Extracellular vesicle (EV) transcriptomes are widely used to build competing endogenous RNA (ceRNA) networks. In these networks one RNA is thought to relieve another from microRNA repression by competing for the same microRNAs. They rest on one observation that transcript pairs sharing more microRNA families are more strongly coexpressed, read as competition. Kinetic theory predicts the same pattern but also shows that a shared microRNA pool correlates two transcripts without any competition. Which of the two drives the pattern had not been measured in EV cargo. Methods adjusting ceRNA inference for confounders exist, although none of the ninety one indexed EV or exosomal ceRNA network studies reports a permutation or null model test of its edges. This study therefore measured how much of the shared family gradient is binding degree and how much survives strict matching, which has not previously been done in EV cargo. We used exoRBase profiles of 2,125 blood EV and 125 urine EV samples plus an independent neurodegenerative plasma EV cohort. Pairs sharing at least K microRNA families were compared against control pairs matched for expression level and binding degree. Coexpression rose with K, but most of that rise disappeared once each pair was compared against control pairs binding a similar total number of microRNAs. This removed about 70
Telomerase reverse transcriptase (TERT) is a key regulator of telomere maintenance and tumor progression; however, its downstream mechanisms in renal cell carcinoma (RCC) remain incompletely defined. TERT expression in RCC tissues was analyzed and correlated with clinicopathological features and patient prognosis. Gain- and loss-of-function assays were performed to assess its roles in tumor cell proliferation, migration, apoptosis, and lipid metabolism. Immunoprecipitation–mass spectrometry identified enhancer of rudimentary homolog (ERH) as a candidate downstream effector. Protein interaction, truncation, and ubiquitination assays were conducted to delineate the underlying mechanism. Xenograft models were used for in vivo validation. TERT was markedly upregulated in RCC and associated with advanced stage and unfavorable prognosis. Functional analyses showed that TERT promoted tumor cell proliferation, migration, and lipid accumulation. Mechanistically, TERT directly interacted with ERH through its 457–596 aa region and enhanced ERH protein stability by suppressing RNF4-mediated ubiquitination. Mutation of the K84 ubiquitination site on ERH abolished its degradation and rescued the inhibitory effects of TERT depletion on lipid metabolism and cell proliferation. Consistently, ERH knockdown attenuated TERT-driven tumor growth and lipid metabolic reprogramming in vivo. This study identifies a TERT–ERH–RNF4 regulatory axis in RCC, in which TERT stabilizes ERH via ubiquitination-dependent mechanisms to drive lipid metabolism reprogramming and tumor progression. Targeting this pathway may provide a potential therapeutic strategy for RCC.
Sepsis-associated endothelial injury is a central event driving microcirculatory dysfunction and multiple organ failure; however, effective targeted therapies are lacking. The role of cuproptosis, a recently identified form of programmed cell death, in sepsis-induced endothelial dysfunction has not yet been clearly defined, and this limits the advancement of associated therapeutic approaches. In vitro, human umbilical vein endothelial cells (HUVECs) were exposed to lipopolysaccharide (LPS) to induce endothelial cell injury. The cells were then treated with estradiol (E2) to investigate the protective effects of E2 on cuproptosis-associated alterations in LPS-treated HUVECs. In vivo, endotoxemic mice were treated with E2, and the effects on cytokine levels, survival rate, organ injury, and cuproptosis-related markers were evaluated. The regulatory relationship between SP1 and ATP7B was examined using bioinformatic prediction, loss- and gain-of-function experiments, dual-luciferase reporter assays, and ChIP-PCR. LPS induced endothelial cell injury accompanied by cuproptosis-associated alterations, as evidenced by downregulation of ATP7B, FDX1, LIAS, and PDHB expression and upregulation of HSP70 expression. These changes were accompanied by mitochondrial depolarization, intracellular accumulation of copper, and depletion of glutathione (GSH) and ATP. Copper loading and chelation experiments further supported the involvement of a copper-dependent process. Treatment with E2 partially reversed these alterations and restored ATP7B expression. Predictive bioinformatics and molecular assays demonstrated that SP1 binds to the ATP7B promoter and negatively regulates transcription of the ATP7B gene. E2 inhibited LPS-induced SP1 upregulation, and SP1 knockdown increased ATP7B levels and alleviated endothelial injury and cuproptosis-associated alterations, whereas SP1 overexpression substantially reversed the protective effects of E2. In vivo experiments revealed that E2 treatment of endotoxemic mice significantly improved survival, attenuated multiple organ injury, and ameliorated altered copper homeostasis and cuproptosis-associated molecular changes. Early E2 post-treatment also reversed SP1/ATP7B alterations and reduced elevated copper levels. These findings support the involvement of a copper-dependent, cuproptosis-associated process in endothelial damage induced by LPS and suggest that E2 exerts protective effects on the endothelium at least in part through regulation of the SP1/ATP7B axis and copper homeostasis. The SP1/ATP7B pathway may therefore represent a potential molecular target for further investigation in sepsis-associated endothelial dysfunction.
