Search Results (2,341)

Biochemical recurrence (BCR) after radical prostatectomy (RP) remains a major clinical challenge. Although metabolic reprogramming drives prostate cancer (PCa) progression, its predictive value for BCR and its interplay with the tumor immune microenvironment (TIME) remain incompletely understood. By integrating weighted gene co-expression network analysis (WGCNA) with machine learning, we identified four metabolic-related hub genes (GDPD1, PLA2G7, PTGDS, and SRD5A2) and developed an XGBoost-Cox model that accurately stratified BCR risk (training 5-year AUC: 0.858; validation 5-year AUC: 0.745). SHAP analysis enhanced the model’s interpretability, while immunohistochemistry (IHC) validated differential protein expression of these targets across 32 clinical specimens. Furthermore, immune profiling demonstrated that these genes are closely linked to M2 macrophage-mediated immunosuppression and altered T-cell infiltration. To translate these biomarkers into therapeutic targets, we employed in silico screening, molecular docking, and molecular dynamics simulations, identifying (-)-epigallocatechin gallate (EGCG) as a promising multi-target candidate. Subsequent in vitro assays confirmed that EGCG binds stably to GDPD1, PTGDS, and SRD5A2, effectively suppressing malignant PCa phenotypes and prostate-specific antigen (PSA) secretion. In summary, we established a robust and interpretable model for predicting BCR after RP, and our in vitro validation suggests that EGCG holds promise as a therapeutic agent to delay PCa progression. Full article

Cold stress poses a major threat to global agricultural productivity. As a tropical woody oil crop, oil palm is highly susceptible to chilling damage; however, the molecular mechanisms underlying its cold response remain largely unknown. In this study, we profiled spear leaves of oil palm seedlings exposed to 8 °C for 0, 0.5, 1, 2, 4 and 8 h, using transcriptomic analysis across the full time course, complemented by metabolomic profiling at the 2 h time point. Physiological measurements showed cold stress-associated changes in chlorophyll and malondialdehyde (MDA) levels, as well as in the activities of antioxidant enzymes (SOD, POD, and CAT). Transcriptome analysis identified 31,576 expressed genes, including 9042 differentially expressed genes (DEGs). The highest number of specific DEGs was observed at the 2 h time point. Weighted gene co-expression network analysis (WGCNA) revealed nine co-expression modules with distinct temporal patterns. A total of 46 hub genes were identified, including WRKY, ERF, and seven genes encoding key enzymes involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan (LOC105041937, LOC105056784, LOC105048637, LOC105055093, LOC105038203, LOC105033050, and LOC105037948). Metabolomic analysis detected 98 differentially accumulated metabolites, which were enriched in the phenylalanine, tyrosine, and tryptophan pathway. qRT-PCR analysis showed that WRKY and ERF expression peaked at 2 h, coinciding with phenylalanine accumulation. In summary, this study describes the temporal dynamics of the cold stress response in oil palm, identifies the 2 h time point as a transition period, and provides a set of prioritized hub genes for further functional validation. These findings may support future breeding efforts aimed at improving cold tolerance in oil palm. Full article

Lutein is a dietary xanthophyll carotenoid with recognized antioxidant and immunomodulatory potential, yet the molecular basis underlying its nutritional effects in laying hens remains insufficiently understood. Here, liver transcriptomic profiling and 16S rRNA sequencing were combined to investigate the response of laying hens to dietary lutein supplementation. A total of 951 differentially expressed genes were identified in the liver, indicating marked transcriptional remodeling after lutein supplementation. Functional enrichment, gene set enrichment, and weighted gene co-expression network analyses consistently showed that these changes were mainly associated with metabolic regulation, redox/stress adaptation, and immune-related communication. In parallel, lutein supplementation changed cecal microbial community structure and shifted specific microbial biomarkers. Integrated correlation analyses further identified candidate host–microbiota association patterns, including a KLF2/FOXO3/Faecalibacterium axis and a KLF2/IL8L2/Prevotellaceae_Ga6A1_group axis. Overall, dietary lutein was associated with coordinated changes in the hepatic transcriptional profile and cecal microbial community structure, which converged on these two functional directions. These findings provide new insight into the nutritional effects of lutein in laying hens and identify candidate pathways and microbial nodes for future functional validation in poultry feeding systems. Full article

