Search Results (607)

Topmouth culter (Culter alburnus) is one of the most economically important freshwater fish in China, but intensive aquaculture has caused germplasm degradation and reduced growth performance, while the genetic basis underlying growth variation in this species remains poorly understood. This study aimed to identify major-effect loci and candidate genes associated with growth-related traits to support molecular breeding. Whole-genome resequencing (average depth 11.44×) was performed on 300 individuals derived from random mating among three geographic populations (Danjiangkou, Taihu, and Poyang Lake); 239 individuals with complete phenotypic records were retained for a genome-wide association study (GWAS) of five growth-related traits, including body weight (BW), body weight without viscera (BWW), total length (TL), body length (BL), and body height (BH). After stringent filtering, 7,597,008 high-quality single-nucleotide polymorphisms (SNPs) were obtained, and association analysis was conducted using a linear mixed model, followed by Benjamini–Hochberg false discovery rate correction and 1000-permutation testing for BW and BL. Six genome-wide significant SNPs and 473 suggestive SNPs were identified, with individual significant SNPs explaining over 11% of phenotypic variance, indicating candidate loci of putatively moderate-to-large effect. Significant SNPs were predominantly clustered on chromosomes 16 and 19. Four candidate genes—aig1, cacna1b, pgm5, and bcr—were identified, with functions related to lipid metabolism, muscle structure, and cell proliferation. This first population-level GWAS in topmouth culter provides valuable molecular markers for marker-assisted selection and lays a foundation for accelerated genetic improvement of this species. Full article

Single-cell omics technologies have transformed the study of cellular heterogeneity, enabling high-resolution analysis of tissue development and complex traits. In sheep and goats, these approaches have been applied to skin, hair follicles, reproductive organs, metabolic tissues, and adipose tissue, revealing cell type-specific regulatory programs underlying traits such as wool quality, fertility, growth, and fat deposition. However, most studies rely on single-cell RNA sequencing (scRNA-seq) and are limited by incomplete genome annotation, insufficient coverage of production traits, and weak integration with population genetics, restricting their application in molecular breeding. This review summarizes advances in single-cell omics in sheep and goats, focusing on tissue development and trait formation. We further discuss emerging strategies that integrate single-cell multi-omics, spatial transcriptomics, and population genetics to resolve regulatory mechanisms in a cell type-specific and spatially informed context. Finally, we discuss CRISPR/Cas9-based validation to link genotype and phenotype, accelerating gene discovery and precision breeding in small ruminants. Full article

Variants in the human PAX4 gene are associated with both monogenic and complex forms of diabetes, yet their pathogenic effects remain difficult to define in models that accurately mimic human islet architecture and neonatal metabolic transitions. Here, we created a porcine PAX4 loss-of-function model using CRISPR/Cas9 cytidine deaminase base editing to introduce a premature stop codon in the PAX4 coding sequence. PAX4 knockout piglets developed severe hyperglycemia within 24 h of birth, followed by rapid postnatal clinical deterioration and uniform death by day 3. Biochemical analysis showed significant diabetic decompensation, including electrolyte imbalances, hyperosmolality, azotemia, dyslipidemia, and metabolic acidosis. Gross and histological examinations revealed notable pancreatic hypoplasia with preservation of exocrine tissue. Single-nucleus RNA sequencing and immunohistochemistry demonstrated an almost complete loss of insulin- and somatostatin-producing β- and δ-cells, respectively, with relative preservation of glucagon-expressing α-cells. Overall, these results establish PAX4 as a crucial factor in pancreatic endocrine development and postnatal glucose regulation in a large-animal model. This platform offers a human-relevant system for studying diabetes-associated PAX4 variants and for testing regenerative and gene-based therapies for insulin-deficient diabetes. Full article

