Search Results (886)

Estrogen is a key regulator of skeletal muscle growth and metabolism in birds, yet its specific roles in female chickens remain poorly defined. To address this gap, we established an estrogen-deficient model by surgically removing the ovaries of Wuding hens, a Chinese indigenous slow-growing breed. Growth traits, carcass yield, and meat quality were evaluated across different ages, complemented by histological examination, serum biochemical analysis, and multi-omics approaches (transcriptomics, proteomics, and lipidomics). Ovariectomized hens maintained somatic growth for a longer period and reached greater body weight and carcass yield at 330 days compared with intact controls. Thigh muscle tenderness was also enhanced in the absence of estrogen, despite no long-term differences in muscle fiber morphology. Lipidomic analysis revealed a transient increase in intramuscular triglyceride content at mid-growth (240 days), pointing to altered lipid storage and distribution. Integrated omics profiling further demonstrated significant changes in the mitogen-activated protein kinase (MAPK) and mechanistic target of rapamycin (mTOR) signaling pathways, accompanied by differential expression of key metabolic and structural genes, including mitogen-activated protein kinase 8 (MAPK8), fatty acid binding protein 4 (FABP4), ankyrin 1 (ANK1), and coenzyme Q6 monooxygenase (COQ6). These molecular adjustments suggest that estrogen withdrawal triggers broad reprogramming of muscle signaling and lipid metabolism. Overall, this study highlights the multifaceted role of estrogen in coordinating growth, muscle quality, and lipid homeostasis in hens and provides a functional model for studying estrogen deficiency in poultry with implications for meat quality improvement. Full article

Congenital heart defects (CHDs) occur in 50–75% of patients with 22q11.2 deletion syndrome (22q11.2DS), ranging from mild to severe manifestations. The genetic and environmental factors contributing to variable CHD phenotypes in 22q11.2DS are largely unknown. In this study, we used a mouse model of 22q11.2DS, termed Df1/+, to evaluate the effect of maternal vitamin A (VitA) dietary imbalance (supplementation or deficiency) on the incidence of aortic arch defects (AADs), which is a common type of CHD observed in both 22q11.2DS patients and Df1/+ mouse embryos. While most groups showed a previously observed 30% AAD incidence, two groups exhibited significantly higher rates: (1) Df1/+ embryos from WT mothers on a VitA-Supl diet (51% AADs) and (2) Df1/+ embryos from Df1/+ mothers on a VitA-Def diet (45% AADs). Thus, a low or high maternal VitA diet can increase the frequency of AADs in embryos depending on the maternal genotype. Transcriptomic analysis of the hearts of these high-risk embryos at embryonic day (E)18.5 revealed downregulation of key genes (Hdac3, Ptgds, Sirt5, Pfkm, and Lclat1) associated with energy metabolism pathways, such as oxidative phosphorylation and glycolysis, suggesting impaired cardiac recovery mechanisms. In conclusion, our findings demonstrate that altered VitA exposure can exacerbate AAD incidence in a maternal-genotype-dependent manner, highlighting the complex interplay between embryonic and maternal genetic background and environmental factors in CHDs associated with 22q11.2DS. Full article

Background: Low birth weight (LBW) is correlated with gut microbiota dysbiosis and intestinal barrier function disruption, increasing susceptibility to enteric diseases. These alterations underscore the critical need to identify key regulators of gut homeostasis, among which bile acids are increasingly recognized as pivotal for barrier integrity, microbial ecology, and host metabolism. Methods: Eight pairs of LBW (the initial BW was 0.850 ± 0.053 kg) and normal-birth-weight (NBW; 1.488 ± 0.083 kg) piglets were compared to evaluate cecal morphology and bile acid profiles. Subsequently, sixteen LBW piglets and eight NBW piglets were allocated into three groups: NBW (1.563 ± 0.052 kg), LBW control (LBW-CON; 0.950 ± 0.120 kg), and LBW with bile acid supplementation (LBW-bile powder; 0.925 ± 0.116 kg). Piglets in the LBW-bile powder group received 25 mg/kg BW of bile powder (hyodeoxycholic acid-enriched) by daily oral gavage for 14 days. Results: LBW piglets exhibited retarded cecal development and lower abundance of hyocholic acid species (p = 0.006). Importantly, bile powder supplementation significantly improved cecal length (p = 0.009) and mucosal thickness (p = 0.020) compared with LBW-CON piglets. Microbial analysis showed that the microbial dysbiosis index was restored to near-normal levels. Transcriptomic analysis revealed impaired extracellular matrix structure and mucus secretion in LBW piglets. Notably, bile powder supplementation markedly upregulated the protein expression of WNT8B (p < 0.001) and the bile acid receptors (i.e., GPBAR1 and FXR), alongside enhanced tight junctions and the goblet cell marker mucin-2 expression (p < 0.05). Conclusions: These findings suggest that specific bile acid supplementation improves gut barrier function and partially supports cecal development in LBW piglets. Full article

