Search Results (10,350)

Studies have shown that the iron concentration in the peritoneal fluid of women is associated with the severity of endometriosis. Therefore, investigation of iron metabolism-related genes (IM-RGs) in endometriosis holds significant implications for both prevention and therapeutic strategies in affected patients. Differentially expressed IM-RGs (DEIM-RGs) were identified by intersecting IM-RGs with differentially expressed genes derived from GSE86534. Mendelian randomization analysis was employed to determine DEIM-RGs causally associated with endometriosis, with subsequent verification through sensitivity analyses and the Steiger test. Biomarkers associated with IM-RGs in endometriosis were validated using expression data from GSE86534 and GSE105764. Functional annotation, regulatory network construction, and immunological profiling were conducted for these biomarkers. Single-cell RNA sequencing (scRNA-seq) (GSE213216) was utilized to identify distinctively expressed cellular subsets between endometriosis and controls. Experimental validation of biomarker expression was performed via reverse transcription–quantitative polymerase chain reaction (RT-qPCR). BMP6 and SLC48A1, biomarkers indicative of cellular BMP response, were influenced by a medicus variant mutation that inactivated PINK1 in complex I, concurrently enriched by both biomarkers. The lncRNA NEAT1 regulated BMP6 through hsa-mir-22-3p and hsa-mir-124-3p, while SLC48A1 was modulated by hsa-mir-423-5p, hsa-mir-19a-3p, and hsa-mir-19b-3p. Immune profiling revealed a negative correlation between BMP6 and monocytes, whereas SLC48A1 displayed a positive correlation with activated natural killer cells. scRNA-seq analysis identified macrophages and stromal stem cells as pivotal cellular components in endometriosis, exhibiting altered self-communication networks. RT-qPCR confirmed elevated expression of BMP6 and SLC48A1 in endometriosis samples relative to controls. Both BMP6 and SLC48A1 were consistently overexpressed in endometriosis, reinforcing their potential as biomarkers. Moreover, macrophages and stromal stem cells were delineated as key contributors. These findings provide novel insights into therapeutic and preventive approaches for patients with endometriosis. Full article

The widespread use of neonicotinoid insecticides has led to increasing resistance in non-target organisms, including the egg parasitoid Trichogramma dendrolimi, a crucial biological control agent. Film-residue bioassays on 17 geographic strains revealed striking inter-strain variability in susceptibility to imidacloprid, with mortality at a discriminating dose of 0.1 mg/L ranging from 25.7% to 87%. The most tolerant (FS) and least tolerant (HA) strains were subsequently selected for evaluation of biological parameters and comparative transcriptomics. Tolerant strains (FS) showed adaptive trade-offs: extended longevity (5.47 ± 0.57 d) and emergence (93.6 ± 1.9%), but reduced fecundity (54.6 ± 4.9 eggs) compared to HA. Transcriptome analysis revealed 2115 differentially expressed genes, with GO enrichment highlighting metabolic and detoxification pathways. KEGG analysis the most enriched pathways were “Protein digestion and absorption” and “Neuroactive ligand-receptor interaction”. RT-qPCR confirmed overexpression of CYP4C1, CYP6K1, and GstS1 in FS, indicating their potential roles in metabolic resistance if present. This study presents preliminary evidence of potential fitness trade-offs and molecular mechanisms that could underly imidacloprid resistance in T. dendrolimi, which may lead to important insights for resistance monitoring and more sustainable integrated pest management strategies. Full article

Saline-alkali stress seriously affects the growth and development of crops. Sorghum bicolor (L.), a C4 plant, is an important cereal crop in the world, and its growth and geographical distribution are limited by alkali conditions. In this study, sorghum genotypes with different alkaline resistance (alkaline-sensitive Z1 and alkaline-tolerant Z14) were used as experimental materials to explore the effects of alkali on sorghum seedlings. RNA-seq technology was used to examine the differentially expressed genes (DEGs) in alkali-tolerant Z14 to reveal the molecular mechanism of sorghum response to alkali stress. The results showed that plant height, root length, and biomass of both cultivars decreased with time under 80 mM NaHCO₃ treatment, but Z14 showed better water retention abilities. The photosynthetic fluorescence parameters and chlorophyll content also decreased, but the Fv/Fm, ETH, ΦPSII, and chlorophyll content of Z14 were significantly higher than those of Z1. The level of reactive oxygen species (ROS) increased in both sorghum varieties under alkali stress, while the enzyme activities of SOD, POD, CAT, and APX were also significantly increased, especially in Z14, resulting in lower ROS compared with Z1. Transcriptome analysis revealed around 6000 DEGs in Z14 sorghum seedlings under alkali stress, among which 267 DEGs were expressed in all comparison groups. KEGG pathways were enriched in the MAPK signaling pathway, plant hormone signal transduction, and RNA transport. bHLHs, ERFs, NACs, MYBs, and other transcription factor families are actively involved in the response to alkali stress. A large number of genes involved in photosynthesis and the antioxidant system were found to be significantly activated under alkali stress. In the stress signal transduction cascades, Ca²⁺ signal transduction pathway-related genes were activated, about 23 PP2Cs in ABA signaling were upregulated, and multiple MAPK and other kinase-related genes were triggered by alkali stress. These findings will help decipher the response mechanism of sorghum to alkali stress and improve its alkali tolerance. Full article