Background/Objectives: Iron deficiency remains a prevalent condition, needing specific laboratory tests for diagnosis. This study aimed to evaluate whether routine complete blood cell count (CBC) parameters can be used within a machine learning framework to predict low ferritin and low transferrin saturation, used as biochemical markers of altered iron status, potentially supporting more targeted laboratory test utilization. Methods: In this single-center retrospective outpatient study, we analyzed 32,437 records from subjects undergoing both complete blood cell count and iron metabolism testing between 2023 and 2026. Low ferritin and low transferrin saturation were defined using sex-specific thresholds. Low ferritin was present in 14,344 subjects (44.2%), whereas low transferrin saturation was present in 7791 subjects (24.0%). After cleaning data and excluding incomplete records, demographic variables and CBC indices were tested as potential predictors. The dataset was split into training and test sets with stratified sampling. Multiple supervised machine learning models, including logistic regression, decision tree, random forest, XGBoost, support vector machine, k-nearest neighbors, and Naive Bayes, were trained. Hyperparameter tuning and model selection were performed using repeated stratified 10-fold cross-validation, optimizing the area under the curve (AUC). Model performance was assessed by AUC, sensitivity, and specificity, and validated on an independent test set. Results: All models showed predictive capability for low ferritin and low transferrin saturation using CBC parameters alone. Ensemble methods, especially random forest and XGBoost, reached the best performance (AUC values of 0.80–0.87 for ferritin and 0.85–0.96 for transferrin saturation). Sensitivity and specificity were balanced, supporting clinical screening applicability. Results were maintained across validation and confirmed in the test set. Prediction of transferrin saturation showed slightly higher accuracy than ferritin. Feature importance analysis identified mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and red blood cell distribution width (RDW) as key predictors. Conclusions: CBC-based machine learning models may help identify subjects with low ferritin or low transferrin saturation, supporting subsequent targeted assessment of iron status. Full article

Autoimmune myocarditis frequently progresses to inflammatory cardiomyopathy through dysregulated immune–stromal interactions. This study employs single-nuclei RNA-sequencing (snRNA-seq) to profile 46,233 cardiac nuclei from the experimental autoimmune myocarditis (EAM) mouse model at four timepoints: day 0 (healthy), day 14 (inflammation), day 21 (acute inflammation), and day 40 (late cardiac remodelling). Single-nuclei RNA profiling identified 18 transcriptionally distinct cell populations. Global cell–cell communication analysis revealed a dramatic peak of intercellular signalling at day 14 (5907 interactions), with fibroblast subpopulations and macrophages as dominant hubs, followed by partial resolution at day 21 (2264 interactions) and renewed remodelling at day 40 (4862 interactions). Subclustering of the macrophage compartment identified five subpopulations: Mac-TLF, Mac-MHCII, Mac-rMHCII, Mac-ResL, and Classical Monocytes. Tissue-resident macrophages (Mac-TLF, CCR2-) dominated at healthy state (~55%) but were rapidly depleted at day 14, coinciding with a dramatic influx of recruited CCR2⁺ macrophages (Mac-rMHCII), which expanded to over 70% of the compartment and maintained dominance through day 40. At inflammation (day 14), the expanded Mac-rMHCII subpopulation displayed a strongly pro-inflammatory signature (Il1b, Stat2, Parp14, Apoe), and the overall macrophage compartment was enriched for cytokine response, Fc-gamma receptor, and Notch signalling pathways, while downregulating homeostatic and mitochondrial metabolic programmes, potentially contributing to impaired efferocytosis and cardiomyocyte dysfunction. Macrophage-centred communication networks expanded markedly at day 14 (1047 interactions), with resting fibroblasts (FB-R) as the primary signalling partner, driving pro-inflammatory stromal activation marked by upregulation of Ccl2, Ccl7, and Csf2. Intra-macrophage subcluster communication also intensified at this timepoint (447 interactions). These findings delineate the temporal and functional heterogeneity of cardiac macrophages during EAM progression and identify key immune–stromal interactions driving pathological cardiac remodelling. The coexistence of pro-inflammatory and transitional reparative macrophage subsets highlights the limitations of broad immunosuppression and supports precision strategies targeting CCR2-mediated recruitment, the SPP1 signalling axis, and macrophage–fibroblast crosstalk as therapeutic avenues in myocarditis and its progression. Full article