Ochratoxin A (OTA) is a major mycotoxin contaminant in grapes and their products, and Aspergillus carbonarius is its main producer. Controlling the growth of A. carbonarius is therefore critical for mitigating OTA contamination. Plant-derived perillaldehyde, with good antifungal activity and safety, has garnered growing attention. However, current understanding of how perillaldehyde affects A. carbonarius growth and OTA production remains poorly characterized. In this study, we systematically investigated the antifungal and antimycotoxigenic effects of perillaldehyde against A. carbonarius and explored the underlying mechanisms. The results showed that perillaldehyde could alter the mycelial morphology and damage the cell integrity of A. carbonarius. Additionally, perillaldehyde could diminish the total antioxidant capacity and impair the energy metabolism of A. carbonarius. Transcriptome analysis showed that the expressions of all the known conserved OTA biosynthetic genes and two OTA transport-related genes were significantly down-regulated, indicating that perillaldehyde could directly inhibit their expression. In conclusion, perillaldehyde can significantly inhibit OTA production by directly disrupting OTA biosynthesis and transport and inhibiting the growth of A. carbonarius. Thus, perillaldehyde has the potential to be used as a natural fungicide or alternative food preservative in grapes and their products, owing to its strong antifungal and antimycotoxigenic effects on A. carbonarius. Full article

The RTgill-W1 cell line serves as an alternative for acute fish toxicity testing. This study aims to study the reliability of the RTgill-W1 cell line in copper cytotoxicity using transcriptomic analysis followed by comparison with existing literature. As a result, the study found that the average EC50 (375 μg/L ± 181 μg/L) in cell viability was similar to previous literature results (0.093–530 μg/L), suggesting the system’s reliability as an alternative. The transcriptome changes of the RTgill-W1 cell line caused by copper exposure are supported by the existing literature on individual fish. For example, osmoregulatory disturbances, regulation of Na⁺/K⁺-ATPase activity, oxidative stress, apoptosis, energy metabolism alterations, metal detoxification, and chaperone protein expression were found in the RTgill-W1 cell line in response to copper exposure, indicating the utility of this cell line for transcriptome analysis. Finally, through RT-PCR confirmation and literature analysis, this study suggests that sirtuin 1, sirtuin 4, Na⁺/K⁺-ATPase, aifm4, bcl2, carbonic anhydrase, hsp70, hsp30, and other biomarkers could be used for detecting copper stress in aquatic organisms. This study is helpful for understanding the toxicity mechanism of copper and can be referred to as scientific data for regulating copper release into the aquatic environment. Full article

Uterine leiomyomas or fibroids are a common but pernicious benign tumor impacting between 70–80% of women of reproductive age. Despite their high prevalence, the etiology of uterine fibroids is not fully understood. This review aims to highlight the distinct metabolic features that uterine fibroids adopt to meet biosynthetic demands, support proliferation, extracellular matrix production, survival, and fibrosis. Specifically, we posit the role of glycolytic reprogramming—an adaptation in fibrosis across organs (lung, kidney, heart, and liver) as a major contributor to uterine fibroid development. Previous genetic, transcriptomic, proteomic, and metabolic studies have drawn strong links between metabolism and uterine fibroid biology and identified genotype-specific metabolic alterations such as fumarate hydratase (FH) deficiency and mediator of RNA polymerase II transcription (MED12) gene mutations. Studies in non-uterine models have linked glycolysis to ECM production and fibrosis through activation of transforming growth factor-beta (TGF-β) and the canonical Wnt pathway (Wnt/β-catenin) signaling, supporting them as potential key pathways in uterine fibroid pathogenesis via glycolytic reprogramming. Other metabolic regulators, such as hypoxia-inducible factor 1-alpha (HIF-1α), mammalian target of rapamycin (mTOR), and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), may also sustain the fibrotic phenotype through coupling signaling that drives ECM production to metabolic programming. Overall, the proposed metabolic perspective of uterine fibroid pathogenesis invites further exploration of mechanistic investigation in uterine-specific models and therapeutic targeting through larger cohort studies. Full article