Background: Coronary heart disease (CHD) has a high global disease burden. According to traditional Chinese medicine theory, the main syndrome type of CHD is the syndrome of intermingled phlegm and blood stasis (SI-GPBS). Tanyu Tongzhi Decoction (TYTZD) exerts clear cardioprotective effects on CHD patients with SI-GPBS, while its specific regulatory mechanism remains unclear. Methods: Clinical serum proteomics and network pharmacology were used to screen key targets and pathways for CHD with SI-GPBS. An APOE^−/− mouse model of CHD complicated with SI-GPBS was established and treated with TYTZD. Transcriptomics, proteomics and WGCNA were combined to screen core genes, with Western blotting, immunofluorescence, co-localization analysis and Carstairs staining for target verification and observation of coronary microthrombosis and endothelial injury. Results: A total of 754 differentially expressed proteins were identified in CHD patients with SI-GPBS, significantly enriched in the platelet activation pathway, with ITGA2B as the upregulated core hub protein. Network pharmacology found 94 active ingredients and 144 therapeutic targets of TYTZD for CHD with SI-GPBS, and key components bound well with ITGA2B. In APOE^−/− mice with SI-GPBS, TYTZD improved cardiac function, reduced blood lipids, myocardial enzymes, aortic lipid deposition and myocardial damage, downregulated ITGA2B, F2RL2, FGA and FGB, inhibited integrin αIIbβ3 signaling, restrained endothelial activation and reduced coronary microthrombosis. Conclusions: TYTZD treats CHD with SI-GPBS mainly by inhibiting platelet activation, improving endothelial dysfunction, and reducing coronary microthrombosis. This study provides experimental basis for TYTZD’s clinical application in CHD with SI-GPBS and new ideas for TCM syndrome–disease combination research. Full article

Stem lodging significantly reduces soybean yield stability, particularly under dense planting and intercropping systems. Stem breaking strength is a key component of lodging resistance, but its genetic basis remains incompletely understood. In this study, an F₂ population consisting of 167 individuals derived from a cross between nanxiadou25 (NXD25, high stem breaking strength) and Shiyuehuang (SYH, low stem breaking strength) was analyzed using bulked segregant analysis with whole-genome resequencing (BSA-Seq) to identify loci associated with stem breaking strength. The trait showed broad quantitative variation in the F₂ population, ranging from 20.1 to 673.7 N. Two extreme bulks were constructed using 30 plants with the highest values and 30 plants with the lowest values. QTL-seq detected 21 candidate intervals at the 95% confidence level, among which, three major loci on Chr07, Chr13, and Chr16 exceeded the 99% threshold and were designated qBR7.2, qBR13.1, and qBR16.1. By integrating large-effect SNP/InDel variation, marker development, RNA-seq profiling, and qRT-PCR validation, nine candidate genes were retained for further study, and three marker-linked genes were highlighted as high-priority candidates. RNA-seq identified 9617 differentially expressed genes between the two parents. In addition, three co-dominant InDel markers, Chr07_01, Chr13_17, and Chr16_83, showed phenotype-consistent polymorphism in extreme F₂ individuals. These findings provide valuable loci, candidate genes, and molecular markers for soybean lodging-resistance breeding. Full article

