Search Results (559)

Spermatogonial stem cells (SSCs) are unipotent germline cells with emerging pluripotent potential under specific in vitro conditions. Understanding their capacity for reprogramming and the molecular mechanisms involved offers valuable insights into regenerative medicine and fertility preservation. SSCs were isolated from Oct4-GFP C57BL/6 transgenic mice using enzymatic digestion and cultured in defined media. Under these conditions, ES-like colonies emerged expressing pluripotency markers. These cells were characterized by immunocytochemistry, teratoma assays, and transcriptomic analyses using bulk and single-cell RNA sequencing datasets. Gene expression profiles were compared with ESCs and SSCs using datasets from GEO (GSE43850, GSE38776, GSE149512). Protein–protein interaction (PPI) networks and co-expression modules were explored through STRING, Cytoscape, and WGCNA. ES-like cells derived from SSCs exhibited strong expression of OCT4, DAZL, and VASA. Transcriptomic analysis revealed key differentially expressed genes and shared regulatory networks with ESCs. WGCNA identified key co-expression modules and hub regulatory RNA binding genes (Ctdsp1, Rest, and Stra8) potentially responsible for the reprogramming process. Teratoma assays confirmed pluripotency, and single-cell RNA-seq validated expression of critical markers in cultured SSCs. This study demonstrates that SSCs can acquire pluripotency features and be reprogrammed into ES-like cells. The integration of transcriptomic and network-based analyses reveals novel insights into the molecular drivers of SSC reprogramming, highlighting their potential utility in stem cell-based therapies and male fertility preservation. Full article

Populus koreana emits a wide array of volatile organic compounds (VOCs) with potential ecological functions; however, the tissue-specific distribution and underlying regulatory mechanisms of these compounds remain poorly understood. This study employed an integrated approach combining gas chromatography-mass spectrometry (GC-MS)-based metabolomics and RNA-seq to systematically profile VOC composition and gene expression in terminal buds, stems and leaves of P. koreana. A total of 207 VOCs were identified, predominantly terpenes and aromatic compounds, exhibiting distinct tissue-specific accumulation patterns. Terminal buds were enriched in limonene and caryophyllene, while leaves showed higher concentrations of alcohols and phenolic aldehydes. Transcriptomic analysis revealed 12,733 differentially expressed genes (DEGs) among the three organs, with substantial enrichment in terpenoid and phenylpropanoid biosynthetic pathways. Notably, key upregulated genes in buds, including TPS21 and PAL1, correlated with observed VOC profiles. Weighted gene co-expression network analysis (WGCNA) further identified 6365 genes strongly associated with bud-specific VOC biosynthesis. Integrated omics analyses indicated coordinated regulation of phenylalanine metabolism and transcription factors in VOC production. These findings illuminate the molecular mechanisms underlying tissue-specific VOC accumulation in P. koreana, enhancing our understanding of metabolic specialization and ecological adaptation in woody plants. Full article

Anthocyanins, key flavonoid-derived secondary metabolites, not only confer diverse pigmentation but also function in photoprotection, antioxidative defense, and cold acclimation. In woody species, bark anthocyanin turnover is tightly linked to environmental adaptation, stress resilience, and ornamental traits, yet its molecular regulation remains largely unresolved. Here, we investigated Salix alba L. bark by integrating anthocyanin quantification, transcriptome profiling, and weighted gene co-expression network analysis (WGCNA) to dissect the temporal dynamics and regulatory architecture of anthocyanin degradation. Anthocyanin content peaked at D2 (late December 2024), declined through D3 (mid-January 2025) and D4 (mid-February 2025), and partially rebounded at D5 (early March 2025), coinciding with peak expression of structural genes LAC1/2, POD1/2, and BGLU10. These enzymes co-expressed with multiple transcription factors, including MYB, bHLH, and WRKY families, forming putative core modules. Functional enrichment indicated that differentially expressed genes were enriched in redox processes, glycoside hydrolysis, flavonoid metabolism, and hormone signaling, suggesting a degradation mechanism mediated by reactive oxygen species, glycosidic cleavage, and hormone–transcription factor interplay. This study provides the first comprehensive framework of bark anthocyanin degradation in white willow, advancing the understanding of pigment dynamics, gene–environment crosstalk, and breeding strategies for ornamental woody plants. Full article

