Search Results (5,426)

Background/Objectives: Our prior epigenome-wide association study (EWAS) on multiple sclerosis (MS) identified myeloid-associated methylation signatures and an association with enhancer regions. Here we compared differential DNA methylation across three central nervous system inflammatory disorders: MS, neuromyelitis optica (NMO), and neurologic post-acute sequelae of COVID-19 (neuro-PASC). Methods: Whole-blood DNA was profiled on Infinium MethylationEPIC arrays. Analyses included EWAS at the CpG level, differentially methylation region (DMR) analysis, and gene regulatory-element enrichment using Locus Overlap Analysis (LOLA). Limma linear models were adjusted for race, EPIC array version, age, sex, disease-modifying treatment class, and blood cell composition. Results: All three diseases were associated with broad CpG-level differential methylation. The most robust findings were disease-specific DMR signatures in gene regulatory regions. All three diseases shared Lamin B1-anchored chromatin states as an architectural genomic feature but differed in immune regulatory transcription factor binding sites (TFBS), RNA polymerase (Pol II) occupancy, and DNase accessibility. MS was enriched for TFBS in myeloid CEBPB and SPI1/PU.1 and lymphocyte-associated RUNX3, EBF1, and BATF. MS hypomethylated DMRs were concentrated at active enhancers and myeloid TFBS, suggestive of chronic myeloid activation. NMO showed the clearest promoter and B lymphocyte associated profile. Neuro-PASC was associated with hematopoietic DNase accessibility and TFBS for BATF and EBF1. Conclusions: These results suggest that DNA methylation in MS, NMO, and neuro-PASC differ meaningfully in regulatory architecture rather than conforming to a single shared disease-associated methylation model. A long-term goal is to develop immune therapies for newly recognized diseases such as neuro-PASC. Full article

Background: Spinal cord injury (SCI) triggers secondary injury processes involving neuroinflammation and systemic immune remodeling. The endocannabinoid system (ECS) has been implicated in neuroimmune regulation, but its transcriptional relationship with immune remodeling and its translational relevance in human SCI blood remain incompletely defined. Methods: A cross-species discovery–validation–translation framework was applied using a rat spinal cord discovery cohort (GSE45006), an independent mouse validation cohort (GSE171441), and a human peripheral white blood cell cohort (GSE151371). Analyses included differential expression profiling, ECS-focused assessment, cross-species comparison, immune-cell signature scoring, ECS–immune correlation analysis, receiver operating characteristic (ROC) analysis, LASSO-based biomarker prioritization, network analysis, disease enrichment, drug–gene interaction querying, and transcription factor/microRNA regulatory annotation. Results: ECS-related transcriptional remodeling was identified across rodent and human datasets in a compartment-dependent manner. In human SCI blood, CNR2, PTGS2, and DAGLB were significantly altered and showed biomarker-prioritization potential. Human SCI blood also showed innate immune enrichment, adaptive immune depletion, and significant ECS–immune correlations. The integrated 28-gene SCI–ECS immune panel formed a functionally coherent protein–protein interaction (PPI) network enriched in immune-response pathways. Disease enrichment supported an immune/inflammatory pathological context, whereas DGIdb identified hypothesis-generating drug–gene relationships involving ECS-related targets. ChEA 2022 revealed nominal transcription factor annotations that did not survive multiple-testing correction, and miRNet identified database-derived miRNA regulators of panel genes. In a secondary sensitivity analysis, the combined ECS signature also retained discriminatory performance against non-CNS trauma controls, suggesting that the observed transcriptional pattern was not fully attributable to generalized trauma-related responses. Conclusions: This study proposes an ECS-associated immune remodeling signature in SCI with translational biomarker-prioritization and pharmacologic target-annotation context in human peripheral blood. These findings are exploratory and require prospective and functional validation. Full article