Acaryochloris marina is a distinctive cyanobacterium that uses chlorophyll d as its primary photosynthetic pigment and possesses two major light-harvesting systems: membrane-integral chlorophyll-binding Pcb/CBP complexes and water-soluble phycobiliproteins. How these antenna systems respond at the transcriptome level to contrasting light environments remains incompletely characterized. Here, we re-analyzed a publicly available RNA-seq dataset for A. marina MBIC11017 (NCBI BioProject PRJNA1130970), comparing cells grown under low-irradiance far-red light (LL-FR; 1.5–2 µmol photons m⁻² s⁻¹, 710-nm peak) and high-irradiance white light (HL-WL; 30–35 µmol photons m⁻² s⁻¹). Because light quality and irradiance both differ in this experimental design, the two effects cannot be separated; all transcriptional changes are therefore interpreted as responses to the combined LL-FR versus HL-WL contrast rather than to far-red wavelength alone. Of 8439 expressed genes, 1810 (21.4%) were significantly differentially expressed (adjusted p < 0.05). Using GFF-verified locus tags which corrected mis-annotations propagated in earlier analyses, the PS-I core gene set showed a mean log₂ fold-change of +1.96 (3.9-fold; 11/11 loci significant), whereas the PS-II core gene set showed a mean log₂ fold-change of +1.10 (2.1-fold; 12/20 loci significant). Light-harvesting genes showed the strongest response: 17/18 phycobiliprotein-pathway genes in KEGG amr00196 were upregulated, together with multiple putative Pcb/CBP loci (mean antenna log₂FC = +3.51; 11.4-fold). Weighted gene co-expression network analysis placed the antenna-associate genes examined here within a module positively correlated with the LL-FR condition (r = 0.802, p = 0.017), and STRING analysis supported an enriched network of predicted or known protein associations (1115 nodes, 4763 edges; PPI enrichment p < 1.0 × 10⁻¹⁶). Recent matched-irradiance experiments indicate that, at equal photon flux, far-red wavelengths reduce phycobilisome content relative to white light. The transcriptional pattern reported here is therefore most parsimoniously interpreted as predominantly a low-irradiance response, with possible wavelength-associated CA5 contributions that cannot be isolated in the present design. Overall, the analysis reveals coordinated transcript-level changes across plasmid-encoded reacquired phycobiliprotein genes, chromosomal Pcb/CBP loci, chlorophyll biosynthesis genes, and photosystem core genes, consistent with coordinated regulation of light-harvesting components in A. marina. Full article

Thyroid hormones (THs) are essential regulators of human brain development, and disrupted TH availability during pregnancy or early life is linked to adverse neurodevelopmental outcomes. Concerns that environmental chemicals interfere with TH signalling have increased the need for human-relevant in vitro systems to identify thyroid hormone system-disrupting chemicals (THSDCs) for risk assessment. Here, we compared two human-induced pluripotent stem cell (hiPSC)-derived brain organoid models for THSDC assessment: (i) human cortical organoids (COs) generated by unguided differentiation, offering higher architectural complexity but lower throughput; and (ii) neural stem cell-derived organoids (NSCOs), designed for scalability with reduced cellular diversity. Both models expressed key TH handling components, including the transporter SLC16A2 (MCT8) and the inactivating enzyme DIO3. Using LC–MS/MS, we show that exogenous T3 is depleted from culture media and metabolized to 3,3′-T2 and 3′-T1 in both models, alongside upregulation of T3-responsive genes (HR, KLF9, DIO3, SEMA3C). Pulse and chronic co-exposures to reference disruptors iopanoic acid (IA, deiodinase inhibitor) and silychristin (SC, MCT8 inhibitor) altered T3 metabolism and modulated T3-responsive transcriptional endpoints. In NSCOs, high-content imaging revealed treatment-associated changes in cell composition, with chronic T3 reducing the SOX2-positive progenitor pool and THSDCs blocking this effect. Together, these findings provide a framework for organoid qualification—linking TH handling, transcriptomic responsiveness, and scalable phenotypic readouts—as a necessary step toward model validation and implementation of brain organoids in THSDC risk assessment pipelines. Full article

Precision nano-fertilization offers transformative potential for sustainable improvement of grape quality, yet the underlying molecular mechanisms remain poorly understood. Here, we investigated the effects of foliar-applied nano zero-valent iron (nZVI) and potassium dihydrogen phosphate (KH₂PO₄), in combination, on berry quality and secondary metabolic reprogramming in Vitis vinifera cv. Marselan. The combined nZVI/KH₂PO₄ treatment improved photosynthetic capacity, Fe/P co-accumulation, and berry quality traits including soluble solid content, sugar–acid ratio, and phenolic and aroma metabolite profiles. Crucially, integrated transcriptomic and metabolomic profiling identified 631 differentially expressed genes and 838 differentially accumulated metabolites, converging on flavonoid biosynthesis and glutathione metabolism as the dominant regulatory axes. Correlation network analysis pinpointed five hub regulatory genes—VvHCT, VvFLS1, VvLAR1/2, VvUGT88F5, and VvODC—as central orchestrators of nanomaterial-driven metabolic reprogramming: VvHCT and VvFLS1 coordinately redirected carbon flux toward hydroxycinnamic acid conjugates and flavonol accumulation, while VvLAR1/2 governed proanthocyanidin polymerization, and VvUGT88F5 modulated glycosylation-dependent metabolite stabilization. Notably, VvODC linked polyamine metabolism to glutathione-mediated stress buffering, revealing a previously uncharacterized crosstalk between nano-iron signaling and antioxidant reprogramming. These findings establish a mechanistic framework in which nZVI and KH₂PO₄ synergistically remodel the secondary metabolome through discrete yet interconnected transcriptional nodes, providing molecular targets for nano-enabled precision viticulture and broader applications of engineered nanomaterials in high-value crop improvement. Full article