Phage therapy is a promising alternative strategy for treating infections caused by multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa), which urgently requires alternative therapies especially due to its ability to form persistent biofilms. In this study, a novel temperate phage, named vB_PaeS_GZMU_S12, was isolated and comprehensively characterized. Despite its temperate genomic features, it exhibited broad-spectrum lytic activity and effective antibiofilm effects. The phage demonstrated lytic activity against 30 out of 72 tested P. aeruginosa strains, resulting in a lytic rate of 41.7
Ischemic stroke triggers complex multicellular responses across neurons, glia, and the neurovascular unit, but the temporal coordination among these cell types remains incompletely understood. In this study, we integrated five publicly available mouse single-cell RNA sequencing datasets spanning the acute, subacute, and recovery phases after middle cerebral artery occlusion (MCAO), together with complementary rat single-nucleus RNA-seq data, to establish a time-resolved transcriptomic framework of post-ischemic brain repair. Integrative single-cell analysis identified candidate multicellular communication patterns linking microglia, astrocytes, oligodendrocyte lineage cells, endothelial cells, and neurons during post-ischemic remodeling. Microglia exhibited an early transition from inflammatory activation toward lipid metabolic and neuroprotective programs. Astrocytes shifted from injury-associated reactive states to reparative phenotypes and emerged as central coordinators of intercellular communication. Oligodendrocyte progenitor cells activated maturation programs associated with remyelination, while the neurovascular unit underwent coordinated remodeling characterized by dynamic signaling interactions among astrocytes, microglia, endothelial cells, and neurons. Selected glial and neurovascular signaling patterns were also detectable in the complementary rat snRNA-seq data. Our analysis suggests that post-ischemic brain repair involves time-associated multicellular programs integrating inflammation resolution, astrocyte-mediated repair, oligodendrocyte maturation, and neurovascular remodeling. These findings provide a hypothesis-generating transcriptomic framework for understanding stage-associated brain repair after ischemic stroke and may inform the development of time-aware therapeutic strategies targeting cell-state transitions and intercellular communication.
Elevated plasma phenylalanine (PHE) is associated with adverse outcomes in heart failure (HF), but whether PHE is only a marker of systemic severity or can modify ischemic vulnerability remains unclear. We evaluated the prognostic value of the PHE–phenylpyruvate (PPA) axis and examined how PHE affects mitochondrial stress responses after ischemic injury and whether 5-methoxytryptophan (5-MTP) mitigates these effects. Plasma levels of PHE and PPA were analyzed in 191 patients with ischemic HF from the cardiac intensive care unit to assess 90-day mortality. A rat myocardial infarction (MI) model was used to assess PHE-related metabolites in infarct and peri-infarct-enriched left ventricular tissue during chronic post-MI remodeling. HL-1 cardiomyocytes were subjected to oxygen–serum–glucose deprivation (OSGD) with or without PHE and 5-MTP. Cell metabolic activity, ATP levels, mitochondrial respiration, extracellular acidification rate-defined glycolytic function, pyruvate supplementation, dichloroacetate response, cell-death patterns, intracellular PHE-related metabolites, and quantitative proteomics were analyzed. In the clinical cohort, elevated PHE was independently associated with 90-day mortality after adjustment for estimated glomerular filtration rate, C-reactive protein, and albumin, supporting PHE as a short-term prognostic and candidate risk-stratification biomarker. Post-MI myocardium showed tissue-level accumulation of PHE-related metabolites. In HL-1 cells, 20 mM PHE exacerbated OSGD-induced mitochondrial dysfunction, ATP reduction, glycolytic reserve exhaustion, and mixed cell-death signaling. Pyruvate failed to rescue ATP, while dichloroacetate partially restored ATP, suggesting pyruvate dehydrogenase-sensitive vulnerability. Proteomics revealed pathway-level suppression of oxidative phosphorylation; 5-MTP partially shifted mitochondrial and metabolic signatures toward recovery without uniformly lowering intracellular PHE. PHE is a short-term prognostic marker and, under high-dose experimental stress, a potential modifier of ischemic bioenergetic vulnerability. 5-MTP appears to act mainly through downstream mitochondrial stress resilience. These findings support PHE-related metabolic stress as a clinically relevant risk signal and experimental modifier of ischemic myocardial vulnerability, while further validation is required before PHE-guided therapeutic strategies can be proposed. Not applicable.