Mitochondrial transcription factor A (TFAM) is essential for mitochondrial DNA (mtDNA) maintenance and function, but its role in glioblastoma (GBM) remains largely unexplored. Analysis of patient astrocytomas and TCGA datasets has revealed progressive TFAM downregulation with increasing malignancy, with the lowest expression in glycolytic/plurimetabolic (GPM) subtypes. Functional and transcriptomic profiling of mesenchymal GBM cell lines showed that TFAM silencing in GPM-type U87MG cells enhanced proliferation, S-phase entry, reactive oxygen species (ROS) production, and adhesion, while reducing motility. These changes were correlated with upregulation of LDHC and TRAF2 and downregulation of androgen receptor-linked motility genes and LOXL2. By contrast, TFAM loss in mitochondrial (MTC)-type A172 cells caused minimal phenotypic alterations, associated with elevated SOD1 expression and activation of antioxidant, mitochondrial membrane, and survival pathways, alongside suppression of oxidative phosphorylation and vesicle-trafficking genes. TFAM overexpression reduced proliferation in U87MG but had a limited impact on A172 cells. Taken together, these findings establish TFAM as a subtype-specific regulator of GBM cell proliferation, redox balance, and motility. TFAM loss drives a proliferative, ROS-sensitive phenotype in GPM-type cells, while eliciting adaptive, stress-resilient programs in MTC-type cells. This study identifies TFAM and downstream effectors, TRAF2 and LOXL2, as potential therapeutic targets, supporting the development of metabolic subtype-tailored strategies for GBM treatment. Full article

CaMK4, a calcium/calmodulin-dependent protein kinase, is an important mediator of cellular signal transduction, yet its role in the regulation of skeletal muscle satellite cells (MuSCs) in goats has remained unclear. In this study, CaMK4 overexpression and knockdown models were established, and integrated transcriptomic and proteomic analyses were performed to systematically elucidate its regulatory network. CaMK4 overexpression altered key pathways associated with cell proliferation and muscle development, including cAMP, PI3K-Akt, and actin cytoskeleton regulation, while proteomic data highlighted calcium signaling and JAK-STAT pathways. Conversely, CaMK4 knockdown enhanced MuSC proliferation by upregulating cell cycle-related genes and proteins. Integrated analyses further identified that Galectin-9 (LGALS9), Collagen triple helix repeat containing-1 (CTHRC1), Hyaluronan Synthase 1 (HAS1), and L-Threonine Dehydrogenase (TDH) may serve as potential key nodes regulating cell cycle, apoptosis, and metabolic control. This suggests a regulatory role for CaMK4. Collectively, these findings provide a mechanistic framework for understanding CaMK4 function in ruminant muscle development and may offer insights for improving goat muscle growth, meat quality traits, and production efficiency. Full article

Monascus pigments (MPs), natural food colorants produced by Monascus spp., have been traditionally used in China and Southeast Asia. Our prior work demonstrated that altered cell wall architecture in M. purpureus M9 significantly enhances pigment synthesis and secretion, although biosynthetic regulation under combined cell wall stress and acidic conditions remains unexplored. This study employed comparative transcriptomics to investigate coordinated regulation of MP production by pH stress and modified cell wall polysaccharides in wild-type (M9-WT) and UDP-galactopyranose mutase-deficient (M9-KO) strains at pH 5.0 and 3.0. At pH 5.0, MpglfA knockout enhanced MP secretion through cell wall restructuring involving differential expression total 67 genes (DEGs) of primary metabolism. Acidic stress (pH 3.0) significantly increased DEGs (168 up/643 down) in M9-KO versus M9-WT, inducing amino acid/fatty acid degradation pathways that generate MP precursors (acetyl-CoA/propionyl-CoA) and accelerating metabolic transition toward secondary metabolism. Concurrently, M9-KO adopted survival strategies featuring growth suppression and acid stress pathway activation to coordinate osmotic adaptation. Glucan synthase genes exhibited greater pH sensitivity than galactomannan-related genes, while MP biosynthetic genes were transcriptionally repressed in M9-KO under higher acidity. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment and the series test of cluster confirmed that primary metabolic pathways, particularly nitrogen/carbon metabolism, critically regulate MP biosynthesis. Transcriptomic analysis under limited pH regimes revealed that antagonistic regulators ROX1 and SPT15 mediated pH-responsive transcriptional reprogramming, potentially regulating specific MP biosynthesis (e.g., monascus orange pigments). This work established theoretical foundations for manipulating cell wall composition to enhance MP production efficiency. Full article

