Search Results (1,179)

Objectives: This study aimed to identify ferro-aging-related hub genes in chronic kidney disease (CKD) and elucidate their potential roles in proximal tubular (PT) cells. Methods: Differential expression analysis was performed using GSE104954, and the differentially expressed genes were intersected with a set of ferro-aging-related genes. Feature selection was conducted using the least absolute shrinkage and selection operator (LASSO), support vector machine–recursive feature elimination (SVM-RFE), and random-forest algorithms. The findings were externally validated in GSE180394. Single-cell transcriptomic data from GSE183276 were then used to define the cellular localization and expression profile of the hub genes, and their regulatory networks were investigated using scTenifoldKnk-based in silico knockout and gene set enrichment analysis (GSEA). Results: Fourteen candidate genes were identified, of which IRF7 and SOCS2 were consistently selected by all three machine-learning algorithms. SOCS2 was significantly downregulated in both the discovery and validation cohorts and showed strong tissue-level discriminatory performance in the discovery cohort, with more modest performance in the external cohort. Single-cell analysis showed that SOCS2 downregulation occurred predominantly in PT cells; CKD PT cells also exhibited increased ACSL4 expression and the enrichment of the ferroptosis pathway. In silico SOCS2 knockout further identified 77 significantly perturbed genes, primarily associated with mitochondrial oxidative phosphorylation, oxidative stress, and metabolic homeostasis. Conclusions: Collectively, these findings identify SOCS2 as a candidate gene associated with a ferro-aging-related transcriptomic signature in CKD PT cells. The observed changes in ACSL4, ferroptosis-related pathways, mitochondrial oxidative phosphorylation, and oxidative stress networks are compatible with, but do not establish, a ferro-aging phenotype. Further functional validation is required to determine whether SOCS2 contributes causally to iron–lipid dysregulation and tubular injury in CKD. Full article

The widespread consumption of ultra-processed foods increases exposure to advanced glycation end-products (AGEs), key mediators of oxidative stress and chronic low-grade inflammation. Although AGEs contribute to adult metabolic dysfunction, their early molecular correlates in pediatric populations remain insufficiently defined. Extracellular vesicle (EV)-associated miRNAs represent stable, non-invasive indicators of systemic stress responses. This study evaluated the association between urinary AGEs and urinary EV-associated miRNAs in 94 Italian children and adolescents from the I.Family cohort. Fluorescent AGEs were quantified via spectrofluorimetry, and EV-enriched urinary miRNAs were profiled using next-generation sequencing. Differential expression and multivariable generalised linear models (adjusted for age, sex, BMI z-score, and hs-CRP) were performed. Differential expression analysis revealed a significant upregulation of hsa-miR-4516 in participants with high versus low urinary AGE levels (fold change = 2.31; FDR = 0.024). In multivariable continuous models, hsa-miR-4516 remained the primary AGE-associated miRNA, though the association attenuated following adjustment for BMI z-score and hs-CRP. Functional enrichment and network analyses highlighted pathways governing oxidative stress responses, proteostasis, and cellular survival. Overall, urinary EV-associated miRNAs may reflect coordinated biological responses to dietary AGE burden rather than serving as direct exposure biomarkers, offering integrated, non-invasive insights into early metabolic and inflammatory adaptations in children. Full article