Fat deposition is an important factor that affects meat production and its quality in livestock animals, including poultry. Non−coding RNAs (ncRNAs) play an important role in duck fat deposition. This study aims to systematically identify key regulatory molecules involved in fat deposition in 8−day−old Cherry Valley ducks through transcriptomic sequencing across four sample groups: intramuscular pre−adipocytes (IMP−0), intramuscular adipocytes after 4 days of induction (IMP−4), subcutaneous pre−adipocytes (SCP−0), and subcutaneous adipocytes after 4 days of induction (SCP−4). Differential expression analysis preliminarily identified several circRNAs and miRNAs differentially expressed during adipocyte differentiation, including novel_circ_000012, novel_circ_000037, novel_circ_000089, as well as miR−501−y, miR−378−y, and miR−3968−y. Further co−expression network analysis revealed that the network constructed during intramuscular adipocyte differentiation comprised 17 nodes and 39 edges, while the network constructed during subcutaneous adipocyte differentiation was larger, containing 39 nodes and 50 edges. Based on connectivity screening, we identified several key miRNAs, such as novel−m0630−5p, novel−m0485−5p, novel−m0672−5p, miR−5126−y, and miR−1408−y. Notably, this study uncovered several novel ceRNA regulatory axes during intramuscular and subcutaneous adipocyte differentiation, including novel_circ_001327/miR−141−y/Zdhhc1, novel_circ_002268/miR−2478−y/ACLY, and novel_circ_002268/miR−3963−x/ACLY. These findings provide crucial molecular insights into the specific deposition mechanisms of intramuscular versus subcutaneous fat in meat ducks, offering valuable targets for molecular breeding programs aimed at improving meat quality. Full article

Early B-cell development is primarily regulated at the transcriptional level and comprises the consecutive differentiation stages B-cell progenitor, pro-B-cell and pre-B-cell. These entities provide the cells of origin in B-cell precursor acute lymphoid leukemia (BCP-ALL) that show aberrations of developmental transcription factors (TFs), representing major oncogenic drivers. Analysis of physiological TFs in these developmental entities helps us to understand their normal and disturbed activities and regulatory connections. Here, we focused on NKL-subclass homeodomain TF NKX6-3, which is active in both normal B-cell progenitors and TCF3::PBX1 fusion gene-positive BCP-ALL cases. By performing siRNA-mediated knockdown and forced expression experiments in BCP-ALL model cell lines, we established a gene regulatory network for NKX6-3 together with TALE-class homeodomain TFs IRX1 and MEIS1, as well as ETS-TF SPIB. Importantly, NKX6-3 was activated by TCF3::PBX1, underlying their co-expression in BCP-ALL. Furthermore, comparative expression profiling analysis of public BCP-ALL patient data revealed TGFb-pathway in-hibitor CD109 as a downregulated target gene of NKX6-3. TGFb-signalling, in turn, enhanced NKX6-3 expression, indicating mutual activation. Finally, RNA-seq analysis of BCP-ALL cell line RCH-ACV after NKX6-3 knockdown revealed MPP7 as an upregulated target gene of both NKX6-3 and TCF3::PBX1, revealing a role for the HIPPO-pathway in B-cell progenitors and TCF3::PBX1-positive BCP-ALL. Collectively, our data introduce novel players and regulatory connections to normal and aberrant TF-networks in B-cell progenitors to serve as potential diagnostic markers or therapeutic targets. Full article