Anthocyanins are major determinants of both the color and nutritional quality of fruit. Their accumulation in plant tissues depends on biosynthesis as well as efficient transport into the vacuole, a process in which glutathione S-transferases (GSTs) are believed to play an important role. Through genome-wide identification and analysis, this study identified 39 Chinese plum (Prunus salicina) glutathione S-transferase (PsGST) genes. Phylogenetic analysis grouped these PsGST genes into seven subfamilies. Dispersed duplication appeared to be the main driver of family expansion, and the duplicated genes appear to have largely evolved under purifying selection. The cultivar ‘Fengweimeigui’ (FWMG), with purple peel and red pulp, and the cultivar ‘Fengweihuanghou’ (FWHH), with yellow peel and yellow pulp, were used as contrasting materials because of their distinct anthocyanin pigmentation. We then profiled anthocyanin accumulation and the expression patterns of all PsGST genes across fruit development using quantitative real-time PCR (qRT-PCR). PsGSTF8 was identified as a candidate gene, and its expression patterns in both peel and pulp were consistent with anthocyanin accumulation, with higher relative transcript levels in the deeply colored cultivar ‘FWMG’ and undetectable expression in ‘FWHH’. The transient overexpression of PsGSTF8 in Chinese plum fruit promoted anthocyanin accumulation, and the complementation of the Arabidopsis thaliana transparent testa 19 (tt19) mutant further supported the potential role of PsGSTF8 in anthocyanin accumulation and GST-mediated transport. These results provide new clues for understanding potential GST-mediated anthocyanin transport and accumulation and offer a basis for the further investigation of the molecular mechanisms underlying fruit coloration in Chinese plum. Full article

Endothelial dysfunction is an early event in the development of cardiovascular diseases and is characterized by impaired barrier function, inflammatory activation of endothelial cells (ECs), and alterations in lipid metabolism. In addition to typical (mononuclear) endothelial cells (TECs), multinucleated variant endothelial cells (MVECs) are present within the vascular wall; however, their functional role remains poorly understood. The aim of the present study was to investigate the molecular and functional characteristics of MVECs and their potential contribution to the development of endothelial dysfunction. Primary human umbilical vein endothelial cells (HUVECs) were used, and multinucleated cells were generated by polyethylene glycol-induced fusion. Cells were incubated under control conditions or exposed to low-density lipoproteins (LDL; 100 µg/mL, 24 h). A comprehensive analysis was performed, including transcriptomic and proteomic (secretome) profiling using gene set enrichment analysis (GSEA), as well as functional assays assessing transendothelial LDL transport, intracellular cholesterol accumulation, macrophage migration, and the expression and secretion of pro-inflammatory cytokines (IL-6, IL-8). MVECs exhibited pronounced differences compared to TECs. GSEA revealed reduced enrichment of pathways related to canonical nuclear factor kappa B (NF-κB) signaling and negative regulation of NF-κB transcription factor activity, actin cytoskeleton organization, focal adhesion assembly, basement membrane organization, and vesicle-mediated transport in MVECs relative to TECs, indicating impaired cytoskeletal integrity, altered cell–matrix interactions, dysregulated inflammatory signaling, and reduced vesicular trafficking activity. Functionally, MVECs demonstrated an increased capacity for cholesterol accumulation and enhanced transendothelial migration of macrophages. Notably, transendothelial LDL transport across the MVEC monolayer was not increased, suggesting a predominance of intracellular lipid accumulation. MVECs also exhibited a pronounced pro-inflammatory phenotype, characterized by elevated expression and secretion of IL-6 and IL-8. Taken together, these findings indicate that MVECs represent a functionally altered endothelial phenotype with impaired barrier function, dysregulated lipid metabolism, and enhanced inflammatory activity. Local accumulation of MVECs within the vascular wall may contribute to the formation of pro-atherogenic regions and play a role in the initiation and progression of endothelial dysfunction. Full article