Background: Diabetic cardiomyopathy (DCM) is a serious cardiovascular complication specific to diabetes mellitus, with rising global prevalence. Ferroptosis, an iron-dependent form of regulated cell death driven by lethal lipid peroxidation, has been implicated in the pathogenesis of DCM. However, the key regulatory genes remain poorly characterized. This study aimed to identify and validate ferroptosis-related signature genes in DCM. Methods: Three murine transcriptomic datasets (GSE123975, GSE155377, and GSE210611) were retrieved from GEO and merged after batch correction. Differentially expressed genes were intersected with weighted gene co-expression network analysis disease-associated module genes and FerrDb ferroptosis annotations to define the ferroptosis-related differentially expressed gene candidate pool. LASSO regression and random forest selection then prioritized hub genes, defined operationally as candidates consistently prioritized by both machine-learning algorithms rather than by network-topological centrality. Classification performance was evaluated by ROC analysis and validated in two independent cohorts (GSE161931 and GSE274500). mMCPcounter estimated immune and stromal infiltration. ScRNA-seq (GSE290095) and spatial transcriptomic (GSE290094) profiling characterized cellular distribution, predicted cardiomyocyte network perturbations and tissue-level expression patterns. High-fat diet/streptozotocin (HFD/STZ)-induced DCM rat models provided experimental validation. Results: Acot1 and Txnip were identified as hub genes, with strong discriminatory performance in the discovery cohort (AUC = 1.000 and 0.988; in-sample estimates, n = 26) and independent external validation (AUC = 0.951 and 0.988). Immune profiling linked both genes inversely with vessel scores, and Txnip was also linked with eosinophils. Single-cell analysis localized Acot1 enrichment to cardiomyocytes and endothelial cells, while Txnip was broadly expressed across multiple cell types, with elevated levels in DCM. In silico knockout analysis predicted distinct cardiomyocyte network perturbation profiles for Acot1 and Txnip, and spatial transcriptomics revealed modest but disease-specific spatial associations between hub gene expression and ferroptosis driver scores (Acot1: rho = 0.123; Txnip: rho = 0.154). Both genes were significantly upregulated at mRNA and protein levels in HFD/STZ-induced DCM rats, with concurrent GPX4 depletion, ACSL4 accumulation, and FTH1 reduction consistent with ferroptosis activation. Conclusions: This study identifies Acot1 and Txnip as ferroptosis-related molecular signatures in DCM and provides multistep prioritization and validation spanning bulk transcriptomics, single-cell and spatial transcriptomics, and in vivo experimental verification, offering potential targets for ferroptosis-targeted therapeutic intervention. Full article

Background: Diabetic wounds are characterized by chronic inflammation, oxidative stress, impaired angiogenesis, and delayed tissue repair. Ferroptosis has emerged as a potential contributor to diabetic wound pathology; however, its relationship with impaired tissue regeneration remains incompletely understood. Objectives: We investigated cellular and transcriptional responses associated with cerium oxide nanoparticle-conjugated microRNA-146a (CNP-miR146a) treatment and whether wound repair is associated with ferroptosis-protective programs and immune–vascular communication. Methods: Diabetic excisional wounds were treated with CNP-miR146a or phosphate-buffered saline controls. Single-cell RNA sequencing was performed on wound tissues, with primary analyses focused on postoperative Day 7. Cellular composition, ferroptosis-associated programs, pseudotime trajectories, and inferred ligand–receptor communication networks were analyzed. Results: CNP-miR146a treatment was associated with transcriptional remodeling of the diabetic wound microenvironment, with myeloid cells exhibiting a prominent response. Treatment was associated with higher NRF2-related antioxidant, ferroptosis-protective, and iron-homeostasis transcriptional programs and with a repair-associated myeloid state. Pseudotime analysis identified a trajectory from monocytes toward pro-regenerative macrophages accompanied by dynamic expression of antioxidant, iron-homeostasis, and repair-associated genes. CellChat predicted increased immune–vascular communication through angiogenic and extracellular matrix-associated pathways. Endothelial cells exhibited increased NRF2-associated transcriptional programs, angiogenesis-associated gene expression, and endothelial repair markers. Conclusions: CNP-miR146a-mediated wound repair is associated with coordinated ferroptosis-protective and NRF2-related transcriptional programs, pro-regenerative myeloid states, endothelial angiogenesis-associated programs, and predicted immune–vascular communication. These findings identify ferroptosis-associated and immune–vascular transcriptional networks as candidate mechanisms of CNP-miR146a-mediated diabetic wound repair requiring further functional validation. Full article