Rice depends on its root system to perceive drought, a major environmental constraint that leads to severe yield losses worldwide. To dissect the underlying molecular basis, we conducted a comparative analysis of drought-sensitive (WAB) and drought-tolerant (IR65) rice genotypes that exhibited divergent drought tolerance at the seedling stage. After exposure to 15% PEG6000 (−0.4 MPa) for two days, the shoot and root architectural traits of IR65 were better than those of WAB seedlings. Measurements of physio-biochemical parameters (SOD, CAT, POD, APX, H₂O₂, and proline) suggest that IR65 seedling roots exhibit greater ROS scavenging and osmotic adjustment capacity than WAB, aligning with tolerance to PEG-induced water deficiency. Transcriptomic assessments of roots identified 802 commonly differentially expressed genes (DEGs) during the drought time course (12, 24, and 48 h) in WAB and IR65. They were clustered into eight groups based on their expression profiles and mainly enriched in phytohormone signaling, protein phosphorylation, and transcription factors. Using weighted gene co-expression network analysis (WGCNA), nine significant modules were identified based on n = 382 of the DEGs. A total of 12 DEGs up-regulated in IR65 were distributed in five modules, and five of them were selected for rapid functional validation through in vivo yeast expression. The results showed that transgenic yeasts were tolerant to simulated drought conditions (135 mM PEG3350), indicating that these genes would be potential targets for rice improvement in drought tolerance in the future. Full article

Background: Ovarian cancer (OVCA) remains the most lethal gynecologic malignancy, with poor prognosis largely due to late-stage diagnosis and therapy resistance. Pyroptosis, a pro-inflammatory form of programmed cell death, has recently emerged as a regulator of tumor progression and immune regulation. This study aimed to systematically profile pyroptosis-related genes and identify robust biomarkers for OVCA. Methods: Microarray data from the GSE54388 dataset were analyzed to characterize pyroptosis-related gene expression. Immune cell infiltration was assessed using xCell, and pathway enrichment was performed via Gene Set Enrichment Analysis (GSEA). Weighted Gene Co-expression Network Analysis (WGCNA) identified hub genes, followed by Gene Ontology (GO) and Reactome enrichment. Machine learning algorithms (Support Vector Machine, XGBoost, and Generalized Linear Model) were employed for feature selection and biomarker identification. Validation was conducted across independent bulk and scRNA-seq datasets, with GEPIA2 used to compare OVCA and normal samples and KMplot for survival analysis. Results: OVCA samples showed significantly reduced infiltration of CD4⁺ and CD8⁺ T cells, mast cells, monocytes, neutrophils, and immature dendritic cells compared to normal samples. GSEA revealed enrichment of cell cycle-related pathways, implicating pyroptosis-related genes as key regulators of mitotic progression. From 1097 differentially expressed genes, 22 pyroptosis-related DEGs (PYRDEGs) were identified, with nine hub genes (CASP1, CEP55, CHMP4C, HTRA1, IL18, MELK, PKM, PTX3, TNFSF13B) strongly associated with OVCA. Functional enrichment linked these genes to cytokinesis, inflammasome activity, and immune signaling. Machine learning consistently identified CEP55 as the core biomarker, demonstrating high diagnostic accuracy (AUC up to 0.972) and significant upregulation in OVCA samples. Correlation analysis linked CEP55 expression to altered immune cell populations, including positive associations with Th1 and class-switched memory B-cells and negative associations with iDCs, Tregs, and M2 macrophages. CEP55 was highly expressed across bulk and scRNA-seq datasets (cancer epithelial and CD8+ TEMRA cells) and negatively correlated with overall survival (OS) and progression-free survival (PFS). Conclusions: Pyroptosis-related genes play pivotal roles in OVCA pathogenesis. CEP55 emerges as a promising biomarker for early detection and a potential therapeutic target, bridging cell cycle regulation with immune modulation. Full article