Introduction: Glucagon-like peptide-1 receptor agonists (GLP-1 RAs), such as liraglutide (LIR), are widely used in humans to treat type 2 diabetes mellitus, obesity, and non-alcoholic fatty liver disease. In mammals, GLP-1 RAs have been shown to influence hepatic lipid metabolism, although the underlying mechanisms remain unclear. In fish, GLP-1 also plays an important role in regulating hepatic processes, including glycogenolysis, gluconeogenesis, and lipolysis. However, the effects of GLP-1 RAs on liver lipid metabolism in fish remain largely unexplored. Objective: This study aimed to evaluate the effects of LIR on lipid target genes using primary hepatocytes from brown trout as an in vitro model. Methodology: After 24 h, a hepatocyte monolayer culture was established, and cells were exposed for 24 and 48 h to supplemented L-15 medium (control), 0.1% dimethyl sulfoxide in supplemented L-15 medium (solvent control), and five single exposures to LIR at 1, 10, 100, 500, and 1000 nM. After 24 and 48 h, cell viability was assessed using the trypan blue exclusion assay. Gene expression was analysed by real-time qPCR, targeting genes involved in lipogenesis, lipid transport, and cholesterol efflux. Results: No concentration-dependent effects on cell viability were observed. Gene expression analysis showed that LIR exposure modulated the mRNA levels of lipid-related genes, including acetyl-CoA carboxylase (ACC), acyl-CoA long-chain synthetase 1 (Acsl1), and fatty acid synthase (FAS), with time being the main influencing factor. Overall, expression levels were higher at 48 h compared to 24 h. Additionally, dose-dependent effects were observed for ACC expression, with higher LIR concentrations showing significant differences compared to controls. Conclusions: These findings indicate that LIR modulates lipid-related gene expression in primary hepatocytes of brown trout without affecting cell viability. The results suggest that GLP-1 receptor activation may influence key pathways involved in hepatic lipid metabolism, with time-dependent effects playing a predominant role. Overall, this study supports the use of brown trout primary hepatocytes as a suitable in vitro model for investigating hepatic lipid responses to LIR and other GLP-1 receptor agonists, while providing initial insight into their potential effects in fish. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) and osteoporosis (OP) are epidemiologically linked, but shared cell-type-specific molecular features remain unclear. We integrated public single-cell/single-nucleus transcriptomic datasets for OP (GSE147287) and MASLD (GSE289173) with two-sample Mendelian randomization (MR), colocalization, network annotation, macrophage-focused in silico perturbation, and exploratory serum assessment. After quality control, 13,753 OP cells and 42,438 MASLD cells/nuclei were analyzed. Macrophages were consistently identified in both datasets and showed disease-associated expansion. Directionally concordant macrophage differentially expressed genes yielded 147 shared candidate genes, with enrichment mainly involving lipid/sterol metabolism, extracellular matrix and adhesion processes, immune presentation, lysosomal processing, and phagocytic pathways. MR prioritized MUC20 as the only candidate with concordant odds ratios greater than 1 for both OP (OR = 1.044, 95% CI 1.003–1.086) and MASLD (OR = 1.111, 95% CI 1.038–1.189). Colocalization supported shared genetic signals for MUC20 in OP (PP.H4 = 0.855) and MASLD (PP.H4 = 0.816). In silico perturbation suggested a limited but pathway-enriched predicted transcriptional footprint. Serum MUC20 was higher in patients with OP+MASLD than in healthy controls. This integrative analysis identified shared macrophage-associated transcriptional themes and prioritized MUC20 as a candidate molecule for future liver–bone crosstalk studies. Full article