Objectives: Nasopharyngeal carcinoma (NPC) arises in an immune-suppressive milieu that frequently undermines treatment efficacy. TPPP3 has been implicated as a negative regulator of NPC aggressiveness, yet its relevance to immune modulation or chaperone networks remains poorly defined. We therefore sought to determine how TPPP3 shapes the NPC immune landscape and to identify its interacting protein partners. Methods: Public single-cell RNA-sequencing datasets from head and neck squamous cell carcinoma and nasopharyngeal carcinoma were analyzed using R. HK-1 and C666-1 cells stably overexpressing TPPP3 were established. These cells were used to construct humanized xenograft tumor models, with intratumoral immune cell infiltration evaluated by immunohistochemistry. In vitro, the same cells and their controls were indirectly co-cultured with peripheral blood mononuclear cells. Cellular lysates from TPPP3-overexpressing cells were subjected to immunoprecipitation–mass spectrometry and immunofluorescence staining, which identified HSPA8 as a TPPP3-interacting protein. Three groups—control, TPPP3-overexpressing, and TPPP3-overexpressing plus the HSPA8 inhibitor VER155008—were then compared in wound healing, colony formation, cell-cycle, and xenograft assays, with immunohistochemical staining for Ki67, TPPP3, and CD3 performed on tumor sections. Results: TPPP3 transcripts were barely detectable across most tumor cell subsets but showed preferential enrichment in NPC epithelial clusters. Enforced TPPP3 expression curtailed xenograft outgrowth while increasing intratumoral abundance of CD3⁺ T cells, CD8⁺ T cells, and CD11c⁺ dendritic cells. Pharmacological blockade of HSPA8 with VER155008 further enhanced TPPP3-driven suppression of migration, clonogenicity, and tumor expansion, and also altered cell-cycle progression while boosting CD3⁺ T-cell accumulation within grafts. Conclusions: These findings suggest a functional association between TPPP3 and HSPA8 that may contribute to tumor growth suppression and immune microenvironment remodeling in NPC. Pharmacological disruption of HSPA8-dependent proteostasis enhanced TPPP3-associated antitumor activity in both in vitro and in vivo models, indicating that this chaperone pathway represents a candidate mechanism worthy of further mechanistic investigation and therapeutic exploration. Full article

Background: Dystonia is a severe neurological disorder with enigmatic pathogenesis. Current treatment options are limited in preventing the disease progression, underscoring the urgent need for new targeted therapeutic agents to develop more effective therapies. Methods: We performed a proteome-wide Mendelian randomization (MR) study and sensitivity analyses to evaluate the causal relationships between dystonia and proteins. GO and KEGG enrichment analysis of dystonia-associated proteins was conducted. Then, we built PPI network and identified the expression of hub-genes in specific brain neurons in single-cell sequencing data. Additionally, we performed drug enrichment analysis of hub-genes, and employed network pharmacology and molecular docking methods to identify potential drugs for dystonia. Results: Our study identified genetically predicted associations consistent with a potential causal effect between 51 proteins and risk of dystonia. GO and KEGG enrichment analyses revealed that these proteins are involved cellular response to transforming growth factor-β stimulation and cytokine-cytokine receptor interaction. Notably, the PPI network exhibited 21 community relationships within the regulatory network among the 51 dystonia-associated proteins identified. The single-cell RNA annotations for brain cluster specificity revealed Tumor necrosis factor (TNF) was highly expressed in microglia cells. Drug enrichment analysis identified five traditional Chinese medicine monomers (paeoniflorin, artesunate, ginsenoside Rh1, psoralen, and quercetin dihydrate) as candidates for molecular docking analysis. Among these, paeoniflorin-TNF, quercetin dihydrate-TNF, and artesunate-TNF exhibited the highest binding energy (−9.1 kcal/mol). Conclusions: Our molecular-docking analysis suggested that traditional Chinese medicine monomers including paeoniflorin, quercetin dihydrate, and artesunate may serve as promising candidates for future drug development. Full article

Background/Objectives: Osteosarcoma (OS) is an aggressive bone malignancy with a complex tumor microenvironment (TME) that influences therapeutic outcomes and resistance. How neoadjuvant chemotherapy (NACT) reshapes the OS TME at single-cell resolution remains largely undefined. This study aimed to characterize cellular heterogeneity in the OS TME after NACT and identify chemokine-mediated intercellular crosstalk driving chemoresistance. Methods: Single-cell RNA sequencing was performed on surgical specimens from 12 OS patients (6 treatment-naive and 6 post-NACT). After quality control, 77,616 cells (36,214 from naive patients, 41,402 from post-NACT samples) were analyzed through the Seurat pipeline. Unsupervised clustering, differential expression analysis, and cell–cell communication network construction were performed, and candidate signaling axes were validated using transwell assays and Western blotting. Results: Cells were classified into 10 major cell types. Osteoblasts, identified as malignant cells, were partitioned into 11 subpopulations with marked transcriptional heterogeneity and differential PI3K/Akt pathway activity. Post-NACT, stromal and vascular components underwent molecular and functional remodeling, shaping an immune-activated microenvironment. Mononuclear phagocytes resolved into three discrete clusters—monocytes, macrophages, and dendritic cells—with differentiation gradients. Endothelial cells maintained robust CXCL2 expression throughout the therapeutic course. Functional validation via transwell assays and Western blotting confirmed that endothelial-derived CXCL2 promoted macrophage chemotaxis via CXCR2, with corresponding CXCR2 upregulation in macrophages. Conclusions: Collectively, these findings suggest the complex cellular and transcriptional heterogeneity of the OS microenvironment and its chemokine-driven molecular remodeling after NACT, indicating that TME dynamics may be a determinant of therapeutic response and chemoresistance. Full article

