Search Results (1,488)

Pain is a complex process involving dynamic transcriptional changes in cells of the PNS and CNS following injury or inflammation. Among stress-inducible transcription factors, ATF3 has emerged as one of the most robust molecular markers of neuronal injury, particularly in sensory neurons of the DRG. Although ATF3 is widely used as an indicator of axonal damage in experimental pain models, its functional contribution to the initiation, maintenance, and resolution of pain remains poorly understood. Recent transcriptomic and functional studies suggest that ATF3 not only reflects neuronal stress but also orchestrates gene expression programs involved in axonal regeneration, neuroimmune communication, ion channel remodeling, and nociceptor plasticity. Moreover, ATF3 expression has been identified in non-neuronal cell populations, including Schwann cells and satellite glial cells, indicating broader roles in peripheral nerve repair and neuroinflammation. Despite the growing body of experimental evidence, the literature remains fragmented, and no consensus has yet been reached as to whether ATF3 primarily promotes adaptive regeneration or directly contributes to maladaptive pain signaling. This review aims to provide a comprehensive and critical overview of the current understanding of ATF3 biology in pain, building on evidence from transcriptomic and molecular analyses, experimental models of neuropathic, inflammatory, and cancer-associated pain, and emerging mechanistic insights into its role in pain-related neuronal plasticity. This review examines the regulation of ATF3 expression, its downstream transcriptional targets, its interactions with inflammatory signaling pathways, and its potential value as a therapeutic target. By consolidating current evidence and highlighting existing knowledge gaps, this review seeks to clarify the multifaceted role of ATF3 in pain pathophysiology. Full article

Iron (Fe) deficiency and cadmium (Cd) contamination often co-occur in agricultural systems, yet the way in which Fe deficiency modulates Cd translocation remains unclear. Here, we investigated root cell wall modifications mediating Cd accumulation in two peanut cultivars with contrasting Fe deficiency tolerance. Fe deficiency significantly increased root Cd concentrations in both cultivars but reduced Cd translocation to shoots, an effect more pronounced in the tolerant cultivar Silihong. Cell wall analysis revealed cultivar-specific compositional changes: pectin and cellulose increased under combined Cd exposure and Fe deficiency, while hemicellulose (HC1) decreased. Negative correlations between Fe and Cd accumulation in roots, cell walls, and their components indicate competition between these two metal ions for binding sites in root cell walls. Increased pectin content under combined stress enhances Cd sequestration, while reduced HC1 content facilitates Fe mobilization to shoots. Transcriptomic analysis identified hub genes associated with cell wall modification, including pectinesterases (PME2/4/29/63), beta-galactosidases (BGAL3/5/8), polygalacturonases (PGs), pectin acetylesterases (PAE8), xyloglucan endotransglucosylase/hydrolases (XTH8/31) and laccases (LAC7/11/15). Under combined stress, Silihong exhibited superior Cd immobilization, characterized by higher Cd accumulation in HC1 and cellulose fractions, stronger induction of PME, PAE8 and LAC genes, and greater suppression of XTHs, PGs, and BGALs. Our findings demonstrate that Fe deficiency restricts Cd translocation by remodeling root cell walls, increasing pectin and cellulose while modulating hemicellulose integrity, thereby creating an expanded apoplastic reservoir that traps Cd. This structural detoxification mechanism, operating downstream of uptake transporters, identifies key cell wall components and regulatory genes as potential targets for breeding peanut cultivars with improved food safety. Full article