Background/Objectives: Managing bone diseases demands novel, natural compounds to bypass the heavy side effects of current therapies. Honey is well-known for its therapeutic traits, yet we know very little about how specific floral varieties impact bone tissue. This study confronts this gap by comparing how acacia, chestnut, and coriander honeys drive human osteoblast behavior in vitro. Methods: After mapping the phenolic/flavonoid profiles and antioxidant capacities of these honeys, we tested them on hFOB 1.19 human osteoblasts. We tracked cell migration via scratch assays and validated osteogenic maturation through Alkaline Phosphatase (ALP) activity and Alizarin Red (AR) mineralization over 7 days. Confocal time-lapse imaging with pharmacological inhibitors monitored intracellular calcium dynamics, while gene shifts were analyzed via qRT-PCR. Results: Coriander honey (CH) packed the highest polyphenol levels and antioxidant power. Biologically, while all honeys accelerated scratch closure, CH drove cell motility most potently. Remarkably, a 7-day treatment with these honeys sparked a significant and robust increase in ALP activity and mineralization, surpassing the osteogenic induction observed with standard osteoinductive media. Mechanistically, CH triggered a sharp [Ca²⁺] spike, relying on external calcium entry and IP3-dependent internal release via PLC activation. qRT-PCR confirmed this anabolic shift via OPG and OPN upregulation. Conclusions: Honey exerts pronounced multi-level osteopromotive effects at both the functional and transcriptional levels, tightly linked to its botanical source. Among the variants, coriander honey stands out for its exceptional ability to fast-track osteoblast migration, differentiation, and early mineral deposition. Therefore coriander honey represents a promising in vitro candidate that warrants further preclinical evaluation for bone repair applications. Full article

Candidozyma auris (formerly known as Candida auris) has emerged as a formidable clinical fungal pathogen as a result of its multidrug resistance and persistent colonization capabilities. In this study, three clinical C. auris strains (namely C. auris strain 01, C. auris strain 03, and C. auris strain 13) with distinct origins were characterized to investigate their phenotypic variations and mechanisms of azole resistance. Comprehensive profiling revealed significant inter-strain differences in biofilm formation, cell surface hydrophobicity, adhesion capacity, and phospholipase activity. Testing for antifungal susceptibility showed that the three clinical strains exhibited different minimum inhibitory concentrations for multiple azoles (fluconazole, voriconazole, and itraconazole) and echinocandins (anidulafungin and micafungin). Sequencing identified Y132F mutations in the ERG11 gene of the three clinical strains. Mechanistic investigations demonstrated that fluconazole exposure significantly upregulated the expression of efflux pump genes (CDR1 and CDR2) and the genes encoding their transcriptional regulators (MDR1 and TAC1b). In a murine skin colonization model, comparing data from the standard strain C. auris strain CBS12766 and clinical strains of C. auris strain 03 and C. auris strain 13 exhibited a significantly higher fungal burden of tissue, whereas strain C. auris strain 01 showed an intermediate level. Host immunity response analysis revealed that expression of the IL-1β gene was significantly elevated in C. auris strain CBS12766-infected mice, while expression of IL-6 and CXCL-1 genes was predominantly increased in the C. auris strain 01, with TNF-α gene expression levels being comparable across all strains. Histopathological examination confirmed local infiltration of inflammatory cells and mild epidermal edema, indicating active host immune engagement. Overall, our findings highlighted substantial phenotypic heterogeneity, different colonization capacities, and differences in expression of inflammatory cytokines among the C. auris strains. Further investigations into fluconazole-response mechanisms identified enhanced efflux pump activity, along with ERG11 gene Y132F mutations and transcription factor modulation among these clinical strains. Full article

Pepper (Capsicum annuum L.) is an important horticultural crop whose growth, development, and yield formation are severely constrained by heat stress. The Mediator complex is a key transcriptional co-regulator in plants and plays important roles in developmental processes and stress responses. However, the MED gene family and its functions in heat stress responses remain largely unexplored in pepper. Using the chromosome-level reference genome of the cultivated pepper (Capsicum annuum var. annuum) cultivar Zhangshugang, a total of 49 CaMED genes were identified and classified into four conserved Mediator modules, namely the head, middle, tail, and kinase modules. Comprehensive bioinformatic analyses showed that CaMED genes are evolutionarily conserved across species, whereas differences in gene structure and sequence characteristics among family members may contribute to their functional diversification. Promoter analysis further showed that these genes contain abundant cis-acting elements related to light, phytohormone, and stress responses. Transcriptome analysis of the 49 identified CaMED genes showed distinct tissue-specific expression patterns, with many members showing preferential expression during early flower development and late placenta development. Furthermore, expression profiling of all CaMED genes using publicly available transcriptome datasets under 42 °C heat-stress conditions, followed by RT-qPCR validation of selected candidates, showed that CaMED25a displayed a relatively stable heat-responsive expression pattern. Virus-induced gene silencing of CaMED25a compromised heat tolerance in pepper plants under heat stress, as evidenced by increased H₂O₂ accumulation and significantly reduced expression of heat defense-related genes, including CaHSP18, CaHSP25.9, and CaHSP70.1. Taken together, this study provides an integrated analysis of the pepper CaMED gene family and reveals the positive contribution of CaMED25a to heat stress tolerance. These findings lay the groundwork for subsequent studies on CaMED gene function and the molecular regulation of high-temperature responses in pepper. Full article