Heterosis utilization is an effective strategy to improve crop yield, stress resistance, and quality, and has been widely used in crop breeding. Soybean is an important oil and protein crop worldwide with heterosis, but the genetic basis of soybean heterosis remains largely unclear. Whole-transcriptome analysis provides a new technical approach to explore the molecular mechanism of heterosis. In this study, HYBSOY2, a registered soybean hybrid variety with the strongest heterosis in China, together with its female parent JLCMS47A, maintainer line JLCMS47B, and male parent JLR2, were used as experimental material. Whole-transcriptome sequencing was performed using RNA extracted from seedling leaves. After mapping high-quality reads to the soybean reference genome, 57 co-expressed differentially expressed genes (DEGs) were identified in HYBSOY2 compared with both JLCMS47B and JLR2. GO and KEGG enrichment analyses shows that these DEGs were mainly enriched in ADP binding, oxidoreductase activity, fatty acid elongation, and pyruvate metabolism. A total of 787 transcription factors were identified between HYBSOY2 and its parents, most of which shows parental expression-level dominance, with the MYB family accounting for the highest proportion. In addition, 10 differentially expressed lncRNAs were detected between HYBSOY2 and its parents. In the comparison between HYBSOY2 and JLCMS47B, 18 differentially expressed miRNAs were identified, among which up-regulated miR396d functions in promoting leaf development and enhancing drought tolerance. In the comparison between HYBSOY2 and JLR2, 20 differentially expressed miRNAs were found, including down-regulated miR172c which is involved in flowering promotion. A total of 12 DEGs were further verified by qRT-PCR, which may be closely related to soybean heterosis. This study provides a comprehensive transcriptomic profile at the seedling stage of the hybrid soybean and offers valuable information for hybrid soybean breeding. These results lay a foundation for further revealing the molecular mechanism underlying soybean heterosis. Full article

High-throughput single-cell RNA sequencing (scRNA-seq) has substantially advanced plant transcriptional landscapes. However, decoding cell-type-specific transcriptional regulation in non-model crops like tomato (Solanum lycopersicum) remains challenging. An integrated computational pipeline was applied using high-dimensional weighted gene co-expression (hdWGCNA) and ensemble machine learning to analyze tomato leaf single-cell transcriptomes. Unsupervised clustering identified 19 cell subpopulations mapped to five major cell-types: mesophyll cells (50.6%), guard cells (31.0%), trichomes (8.3%), vascular cells (7.5%), and lamina epidermis (2.6%). hdWGCNA revealed eight cell-type-specific modules, linking mesophyll cells to photosynthesis and guard cells to redox homeostasis. Machine learning classifiers prioritized candidate transcription factors (TFs), with XGBoost achieving the highest accuracy (0.85) to define cell identity. A consensus of 33 core TFs was identified, from which four candidate TFs (SlWRKY-78, SlWRKY-75, SlERF-57, and SlGLK-49) were selected for in silico knockout (KO) analysis. The simulations predicted that these knockouts might dysregulate core functional pathways, such as serine-type endopeptidase inhibitor activity and protein binding. Furthermore, CellOracle simulations suggested that the virtual deletion of the guard-cell-associated SlWRKY-78 and SlWRKY-75 could induce a directional trajectory shift from the terminally differentiated guard cells back to the less differentiated mesophyll territory. These findings provide a promising computational framework for deciphering cell-type-specific regulatory programs in horticultural crops. Full article

