic tissue and the pancreatic beta cell line INS-1 via polymerase chain reaction and Western blotting analyses. Hematoxylin and eosin staining and histopathological analysis were performed to determine the localization of Piezo2, insulin, and glucagon in the islets of Langerhans from mouse pancreas. Immunofluorescence revealed that Piezo2 colocalized with insulin, glucagon, pancreatic polypeptide (PP, a pancreatic cell marker), and insulin/PP (suggesting Ppy-lineage beta cells). Piezo2 expression is significantly reduced in islets from HFD-fed mice and downregulated under high glucose conditions in INS-1 cells. Stretch stimulation, with or without D-GsMTx4 (a Piezo2-specific inhibitor), enhanced glucose-stimulated insulin secretion, whereas ruthenium red (a non-specific Piezo channel inhibitor) did not alter the response to high glucose. Conclusions: These findings demonstrate Piezo2 expression in pancreatic islets and suggest that it is enriched in beta cells and Ppy-lineage beta cells, minority in alpha cells and is responsive to metabolic stress. Although Piezo2 may contribute to beta-cell adaptation, its role in insulin secretion remains unclear. Full article

Characterized by its highly aggressive behavior and propensity for metastasis, osteosarcoma remains a formidable clinical challenge with restricted treatment modalities. Cancer stem-like cells (CSCs) are widely recognized as central orchestrators of oncogenic progression and therapeutic intractability; however, the precise epigenetic regulations governing these processes are yet to be fully elucidated. Here, we investigated the role of the long non-coding RNA DANCR in regulating osteosarcoma stemness. DANCR expression was significantly upregulated in human osteosarcoma tissues and positively correlated with the stemness markers CD133, SOX2, and CD90. Functional assays demonstrated that DANCR overexpression enhanced stem-like properties, including an enriched CD133+/CD44+ cellular fraction and enhanced spheroid-forming capacity, concurrently accelerating in vitro cellular proliferation, migration, and invasive potential. In a xenograft mouse model, DANCR upregulation promoted in vivo tumor growth and lung metastasis. Mechanistically, dual-luciferase reporter assays and RNA immunoprecipitation (RIP) revealed that DANCR acts as a competing endogenous RNA (ceRNA) by sponging miR-145-5p, thereby facilitating the de-repression of CD133 and contributing to Akt/mTOR signaling activation. In addition, DANCR/miR-145-5p modulation was associated with changes in autophagy-associated markers. Collectively, these findings identify the DANCR/miR-145-5p/CD133 axis as a regulator of osteosarcoma stemness and progression, providing new insights into tumor biology and highlighting a potential molecular target for therapeutic investigation. Full article

Background: Cellular senescence is accompanied by mitochondrial dysfunction and decline in type I collagen production, contributing to age-related tissue deterioration. However, the post-transcriptional mechanisms underlying senescence-associated collagen decline remain poorly understood. Methods: Here, we investigated the effects of chlorella hot water extract (CHWE) on mitochondrial function and collagen production in senescent human fibroblasts. Results: CHWE restored mitochondrial membrane potential, ATP production, and redox balance through upregulation of SOD2. Notably, CHWE increased collagen protein levels without altering COL1A1 mRNA, indicating post-transcriptional regulation. miRNA profiling across young, senescent, and CHWE-treated senescent fibroblasts revealed that miR-193a-5p was upregulated during senescence (1.73-fold) and normalized by CHWE treatment. Functional validation confirmed that miR-193a-5p mimic suppressed COL1A1 protein. These findings identify a senescence–miR-193a-5p–COL1A1 axis in which age-dependent miR-193a-5p accumulation represses collagen translation, and CHWE reverses this process. By simultaneously restoring mitochondrial bioenergetic capacity and relieving miRNA-mediated translational repression, CHWE promotes efficient collagen recovery in senescent cells through complementary mechanisms. Conclusions: This study reveals a translational regulatory mechanism of collagen decline during cellular aging and highlights CHWE as a functional food supplement and a potential multi-target agent for age-related tissue deterioration. Full article