Immunosenescence is a critical driver of tumor initiation and progression. In this study, we systematically characterized immune cell senescence by integrating transcriptomic profiles from 17 physiologically aged tissues with pan-cancer single-cell datasets, encompassing 206 samples across nine cancer types. Cross-tissue comparison of senescence-associated alterations, integrated with spatial transcriptomics, revealed that malignant cells triggered senescence in the core myeloid subpopulation designated Mac_DAB2 via a conserved MIF-CD74 signaling axis. By integrating shared myeloid differentiation programs across normal tissues and the tumor microenvironment (TME) with their transcriptional regulatory networks, we defined a myeloid senescence-associated gene (MSAG) signature. This signature successfully distinguishes a senescence-associated, immunosuppressive subtype linked to poor prognosis in pan-cancer cohorts. Finally, we established the MSAG.SIG prognostic model using an ensemble framework of 117 machine learning algorithms, which demonstrated robust and consistent predictive performance across multiple independent cohorts. Overall, this study elucidates the mechanisms underlying TME-driven myeloid senescence, establishes MSAG as a conceptual framework for characterizing myeloid immunosenescence, and provides a clinically relevant pan-cancer prognostic tool with translational potential. Full article

Reverse transcription quantitative real-time PCR (RT-qPCR) is a highly efficient and sensitive technique for quantifying gene transcript levels. The accuracy of gene expression analysis depends critically on the selection of appropriate reference genes for normalization, which is essential to minimize technical variation arising from differences in RNA quality, reverse transcription efficiency, and sample handling. Schisandra chinensis is a medicinally important plant with a long history of use in traditional Chinese medicine and has gained increasing global recognition. In recent years, a growing number of studies have employed molecular biology approaches to investigate the molecular mechanisms underlying secondary metabolite biosynthesis in S. chinensis. However, systematically validated reference genes for RT-qPCR analysis in this species have not yet been established. In the present study, the expression stability of eleven candidate reference genes was evaluated across different tissues and under various abiotic stress conditions in S. chinensis using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. Comprehensive analysis revealed that PP2A15 and UBC2 were the optimal reference gene combination for leaves; UBC2 and UBC11 for stems; RPL6 and PP2A15 for roots; RPL21 and RPL6 for fruits; and RPL6 and UBC11 as the best-performing pair across all tissue types. Under abiotic stress conditions, UBC11 and UBC2 exhibited the highest stability in both leaves and roots under salt stress; UBC2 and GPN1 proved most stable under alkaline stress; UBC2 and RPL6 were identified as the most suitable combination under drought stress; and UBC2 and UBQ12 demonstrated consistently stable expression across all three abiotic stress treatments. The reliability of these reference gene combinations was further validated by examining the expression profiles of three target genes. Collectively, these findings establish a validated reference gene toolkit for future gene expression studies in S. chinensis, particularly for the functional characterization of genes involved in lignan biosynthesis and abiotic stress responses. Full article