RNA-omics technologies have expanded poultry transcriptome research beyond tissue-level gene abundance. They now resolve intact transcripts, RNA chemical modifications, cellular origins, and spatial locations. This review centers on a core question: what specific, previously inaccessible RNA information does each RNA-omics technology provide? Based on their primary measurement targets, we categorize these technologies into four groups: bulk transcriptome and small RNA sequencing for analyzing gene expression and regulatory RNA networks; long-read and direct RNA sequencing for resolving transcript isoforms; epitranscriptomic methods for detecting RNA modifications; and single-cell and spatial transcriptomics for identifying the cellular origins and spatial distributions of signals. Methods for resolving RNA structure, RNA–protein interactions, and translation status (e.g., structure probing, CLIP-type mapping, and ribosome profiling) remain in their infancy in poultry, leaving translation and RNA–protein regulation largely unmeasured in tissues such as the oviduct, the lipogenic liver and nucleated erythrocytes. For each category, we discuss its direct measurement targets and primary outputs, the additional information it provides compared to established methods, representative applications in poultry, and its inherent limitations. Building on this framework, we discuss how to select and combine technologies based on specific research questions and summarize their applications in studies of production performance and product quality, reproduction, and health and resilience. Different technologies measure distinct types of RNA features and are not simply interchangeable. Future research must place greater emphasis on matching technologies to scientific questions, integrating complementary data, and improving three foundations: the annotation of poultry transcripts and non-coding RNAs, standardized analytical pipelines, and functional validation systems. Full article

Background/Objectives: The recent advances in pulmonary delivery have shifted the paradigm to the development of inhalable drug-loaded polysaccharide particles that can be positioned at the respiratory interface while reducing the systemic exposure. Quercetin has broad anticancer activity but remains difficult to translate because of its poor aqueous solubility, limited bioavailability and rapid metabolic loss. Here, we report quercetin-loaded chitosan/Salvia hispanica polysaccharide nanoparticles as a natural polyelectrolyte nanocarrier for pulmonary delivery in lung cancer. Methods: Central composite design (CCD) and artificial neural network (ANN) models were used for mapping the factors to responses. Results: The models displayed a higher predictive accuracy and optimization reliability for identifying the optimized formulation. The optimized nanoparticles showed a quasi-spherical morphology (mean hydrodynamic diameter = 331 ± 14.34 nm) with cationic ζ-potential of +36.3 ± 2.56 mV and polydispersity index of 0.15. The optimized formulation showed acceptable powder-flow characteristics, an encapsulation efficiency of 73.8 ± 0.73%, drug loading of 14.20 ± 0.22%, and biphasic release with sustained quercetin release over 48 h. In A549 and H460 cell lines, nanoencapsulation increased the antiproliferative effect of quercetin relative to the free compound, yielding lower IC₅₀ values after 48 h of exposure. The nanoparticles showed greater suppression of wound closure, increased reactive oxygen species fluorescence and clear cellular uptake. Blank nanoparticles produced only limited effects. Conclusions: These results indicate that CCD/ANN-guided chitosan/Salvia hispanica polysaccharide nanoparticles provide a promising nanodelivery tool for quercetin delivery and enhanced in vitro activity in lung cancer cells, while the observed aerosol performance advocates further investigation of their pulmonary delivery potential. Full article