Earle’s balanced salt solution (EBSS) is a classical autophagy inducer that provides a special culture environment lacking amino acids and serum, causing cell starvation. However, the production of relevant omics data surrounding EBSS-induced autophagy is still in the early stage. The objective of this study was to identify new potential functional proteins in the autophagy process through omics analysis. We selected EBSS-induced autophagy as our research object and uncovered autophagy-regulatory proteins using RNA-seq analysis. Western blotting showed that EBSS increased LC3B-II protein levels in NRK cells, reaching the maximum amount at 2 h of culture. Then, we used next-generation sequencing to obtain quantified RNA-seq data from cells incubated with EBSS and the bowtie–tophat–cufflinks flow path to analyze the transcriptome data. Using significant differences in the FPKM values of genes in the treated group compared with those in the control group to indicate differential expression, 470 candidate genes were selected. Subsequently, GO and KEGG analyses of these genes were performed, revealing that most of these signaling pathways were closely associated with autophagy, and to better understand the potential functions and connections of these genes, protein–protein interaction networks were studied. Considering all the conclusions of the analysis, 27 candidate genes were selected for verification, where the knockdown of Txnrd1 decreased LC3B-II protein levels in NRK cells, consistent with the results of confocal experiments. In conclusion, we uncovered autophagy-regulatory proteins using RNA-seq analysis, with our results indicating that TXNRD1 may play a role in regulating EBSS-induced autophagy via an unknown pathway. We hope that our research can provide useful information for further autophagy omics research. Full article

NRDE2 is a highly conserved protein implicated in post-transcriptional gene silencing in Schizosaccharomyces pombe and Caenorhabditis elegans and has been shown to modulate splicing in mammals. To explore whether NRDE2 participates in additional processes in human cells, we performed tandem affinity purification followed by proteomic analysis of NRDE2 from nuclear extracts of HEK293T and HeLa cells. Our analysis confirmed the interaction of NRDE2 with its well-characterized partner, the MTR4 helicase (MTREX), as well as with multiple splicing factors. Notably, we also identified interactions with chromatin-associated proteins involved in transcription, including the Polymerase-Associated Factor 1 (PAF1) complex and elongating forms of RNA polymerase II (RNAPII). To further investigate NRDE2 function, we conducted RNA-seq following its transient depletion. Differential expression analysis revealed that loss of NRDE2 alters the expression of thousands of genes. Consistent with earlier reports, we observed splicing defects, particularly intron retention; however, our results indicate that the impact of NRDE2 on intron retention is more extensive than previously recognized. Moreover, intron retention was frequently associated with reduced mRNA expression. Together, these findings suggest that NRDE2 associates with both transcriptional and splicing machineries and plays a broader role in RNA processing than previously appreciated. Full article

Obesity is an epidemic with myriad health effects, but little is understood regarding individual obese phenotypes and how they may respond to therapy. Epigenetic changes associated with obesity have been detected in blood, liver, pancreas, and adipose tissues. Previous work using human organoids found that dietary glucose hyperabsorption is a steadfast trait in cultures derived from some obese subjects, but detailed transcriptional or epigenomic features of the intestinal epithelia associated with this persistent phenotype are unknown. This study evaluated differentially expressed genes and relative chromatin accessibility in intestinal organoids established from donors classified as non-obese, obese, or obese hyperabsorptive by body mass index and glucose transport assays. Transcriptomic analysis indicated that obese hyperabsorptive subject organoids have significantly upregulated dietary nutrient absorption transcripts and downregulated type I interferon targets. Chromatin accessibility and transcription factor footprinting predicted that enhanced HNF4G binding may promote the obese hyperabsorption phenotype. Quantitative RT-PCR assessment in organoids representing a larger subject cohort suggested that intestinal epithelial expression of CUBN, GIP, SLC5A11, and SLC2A5 were highly correlated with hyperabsorption. Thus, the obese hyperabsorption phenotype was characterized by transcriptional changes that support increased nutrient uptake by intestinal epithelia, potentially driven by differentially accessible chromatin. Recognizing unique intestinal phenotypes in obesity provides a new perspective in considering therapeutic targets and options with which to manage the disease. Full article