With estrus confined to three winter months, early pregnancy detection is essential for reproductive management in farmed sika deer. However, the development of reliable non-invasive early pregnancy detection techniques has been hindered by limited understanding of their reproductive physiology. To identify pregnancy-specific biomarkers in sika deer, we performed RNA-sequencing (RNA-Seq) on maternal peripheral blood collected on days 0, 7, 15, and 20 after artificial insemination. Using time-series clustering analysis and weighted gene co-expression network analysis (WGCNA), we identified key genes and pathways at each stage. Notably, maternal-fetal recognition-related interferon-stimulated genes (ISGs; IFNAR1/2, STAT1/2, MX1/2, and RSAD2), anti-apoptotic and immune-regulatory genes (BCL2, XIAP, and IL10), and cysteine metabolism genes (CTH, CBS, GCLC, and GCLM) were upregulated by day 7, suggesting their role in supporting corpus luteum development through immune regulation and redox homeostasis. By days 15–20, upregulated genes were enriched in pathways related to mitochondrial function, cell adhesion, and cell cycle regulation, indicating their involvement in embryo adhesion and syndesmochorial placentation. In conclusion, this study demonstrates that ISGs, immune-regulatory genes and cysteine metabolism genes are detectable as early as day 7 post-insemination, highlighting their promise as early pregnancy biomarkers and providing a molecular basis for non-invasive diagnostic development in sika deer. Full article

Glyphosate is one of the most widely used herbicides in agricultural, horticultural, and urban environments. However, its residue accumulation and oxidative damage pose serious threats to crop health and food safety. In this study, we evaluated the potential of epigallocatechin gallate, a natural polyphenol derived from tea, to alleviate glyphosate-induced stress in melon (Cucumis melo L.). LC-MS/MS analysis revealed that EGCG significantly reduced glyphosate residues in plant tissues. Transcriptome analysis indicated that glyphosate induced extensive transcriptional reprogramming, activating genes involved in detoxification and antioxidant defense. Co-treatment with glyphosate and EGCG partially mitigated this stress response and redirected gene expression toward secondary metabolic pathways, particularly flavonoid and phenylalanine biosynthesis. Under herbicide stress, EGCG restored the transcription of key flavonoid biosynthetic genes, including PAL, C4H, CHI, and OMT. Meanwhile, EGCG also modulated the expression of APX, SOD, and GST, suggesting a selective effect on antioxidant systems. Co-expression network analysis identified key hub genes associated with oxidative stress and flavonoid metabolism. These findings demonstrate the dual regulatory role of EGCG in suppressing acute oxidative stress while enhancing metabolic adaptability, highlighting its potential as a natural additive for reducing herbicide residues in fruit crops. Full article

Background/Objectives: Neurodegenerative diseases (NDs) such as Alzheimer’s (AD), Parkinson’s (PD), Huntington’s (HD), and Amyotrophic Lateral Sclerosis (ALS) are clinically distinct but share overlapping molecular mechanisms. Methods: To identify conserved systemic signatures, we analyzed blood RNA-Seq datasets using Weighted Gene Co-Expression Network Analysis (WGCNA), differential expression, pathway enrichment, and miRNA–mRNA network mapping. Results: Two modules, the red and turquoise, showed strong preservation across diseases. The red module was enriched for cytoskeletal and metabolic regulation, while the turquoise module involved immune, stress-response, and proteostatic pathways. Discussion: Key hub genes, such as HMGCR, ACTR2, MYD88, PTEN, EP300, and regulatory miRNAs like miR-29, miR-132, and miR-146a, formed interconnected networks reflecting shared molecular vulnerabilities. The absence of classical heat shock proteins in preserved blood modules highlights tissue-specific expression differences between blood and neural systems. Several hub genes overlap with known pharmacological targets, suggesting potential in translational relevance. Conclusions: Together, these findings reveal conserved blood-based transcriptional modules that suggest parallel central neurodegenerative processes and may support future biomarker development and possible therapeutic exploration. Full article

Mealybugs are high-priority quarantine pests in fresh-produce trade due to cryptic habits, broad host ranges, and market-access risks. Phytosanitary irradiation (PI) provides a non-residual, process-controlled option that is increasingly integrated with modified-atmosphere (MA/MAP) logistics. Because molecular oxygen enhances indirect radiation damage (oxygen enhancement ratio, OER), oxygen limitation may modulate PI outcomes in mealybugs. The Jack Beardsley mealybug (Pseudococcus jackbeardsleyi) has an IPPC-adopted PI treatment of 166 Gy (ISPM 28, PT 45). We exposed adult females to 166 Gy under air and 1% O₂ and generated whole-transcriptome profiles across treatments. Differentially expressed genes and co-differentially expressed genes (co-DEGs) were integrated with protein–protein interaction (PPI) and regulatory networks, and ten hubs were validated by reverse transcription quantitative PCR (RT-qPCR). Hypoxia attenuated irradiation-induced transcriptional disruption. Expression programs shifted toward transport, redox buffering, and immune readiness, while morphogen signaling (Wnt, Hedgehog, BMP) was coherently suppressed; hubs including wg, hh, dpp, and ptc showed stronger down-regulation under hypoxia + irradiation than under irradiation alone. Despite these molecular differences, confirmatory bioassays at 166 Gy under both atmospheres (air and 1% O₂) achieved complete control. These results clarify how oxygen limitation modulates PI responses in a quarantine mealybug while confirming the operational efficacy of the prescribed 166 Gy dose. Practically, they support the current international standard and highlight the value of documenting oxygen atmospheres and managing dose margins when PI is applied within MA/MAP supply chains. 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