L-carnitine plays a central role in mitochondrial fatty acid transport and cellular energy regulation; effects on the biochemical phenotype of brain cancer cells remain insufficiently characterized. Here, we applied confocal Raman spectroscopy and imaging to investigate the biochemical alterations induced by L-carnitine supplementation—administered as its tartrate salt—in human astrocytoma cells. Raman spectral analysis revealed distinct changes in lipid-, protein-, nucleic acid-, and cytochrome-associated vibrational features following 24 h of treatment, suggesting alterations in mitochondrial activity and cellular energy-related processes. Principal component analysis identified PC1 (93.87%) as representing the intrinsic biochemical composition of the cells, whereas PC2 (1.19%) and PC3 (0.59%) captured subtle yet consistent variations in lipid organization, protein conformation, and redox-sensitive vibrational features associated with L-carnitine exposure. Pearson correlation analysis of Raman cluster spectra indicated biochemical differences across cellular compartments, with the most pronounced changes observed in lipid droplets, supporting modifications in lipid-associated cellular processes. These findings demonstrate that Raman imaging provides a sensitive, label-free platform for resolving L-carnitine-induced biochemical heterogeneity at the single-cell level. Overall, this study highlights vibrational spectroscopy as a powerful tool for characterizing cellular responses to metabolic modulators and provides insight into the biochemical impact of exogenous L-carnitine in brain cancer cells. Full article

Gastric adenocarcinoma (STAD) exhibits extensive intratumoral heterogeneity that contributes to tumor progression and therapeutic resistance. In this study, we integrated single-cell RNA sequencing and bulk transcriptomic analyses to characterize malignant epithelial subtypes in STAD. Among seven identified tumor subtypes, the OLFM4-associated C3 subtype exhibited enriched palmitoylation-related signatures and altered metabolic activities, particularly glycolysis-related pathways. Functional enrichment analyses further supported the enrichment of multiple energy metabolism pathways. To evaluate the association between OLFM4 and metabolic regulation, recombinant OLFM4 treatment and siRNA-mediated OLFM4 knockdown were performed in gastric cancer cell lines. OLFM4 upregulation increased the expression of ZDHHC2 and GLUT1, accompanied by enhanced glucose uptake and elevated ATP production, whereas OLFM4 silencing reduced ZDHHC2 and GLUT1 expression. In addition, a prognostic risk model derived from C3 subtype-associated genes (MUC16, RALA, and PCBD1) effectively stratified STAD patients and was associated with immune checkpoint expression and immune infiltration. Collectively, our findings identify an OLFM4-associated gastric cancer cell state with palmitoylation-related signatures and altered metabolic activities, highlighting its potential relevance to metabolic heterogeneity in gastric adenocarcinoma. Full article

Background/Objectives: Whether anesthetic maintenance influences tumor biology in cervical cancer remains unsettled. We examined whether plasma extracellular vesicles (EVs) collected during sevoflurane or propofol anesthesia differentially affect HeLa cell behavior and explored lipidomic alterations associated with the biologically active EV condition. Methods: In a single-center prospective observational cohort, paired plasma samples were collected before anesthesia induction and before wound closure from 53 patients with stage II cervical cancer undergoing radical surgery under sevoflurane (n = 28) or propofol (n = 25) anesthesia. EV preparations were characterized by transmission electron microscopy, nanoparticle tracking analysis, and immunoblotting for EV markers. Their effects on HeLa cell proliferation, invasion, and wound closure, as well as HUVEC tube formation, were examined in vitro. EV miRNA profiles were analyzed by small-RNA sequencing. Lipidomic profiling by LC-MS and immunoblot analysis of EGFR/PKCα/NF-κB signaling were performed in recipient HeLa cells exposed to sevoflurane-associated EVs. Results: EVs collected after sevoflurane anesthesia increased HeLa cell proliferation, invasion, and wound closure and enhanced endothelial branching in HUVEC tube-formation assays, whereas post-propofol EVs showed no comparable phenotype. Small-RNA sequencing identified distinct anesthesia-associated EV miRNA changes, with the sevoflurane-related signature enriched in glycerolipid metabolism, glycerophospholipid metabolism, glycosylphosphatidylinositol-anchor biosynthesis, phosphatidylinositol signaling, and inositol phosphate metabolism. In HeLa cells treated with post-sevoflurane EVs, lipidomic analysis showed clear separation from pre-sevoflurane EV-treated cells and identified increased diacylglycerol (DG) species, including DG (16:1/18:2), DG (16:0/16:1), DG (18:2/18:2), DG (18:2/20:4), and DG (16:0/18:2). These changes were accompanied by higher p-EGFR, PKCα, and p-NF-κB p65 levels. Several DG species correlated positively with proliferation and invasion readouts and inversely with residual wound area. Conclusions: Plasma EVs collected after sevoflurane anesthesia were associated with a more aggressive phenotype in recipient cervical cancer cells and with lipid remodeling characterized by DG accumulation and altered EGFR/PKCα/NF-κB signaling. The data support an exploratory mechanistic model linking sevoflurane-associated EV cargo to metabolic reprogramming in cervical cancer cells. Full article