Cellular senescence and chronic inflammation are core drivers of heart disease, but whether these two processes act synergistically or exhibit a decoupled pattern across different diseases and cell types remains unclear. Here, we integrated three independent human heart snRNA‑seq datasets from patients with acute myocardial infarction (MI), dilated cardiomyopathy (DCM), and heart failure (HF). Cellular senescence was quantified using the human universal senescence index (hUSI) and the SenMayo gene set (SAUL_SEN_MAYO; MSigDB). Inflammation was assessed using both a curated 23‑gene core signaling signature and unbiased Hallmark pathway analyses; the latter revealed consistent activation of inflammation‑associated pathways (e.g., TNF‑α/NF‑κB) across all three diseases. Compared with controls, the senescence score was significantly decreased in all three diseases, whereas the inflammation score was increased, revealing a consistent decoupled pattern (inflammation elevation with senescence reduction) across heart diseases. To quantify this deviation, the Inflammation‑Senescence Deviation Index (ISDI) was defined as the inflammation Z‑score minus the senescence Z‑score, with positive values indicating relative predominance of inflammation over senescence. Endothelial cells were identified as the only major cell type showing a robust and consistent shift toward inflammation dominance in all three datasets. Mechanistically, the TNF‑alpha signaling via NF‑κB pathway was activated while the p53 pathway was suppressed in disease endothelial cells. A 10‑gene down‑regulated signature derived from DCM endothelial cells showed consistent down‑regulation across the three snRNA‑seq datasets. In a clinical association analysis of LVAD therapy for end‑stage heart failure, NF‑κB pathway activity significantly distinguished non‑responders from responders, whereas senescence scores showed no difference and the inflammation score showed only a non‑significant trend. This signature was validated in six independent external cohorts, and the decoupled pattern itself was confirmed in an independent pediatric DCM snRNA‑seq dataset. These findings challenge the traditional synergistic model of senescence and inflammation in heart disease and highlight inflammation dominance as a conserved feature. The specific association of NF‑κB pathway activity with clinical outcome suggests that targeting inflammatory pathways (e.g., NF‑κB signaling) may have higher therapeutic priority than modulating senescence programs. Integration of three human heart snRNA‑seq datasets (MI, DCM, HF) reveals a decoupled pattern: inflammation increases while senescence decreases across diseases. Endothelial cells are the most consistently affected cell type in all three datasets. In endothelial cells, p53 pathway suppression is consistently observed across all three diseases, while NF‑κB pathway activation is present in DCM and HF but shows heterogeneous regulation in MI. NF‑κB pathway activity, but not senescence, distinguishes LVAD responders from non‑responders, and the decoupled pattern is validated in external cohorts.
Heart failure (HF) is clinically associated with aggravated breast cancer (BC) progression; however, the integrative genomic mechanisms underlying this cardio-oncological crosstalk remain poorly understood. We conducted integrative bioinformatics analyses combining weighted gene co-expression network analysis (WGCNA) and machine learning algorithms to screen key hub genes involved in HF and BC progression. The candidate gene Col10a1 was further validated using myocardial infarction (MI)-induced HF xenograft mouse models, paired clinical plasma and tumor specimens, and comprehensive in vitro functional assays. COL10A1 expression was higher in breast cancer patients with CVD than in BC-only patients. Given the limited sample size, these findings were considered exploratory. Mechanistically, elevated Col10a1 was associated with activation of the transforming growth factor‑β (Tgf-β)/Smad signaling pathway and induction of epithelial–mesenchymal transition (EMT). In vivo, the HF microenvironment markedly accelerated BC tumor growth and was accompanied by enhanced Col10a1 expression and Tgf-β signaling activation. In vitro, cardiomyocyte-derived Col10a1 significantly promoted the proliferation, migration, and invasion of BC cells, whereas Col10a1 knockdown significantly attenuated these malignant phenotypes. Our study identifies a potential regulatory link between HF and BC and provides preliminary mechanistic insights into the role of Col10a1 in BC progression under cardiac injury conditions. Col10a1 may serve as a candidate mediator in the interaction between cardiac injury and BC progression.