Background: A high-fat diet (HFD) contributes to cardiometabolic disease. Gut microbiota-derived metabolites may participate in this process, but their contribution to lipid regulation is not well defined. Indoxyl sulfate (IS), a microbiota-derived metabolite, has been linked to vascular and metabolic dysfunction. Its role in lipid metabolism remains unclear. Methods: In Part A, plasma and urinary concentrations of IS were measured in plasma and urine from HFD-fed rats in which dyslipidemia had developed, together with controls. In Part B, HepG2 cells were exposed to IS, and cell viability and selected cholesterol metabolism-related transcripts and proteins were assessed. In Part C, 10-week-old, male Sprague–Dawley rats maintained on a standard diet received vehicle or IS at two doses for 8 weeks. Hepatic expression of LDLR, SREBP-2, HMG-CoA reductase, and related cholesterol metabolism markers were measured by quantitative real-time PCR and Western blotting. Results: In Part A, higher plasma IS concentrations and higher daily urinary IS excretion were found in samples collected from HFD-fed rats compared to controls. In HepG2 cells, IS reduced cell viability at higher concentrations and increased LDLR mRNA and protein expression. In IS-treated rats, total cholesterol, LDL-cholesterol, and triglycerides increased in a dose-dependent manner. Hepatic SREBP-2 and HMG-CoA reductase protein levels were increased at both IS doses, whereas LDLR protein abundance was increased at the higher dose. Moreover, serum PCSK9 levels were reduced in IS-treated rats. Conclusion: IS increased in HFD-fed rats. IS altered cholesterol metabolism-related pathways in HepG2 cells and in rats. In vivo IS administration increased circulating lipids and hepatic proteins involved in cholesterol synthesis and uptake. These findings indicate that IS may contribute to disturbed lipid homeostasis, although its role in HFD-induced dyslipidemia requires further mechanistic confirmation. Full article

The proliferation of methicillin-resistant Staphylococcus aureus (MRSA) in food processing is an escalating public health issue. This circumstance has intensified the quest for ecological alternatives to impede pathogen proliferation and avert food degradation. This study firstly investigated the chemical compositions of three essential oils (EOs) sourced from Eucalyptus, Rosemary and Lavender plants using GC-MS. Subsequently, the antibacterial and antibiofilm activities of the tested EOs were assessed against MRSA strains. The effects of these EOs on the expression of antibiotic resistance-related (mecA), virulence regulatory (agrA and sarA), and enterotoxin (sea) genes in MRSA strains were also evaluated by real-time PCR. Concerning the composition analyses performed on the EOs, our results revealed a total of 82 compounds, which accounted for 99.20, 98.10 and 92.78% of Eucalyptus, Rosemary and Lavender EOs, respectively. The anti-staphylococcal activity showed that Eucalyptus EO had the greatest effect, with diameter of inhibition exceeding 41 mm. Moreover, the association between Rosemary EO and the antibiotic (cefoxitin) highlighted the enhancement of the antibacterial effect against the MRSA reference strain. Additionally, Eucalyptus EO showed the highest inhibitory effect against both strains, with MIC values ranging from 0.781 to 1.563 mg/mL, followed by the Rosemary and Lavender EOs. All the tested EOs displayed a bactericidal effect against the tested MRSA strains. Regarding the antibiofilm activity, Rosemary and Lavender EOs had varying impacts on the pre-formed biofilms, with percentage reduction values ranging from 36% to 73% and 37% to 68%, respectively. Finally, the mRNA expression of the MRSA gene A mecA and virulence genes agrA, sarA and sea declined following EO treatment compared with the control. The findings of this study highlighted the efficacy of locally tested EOs in reducing MRSA biofilm formation and the expression of virulence factors and suggested their potential use in food safety and culinary applications. Full article

The spatial organization of the eukaryotic nucleus plays a pivotal role in regulating pre-mRNA splicing; however, the underlying principles governing this organization remain incompletely understood. Recent advances in imaging and sequencing technologies have revealed that splicing regulation is orchestrated across multiple hierarchical levels, from nanoscale protein–RNA interactions to large-scale nuclear architecture. Intrinsically disordered regions (IDRs) in RNA-binding proteins (RBPs) mediate multivalent interactions that drive liquid–liquid phase separation, leading to the formation of dynamic biomolecular condensates, such as nuclear speckles, paraspeckles, and nuclear stress bodies (nSBs). These structures act as functional hubs that modulate RNA processing efficiency and respond to cellular stress. In addition, emerging evidence highlights nucleus-wide RBP meshworks that spatially organize co-transcriptional splicing through dynamic RNA-dependent interactions. The interplay between these condensates and meshworks forms a spatially organized network that fine-tunes the efficiency and fidelity of pre-mRNA splicing. Collectively, this review presents a unified model in which phase separation and higher-order nuclear architecture coordinately regulate transcriptomic output in space and time. Full article