Rice (Oryza sativa L.) is one of the major food crops. Yield and quality are affected by premature leaf senescence, a complex and tightly regulated developmental process. To elucidate the molecular regulatory mechanism controlling rice leaf senescence, the integrative transcriptome, metabolome and weighted gene co-expression network analysis (WGCNA) of flag leaves in five development stages (FL1–FL5) was performed. In this study, a total of 9412 differential expressed genes (DEGs) were identified. To further mine DEGs related to leaf senescence, a total of five stage-specific modules were characterized by WGCNA. Among them, two modules displayed continuous down-regulated and up-regulated trends from stages FL1 to FL5, which were considered to be highly negatively and positively correlated with the senescence trait, respectively. GO enrichment results showed that the genes clustered in stage-specific modules were significantly enriched in a vast number of senescence-associated biological processes. Furthermore, large numbers of senescence-related genes were identified, mainly participating in transcription regulation, hormone pathways, degradation of chlorophyll, ROS metabolism, senescence-associated genes (SAGs), and others. Most importantly, a total of 40 hub genes associated with leaf senescence were identified. In addition, the metabolome analysis showed that a total of 309 differential metabolites (DMs) were identified by WGCNA. The integrative transcriptome and metabolome analysis identified a key hub gene OsBELH4A based on the correlation analysis conducted between 40 hub genes and 309 DMs. The results of function validation showed that OsBELH4A overexpression lines displayed delayed leaf senescence, and significantly increased grain number per plant and grain number per panicle. By contrast, its knockout lines displayed premature leaf senescence and reduced grain yield. Exogenous hormone treatment showed that OsBELH4A significantly responded to SA and auxin. These findings provide novel insights into leaf senescence, and further contribute to providing genetic resources for the breeding of crops resistant to premature senescence. Full article

Cell division is critical for the survival, growth, pathogenesis, and antibiotic susceptibility of Mycobacterium tuberculosis (Mtb). However, the regulatory networks governing the transcription of genes involved in cell growth and division in Mtb remain poorly understood. This study aimed to investigate the impact of BlaI overexpression on cell division and growth in Mtb and elucidate the underlying mechanisms. Mycobacterium smegmatis mc²155 was used as the model organism. Recombinant strains overexpressing BlaI were constructed. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), ethidium bromide and Nile red uptake assays, minimum inhibitory concentration (MIC) determination, drug resistance analysis, quantitative real-time PCR (qRT-PCR) assays, and electrophoretic mobility shift assay (EMSA) were employed to assess changes in bacterial morphology, cell wall permeability, antibiotic susceptibility, gene transcription levels, and the interaction between BlaI and its target genes. Overexpression of BlaI disrupted bacterial division in M. smegmatis, leading to growth delay, cell elongation, and formation of multi-septa. It also altered the lipid permeability of the cell wall and enhanced the sensitivity of M. smegmatis to β-lactam antibiotics. BlaI overexpression affected the transcription of cell division-related genes, particularly downregulating ftsQ. Additionally, BlaI negatively regulated the transcription of Rv1303—a gene co-transcribed with ATP synthase-encoding genes—inhibiting ATP synthesis. This impaired the phosphorylation of division complex proteins, ultimately affecting cell division and cell wall synthesis. Overexpression of BlaI in Mtb interferes with bacterial division, slows growth, and alters gene expression. Our findings identify a novel role for BlaI in regulating mycobacterial cell division and β-lactam susceptibility, providing a foundation for future mechanistic studies in M. tuberculosis, with validation required to assess relevance to clinical tuberculosis—though validation in M. tuberculosis and preclinical models is required. Full article