Insects lack adaptive immunity and rely exclusively on innate immune system for pathogen defense. However, the specific role of BmToll9-2, a key Toll receptor in the silkworm (Bombyx mori), in mediating immune responses, particularly against bacterial challenges in the larval fat body, remains incompletely understood. To address this gap, this study employed a combination of molecular approaches, including RNA interference (RNAi) targeting BmToll9-2, bacterial challenges with heat-inactivated Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive), and quantitative real-time PCR (qPCR) to assess the transcriptional changes of BmToll9-2 and immune-related genes in the fat body, a key immune tissue. Quantitative analysis showed that after BmToll9-2 RNAi, bacterial challenges significantly upregulated BmToll9-2 expression in the fat body at 12 h post-challenge, whereas BmToll9-2 silencing alone notably downregulated most downstream signaling genes of the Toll pathway by 53.07–83.14%, as well as 11 immune effector genes, including antimicrobial peptide genes, by 64.48–93.40%. Importantly, feeding bacteria post-RNAi reversed these downregulations: E. coli induced a stronger upregulation of both signaling and effector genes compared to S. aureus. This study provides transcriptional evidence that BmToll9-2 may act as a positive regulator of the Toll pathway signaling and antimicrobial peptides in silkworm larval fat body, facilitating robust and rapid immune signaling. This study deepens our understanding of Lepidopteran innate immunity by elucidating key molecular mechanisms, thereby providing a solid foundation for refining RNAi-based pest control strategies. Full article

Background/Objectives: RNA interference (RNAi) represents a promising therapeutic approach for silencing oncogenes involved in cancer progression by utilizing small interfering RNA (siRNA). However, siRNA requires an efficient delivery system to overcome cellular uptake and endosomal escape barriers. This study aimed to evaluate a multifunctional tandem peptide, GE11-599, designed to enhance the targeted delivery of siRNA and maintain its bioactivity in glioblastoma (GBM) cells. Methods: The GE11-599 peptide, consisting of an EGFR-targeting GE11 motif and a 599 fusogenic domain, was complexed with siRNA via electrostatic interactions to form nanoparticles. We assessed nanoparticle physicochemical properties, protection of siRNA from serum and RNase degradation, and cellular uptake in two GBM cell lines (U118MG and U87MG). Mechanistic studies evaluated receptor-mediated endocytosis and the subsequent escape from endosomes. Functional assays quantified STAT3 gene silencing and downstream effects on cell migration following treatment with GE11-599–siSTAT3 complexes. Results: GE11-599 formed positively charged, monodisperse nanoparticles capable of protecting siRNA from degradation. The tandem peptide significantly enhanced cellular internalization through EGFR-mediated endocytosis and facilitated endosomal escape of siRNA. Treatment with GE11-599–siSTAT3 resulted in robust gene silencing, achieving up to an 80% reduction in STAT3 mRNA expression. Downstream functional assessment showed a 40% decrease in migration in GBM cells treated with GE11-599–siSTAT3 complexes. Conclusions: The GE11-599 tandem peptide effectively enhances cell-specific internalization and endosomal escape of siRNA in GBM cells, resulting in increased siRNA bioactivity and functional gene silencing. These findings support GE11-599 as a promising siRNA delivery platform for targeting EGFR-expressing cancers. Full article

Yellow leaf phenotypes represent an important trait in pepper and enrich genetic germplasm resources. Previous studies have primarily examined leaf yellowing caused by defects in chlorophyll biosynthesis, whereas the functions of chlorophyll degradation-related genes remain less well characterized. In this study, a yellow leaf phenotype (NY) was identified. Transmission electron microscopy and RNA-seq showed that differentially expressed genes were concentrated in photosynthesis- and chlorophyll-related pathways. CaCLH1 was then demonstrated to promote chlorophyll degradation. Yeast one-hybrid analysis identified the CabHLH18-like gene as a direct interactor with the CaCLH1 promoter and as a positive regulator of CaCLH1 transcription. The CabHLH18-like gene was highly expressed in yellow leaf pepper. The CabHLH18-like gene was subsequently isolated and characterized, revealing nuclear localization and transcription factor activity. Functional analysis showed that silencing the CabHLH18-like gene increased chlorophyll content, whereas its overexpression reduced chlorophyll content. These findings indicate that CaCLH1 is a direct downstream target of the CabHLH18-like gene and contributes to CabHLH18-like-gene-mediated regulation of leaf yellowing in pepper. This study refines mechanistic understanding of leaf yellowing and provides a foundation for future research and breeding applications in pepper. Full article