RNA interference (RNAi) represents a promising alternative to chemical insecticides, but its efficacy depends on efficient double-stranded RNA (dsRNA) uptake, a process poorly characterized in thrips. To enable sufficient dsRNA production for functional studies, we first optimized an E. coli expression system by constructing a vector containing three tandem terminators, which substantially enhanced dsRNA yield by approximately 11-fold. Using this optimized production system, this study identified a conserved muscle actin fragment for dsRNA synthesis and evaluated RNAi responses in Megalurothrips usitatus and Frankliniella occidentalis. Insect mortality, target-gene suppression, and transcriptomic responses were evaluated via RT-qPCR and RNA-seq analyses using artificial diets supplemented with muscle actin dsRNA. The designed dsactin shared > 97% sequence identity between the two species. Oral ingestion of 1500 ng µL⁻¹ dsRNA caused concentration-dependent mortality (72% in M. usitatus, 48% in F. occidentalis) and significant down-regulation of muscle actin mRNA within 72 h. Transcriptomic analysis in M. usitatus revealed upregulation of genes associated with clathrin-mediated endocytosis and SID-1-like transmembrane transport, suggesting a potential dual-pathway model for dsRNA uptake. These findings provide correlative insights into RNAi efficiency in thrips. Full article

Background: Angiopoietin-like 3 (ANGPTL3) and proprotein convertase subtilisin/kexin type 9 (PCSK9) are key regulators of lipid homeostasis. We have previously shown that gene silencing of ANGPTL3 significantly induces PCSK9 expression in the human hepatoma cell line Huh7. Here, we investigated the biological significance of this regulation in the cultured human hepatoma cell line Huh7. Methods: We performed an RNA-seq analysis in Huh7 cells transfected with siRNA-ANGPTL3, siRNA-PCSK9, and double siRNA-ANGPTL3/PCSK9. Selected findings were assessed by RT-qPCR, Western blotting, and ELISA. Results: Among 13,945 detected transcripts, 192 genes were differentially expressed after ANGPTL3 silencing, 88 after PCSK9 silencing, and 219 after combined ANGPTL3/PCSK9 silencing, compared with scramble-siRNA controls. When ANGPTL3 gene expression was silenced, we observed a compensatory induction in PCSK9 mRNA and protein expression. Bioinformatic analysis revealed that gene silencing of ANGPTL3 or both ANGPTL3/PCSK9 suppresses serpin family A member 1 (SERPINA1), which encodes α1-antitrypsin, and lectin mannose-binding 1 (LMAN1). These data were confirmed by Western blot and RT-PCR analysis. In addition, ANGPTL3-siRNA, alone or combined with PCSK9-siRNA, significantly increased FV and FVIII mRNA expression and secretion in conditioned medium. Conclusions: Our data identified SERPINA1 and LMAN1 as genes downregulated in response to ANGPTL3 silencing in Huh7 hepatoma cells, which was also associated with increased expression of FV and FVIII. Our study suggests a potential link between ANGPTL3 silencing and coagulation-related processes, extending the biological relevance of ANGPTL3 beyond lipid metabolism. Full article

Clinical genomics has traditionally focused on protein-coding variation, yet many pathogenic mechanisms arise through alterations in RNA processing, stability, localisation, translation, and surveillance. Prior reviews have addressed individual RNA layers, splicing, non-coding RNAs, RNA therapeutics, or RNA diagnostics in isolation. This review presents an integrated, mechanism-matched framework linking RNA-level disease mechanisms to diagnostic reasoning and therapeutic selection across all major RNA layers, offering a practical resource for clinical geneticists and translational researchers. I examine how splicing defects, pseudoexon inclusion, polyadenylation disruption, RNA editing loss, untranslated-region variants, premature termination codons, stop-loss variants, RNA-binding protein dysfunction, non-coding RNA dysregulation, altered codon usage, ribosome stalling, and surveillance pathway failure, including nonsense-mediated decay, nonstop decay, and no-go decay, each create distinct and mechanistically addressable disease states. A central argument of this review is that treatment selection must be mechanism-matched rather than gene- or variant-class-based: splice defects may require antisense oligonucleotide (ASO)-mediated correction or small-molecule splice modulation; toxic transcripts may require ASO- or siRNA-mediated silencing; haploinsufficiency may require mRNA replacement or transcript rescue; premature termination codons are candidates for readthrough only when transcript and protein context are favourable. I further argue that RNA sequencing, long-read transcriptomics, allele-specific expression analysis, and functional assays are essential for both diagnosis and therapeutic stratification. The framework described here moves clinical variant interpretation beyond descriptive classification toward mechanism-based, RNA-centric precision medicine. Full article