Enhancer of Zeste Homolog 2 (EZH2) is a key epigenetic regulator known for its role in global gene silencing and is involved in a variety of cellular processes, including cell survival, proliferation, invasion, and self-renewal. As a core component of the Polycomb Repressive Complex 2 (PRC2), EZH2 catalyzes the trimethylation of histone H3 at lysine 27 (H3K27me3), leading to chromatin compaction and transcriptional repression. Dysregulated EZH2 expression is observed in a wide range of solid tumors and hematological malignancies and is frequently associated with increased metastatic potential and poor clinical outcomes. While EZH2 primarily mediates gene silencing through its canonical PRC2-dependent activity, it also exerts oncogenic effects via non-canonical mechanisms. In its non-canonical role, EZH2 acts independently of PRC2, interacting with other signaling molecules as a transcriptional activator or co-activator, thereby promoting the activation of oncogenic pathways. Through both canonical and non-canonical mechanisms, EZH2 significantly contributes to tumor initiation and its subsequent progression. Given its critical role in oncogenesis and cancer progression, EZH2 is under investigation as a potential biomarker for cancer diagnosis and prognosis. This review provides a comprehensive overview of EZH2’s function and oncogenic roles across human cancers. Enhanced insight into EZH2’s complex regulatory network may facilitate the development of more effective strategies to manage EZH2-driven malignancies. Full article

Amyotrophic lateral sclerosis (ALS) is a terminal neurodegenerative disease, marked by considerable clinical and molecular heterogeneity. While several genetic drivers have been linked to familial ALS (fALS), the biology of sporadic ALS (sALS)—which accounts for the majority of ALS cases—remains poorly defined. To address this gap, we analyzed 247 bulk mRNA-sequenced post-mortem tissue samples from the lumbar spinal cord and motor cortex and compared expression profiles between fALS, sALS, and controls. Variance-stabilized DEGs from DESeq2 analysis were used as inputs for weighted gene co-expression network analysis (WGCNA). Finally, gene ontology was used to identify transcriptomic signatures and biological pathways unique to sALS and fALS. In the spinal cord, sALS samples exhibited specific downregulation of mitochondrial complex I subunits (e.g., NDUFS8 and NDUFB7) and regulatory genes (e.g., AURKAIP1 and ATP5F1D), suggesting compromised metabolic resilience. In the motor cortex, a co-expression module associated with adaptive immune function and leukocyte infiltration was downregulated in sALS yet upregulated in fALS, indicating distinct inflammatory pathways between these two forms of ALS. Together, our findings highlight that while sALS and fALS are largely the same disease, they exhibit distinct transcriptomic signatures. By accounting for mode of inheritance in study designs—particularly sALS, which represents ~90% of ALS cases—researchers may reveal deeper insights into ALS pathology. This perspective could enable more targeted therapeutic strategies, ultimately improving outcomes for all ALS patients. Full article

The sweetpotato (Ipomoea batatas [L.] Lam) is a globally significant crop, valued for its nutritional and economic importance. The tuberous roots of the sweetpotato are rich in carotenoids, which contribute to their vibrant colors and health benefits. This study focuses on three elite fresh-consumption sweetpotato cultivars: “Kokei No. 14,” “Xinxiang,” and “Zheshu81” with distinct flesh colors. To elucidate the metabolic pathways and genetic mechanisms underlying carotenoid biosynthesis in the sweetpotato, 20 types of carotenoids were quantified using targeted metabolomic analyses, and the key genes involved in carotenoid synthesis were identified with transcriptomic analyses. The results revealed significant differences in carotenoid content and composition among the cultivars, with “Zheshu81” exhibiting the highest carotenoid levels. Weighted gene co-expression network analysis further highlighted key regulatory genes and transcription factors influencing carotenoid accumulation. This study identifies key transcriptional regulators associated with carotenoid accumulation, sheds light on sweetpotato carotenoid biosynthesis mechanisms, and lays a foundation for breeding to improve its nutritional quality and flesh color. Full article