Central chondrosarcoma is the second most common primary malignant bone tumour, and grade progression markedly worsens prognosis. The contributions of lipid metabolic reprogramming and epigenetic co-dysregulation to grade progression remain poorly characterised. We integrated a bulk RNA-seq discovery cohort of 53 graded central chondrosarcomas (GSE299759) with a single-cell analysis of eight chondrosarcomas (GSE184118). Because the atypical cartilaginous tumour (ACT) and dedifferentiated groups each comprised only three samples, the Grade 3 versus Grade 2 contrast was pre-specified as the primary comparison. Curated panels of 44 lipid metabolism genes and 50 epigenetic regulators were assessed by differential expression and a correlation-based connectivity ranking, evaluated by permutation testing. In the primary Grade 3 versus Grade 2 comparison, SQLE, ACACA, and FASN were upregulated (FDR < 0.05), indicating a grade-associated increase in de novo lipogenesis. In the exploratory Grade 3 versus ACT comparison, additional lipid genes (HMGCR, LDLRAP1) and the epigenetic regulators EHMT2 and SIRT2 showed altered expression, although the small ACT group limits these estimates. A connectivity ranking highlighted FASN, KMT2C, TET2, SETD5, and KDM5B; permutation testing confirmed this co-expression structure was non-random (p < 0.0001). Single-cell analysis showed FASN, SETD5, and KDM5B are expressed predominantly in malignant cells, whereas KMT2C and TET2 are not, indicating cell-type heterogeneity. De novo lipogenesis upregulation is the most consistent lipid alteration in high-grade central chondrosarcoma, nominating SQLE, ACACA, and FASN as candidates for experimental investigation. Full article

Dormancy is an important factor influencing colorectal cancer (CRC) metastasis through diverse metabolic pathways and cell types. To elucidate its molecular mechanisms, bulk transcriptomic pathway scoring was integrated with single-cell RNA sequencing of epithelial, cancer stem, and immune cells to identify CRC dormancy-associated genes (CDAGs). Twenty-three CDAGs were identified. These genes were found to play a regulatory role in dormancy by participating in metabolic processes affecting energy supply or substance synthesis. In two independent CRC cohorts (GSE41258, GSE41568), machine learning models using these genes distinguished metastatic samples with area under the curve (AUC) of 0.79–0.87. High CDAG expression was associated with better recurrence-free survival in GSE41258 (p = 0.005), which remained significant after adjusting for age, sex, and adjuvant chemotherapy (p = 0.037). The prognostic value was validated in The Cancer Genome Atlas (TCGA) Colon and Rectal Cancer for progression-free survival (p = 0.004). Moreover, 20 CRC dormancy-associated drugs were identified, 12 of which were reported to be associated with CRC, two with experimental evidence of inhibiting CRC metastasis or recurrence. This study provided metabolic-oriented genes for characterizing CRC dormancy, which could distinguish metastatic samples and had independent prognostic value, and offered a foundation for further development of targeted therapeutic strategies. Full article