This review delineates age-related changes in articular hyaline cartilage and chondrocyte senescence, distinguishing physiological aging processes from osteoarthritis (OA) pathogenesis — a distinction frequently conflated in the scientific literature. Aging cartilage exhibits impaired homeostasis and progressive macroscopic alterations — including thinning and ectopic calcification — as well as molecular hallmarks such as glycosaminoglycan (GAG) depletion, advanced glycation end-product (AGE) accumulation, and inflammaging. These alterations predispose joints to degeneration and elevate OA risk, yet do not inevitably precipitate disease. Chondrocyte senescence is further examined in tissue aging, OA pathology, and two-dimensional culture models, emphasizing tissue-specific triggers, including mechanical overload (e.g., Piezo1-mediated), oxidative stress, mitochondrial dysfunction (impaired mitophagy and ROS surge), and replicative exhaustion (including passaging). Emerging evidence establishes chondrocyte senescence as a modifiable driver of joint degeneration, thereby supporting the development of targeted interventions to attenuate cartilage aging and forestall early OA development.
TB is a serious health challenge globally, with more than 10 million new cases every year and rising MDR and XDR variants diminishing the efficacy of existing chemotherapeutics. Although BCG vaccination confers protection in children, its limited ability to prevent adult pulmonary TB reveals the urgent need for next-generation vaccines proficient in inducing robust and durable immunity. PE and PPE protein families of M. tb, constituting nearly 10
Sepsis is defined by a dysregulated host immune response that encompasses both hyperinflammation and concurrent immunoparalysis. Rather than isolated cell defects, a dynamic multicellular network—involving neutrophils, macrophages, T cells, dendritic cells, and platelets—drives this maladaptive state through cytokine and metabolic crosstalk. Here, we review how cell-cell interactions within this network promote the transition from acute inflammation to sustained organ dysfunction, and we outline emerging precision strategies, including immune checkpoint modulation, metabolic intervention, and biomarker-guided timing, that target critical network nodes. We further highlight the fundamental distinction between PPAR-mediated immune tolerance, which preserves antimicrobial competence, and pathological immunoparalysis marked by reduced monocyte HLA-DR expression, arguing that their differential recognition is essential for matching therapy to immune trajectory. Integrating these network-based approaches into clinical practice holds the promise of rebalancing immunity and improving outcomes in sepsis. Not applicable.
Shigella phages are the major sources of genetic variability for Shigella sp. populations, but the evolutionary relationships among these phages remain unclear. To bridge the gap, we analyzed 371 complete phage genomes using a multi-scale framework integrating ANI clustering, protein-family diversity, gene-sharing networks, reticulate membership patterns, evolutionary modules, and proteomic phylogeny. ANI revealed a highly structured genomic landscape with 104 clusters, including several large lifestyle-pure groups. Virulent phages dominated by Straboviridae and Andersonviridae formed tight islands, whereas temperate phages assembled into broader, taxonomically mixed units enriched for Peduoviridae, Casjensviridae, and related lineages. The gene-sharing network exposed a strong lifestyle asymmetry: the largest connected component was dominated by temperate phages. In contrast, the highest-degree hubs were dominated by virulent Straboviridae phages, reflecting conserved structural/replication blocks in virulent lineages. In the case of betweenness, temperate genomes were predominant, indicating their role as evolutionary bridges. Membership analysis showed that most genomes exhibited strongly concentrated cluster signatures, demonstrating the dominance of consistent lineage backbones, and that very few temperate phages displayed broadened memberships consistent with concept of mosaicism. Module profiling revealed a two-tier module architecture, consistent head-tail replication modules conserved across major families, and a fluid accessory layer enriched for regulatory, host-interaction, lysis, and hypothetical proteins. These accessory modules were cluster-restricted or scattered across a few lineages, consistent with episodic gene flow, niche-specific adaptation, and mobile genomic islands. The proteomic tree demonstrated that all detected ICTV families formed monophyletic clades, with a strong phylogenetic signal for lifestyle and lifestyle transitions representing rare, evolutionarily costly events. Together, these results show that Shigella phages evolve through the interplay of deep lineage structure, lifestyle-specific evolutionary constraints, and modular gene exchange, producing a structured genomic relationship among Shigella bacteriophages.