Background: Prostate cancer (PCa) is a leading cause of cancer-related mortality worldwide, highlighting the need for improved prognostic tools. The integration of artificial intelligence (AI) and machine learning (ML) with multi-omics data offers new opportunities for biomarker discovery and risk stratification. Methods: We integrated bulk transcriptomic data from GSE116918 (training, n = 248) and three cross-cohort consistency evaluation cohorts (TCGA-PRAD, GSE70769, GSE46602), focusing on 1087 epithelial–mesenchymal transition (EMT)-associated genes. Using consensus clustering, weighted gene co-expression network analysis (WGCNA), and 91 machine learning algorithm combinations (including Random Forest, Lasso, and CoxBoost), we constructed a prognostic signature. SHAP analysis was used for model interpretability. Single-cell RNA sequencing (scRNA-seq, GSE268307, 10,672 cells) and spatial transcriptomics (10× Genomics Visium FFPE) provided hypothesis-generating evidence; spatial analysis was based on one tissue section. Results: A three-gene signature (INHBA, FAP, ITGBL1) effectively stratified patients into high- and low-risk groups, with the high-risk group showing significantly worse metastasis-free survival (HR = 1.61, 95% CI: 1.39–1.87; 4-year AUC = 0.93 in the training cohort; external AUCs ranged from 0.62 to 0.77). CytoTRACE inferred high differentiation potential of COMP+ fibroblasts, and Monocle3 inferred a transcriptional transition from COMP+ toward NELL2+ fibroblasts. BayesPrism deconvolution suggested that high inferred COMP+ fibroblast abundance was associated with poor prognosis and advanced T stage. NicheNet analysis prioritized BMP7 as a key upstream ligand, with downstream targets enriched in TGF-β signaling and stem cell pluripotency pathways. Conclusions: This study presents a machine learning-based multi-omics framework for prostate cancer risk stratification. The three-gene signature provides a new exploratory prognostic model while inferring a COMP+ to NELL2+ transcriptional transition. These findings may inform future hypothesis-driven studies of treatment sensitivity, pending experimental validation, and demonstrate the value of AI-driven multi-omics integration for precision oncology. Full article

The efficacy of adoptive cell transfer (ACT) therapy in solid tumors is often limited by the functional exhaustion and insufficient persistence of infused CD8⁺ T cells within the tumor microenvironment. Through the integrated analysis of single-cell transcriptomic data, this study identified enolase 1 (ENO1), a key rate-limiting enzyme in glycolysis, as a core gene highly correlated with the superior anti-tumor phenotype of tumor-infiltrating lymphocytes (TILs). However, in vitro functional validation demonstrated that the overexpression of Eno1 failed to substantially enhance the anti-tumor efficacy of mouse T cells, suggesting the presence of a downstream metabolic regulatory node within the glycolytic cascade that restricts the conversion of carbon flux. To overcome this limitation, we introduced the small molecule activator TEPP-46 to target a crucial downstream metabolic hub, pyruvate kinase M2 (PKM2). Transcriptome sequencing confirmed that PKM2 activation successfully induced systemic metabolic rewiring in CD8⁺ T cells and broadly upregulated the expression of cytotoxicity- and memory-related genes. In an in vivo B16-OVA melanoma model, OT-1 T cells subjected to In vitro TEPP-46 pretreatment exhibited significantly enhanced tumor-suppressive capabilities and effectively promoted the preferential differentiation of T cells into central memory T cells (Tcm). In summary, this study highlights the importance of targeting downstream metabolic nodes to bypass intrinsic metabolic restrictions in T cells. It demonstrates that in vitro metabolic pretreatment via PKM2 activation represents an effective translational strategy for optimizing the anti-tumor efficacy of ACT cell products. Full article

Background: Trophoblast retrieval and isolation from the cervix (TRIC) has emerged as a promising alternative to invasive prenatal diagnostic procedures. However, contamination by maternal immune cells remains a major challenge that may compromise trophoblast purity and the reliability of downstream fetal genetic analyses. Methods: Maternal immune cells were selectively depleted by immunomagnetic sorting using antibodies targeting CD45 or CD56. The remaining cells were subsequently enriched for HLA-G-positive trophoblasts and characterized by immunofluorescence and gene-expression analyses using CD45, CD56, HLA-G, cytokeratin 7 (CK7), and β-human chorionic gonadotropin (β-hCG). Results: Compared with CD45-mediated depletion, CD56-mediated depletion demonstrated more efficient removal of maternal immune cells, as indicated by significantly reduced CD56 expression. CK7 expression showed an increasing trend following CD56 depletion, whereas β-hCG expression remained largely unchanged. Immunofluorescence analysis further demonstrated a significant increase in the proportion of CK7⁺/β-hCG⁺ trophoblast cells after CD56 depletion. Conclusions: Among the evaluated depletion strategies, CD56-mediated depletion demonstrated a more favorable profile for trophoblast-associated characteristics than CD45-mediated depletion, suggesting its potential contribution to further methodological optimization of trophoblast isolation in TRIC-based noninvasive prenatal genetic testing. Full article