Background: Chronic obstructive pulmonary disease (COPD) is associated with systemic inflammation and increased cardiovascular comorbidity, yet peripheral blood molecular markers for cardiovascular comorbidity-related stratification in COPD remain poorly defined. Methods: In this study, PBMC transcriptomic datasets from a COPD cohort (GSE42057) and a CAD cohort (GSE113079) were analyzed using weighted gene co-expression network analysis (WGCNA) to identify disease-associated modules, followed by overlapping gene screening. Machine-learning models were then applied to prioritize the shared genes. External validation was performed in an independent COPD cohort (GSE54837) and an independent CAD cohort (GSE250283). Immune-cell deconvolution and single-cell transcriptomic analysis of a CAD dataset (GSE269269) were further used to characterize the immune and cellular context of the leading candidate. Finally, RT–qPCR was performed in an institutional PBMC cohort for experimental validation. Results: A total of 169 shared genes were identified, with enrichment in immune, mitochondrial, oxidative phosphorylation, and metabolic pathways. RTN4 was the most consistently validated candidate across COPD and CAD cohorts and was associated with poorer lung function, advanced GOLD stages, and monocyte-related immune patterns. In CAD single-cell data, RTN4-associated signals were mainly localized to monocytes, particularly intermediate monocytes under plaque rupture conditions, with enrichment of immune, antigen-presentation, oxidative-stress, and metabolic pathways. RT–qPCR confirmed increased RTN4 mRNA expression in COPD and a further increase in patients with COPD and comorbid CAD despite comparable FEV1% predicted between the two COPD groups. Conclusions: These findings suggest that elevated RTN4 expression may serve as a PBMC-derived, monocyte-associated candidate molecular feature related to COPD–CAD comorbidity. Full article

Chronological skin aging is a complex biological process characterized by progressive collagen degradation and cellular senescence. Among the molecular regulators implicated in these hallmarks, miR-34a has emerged as a critical mediator linking inflammation and senescence pathways. Consequently, this study aimed to investigate the anti-aging potential of Helix aspersa snail mucus, with particular emphasis on its modulation of miR-34a-associated molecular mechanisms, and to explore liposomal encapsulation as a strategy to improve its topical performance and user acceptability. Snail mucus was collected and characterized using LC–ESI–QTOF–MS/MS, while its antioxidant activity was assessed by DPPH and FRAP assays. Afterward, mucus-loaded liposomes were developed and optimized. Aged mice were assigned to control aged, Lipo, free mucus, and Lipo-mucus groups, alongside a young control group. Anti-aging efficacy was evaluated through wrinkle grading, skin moisture determination, histological examination, and collagen assessment by Masson’s trichome staining. miR-34a-5p, its target genes, and related aging-associated genes were also determined, followed by upstream regulatory network prediction using X2Kweb. The optimized formulation exhibited nanoscale particle size, high encapsulation efficiency, enhanced skin retention, and improved spreadability. Compared with free mucus, Lipo-mucus significantly increased the epidermal and dermal deposition of total protein and allantoin. Both treatments exerted remarkable anti-aging effects, evidenced by improved skin architecture and enhanced collagen deposition. These effects were associated with modulation of the miR-34a-5p-driven senescence hub. Collectively, liposomal encapsulation enhanced the cutaneous delivery, cosmetic properties, and anti-aging efficacy of H. aspersa mucus, supporting its potential as a mechanism-based cosmeceutical intervention for chronological skin aging. Full article

The neurovascular unit (NVU) is composed of a diverse array of cells and an extracellular matrix (ECM). Neural cells and blood vessels are intricately interconnected, forming a cohesive whole. Specific cellular components and structures within the NVU play an indispensable role in maintaining homeostasis of the central nervous system (CNS). With the advancement and maturation of cell co-culture technology, various three-dimensional (3D) NVU models continue to emerge, offering a more objective and comprehensive perspective for in vitro studies of CNS diseases. Specifically, these 3D NVU models include Transwell Chamber models, gel-polydimethylsiloxane (PDMS)-based 3D models, self-assembled NVU models and microfluidic NVU models, which reconstruct the complex NVU architecture to varying degrees. This review systematically summarizes multiple 3D construction strategies for in vitro NVU to overcome the limitations of conventional cellular tests or animal experiments, highlights the critical roles of biomimetic gel in recapitulating native cell-gel crosstalk, comparatively analyzes four major 3D NVU technical routes in terms of cellular composition, vascular morphology, barrier performance, and reproducibility, categorizes application scenarios of 3D NVU platforms oriented to practical research demands, including oxygen-glucose deprivation/reoxygenation (OGD/R) injury modeling, blood-brain barrier (BBB) permeability assay, CNS drug penetration screening, neuroinflammation and neurotoxicity evaluation, proposes practical principles for model selection under different experimental purposes, and concludes with current bottlenecks, including imperfect vascular network maturation and lack of unified evaluation criteria, together with future perspectives for standardized 3D NVU in vitro. By comparing the advantages and limitations of these approaches, we aim to clarify their optimal applicability for investigating specific pathological mechanisms and screening potential therapeutics. Full article