Oral squamous cell carcinoma (OSCC) represents a major global health burden, characterized by poor prognosis and limited improvement in survival over recent decades. Increasing evidence indicates that oral carcinogenesis is not solely driven by host genetic alterations but is significantly influenced by the oral microbiome through complex bidirectional interactions. This narrative review synthesizes current knowledge on the crosstalk between oral microbial communities and host genomic instability, with a specific focus on mutation-driven mechanisms. We discuss how microbial dysbiosis contributes to DNA damage, mutational signatures, epigenetic reprogramming, and immune modulation, thereby facilitating malignant transformation. Unlike previous reviews that address microbiome–cancer associations broadly, this work explicitly maps the mechanistic chain from microbial genotoxins through specific DNA repair pathway disruption to mutation accumulation in OSCC, and devotes substantial attention to the underexplored reverse direction—how host immune gene polymorphisms, DNA repair defects, and metabolic reprogramming shape the microbial niche. A comparative analysis with recent high-impact reviews is included. Finally, we outline emerging research directions, including multi-omics integration, single-cell and spatial transcriptomics, microbiome-targeted therapeutics, and artificial intelligence-assisted precision oncology approaches. Full article

Vibrio splendidus is an important opportunistic pathogen that causes diseases in aquatic animals, and its persisters increase the difficulty of aquaculture disease control. The stringent response is a central pathway in bacteria for coping with environmental stress, and the signaling molecule (p)ppGpp, synthesized under the regulation of RelA/SpoT homologs, is closely associated with persister formation and virulence modulation. However, the regulatory mechanisms linking the stringent response to persister formation and virulence in V. splendidus remain unclear. In this study, the core gene deletion strains ΔrelA and ΔrelAΔspoT were constructed via homologous recombination. Combined with D₂O single-cell Raman spectroscopy, transcriptomics, and phenotypic assays, we systematically characterized the biological effects of stringent response inactivation. The results showed that the loss of relA and spoT significantly reduced persister formation and key virulence traits while enhancing biofilm formation. Single-cell Raman spectroscopy analysis indicated that persisters remained metabolically active, accompanied by changes in different cellular components. Transcriptome analysis revealed that the absence of stringent response affected multiple pathways, including ribosomal function, energy metabolism, two-component systems, and quorum sensing. Additionally, the sigma factor RpoS may potentially exert a compensatory function in ΔrelAΔspoT strain, but this requires further validation. In conclusion, the stringent response positively regulates persister formation and virulence in V. splendidus, despite the existence of complex regulatory mechanisms. This study provides a theoretical basis for the development of anti-infective strategies targeting stringent response in aquatic pathogens. Full article

Black rice is abundant in polyphenolic antioxidants, but conventional thermal processing degrades these heat-sensitive compounds, limiting their bioactivity. Although single-strain fermentation can improve the extraction of bioactive components, it remains challenging to simultaneously balance the flavor and bioactivity of fermented black rice products. Low-temperature co-fermentation with yeast and lactobacillus has emerged as a promising strategy to enhance both the flavor profile and functional quality of fermented foods. Therefore, this study investigates the effects of low-temperature co-fermentation with Saccharomyces cerevisiae and Lactobacillus bulgaricus 134 on the quality of black rice slurry. The efficacy was systematically evaluated by monitoring fermentation kinetics, conducting polyphenol and anthocyanin metabolomics analysis, performing flavoromics analysis, and combining in vitro ABTS radical scavenging assays with a Caco-2 cell-based oxidative stress model. The results showed that this process activated β-glucosidase within the first 24 h of fermentation. By activating terpenoid and phenolic metabolic pathways, it maximized the accumulation of anthocyanins and short-chain esters during 30–36 h, which conferred the product with prominent fruity and sweet notes. Fermented black rice slurry (FBRS) exhibited potent ABTS radical scavenging activity. In the Caco-2 oxidative stress model, FBRS pretreatment restored cellular viability, upregulated the activity of endogenous antioxidant enzymes, and reduced MDA content. This study provides a theoretical foundation for developing high-nutritional, flavor-enhanced fermented black rice products. Full article