Leaf senescence is the final, programmed stage of leaf development, marked by nutrient remobilization and tightly regulated molecular events. Although alternative splicing has emerged as a major regulator of plant development, its role in isoform switching during leaf aging remains poorly understood. To address this, we conducted a genome-wide analysis of isoform switching in Arabidopsis, leveraging publicly available RNA-seq data from mature (16-day-old) and senescent (30-day-old) leaves, analyzed with the IsoformSwitchAnalyzeR package. Between these two developmental stages, we identified 269 genes exhibiting 377 significant isoform switches collectively predicted to alter protein localization, coding potential, and transcript stability. Experimental validation confirmed predicted switching at the PUS3 (Pseudouridine Synthase 3) locus, with sequence analysis revealing an age-dependent shift from mitochondrial-targeted to cytoplasmic isoforms. Gene Ontology enrichment analysis of switching genes revealed 82 significant terms, prominently associated with metabolism, gene expression, developmental regulation, and stress responses. Interestingly, we found nearly one-third of switching genes to overlap with known targets of the splicing factor SR45, with enrichment in pathways related to nucleotide and amino acid metabolism, energy production, and developmental processes. Correspondingly, dark-induced senescence assays revealed accelerated senescence in the sr45 mutant, confirming SR45′s role in regulating leaf aging. Specific complementation of SR45′s two isoforms revealed contrasting functions, with SR45.1 restoring normal senescence timing while SR45.2 failed to complement. Taken together, our findings demonstrate that differential isoform usage, orchestrated by specific splicing regulators, plays a critical role in leaf aging. This insight opens new avenues for manipulating senescence and engineering stay-green traits in crops. Full article

Calcium-dependent protein kinases (CDPKs) are key Ca²⁺ sensors in plants, mediating responses to abiotic stresses via phosphorylation signaling. In the halophyte Nitraria sibirica, which thrives in saline soils, we identified 19 CDPK genes (NsCDPKs) and classified them into four canonical angiosperm clades, highlighting conserved functional modules. Promoter analysis revealed diverse cis-acting elements responsive to light, hormones (ABA, MeJA, auxin, GA, SA), and abiotic stresses (drought, cold, wounding), along with numerous MYB binding sites, suggesting complex transcriptional regulation. Transcriptome profiling under salt stress (100 and 400 mM NaCl) showed induction of most NsCDPKs, with several genes significantly upregulated in roots and stems, indicating coordinated whole-plant activation. These salt-responsive NsCDPKs were also upregulated by cold but repressed under PEG-simulated drought, indicating stress-specific regulatory patterns. Fifteen MYB transcription factors, differentially expressed under salt stress, were predicted to interact with NsCDPK promoters, implicating them as upstream regulators. This study identified a potential salt- and cold-responsive CDPK regulatory module and a MYB-mediated transcriptional hierarchy in N. sibirica, providing insights into the molecular mechanisms of salinity adaptation and highlighting candidate genes that could be explored for improving salt tolerance in crop species. Full article

Walnuts (Juglans regia L.) are an economically important woody crop, but spring frost poses a serious threat to their growth and productivity. However, the molecular mechanisms underlying walnut responses to freezing stress remain largely unknown. In this study, transcriptome analyses were performed on cold-tolerant and cold-sensitive walnut varieties subjected to freezing stress. A total of 9611 differentially expressed genes (DEGs) responsive to freezing stress were obtained, of which 2853 were common up-regulated and 2880 were common down-regulated in both varieties. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed 15 significantly enriched pathways in both varieties, including flavonoid biosynthesis. A simplified walnut flavonoid biosynthesis pathway was constructed, encompassing 36 DEGs encoding 13 key enzymes, demonstrating that flavonoid biosynthesis in walnut is significantly activated under freezing stress. Furthermore, weighted gene co-expression network analysis (WGCNA) identified a regulatory network centered on the JrCBF genes and uncovered 34 potential interacting genes. Collectively, these findings provide novel insights into the molecular responses of walnut to freezing stress and establish a foundation for elucidating the mechanisms underlying walnut cold tolerance. Full article