Bisphenol A (BPA) is a non-persistent industrial chemical widely used in the production of polycarbonate plastics and epoxy resins. Due to its mass production and versatility, BPA is ubiquitous in environmental matrices, leading to human exposure through ingestion, dermal contact, and inhalation. As a known endocrine-disrupting chemical (EDC) with estrogenic activity, BPA exposure has been associated with reproductive, metabolic, immune, oncogenic, and developmental effects. Mechanistically, BPA is reported to exert its toxic effects via multiple pathways, including alterations in epigenetic microRNA (miRNA) expression. miRNAs are endogenous non-coding RNA molecules that regulate gene expression by targeting mRNAs, thereby influencing a wide range of cellular and metabolic pathways involved in development and disease. Importantly, this review consolidates evidence suggesting that the biological effects of BPA may, in part, be mediated through miRNA-driven epigenetic modifications, affecting numerous downstream proteins and signaling pathways. Altered miRNA expression induced by BPA exposure is implicated in diverse health outcomes, including reproductive dysfunction, oncogenesis, metabolic disorders, and neurodevelopmental abnormalities. Notably, BPA exposure predominantly results in the upregulation of specific miRNAs, such as miR-21 and miR-146a, although tissue-specific and sex-dependent variations are evident. In this review, we provide a comprehensive overview of human, in vivo, and in vitro studies investigating BPA-induced miRNA dysregulation and its associated biological effects. Full article

Root hairs are tubular protrusions of root epidermal cells that expand the root surface area to facilitate water and nutrient uptake. The target of rapamycin (TOR) kinase has been identified as a positive regulator of root hair elongation, and the RHD6-RSL4 bHLH transcriptional cascade is well established as a core module that governs root hair morphogenesis. However, whether TOR signaling acts upstream of the RHD6-RSL4 pathway and how glucose signals are integrated into this transcriptional regulatory network during root hair development remain incompletely understood. In this study, transcriptome profiling combined with pharmacological and genetic functional assays was performed to elucidate the TOR-mediated transcriptional regulatory pathway of root hair elongation in Arabidopsis. Chemical inhibition of TOR triggered genome-wide transcriptional reprogramming in seedling roots, including disruption of auxin and ethylene signal transduction and pronounced downregulation of hundreds of genes related to root hair development. Glucose-activated TOR signaling modulates the expression of root hair-specific (RHS) genes mainly through the core RHD6-RSL4 transcriptional cascade. The transcription of RSL1–RSL5 was strongly dependent on functional TOR activity, whereas RHD6 transcript abundance was specifically induced by glucose–TOR signaling under carbon-starvation recovery conditions. Genetic overexpression of either RHD6 or RSL4 partially rescued root hair elongation defects caused by TOR suppression, confirming that the RHD6-RSL4 cascade functions as a critical downstream transcriptional module of glucose–TOR signaling. Collectively, this work establishes a transcriptional framework in which glucose–TOR signals modulate root hair elongation via transcriptional activation of the master bHLH regulators RHD6 and RSL4. Full article