Background: The m⁷G cap structure, which mimics the natural cap of eukaryotic mRNA, is a critical determinant of mRNA vaccine efficacy, safety, and stability. However, its precise quantification remains challenging due to complex impurity profiles and the high physicochemical similarity between the target cap and related impurities. Although liquid chromatography mass spectrometry (LC-MS) is widely employed for this purpose, current methodologies still face significant limitations, including labor-intensive sample preparation, low analytical throughput, poor reproducibility in quantifying low-level impurities, and a lack of universally applicable strategies across diverse mRNA vaccine platforms. Methods: We systematically optimized sample preparation and LC-MS detection workflows. RNase H-mediated cleavage was compared with DNAzymes, guide DNA probes were rationally designed, and thermostable RNase H was introduced for one-step denaturation and cleavage. To establish an accurate, efficient, and universal sample preparation workflow. Chromatographic conditions were optimized using an ion-pairing reagent system to suppress ESI-MS metal adducts. Eliminating sample purification improves recovery, reduces manual handling errors, and boosts assay efficiency. Results: Through optimally designed guide DNA probes, RNase H cleavage specificity reached ≥98% with high cleavage efficiency, offering higher efficiency than DNAzyme. Furthermore, the incorporation of thermostable RNase H enabled a single-step workflow combining high-temperature denaturation and site-specific cleavage, substantially streamlining sample preparation. On the chromatographic side, optimization of the ion-pairing reagent system effectively suppressed metal adduct formation in electrospray ionization mass spectrometry (ESI-MS). This advancement enabled direct injection of the 5′ cap fragments without purification, achieving high-recovery quantification while demonstrating broad compatibility across mainstream LC-MS platforms. The optimized assay reduces the total analytical workflow from 4~6 h to under 1.5 h. Conclusions: Combining high accuracy, robustness, and broad platform compatibility, this method offers a universal, high-throughput analytical solution for mRNA vaccine quality control and continuous process development. Full article

Galectin-3 (Gal-3) is a β-galactoside-binding lectin implicated in metabolic inflammation, cardiovascular and renal dysfunction, neurodegenerative disorders, and obesity-related pathologies. Although Gal-3 is recognized as a clinically relevant biomarker, the mechanisms controlling its tissue expression and circulating abundance remain poorly defined. O-GlcNAcase (Oga; encoded by Mgea5), the enzyme that removes O-linked β-N-acetylglucosamine (O-GlcNAc) from proteins, regulates nutrient-sensitive signaling and transcriptional processes that overlap with Gal-3 associated disease pathways. To investigate the relationship between metabolic status and Gal-3 expression, male mice were fed a high-fat diet (HFD) for eight weeks to induce obesity. HFD-fed mice exhibited significant increases in body weight and fasting and fed blood glucose levels compared with lean controls, confirming metabolic dysregulation. ELISA revealed approximately threefold higher serum and plasma Gal-3 concentrations in obese mice, indicating enhanced Gal-3 production in diet-induced obesity. To determine whether Oga regulates Gal-3 expression, Oga wild-type (WT), heterozygous (HET), and knockout (KO) mice were analyzed. Circulating Gal-3 protein levels were significantly reduced in Oga KO mice, with intermediate levels in Oga HET animals. RT-qPCR revealed genotype-dependent modulation of Gal-3 (Lgals3) mRNA expression across multiple tissues, demonstrating tissue-specific regulation by Oga. These findings establish Oga as a critical regulator of Gal-3 expression and systemic abundance. The data reveal a mechanistic link between O-GlcNAc signaling enzyme Oga, and lectin-mediated metabolic inflammation, suggesting that Oga activity influences Gal-3 homeostasis and may affect its interpretation as a biomarker in metabolic disease. Full article