EZH2, the catalytic subunit of polycomb repressive complex 2 (PRC2), plays a critical role in neural development by regulating gene expression through the trimethylation of lysine 27 on histone H3 (H3K27me3), which promotes chromatin remodeling and transcriptional repression. Although PRC2 is known to regulate cell fate specification and gliogenesis, its in vivo functions during vertebrate neurodevelopment, particularly at the level of neuronal subtype differentiation, remain incompletely understood. Here, we investigated the consequences of ezh2 loss-of-function during zebrafish brain development, focusing on oligodendrocyte differentiation, cerebellar neurogenesis, and the formation of neurotransmitter-specific neuronal populations. Using whole-mount in situ hybridization, we found that ezh2 inactivation does not alter the expression of oligodendrocyte lineage markers, indicating that early oligodendrocyte precursor cell specification and myelination are preserved. However, a significant reduction in cerebellar proliferation was observed in ezh2-deficient larvae, as evidenced by the downregulation of pcna and cyclin A2, while other brain regions remained unaffected. Notably, the expression of atoh1c, a key marker of glutamatergic cerebellar progenitors, was strongly reduced at 5 days post fertilization, suggesting a selective role for ezh2 in maintaining cerebellar progenitor identity. This was associated with impaired differentiation of both glutamatergic granule cells and GABAergic Purkinje cells in specific cerebellar subregions. In contrast, the expression of markers for other major neurotransmitter systems remained unaffected, indicating a region-specific requirement for ezh2 in neuronal development. Finally, behavioral analysis revealed a hyperlocomotor phenotype in ezh2^−/− larvae, consistent with cerebellar dysfunction. Together, these findings identify ezh2 as a key regulator of progenitor maintenance and neuronal differentiation in the cerebellum, highlighting its crucial role in establishing functional cerebellar circuits. Full article

Major depression (MD) is associated with chronic inflammation and impaired neuroplasticity; however, the cellular mechanisms underlying antidepressant action remain incompletely understood. We performed transcriptomic profiling and functional validation in human microglia treated with venlafaxine (VEN) and vortioxetine (VOR), or with stable ST3GAL5 overexpression (ST3GAL5OE). Differential expression analysis, enrichment studies, and functional assays using NF-κB-RE-NlucP and SIE-NlucP reporter lines were conducted to assess the impact on inflammatory signaling. Microarray analysis identified 41 genes consistently upregulated and 316 consistently downregulated across VEN, VOR, and ST3GAL5OE conditions. Upregulated genes were enriched for synaptic organization, whereas downregulated genes were associated with nitric oxide biosynthesis and pro-inflammatory pathways, including Rap1, MAPK, and PI3K-Akt signaling. Functional assays confirmed that VEN and VOR suppressed cytokine-induced NF-κB and STAT3 activation, effects that were recapitulated by exogenous GM3 treatment and ST3GAL5 overexpression. Chronic exposure to VEN or VOR produced more modest, pathway-specific suppression, supporting convergence on the ST3GAL5–GM3 axis. These findings extend the conventional monoaminergic model of antidepressant action by highlighting the ST3GAL5–GM3 lipid remodeling axis as a novel regulatory pathway that attenuates microglial inflammatory signaling. Although validation in primary microglia and in vivo models is required, our results suggest that this axis could serve as both a therapeutic target and a candidate biomarker for inflammation-associated MD. Full article

Macrophages play a central role in joint inflammation and bone destruction in rheumatoid arthritis (RA). While activator protein-1 (AP-1) transcription factors have been implicated in RA pathogenesis, the specific roles of individual AP-1 members in regulating synovial macrophages remain unclear. To address this, two public single-cell transcriptomic datasets were first analyzed to profile synovial macrophages, and then to identify AP-1 family members and associated pathways via differential expression and gene set enrichment analyses. JUND, FOSL2, and FOSB were found to be highly enriched in the RA synovium, and a distinct CXCL3⁺FOSL2⁺ macrophage subset was identified, characterized by pro-inflammatory, metabolic, and differentiation-related pathways. Intercellular communication analysis further revealed that this CXCL3⁺FOSL2⁺ macrophage subset interacted with ACKR1⁺ endothelial cells within the synovial microenvironment. Validation in a large-cohort bulk transcriptomic dataset, together with functional assays using in vitro FOSL2 knockdown in U937 cell lines, further confirmed FOSL2’s role in promoting macrophage-driven inflammation. Collectively, these findings indicate that CXCL3⁺FOSL2⁺ macrophages drive RA synovitis via the FOSL2/AP-1 axis, highlighting a potential therapeutic target. Full article