The electrical response of conductive textile structures to liquid exposure was investigated as a basis for electrical resistance-based haemorrhage detection. The sensing principle relies on changes in the electrical resistance of the conductive network following liquid exposure, with the resulting resistance variation used as the sensing parameter. Nine conductive textile variants were developed and evaluated, comprising three knitted structures (K1–K3) and six woven structures produced in raw and finished states (W1–W3). The structures incorporated silver-coated polyamide and stainless-steel conductive yarns and were exposed to water, acidic perspiration (pH 5.5), alkaline perspiration (pH 8.0), and saline solution. Saline solution was used as a controlled conductive aqueous medium for comparison and does not reproduce the physical, chemical, rheological, cellular, or biochemical properties of whole blood. Electrical resistance measurements, together with physical and mechanical characterization, scanning electron microscopy (SEM), and Fourier-transform infrared spectroscopy (FTIR), were performed to assess structural stability and electrical response. Saline solution produced the largest resistance variations among the tested liquids, whereas water and perspiration resulted in lower responses. Localized mechanical deformation further induced pronounced resistance changes in several woven structures. Among the evaluated variants, W2 exhibited the most favorable combination of structural stability and electrical responsiveness. These results support further investigation of W2 (conductive yarn: Filix DA5393 yarn) as an electrical resistance-based sensing structure for potential haemorrhage-related liquid detection applications. Full article

Network densification will play a vital role in next-generation cellular networks, as it addresses coverage and capacity issues in the radio access domain. However, new cell deployments can negatively impact neighbor cells, requiring careful planning. Unfortunately, the complexity of advanced radio resource management schemes implemented in Beyond 5G and future 6G networks makes it challenging to predict the impact of radio deployments in the existing cells accurately. This work presents GRIMCELL, a novel data-driven method to estimate the impact of radio deployments (i.e., new carriers, sectors, or sites) on cell performance. For this purpose, GRIMCELL combines radio planning, configuration management and performance management data gathered in commercial vendor equipment. The core of GRIMCELL is a proven message passing graph neural network (XENet) to forecast the performance of both new and existing cells after the deployment. Assessment over data from a commercial LTE-A Pro network has shown that GRIMCELL provides high accuracy and flexibility across diverse deployment scenarios. Full article

Eggshell quality profoundly affects egg commercial value, storage performance and food safety, and its late-period deterioration restricts the sustainable production of long-cycle laying hens. With the poultry industry extending the laying cycle to 100 weeks for the “500 eggs within 700 days” production target, hens suffer severe shell quality degradation after 60 weeks of age, with the eggshell breakage rate rising from 1–2% to 5–8% and resulting in considerable economic losses. Eggshell strength is a moderately heritable polygenic trait determined by delicate biomineralization and ultrastructural organization. Specific functional genes dominate shell mineralization by regulating uterine calcium homeostasis, crystal nucleation and structural assembly. Notably, prominent genotype–age interactions reduce heritability in aged hens, and most identified genetic loci fail to maintain stable late-phase shell quality. Uterine epithelial aging triggers ultrastructural abnormalities, including thickened mammillary layers, reduced palisade layers and disordered pores, impairing shell mechanical resistance and gas exchange. Single-cell multi-omics technologies enable high-resolution profiling of uterine cellular heterogeneity and mineralization-related signaling networks, providing novel approaches to decipher the molecular mechanisms of shell quality decline. This review summarizes eggshell biomineralization, genetic regulation, age-dependent quality deterioration and advanced omics applications, aiming to offer theoretical references for improving late-stage eggshell quality and breeding elite laying hen strains. Full article