Alzheimer’s disease (AD) lacks effective disease-modifying therapeutics. Probiotics, promising neuroprotective candidates, exert benefits mainly by modulating gut-brain-axis (GBA) signaling. This study explored the anti-AD effects and mechanisms of Rhodopseudomonas pseudopalustris (R. pse). Using Caenorhabditis elegans (C. elegans) AD models, we evaluated AD-related phenotypes (learning deficits, paralysis) after R. pse administration, and performed genetic analysis and metabolomic profiling to clarify its regulatory pathways and metabolites. Mechanistically, R. pse significantly alleviated AD-related phenotype in C. elegans. It upregulated γ-glutamylcysteine synthetase (GCS-1) to enhance the glutathione (GSH)-dependent antioxidant defense. Knockout of the oxidation repair enzyme methionine sulfoxide reductase A-1 (MSRA-1) abolished the neuroprotective effects of R. pse, which was rescued by methionine. R. pse also activated activating transcription factor 7 (ATF-7)-mediated innate immunity and transforming growth factor β (TGF-β) signaling, with pantothenic acid as its functional metabolite. Collectively, R. pse is a potential anti-AD bacterium that mitigates AD model pathogenesis by enhancing the cellular antioxidant capacity, providing experimental evidence for bacteria-based AD interventions. Full article

Interferons (IFNs) play vital roles in antiviral immunity, yet the functional diversity of type I IFNs in teleosts remains incompletely characterized. In this study, we identified and characterized a group II type I interferon, designated IFNc (MsIFNc), from largemouth bass (Micropterus salmoides). The cDNA sequence of MsIFNc is 660 bp in length, encoding a 184-amino-acid polypeptide containing a signal peptide and four conserved cysteines predicted to form two disulfide bonds. Phylogenetic analysis confirmed its classification within the teleost IFNc subgroup. Tissue expression profiling revealed constitutive MsIFNc transcription in all examined tissues, with the highest levels in the liver, intestine, and spleen. Moreover, MsIFNc expression was significantly upregulated in the spleen following polyinosinic–polycytidylic acid (polyI:C) stimulation. Recombinant MsIFNc (rMsIFNc) was successfully expressed in Pichia pastoris and significantly enhanced the viability of primary hepatocytes infected with Micropterus salmoides rhabdovirus (MSRV). These results demonstrate that IFNc is an important component of the immune response in largemouth bass, providing a basis for understanding the function of fish IFNc. Full article

Background: Hematopoietic stem cell (HSC) ex vivo culture causes severe loss of repopulation and regenerative capacity without compromising multilineage differentiation, which greatly limits the efficacy of HSC transplantation. The molecular mechanisms underlying culture-triggered HSC dysfunction remain poorly understood. Methods: Human CD34⁺ HSCs were cultured ex vivo for 96 h to establish a culture-induced HSC dysfunction model. Single-cell RNA sequencing was applied to screen key regulatory genes. TSC22D3 function was verified via overexpression assays, and immunodeficient mice were used to assess HSC engraftment. Transcriptomic profiling were performed to explore downstream molecular mechanisms. Results: Ex vivo culture induced G0 quiescence exit, elevated early apoptosis and impaired in vivo repopulation in human CD34⁺ HSCs. TSC22D3 was highly enriched in freshly isolated quiescent HSCs and gradually downregulated during culture. TSC22D3 overexpression restored HSC G0 arrest and improved hematopoietic engraftment in mice. Mechanically, TSC22D3 upregulated HSC self-renewal genes, suppressed cell cycle-related genes (CDK2/4), and activated the P53-P21-P27 pathway. Conclusions: This study demonstrates that TSC22D3 preserves HSC function during ex vivo culture by maintaining stem cell quiescence and restricting excessive proliferation. These findings reveal a novel transcriptional mechanism regulating HSC homeostasis and provide a promising target for improving functional HSC ex vivo expansion for clinical transplantation. Full article