Background and Aims: Little is known about metabolic dysfunction-associated steatotic liver disease (MASLD) as a risk factor for hepatocellular carcinoma (HCC) in non-cirrhotic (HCC-NC) patients. In-house developed mouse models with defective lipid-metabolizing enzyme long-chain 3-hydroxy acyl-CoA dehydrogenase (LCHAD), coded by hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha (HADHA) gene, result in MASLD (steatosis) without cirrhosis leading to HCC-NC. The aims of the current investigations are to assess molecular markers and the associated molecular events that may lead to HCC-NC. Methods: cDNA array study of HCC patients was conducted to assess the expression of HADHA transcripts. Differentially expressed proteins identified between wild-type (WT) and heterozygous mice with no cancer (HT) from a previous study were subjected to Ingenuity Pathway Analysis (IPA). Western blotting was performed to assess the expression of proteins. Results: IPA of the differentially expressed proteins between WT and HT mice results in two biological networks (network 1 and network 2), which pointed to an important role of p53 in HCC-NC. Validation of the levels of MDM2 and p53 also highlights the role of MDM2-p53 axis in HCC-NC. All the focus molecules in network 1 and network 2 are either presented as tumor suppressor/promoter of carcinogenesis or serum markers for early HCC diagnosis. The hepatotoxicity report from IPA further identified four functional groups including liver steatosis, glutathione depletion, hepatocellular carcinoma, and liver hyperplasia/hyperproliferation. Conclusions: This study suggests that impaired fatty oxidation may play a role in the development of HCC associated with steatosis but without cirrhosis (HCC-NC). Defective LCHAD is a novel etiology for HCC. Full article

Citrobacter braakii is an emerging opportunistic pathogen of escalating clinical significance in animal hosts, though its pathogenic mechanisms remain poorly characterized. This study isolated a C. braakii strain (SCGY-1L) from diseased Siniperca chuatsi and confirmed its identity through integrated morphological, physiological, and molecular analyses. Comprehensive genomic sequencing revealed a 5.75 Mb genome comprising one circular chromosome and two plasmids. A Circos plot was constructed to visualize the genomic architecture of strain SCGY-1L, revealing 5482 protein-coding genes, 25 tRNA genes, and 86 rRNA genes. Additionally, 738 virulence-associated genes and 366 antibiotic resistance determinants were annotated, elucidating multidrug-resistant phenotypes including insensitivity to erythromycin and penicillin. Pathogenicity assessment established an LD₅₀ of 1.28 × 10⁶ CFU/mL in infected hosts, with histopathological analysis showing significant hemorrhage and necrosis in target organs (liver, spleen, kidney). Host transcriptome profiling generated 41.21 Gb of high-quality clean data, identifying 2201 differentially expressed genes post-infection (1568 up-regulated; 633 down-regulated). These were significantly enriched in phagocytosis, cytokine-mediated signaling, and inflammatory regulation pathways. These molecular insights establish C. braakii’s mechanistic framework for pathogenesis and host adaptation, providing critical targets for diagnostics and therapeutics against emerging Citrobacter infections. Full article

Coptis trifolia (threeleaf goldthread) offers a valuable comparative system for investigating the evolution and regulation of benzylisoquinoline alkaloid (BIA) synthesis. In this study, we analyzed the leaf and root transcriptomes of C. trifolia using both long-read and short-read RNA-Sequencing. We assembled 41,926 unigenes (≥500 bp) and identified 37 genes related to BIA biosynthesis, including two transcription factors, bHLH1 and WRKY1. The number of BIA genes identified in C. trifolia was comparable to that in other Coptis species. Transcriptome analysis revealed that most of these genes were more highly expressed in roots than leaves. Consistent with previous studies, C. trifolia contained a single (S)-stylopine synthase (SPS) gene homolog, potentially multifunctional for (S)-canadine synthase (CAS), (S)-cheilanthifoline synthase (CFS), and SPS. Transcriptome and untargeted metabolomic data indicated greater variation in root samples than leaf samples, although slightly more differentially expressed transcripts and metabolites were observed in leaves. Targeted metabolite profiling showed higher BIA accumulation in roots, with epiberberine being the most abundant, followed by coptisine, berberine, and columbamine. These results provide essential genomic resources for comparative analysis of the BIA pathway across Ranunculaceae, targeted gene function studies for metabolic bioengineering, and conservation strategies for C. trifolia, a member of an early-diverging clade within the genus with limited genetic resources. Full article