Triple-negative breast cancer (TNBC) remains a major therapeutic challenge due to pronounced molecular heterogeneity, transcriptional plasticity, and frequent treatment resistance. MicroRNA (miRNA)-based strategies have emerged as potential approaches for modulating dysregulated gene expression networks in TNBC; however, the contribution of understudied miRNA families to TNBC-associated regulatory programs remains incompletely understood. This study aimed to investigate the tumor-suppressive role of miR-548f-3p in TNBC and to identify candidate downstream effectors, with particular focus on ANP32E. An integrative analysis combining public transcriptomic datasets, clinical expression profiling, computational target prediction, network-based prioritization, pathway analysis, and single-cell transcriptomic assessment identified miR-548f-3p as consistently downregulated in TNBC. Among candidate downstream targets, ANP32E, a chromatin-associated regulator involved in H2A.Z histone variant dynamics, was identified as a potential effector exhibiting increased expression in TNBC and enrichment within malignant epithelial cell populations. An inverse association between miR-548f-3p and ANP32E expression was observed in patient-derived samples. In breast cancer cell models, miR-548f-3p mimic restoration increased apoptosis, promoted G₀/G₁ accumulation, and reduced migration- and invasion-associated readouts, although measurable effects were also observed in non-tumorigenic MCF-10A cells. These phenotypic changes were accompanied by reduced ANP32E expression at the protein level, indicating that ANP32E expression is responsive to miR-548f-3p restoration. This study supports miR-548f-3p as a candidate tumor-suppressive miRNA in TNBC. The reduction in ANP32E protein expression following miR-548f-3p restoration, together with computational, single-cell, and clinical expression evidence, supports ANP32E as an expression-responsive candidate downstream effector of miR-548f-3p. Further reporter-based and rescue experiments are required to confirm direct 3′UTR-mediated targeting and to define the mechanistic contribution of ANP32E within the broader miR-548f-3p regulatory network. Full article

Background/Objectives: Ephedrae Herba (EH) is widely used in traditional East Asian medicine, but safety concerns regarding its adverse events remain. This study aimed to investigate EH-associated adverse events using clinical pharmacovigilance data and to perform exploratory in silico analyses to propose potential molecular mechanisms underlying these adverse events. Methods: A disproportionality analysis was performed using individual case safety reports from the Korea Adverse Event Reporting System database. EH-containing products were compared with other herbal medicine products using reporting odds ratios (RORs), proportional reporting ratios, and information components. Network pharmacology identified adverse event-related genes and pathways, and protein–protein interaction networks were constructed. Molecular docking predicted direct adverse event-associated targets of ephedrine and compared mechanisms with control compounds (aconitine and spinosin). Results: Four adverse-event signals were detected in the primary analysis: sleep disorder, dry mouth, insomnia, and palpitations. Sensitivity analysis identified four signals, with three (dry mouth, insomnia, and palpitations) consistent across both analyses; constipation emerged only in the sensitivity analysis. Conclusions: Adverse event-associated network analysis predicted key pathways: Neuroactive ligand–receptor interaction, Pathways of neurodegeneration, and Dopaminergic synapse. Molecular docking predicted that ephedrine may act on downstream signaling mechanisms shared by neurotransmitter systems, including the dopaminergic system, distinct from control compounds. Full article

Background: Cerebrovascular diseases have complex pathogenesis and pose a serious threat to human health; thus, novel diagnostic and therapeutic strategies are needed. Small extracellular vesicles (sEVs), commonly referred to as exosomes, are 30–150 nm lipid-bilayer vesicles that shield long noncoding RNAs (lncRNAs) from degradation. Because exosomal lncRNAs are more stable than free lncRNAs in blood and cerebrospinal fluid and can cross the blood–brain barrier, they are promising as biomarkers and therapeutic vectors. This review summarizes the roles and mechanisms of exosomal lncRNAs in cerebrovascular diseases. Methods: This narrative review is based on the experimental literature and focuses on the biological functions and regulatory mechanisms of exosomal lncRNAs in cerebrovascular disorders. Results: As competing endogenous RNAs (ceRNAs), they sequester microRNAs (miRNAs), thereby derepressing downstream target-gene expression and modulating neuronal injury (oxidative stress, apoptosis, neuroinflammation) through the nuclear factor kappa-B (NF-κB) and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) pathways. They show altered profiles in acute stroke (ischemic/hemorrhagic) correlated with neurological deficits, and are relevant to the early diagnosis of chronic diseases (atherosclerosis, aneurysm) and vascular dementia. Conclusions: Exosomal lncRNAs demonstrate promising translational potential in preclinical studies because they combine exosome delivery capabilities with lncRNA regulatory functions, although clinical validation remains limited. Full article