Cisplatin is a widely used antineoplastic agent whose therapeutic efficacy is often limited by its adverse effects on the central nervous system. In this exploratory study, we characterized the transcriptomic impact of a cumulative cisplatin regimen on the male Wistar rat brain using microarray technology. Differentially expressed genes were identified, and their functional roles were investigated through enrichment analyses (KEGG) and Gene Ontology (GO), and the construction of protein–protein interaction (PPI) networks. Our results revealed significant alterations in pathways related to synaptic signaling, neuroplasticity, and cellular metabolism. To generate translational hypotheses, these findings were subsequently correlated in silico with public human lower-grade glioma (LGG) datasets, which suggested a potential association between key cisplatin-regulated genes and clinical prognosis and immune cell infiltration patterns. This manuscript does not include RT-qPCR (or Western blot) validation; results should be interpreted as hypothesis-generating and require orthogonal confirmation. These findings provide a comprehensive transcriptomic map of cisplatin-induced neurotoxicity, offering novel insights into its underlying molecular mechanisms and identifying a rich set of candidate targets for future neuroprotective strategies. Full article

Background/Objectives: Thyroid cancer (TC) is the most common type of endocrine neoplasm and is increasing in incidence, particularly papillary thyroid carcinoma (PTC). Early-stage disease has a favorable prognosis; however, advanced forms, such as anaplastic thyroid carcinoma, complicate treatment. Long non-coding RNAs (lncRNAs), longer than 200 nucleotides and non-coding, together with microRNAs, have emerged as major regulators of TC pathogenesis. This review summarizes data on how dysregulated lncRNAs influence the hallmarks of cancer in thyroid malignancies. Methods: We reviewed the literature on the role of lncRNAs and microRNAs in TC, focusing on their functions as competing endogenous RNAs (ceRNAs), regulators of PI3K/AKT and Wnt/β-catenin pathways, and controllers of epigenetic alterations. Results: Dysregulated lncRNAs contribute to hallmarks including sustained growth, evading suppressors, resisting death, replicative immortality, angiogenesis, invasion, metabolic reprogramming, immune evasion, genomic instability, and tumor-promoting inflammation. ceRNA mechanisms amplify immune evasion by regulating checkpoint proteins and cytokines, altering immune cell activity. Altered lncRNA profiles correlate with aggressiveness, metastasis, and prognosis. Notable lncRNAs, such as H19, MALAT1, and DOCK9-AS2, dysregulate oncogenic pathways and represent potential biomarkers. Conclusions: Advances in therapeutics suggest inhibiting oncogenic lncRNAs or restoring tumor-suppressive lncRNAs via RNA interference, antisense oligonucleotides, or CRISPR/Cas9 editing. New technologies, including single-cell RNA sequencing and spatial transcriptomics, will improve understanding of heterogeneous lncRNA–microRNA networks in TC and support precision medicine. LncRNAs signify both molecular drivers and clinical targets for thyroid cancer. Full article

Benzo[a]pyrene (B[a]P), a ubiquitous environmental pollutant, poses a significant threat to male reproductive health, but the underlying latent molecular mechanisms remain virtually unknown. This study investigated the effects of embryonic B[a]P exposure on testicular function and spermatogenesis in F0 and F1 adult male medaka (Oryzias latipes). Embryos were exposed to sublethal concentrations (2.5, 20, and 80 μg/L) for 8 days and then raised in clean water until they reached adulthood. Transcriptomic analysis of F0 testicular tissues revealed widespread dysregulation of critical pathways. Exposure impaired the brain–pituitary–gonadal axis by disrupting GnRH signaling and downregulating genes encoding key steroidogenic enzymes (CYP17A1, HSD3B2), indicating suppressed testosterone biosynthesis. Concurrently, pathways essential for cellular energy metabolism (AMPK signaling, insulin signaling), amino acid biosynthesis, and cytoskeletal organization (actin cytoskeleton, focal adhesion) were profoundly altered. Furthermore, B[a]P activated apoptotic pathways and disrupted the balance between cell survival (PI3K-Akt signaling) and death, compromising spermatogenic cell fate. These molecular disruptions manifested in drastic physiological impairments, including a reduced gonadosomatic index, decreased sperm motility, and compromised fertilization success in F0 males, although these effects were recovered in the F1 generation. This study provides a comprehensive molecular basis for the long-term reproductive toxicity of early-life B[a]P exposure. Full article