Immune remodeling within the tumor microenvironment (TME) influences the progression and clinical outcome of uterine corpus endometrial carcinoma (UCEC), but the contribution of chemokine-related regulatory genes remains incompletely characterized. This study aimed to evaluate the prognostic relevance of CXCL13 and its association with immune microenvironmental features in UCEC using publicly available transcriptomic and single-cell datasets. RNA-sequencing profiles and clinical annotations from 589 UCEC cases in The Cancer Genome Atlas (TCGA) were analyzed to assess TME composition using ESTIMATE (Estimation of Stromal and Immune cells in MAlignant Tumours using Expression data) and CIBERSORT (Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts), followed by survival analysis, differential gene expression analysis, protein–protein interaction network construction, Cox regression, and gene set enrichment analysis. A public single-cell RNA-sequencing dataset from the Gene Expression Omnibus (GEO; GSE173682) was further used to infer the cellular sources of CXCL13. Elevated CXCL13 expression was associated with favorable overall survival and enrichment of immune-activation pathways. CIBERSORT-based analysis indicated that high CXCL13 expression correlated with increased estimated fractions of CD8⁺ T cells and plasma cells, together with transcriptional features related to tertiary lymphoid structure-associated immune activation, whereas several immunosuppressive cell populations showed lower estimated abundance. Single-cell analysis suggested that CXCL13 was mainly expressed by follicular helper T cells and exhausted CD8⁺ T cells. These findings indicate that CXCL13 may serve as a prognostic biomarker associated with an immune-active TME in UCEC. Further histological, spatial, and functional validation is warranted to confirm its mechanistic role and translational potential. Full article

Ataxia-Telangiectasia (A-T) is a multisystem disorder caused by loss of A-T mutated (ATM) protein activity, characterized clinically by immunodeficiency and cerebellar ataxia. ATM is a master regulator of DNA damage responses and loss of ATM function is accompanied by persistent activation of PARP1 leading to depletion of intracellular NAD⁺ and dysfunction of a series of cellular signalling pathways dependent on NAD⁺, providing a mechanistic rationale for NAD⁺ augmentation therapy. We performed a clinical trial of NAD⁺ augmentation with nicotinamide riboside (NR) over 24 months in A-T patients where we observed improved coordination and eye movements in A-T patients. Here, by using peripheral blood mononuclear cells, we performed longitudinal transcriptome profiling to define molecular signatures of A-T and to assess pathway-level responses to NR supplementation. A-T patients exhibited reproducible transcriptomic alterations involving immune, vascular, and inflammatory pathways. NAD⁺ augmentation was associated with suppression of interferon response genes and modulation of networks correlated with neurological improvement. These findings establish systemic molecular signatures of A-T and identify potential blood-based biomarkers that reflect disease processes and therapeutic response, supporting the use of NAD⁺ augmentation as a disease-modifying strategy in A-T by dampening interferon signalling. Full article

This study aimed to investigate the selective anticancer activity of the curcumin analog PAC (3,5-Bis-4-hydroxy-3-methoxybenzylidene)-N-methyl-4-piperidone). Normal gingival epithelial cells (GECs), cancerous gingival cells (Ca9-22) and tongue squamous carcinoma cells (CAL27) were exposed to increasing concentrations of PAC (0–10 µM) for 24 h. Cell viability and cytotoxicity were evaluated using MTT and LDH assays, while apoptosis and caspase activation were analyzed by Annexin V/PI staining and flow cytometry. Gene-expression profiling was performed using RT² Profiler PCR arrays. PAC significantly inhibited Ca9-22 and CAL27 cell proliferation in a concentration-dependent manner, with an IC₅₀ value of 5 µM, while exerting no noticeable cytotoxic effects on normal GEC. PAC treatment induced significant early and late apoptosis associated with increased caspase activity in both oral cancer cell lines. Transcriptomic analyses revealed extensive modulation of apoptosis-related genes. In Ca9-22 cells, PAC predominantly suppressed anti-apoptotic and survival-associated genes, including BCL2, BIRC3, BIRC5, XIAP, CFLAR, and NFKB1. In contrast, CAL27 cells exhibited a more pronounced pro-apoptotic transcriptional profile characterized by upregulation of TP53, APAF1, CASP1, BID, and TNF. Gene interaction network analyses further demonstrated that PAC targets highly interconnected apoptotic signaling pathways. Collectively, these findings demonstrate that PAC exerts potent selective anticancer activity against OSCC cells through modulation of intrinsic and extrinsic apoptotic pathways. These results further support the therapeutic potential of PAC as a promising multitarget candidate for oral cancer treatment. Full article