Background: Drought tolerance in wheat is a complex trait controlled by multiple regulatory networks, among which calcium-dependent protein kinases (CDPKs) act as important components linking stress perception with downstream cellular responses. However, the functional contribution of individual CDPK members to drought adaptation in wheat remains largely unclear. This study aimed to identify and functionally characterize drought-responsive CDPK genes associated with differential drought responses in wheat. Methods: Two wheat lines derived from the same breeding background exhibiting contrasting drought adaption, 23B1 and 23B39, were subjected to PEG6000-induced osmotic stress. Growth traits, osmotic adjustment-related metabolites, membrane damage indicators, and antioxidant enzyme activity were evaluated. Transcriptomic analysis was performed at early drought-response stages, followed by differential expression analysis, functional enrichment, CDPK family screening, and qRT-PCR validation. The role of TaCDPK22-5A was further investigated using barley stripe mosaic virus (BSMV)-mediated virus-induced gene silencing (VIGS). Results: The drought-responsive line 23B1 maintained stronger growth, accumulated higher levels of proline and soluble sugars, exhibited enhanced peroxidase activity, and showed reduced membrane lipid peroxidation compared with 23B39. Transcriptome analysis revealed extensive transcriptional reprogramming under drought stress, with differentially expressed genes mainly associated with metabolic adjustment, transport regulation, secondary metabolism, and stress-responsive pathways. Among the identified CDPK members, TaCDPK22-5A showed a strong drought-responsive expression pattern in the line exhibiting stronger drought tolerance (23B1). Virus-induced gene silencing of TaCDPK22-5A significantly impaired drought tolerance, resulting in reduced growth, biomass accumulation, and chlorophyll retention under drought conditions. Conclusions: These findings demonstrate that TaCDPK22-5A contributes positively to drought adaptation in wheat and highlight CDPK-mediated calcium signaling as an important regulatory component of drought responses. The identified gene provides a potential target for improving drought resilience in wheat breeding. Full article

Osteoarthritis (OA) is increasingly recognized as a mechanically driven whole-joint disease in which abnormal mechanotransduction initiates a cascade of mitochondrial dysfunction, chronic inflammation, and progressive cartilage degeneration. Among the mechanosensitive molecules identified to date, Piezo1 has emerged as a key mechanosensitive regulator linking pathological mechanical loading to intracellular calcium signaling and downstream cellular responses. Growing evidence indicates that persistent Piezo1 activation promotes mitochondrial calcium overload, excessive reactive oxygen species production, ATP depletion, mitochondrial membrane depolarization, and impaired mitophagy, ultimately amplifying chondrocyte dysfunction and extracellular matrix degradation. In parallel, mitochondrial damage triggers immunometabolic reprogramming through activation of the cGAS–STING pathway and the NLRP3 inflammasome. It also promotes pro-inflammatory cytokines, including interleukin-1β, tumor necrosis factor-α, and interleukin-6. Together, these responses may contribute to a self-perpetuating cycle of inflammation and tissue destruction. This review provides a comprehensive synthesis of recent advances regarding the role of Piezo1 in OA, focusing on the mechanistic links between mechanotransduction, mitochondrial dysfunction, mitophagy, and immunometabolic dysregulation. We further discuss the contribution of mitochondrial quality-control pathways, including PINK1/Parkin-, BNIP3-, and FUNDC1-mediated mitophagy, as well as alterations in mitochondrial dynamics involving DRP1, MFN1, MFN2, and OPA1. Emerging experimental models are discussed as valuable tools for accelerating therapeutic discovery. Finally, we critically evaluate current therapeutic strategies targeting the Piezo1–mitochondria axis, including mechanosensitive channel modulation, mitochondrial protection, mitophagy enhancement, gene therapy, biomaterial-assisted delivery, and nanomedicine. Collectively, current evidence supports the Piezo1–mitochondria–immune axis as an important mechanistic framework contributing to OA pathogenesis and as a potential therapeutic target. Integrating mechanobiology, mitochondrial medicine, and precision-engineered experimental models may facilitate the development of next-generation disease-modifying therapies capable of slowing or preventing osteoarthritis progression. Full article