The Hedgehog (Hh) signaling pathway is activated in diffuse large B-cell lymphoma (DLBCL) and helps facilitate tumor cell survival and proliferation. Currently, the role of the Hh signaling pathway in the prognosis of DLBCL has yet to be thoroughly investigated. RNA-Seq data and scRNA-seq data of DLBCL were collected from the UCSC Xena and GEO databases. A prognostic model related to Hh signaling pathway genes was constructed, and risk stratification was performed. The immune microenvironment characteristics, Hh scores, and drug sensitivity differences of different risk groups were systematically compared. The potential immune regulatory ligand-receptor pairs were screened through cell communication analysis. On this basis, the gene RABEP1, which contributed significantly to the model, was knocked down in SU-DHL-4 cells. Combined with a nude mouse subcutaneous xenograft tumor model, its tumor-promoting effect and impact on Hh signaling activity were verified in vivo and in vitro, as well as at the pathway level. We constructed an 11-gene prognostic model based on Tregs, Tfh and CD8+ T cells with high Hh scores, which demonstrated good stability and predictive ability in multiple datasets. RABEP1, with a prominent contribution to the risk score, was highly expressed in the high-risk group of DLBCL and negatively correlated with the sensitivity of AC220. In vitro and in vivo experiments showed that knockdown of RABEP1 could inhibit tumor growth and promote apoptosis by suppressing Hh signaling (GLI1/PTCH1). By integrating multi-omics data, we developed a prognostic model based on Hh-related genes. Based on an analysis of cell communication among immune cells, we identified several key receptor-ligand pairs. These findings not only provide new molecular biomarkers for predicting DLBCL prognosis but also offer fresh perspectives for therapeutic research targeting the Hh signaling pathway.
Clear cell renal cell carcinoma (ccRCC) ranks among the most common malignant tumors affecting the urinary tract. However, the role of ferroptosis mediated by plasma cells in ccRCC remains poorly understood. In this study, we combined single-cell RNA sequencing (scRNA-seq), spatial transcriptomic RNA sequencing (spRNA-seq), bulk RNA sequencing (RNA-seq) analysis to investigate the comprehensive landscapes of ferroptosis regulators within ccRCC. Expression profiles of ferroptosis markers, drivers and suppressors were depicted in scRNA-seq data via Addmodule Score and Percentage Feature Set algorithms. The marker genes and RNA-seq data were utilized to construct the Plasma Signature (Plasma.Sig), predicting overall survival (OS) of ccRCC patients with machine learning (ML) algorithms. In vitro and in vivo experiments were conducted to validate our bioinformatics findings. Through scRNA-seq and spRNA-seq analyses, we identified a subpopulation of DERL3 + plasma cells with close intercellular interactions with malignant cells, which is also correlated with ferroptosis suppressors in ccRCC. Utilizing marker genes of DERL3 + plasma cells, we developed the Plasma.Sig to predict OS of ccRCC patients accurately and specifically. By bulk RNA-seq analysis, we demonstrated that high DERL3 expression was associated with poor prognosis in ccRCC. Co-culture experiments revealed that knockdown of DERL3 in plasma cells decreased GPX4 expression in ccRCC tumor cells at both mRNA and protein levels. Furthermore, DERL3 knockdown impaired tumor cell proliferation, enhanced lipid peroxidation, and significantly induced ferroptosis in ccRCC tumor cells through the JAK2/STAT3 signaling pathway. Notably, combining DERL3 targeting with anti-PD-1 therapy enhanced the efficacy of immunotherapy in subcutaneous tumor model of ccRCC. Using multi-omics approaches, we identify that targeting DERL3 in plasma cells modulates tumor ferroptosis via the JAK2/STAT3 axis and potentiates immunotherapy response in ccRCC. Our findings highlight ferroptosis-targeting strategies combined with immunotherapy as a promising therapeutic approach for ccRCC. Not applicable.