Severe COVID-19 is characterized by profound thromboinflammatory and immune disturbances, but the network-level relationships among complement–coagulation dysregulation, humoral immune remodeling, and iron-associated immune regulation remain incompletely understood. Here, we performed integrative proteomic and transcriptomic analyses across peripheral blood and lung microenvironments using weighted gene co-expression network analysis (WGCNA), differential network analysis (DiNA), and immune deconvolution. Proteomic network analysis identified a disease-associated module enriched in complement activation, coagulation cascades, platelet degranulation, and acute inflammatory responses. Hub proteins, including C9, LBP, vWF, and F11, were prioritized based on module association and intramodular connectivity. Notably, C9 and LBP were repeatedly identified across WGCNA, DiNA, and differential expression analyses, underscoring their robust association with severe COVID-19-associated molecular network remodeling. Transcriptomic and CIBERSORTx-based immune deconvolution analyses showed altered immune-cell composition in blood and lung tissues, including B-cell and plasma-cell-associated changes. Notably, TFRC displayed cell-type-associated expression changes in naïve B cells and plasma cells, suggesting a potential link between iron-associated immune regulation and humoral immune remodeling. Collectively, these computational findings highlight coordinated complement–coagulation dysregulation, humoral immune remodeling, and TFRC-associated iron-related immune alterations in severe COVID-19, and prioritize TFRC, C9, and LBP as candidate molecular indicators requiring further experimental and clinical validation. Full article

Dental pulp tissue contains mesenchymal stem/progenitor cells that possess high proliferative potential for self-renewal. They are neural-crest derived cells and exhibit multi-lineage differentiation properties. These progenitor stem cells are now recognized as being vital to the dentin regeneration process following injury. Understanding the molecular mechanisms that mediate the differentiation of adult stem cells into odontoblasts and their use in the repair of the dentin–pulp complex is of significant interest in regenerative dental medicine. Dentin Phosphophoryn (DPP), synthesized and processed predominantly by the odontoblasts, functions both as a structural and signaling protein. We had previously demonstrated that DPP activates NF-κB and promotes Wnt5a expression in dental pulp stem cells. In this context, we observed that DPP can activate TAZ, a biologically potent transcriptional coactivator which serves as a downstream element of the NF-κB signaling cascade. Furthermore, binding of NF-κB p65 subunit to the TAZ promoter was facilitated by DPP stimulation, and their interaction was confirmed by ChIP analysis. In addition, DPP-dependent activation of the TAZ/TEAD reporter was confirmed by luciferase activity in DPSCs. Co-immunoprecipitation analysis confirmed the in vivo interaction between TAZ and β-catenin with DPP stimulation. This regulatory complex facilitated TAZ to bind to the conserved TEAD binding motifs of key gene targets involved in odontogenic differentiation such as RUNX2, OSX, OCN, ALP, BMP4, and WNT5A. Some of these genes also contain binding sites for the TCF/LEF transcription factors that interact with the Wnt effector, β-catenin. Activation of TAZ and β-catenin resulted in the upregulation of odontoblast gene expression and reduced expression in the presence of the TAZ–TEAD protein complex inhibitor. Using mandibles of DSPP KO and WT mice, we confirmed reduced TAZ and β-catenin protein levels in the dental pulp cells and in the odontoblasts of DSPP KO mice when compared with WT. Thus, DPP, an extracellular matrix protein, provides biological cues to activate the TAZ signaling pathway that can stimulate the terminal differentiation of DPSCs into functional odontoblasts. Full article

Background/Objectives: Increasing evidence indicates that gliomas co-opt mechanisms of excitatory synaptic transmission and plasticity to support tumor progression, yet these processes remain poorly characterized in lower-grade gliomas (LGGs). Here, we investigated whether genes associated with excitatory synaptic function are linked to patient prognosis in LGG. Methods: A curated panel of 36 synaptic genes was analyzed in LGG using RNA-sequencing and clinical data from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) datasets. Results: Among the genes investigated, DLG2, DLG3, and DLG4, which encode the postsynaptic scaffolding proteins PSD-93, SAP-102, and PSD-95, respectively, showed strong associations with patient overall survival (OS). Higher expression of each gene was consistently associated with longer OS across both datasets. Expression of DLG2–DLG4 was higher in oligodendroglioma and IDH-mutant, 1p/19q co-deleted tumors, and lower in astrocytoma and IDH-wild-type tumors. Furthermore, expression of all three genes positively correlated with a broad gene signature associated with a synaptic gene program, including multiple components of glutamatergic signaling and postsynaptic organization. Conclusions: These findings suggest that elevated expression of DLG2–DLG4 is associated with a transcriptional program resembling differentiated neuron-like features and favorable clinical outcome in LGG. Full article