Background: Apolipoprotein E (APOE) is the strongest genetic risk determinant for late-onset Alzheimer’s disease (AD). The APOE3 allele is risk-neutral, the APOE4 allele increases the risk of developing AD, and the APOE2 allele is neuroprotective. Methods: We utilized RNA sequencing of hemi-brains from a mouse model homozygous for each of these humanized APOE alleles to study gene expression profiles between mice aged 12 months of age (MO) and 18 MO, independent of β-amyloid and tau pathology. Results: More than half of the differentially expressed genes (DEGs) within each genotype were shared with at least one other APOE allele, including 1610 DEGs that were shared across the three genotypes. These DEGs represent changes driven by aging rather than APOE genotype. Aging induced DEGs and biological pathways involving metabolism, synaptic function, and protein synthesis, among others. Alterations in these pathways were also identified by DEGs unique to APOE4, suggesting that the APOE4 allele drives the aging phenotype. In contrast, fewer pathways were identified from DEGs unique to APOE2 or APOE3. Conclusions: Transcriptomic results suggest that the most significant impact on brain-level expression changes in humanized APOE mice is aging and that APOE4 exacerbates this process. These in vivo findings within an established model system are consistent with brain aging being the greatest risk factor for AD and suggest that APOE4 expression promotes an aging phenotype in the brain that interacts with, and contributes to, aging-driven AD risk. Results reinforce the impact age and APOE allele contribute to AD and age-related neurodegeneration, and foster greater mechanistic understanding as well as inform therapeutic intervention. Full article

Analyzing the biochemical and physiological activities of food microbes using molecular and bioinformatics tools is important, offering profound insights into their safety, functional, and applicational roles in food. In this study, Lactiplantibacillus plantarum NMGL2, a well-documented beneficial lactic acid bacteria (LAB) strain, was investigated for its genomic, metabolic, and transcriptomic characteristics. Whole-genome sequencing revealed that this strain possesses a chromosome and two plasmids, with 3320 annotated genes, showcasing pathways involved in carbohydrate metabolism, stress adaptation, and bioactive compound synthesis. Growth studies under various nutritional conditions, including fructose, lactose, exogenous exopolysaccharide (EPS), and soy peptone, demonstrated that nitrogen source alteration significantly enhanced bacterial growth and EPS production. Transcriptomic analysis showed the addition of EPS and soy peptone resulted in similar regulatory patterns, suggesting shared modulation of metabolic pathways, although distinct gene regulation patterns were involved. In contrast, fructose and lactose primarily regulated carbohydrate metabolism without increasing EPS yield. Prophage gene clusters were consistently down-regulated across all experimental conditions, reflecting the strain’s adaptive response. These findings highlight L. plantarum NMGL2’s ability to dynamically adjust its metabolism and gene expression in response to environmental and nutritional changes, offering valuable insights for its application in functional foods and probiotics. These results also imply the potential of LAB strains in bioactive compound production and health-related applications through metabolic engineering. Full article

Background: Meningiomas are common intracranial tumors in adults. Most are benign WHO grade I (GI) tumors, while approximately 20% are diagnosed as more aggressive WHO grade II (GII) and grade III (GIII) meningiomas. The study aimed to identify genes with tumor grade-related expression and to assess their functional relevance. Methods: RNA sequencing (RNA-seq) was performed to analyze transcriptomes of benign meningothelial (n = 19) and fibrous (n = 11), atypical (n = 18) and anaplastic (n = 12) meningiomas. The data were analyzed for differential genes expression and Gene Set Enrichment Analysis (GSEA). A deposited scRNA-seq dataset was used to define meningioma cellular composition and cell type-specific gene expression enabling deconvolution of RNA-seq data. Results: Unsupervised analysis revealed three tumor clusters corresponding to the histological subtypes of meningothelial (GI), fibrous (GI) and atypical/anaplastic (GII/GIII) meningiomas. Differential analysis identified 5518 protein-coding genes with grade-related changes in expression. GSEA showed that high-grade meningiomas were enriched for processes of cell proliferation, ribosome biogenesis, and metabolism, whereas benign tumors were enriched for cell morphogenesis, transmembrane ion transport, and immune regulation. PGK1 was the most significantly grade-related gene and increased expression of phosphoglycerate kinase 1 in GII and GIII tumors was confirmed by immunohistochemistry. Deconvolution of RNA-seq data revealed grade-related changes in the tumor microenvironment, notably a progressive decrease in border-associated macrophages from WHO GI to GIII tumors. Conclusions: In our study, we characterized key genes and processes dysregulated in high-grade meningiomas, including less understood mechanisms such as metabolic reprogramming, disrupted ion transport, altered immune regulation, and differences in the tumor microenvironment between benign and aggressive tumors. Full article