Radiation-induced lung injury (RILI) is a severe complication of thoracic radiotherapy, and effective interventions are still lacking. DNA damage is a primary instigator of RILI, which triggers DNA replication stress that in turn aggravates genome instability, forming a vicious cycle. Here, using a RILI mouse model and the human bronchial epithelial cell line BEAS-2B, we identify the CSN5-MALT1 axis as a critical protective pathway against RILI by alleviating DNA replication stress. The expression of MALT1 and CSN5 were upregulated in both a RILI mouse model and irradiated BEAS-2B cells. Genetic depletion of either MALT1 or CSN5 significantly exacerbated IR-induced DNA damage and replication stress, impaired DNA repair capacity, and reduced cell survival. Mechanistically, CSN5 stabilized the MALT1 protein by reducing its ubiquitination. Rescue experiments established that CSN5 functions upstream of MALT1 to protect cells from IR-induced DNA damage by mitigating replication stress in BEAS-2B cells. Notably, all these effects were only observed upon irradiation and were absent under non-irradiated cells. Our study reveals a CSN5-MALT1 axis which is activated by IR to preserve genome integrity, highlighting a potential therapeutic strategy for RILI.
Ethical oversight for animal research extends to vertebrates in most jurisdictions but excludes the vast majority of invertebrates—a taxonomic boundary that is increasingly difficult to justify given accumulating evidence of sentience in several invertebrate groups. This paper argues that researchers, institutions, and governments should develop voluntary best-practice guidance for invertebrate welfare as a practical and proportionate precautionary response, rather than waiting either for definitive proof of sentience or for formal regulatory solutions. We first review neurobiological and behavioral evidence for sentience in cephalopod mollusks, decapod crustaceans, and insects, concluding that a realistic possibility of sentience exists across all three groups. We then argue that a realistic possibility of sentience—rather than confirmation of sentience—is sufficient to warrant precaution, and show that this standard aligns with existing ethical frameworks in the UK, EU, and US. We further demonstrate that invertebrate use in research is substantial, with estimates ranging from tens of thousands of cephalopods and decapods to billions of insects annually.
Rapsyn is a pivotal scaffolding protein required for clustering nicotinic acetylcholine receptors (nAChRs) at the neuromuscular junction (NMJ). Mutations in Rapsyn are a well-established cause of congenital myasthenic syndromes (CMS), leading to early-onset muscle weakness. However, although Rapsyn is expressed exclusively in skeletal muscle, the specific contribution of muscle-derived Rapsyn to NMJ development and stability has never been directly tested. Previous studies using in vivo Rapsyn silencing suggested a role for Rapsyn in adult NMJ maintenance, but the specific contribution of muscle-derived Rapsyn and the threshold level requirement to maintain adult NMJ integrity remain incompletely understood. Using muscle-specific and inducible Rapsyn knockout mouse models, we examined the role of muscle-derived Rapsyn in NMJ formation, structural maintenance, and neuromuscular function across developmental and adult stages. Homozygous muscular Rapsyn ablation caused neonatal lethality and catastrophic NMJ disorganization. In contrast, grade reduction of Rapsyn expression in adult mice progressively induced fragmented nAChR clusters and activity-dependent neuromuscular dysfunction despite relatively preserved gross NMJ morphology. These findings indicate that reduced Rapsyn expression destabilizes postsynaptic receptor domains and produces features resembling postsynaptic dysfunction observed in myasthenic disorders. This study demonstrates that sustained muscular Rapsyn expression is required for lifelong NMJ integrity and identifies a dose-dependent requirement for maintaining postsynaptic stability. Our findings complement previous studies demonstrating the protective effects of Rapsyn augmentation in experimental autoimmune MG by providing genetic evidence that sustained muscular Rapsyn expression is required for lifelong NMJ stability and postsynaptic resilience.
Dysregulated copper metabolism has attracted increasing attention in neurodegenerative diseases, but its causal position within disease progression remains incompletely defined. Cuproptosis is a copper-dependent form of regulated cell death characterized by aggregation of lipoylated tricarboxylic acid (TCA)-cycle proteins and loss of iron–sulfur (Fe–S) cluster proteins, providing a mechanistically specific framework that is distinct from nonspecific copper-induced oxidative injury. In neurodegenerative settings, cuproptotic stress is most plausibly viewed as a context-dependent mitochondrial lesion whose expression depends on labile copper availability, mitochondrial respiratory dependence, protein lipoylation, and antioxidant reserve. It may increase ferroptotic and apoptotic susceptibility through shared liabilities in glutathione metabolism, Fe–S cluster integrity, and mitochondrial stress signaling. Current evidence further supports a layered response hierarchy in which Nrf2–ATF4 mediates early adaptation, NF-κB–p53 contributes to inflammatory and pro-death amplification, and HIF-1α–MTF1 modifies the vascular and metabolic context. Neuronal vulnerability is disease- and region-specific, whereas astrocytes, microglia, oligodendrocytes, and brain endothelial cells determine whether copper stress is buffered or propagated. We therefore frame copper-driven injury as a disease-stratified, multicellular process and discuss biomarker-guided approaches for distinguishing copper overload, maldistribution, impaired utilization, and downstream inflammatory amplification. Cuproptosis links copper overload to mitochondrial proteotoxic stress Fe-S loss and GSH depletion connect cuproptosis with ferroptosis Nrf2-ATF4 and NF-kB-p53 define adaptive and inflammatory modules Glial buffering may shape copper-driven neuronal vulnerability Biomarker-guided targeting may stratify copper-related neurodegeneration
Ferro-aging, an emerging concept linking ferroptosis and cellular senescence, remains poorly characterized in clear cell renal cell carcinoma (ccRCC). The clinical and immunological implications of ferro-aging-related genes (FARGs) in ccRCC have not been systematically explored. Transcriptomic and clinical data from TCGA-KIRC and E-MTAB-1980 cohorts were integrated with single-cell RNA sequencing data (GSE304466), spatial transcriptomics data (GSE175540), and 6 additional GEO datasets. Differential expression analysis identified ferro-aging-related differentially expressed genes (DEGs), which were subjected to functional enrichment, prognostic model construction via LASSO and multivariate Cox regression, immune landscape characterization, and drug sensitivity prediction. Single-cell analysis and virtual knockout of DPEP1 were performed using the “scTenifoldKnk” R package. In vitro functional assays, including CCK-8, colony formation, wound healing, and Transwell assays, were conducted in A-498 and OS-RC-2 ccRCC cells with DPEP1 overexpression. Intersection of 2,288 DEGs with 95 FARGs yielded 21 ferro-aging-related DEGs, which were enriched in pathways related to oxidative stress, immune inflammation, and HIF-1 signaling. A 9-gene FARGs score demonstrated prognostic performance in both training (5-year AUC = 0.702) and validation (5-year AUC = 0.778) cohorts. High FARGs score was associated with distinct immune infiltration patterns, elevated IC50 values for sunitinib and pazopanib, and increased sensitivity to axitinib and sorafenib. DPEP1 showed the most favorable prognostic association, exhibiting tumor-specific downregulation across multiple cohorts. Single-cell analysis localized DPEP1 predominantly to endothelial cells and B cells, and virtual knockout perturbed antigen processing and presentation pathways. DPEP1 overexpression suppressed ccRCC cell proliferation, colony formation, migration, and invasion in vitro. DPEP1 is a ferro-aging-related tumor suppressor with favorable prognostic significance in ccRCC. The FARGs score provides a tool for risk stratification and therapeutic guidance. DPEP1 represents a promising prognostic and immunological target warranting further investigation.
Under the constraints of ecological protection policies on the Qinghai-Tibet Plateau, the sheep industry must shift from quantitative expansion to meat yield improvement. Oula, Qiaoke, and Ganjia sheep are three Tibetan sheep breeds that exhibit significant differences in growth performance. The myostatin (MSTN) gene is a key negative regulator of muscle development. This study aimed to investigate variations in the MSTN gene—including single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and copy number variations (CNVs)—and analyze the associations of haplotypes and CNVs with body size traits. Thirty-six genetic variants (34 SNPs and 2 InDels) were identified, and six major haplotypes were constructed. The analysis revealed that individuals carrying the H1H3 haplotype combination exhibited a significantly larger cannon circumference. CNV analysis showed that Oula sheep, characterized by larger body size, had a higher frequency of MSTN deletions. Furthermore, individuals with the deletion type displayed significantly greater body weight, body slant length, chest girth, and cannon circumference compared to those with normal copy numbers. Specific MSTN gene variations, notably the H1H3 haplotype combination and the CNV deletion type, are potential genetic markers associated with superior body size traits in Tibetan sheep. These findings provide candidate molecular markers for marker-assisted selection to breed high-meat-performance sheep adapted to the ecological environment of the Qinghai-Tibet Plateau.
