DNA methylation-mediated alterations in Copper(I/II) redox equilibrium underlie lead-induced neurotoxicity.

To investigate the extracellular matrix (ECM) change in choroid and explore the key regulator of choroidal vascular scaffold in axial myopia. Myopia was induced in pigmented rabbits and guinea pigs using the form-deprivation approach. Quantitative label-free proteomics were performed using the samples of rabbits to investigate the differentially expressed proteins (DEPs) in myopic choroid. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment was conducted to explore the potential biomarkers and signal pathways that form the scaffold and regulate the choroid morphology in myopia. Immunoblotting and immunofluorescence were applied to determine the expression and distribution of DEPs in choroid. Adeno-associated virus was used to knock down the expression of COL4A2 to verify its biological function in refraction development and choroid morphology. Long-term form deprivation significantly induced myopia shifts and decreased the choroidal thickness in pigmented rabbits. Proteomic analysis revealed that COL4A2 negatively regulates vasculature development. Masson's trichome staining and immunofluorescence showed decreased choroidal thickness and lumen scaffold deformation with decreased collagen IV in form-deprivation myopia (FDM) choroid. Immunoblotting revealed that COL4A2 rather than COL4A1 contributes to the downregulation of collagen IV in FDM choroid. Dysfunction of COL4A2 hindered choroidal vascular scaffold formation, decreased guinea pig choroidal thickness, and promoted myopia shifts with refraction change and axial elongation. Type IV collagen is a key ECM in construction of the choroidal vascular lumen. COL4A2 is downregulated in FDM choroid, and suppression of COL4A2 impairs the choroid vascular scaffold and promotes myopia shift with decreased choroidal thickness.

PurposeThis study aimed to identify plasma exosomal protein biomarkers for early recognition of acute myocardial infarction (AMI) using label-free quantitative proteomics.MethodsPatients presenting to the Second Affiliated Hospital of Soochow University with chest discomfort between February 2022 and December 2022 were enrolled. Plasma exosomes from a discovery cohort (six AMI patients and six non-AMI controls) were analyzed by mass spectrometry. Differentially expressed proteins (DEPs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Candidate proteins were further validated by western blot (WB) in an independent validation cohort (20 AMI patients and 20 non-AMI controls). Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic potential of the DEPs for AMI.ResultsA total of 24 DEPs were identified, of which 11 were upregulated and 13 were downregulated in AMI patients. WB analysis confirmed the significantly elevated expression of Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4) in AMI-derived exosomes. The area under the ROC curve (AUC) for ITIH4 was 0.8825, indicating high diagnostic accuracy. Correlation analysis revealed a significant positive correlation between plasma exosomal ITIH4 levels and the level of cTnI expression (R = 0.702, P < 0.001), indicates that exosomal ITIH4 may serve as a novel acute-phase reactant during myocardial injury.ConclusionPlasma exosomal ITIH4 is closely associated with AMI and may serve as a promising early diagnostic biomarker.Trial registrationRegistered at the Chinese Clinical Trial Registry (https://www.chictr.org.cn/showproj.html?proj=149623) with No. ChiCTR2200056343 on February 4, 2022. Principal investigator: Jiang Zhu.

Abstract Background Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease with substantial heritability and clinical heterogeneity. Large‐scale genetic studies often lack deep clinical or immunological phenotyping and typically rely on unmatched biobank controls. Our study overcomes this limitation by using carefully matched healthy comparators and integrating genomic, proteomic and pQTL analyses to dissect the molecular underpinnings of HS. Objectives To identify genetic variants associated with HS susceptibility using a genome‐wide association study (GWAS) in a Greek cohort and to determine whether these variants influence systemic inflammation by integrating blood proteomic profiling and protein quantitative trait locus (pQTL) mapping. Methods A case–control study involving 314 HS patients and 81 age‐, sex‐ and comorbidity‐matched healthy comparators of European (Greek) ancestry. Genomic DNA was analysed using GWAS, and inflammatory protein levels were assessed in a subset of participants using the Olink proteomics platform. GWAS meta‐analysis was performed with the FinnGen biobank. Publicly available pQTL datasets were used to evaluate genetic regulation of differentially expressed proteins. Results While the Greek GWAS alone revealed suggestive genetic loci, meta‐analysis with FinnGen identified 60 genome‐wide significant loci, including novel variants near HLA‐DRA . Proteomic profiling uncovered 51 differentially expressed proteins (DEPs), with only four upregulated in HS patients. Severity‐correlated proteins included IL‐6, IL‐17A and FGF21. Integration with pQTL data showed enrichment of HS‐associated SNPs among pQTLs regulating DEPs, supporting the genetic basis for systemic inflammation in HS. Conclusions Our findings support a dual model of HS pathogenesis involving genetically driven epithelial dysfunction and systemic inflammation. The identification of HLA‐DRA ‐associated variants raises the possibility that HS may share features with autoimmune diseases, while the proteomic profile dominated by innate cytokines suggests that an autoinflammatory component is also involved.

Transient overexpression assays and RNA sequencing (RNA-seq) showed that the transcription factor HmPIF1 enhances lead (Pb) tolerance in Hydrangea by improving antioxidant capacity and altering transporter protein expression. Lead (Pb) soil contamination has caused serious ecological and environmental issues. Hydrangea represents a promising candidate species for phytoremediation, whereas research on its Pb-tolerant genes remains relatively limited. This study aimed to explore the Pb tolerance function of HmPIF1 at the physiological and transcriptional levels. Results showed that Pb stress significantly upregulated the expression of HmPIF1. Subcellular localization and transcriptional autoactivation assays demonstrated that HmPIF1 is a nuclear-localized transcription factor without transcriptional autoactivation activity. Transient overexpression experiments confirmed that eight substances, including glutathione reductase, superoxide dismutase, and total protein, were key physiological factors for HmPIF1-enhanced Pb tolerance in Hydrangea leaves, while transcriptomic analysis identified "photosynthesis" and "glutathione metabolism" as likely the core regulatory pathways. Furthermore, HmPIF1 overexpression promoted Pb accumulation in leaves, accompanied by differential expression of ion transporter proteins. Taken together, HmPIF1 positively regulates plant Pb tolerance and enhances Pb uptake in leaves, which may be achieved through multiple regulatory pathways including photosynthesis, antioxidation and ion transporter-mediated processes. These findings provide a theoretical basis for subsequent related research.

Mutations in p53 have been implicated in poor prognosis and reduced sensitivity to 5-fluorouracil (5-FU) treatment in colon cancer. While p53-dependent mechanisms have been widely studies, less is known about how p53 deficiency reshapes cellular signaling and contributes to 5-FU resistance. In this study, we aimed to profile proteomic alterations associated with p53 loss by comparing colon cancer cells with and without p53 expression. Differentially expressed proteins (DEPs) related to cell cycle regulation were of particular interest, as 5-FU treatment induced G1 phase arrest in HCT116 p53 wild-type (WT) cells, whereas p53 knockout (KO) cells predominantly showed S phase arrest. We identified several DEPs in p53 deficient cells following 5-FU treatment. Notably, F3 expression was increased, while aldehyde dehydrogenase family 1 member A4 (ALDH1A3), histone deacetylase 2 (HDAC2), and protein S100-A4 (S100A4) were decreased. The expression levels of these genes were associated with overall survival in patients with colon cancer. These findings highlight proteomic alterations linked to p53 deficiency and support a proposed model in which differential regulation of specific proteins may be associated with reduced sensitivity to 5-FU, providing a basis for future mechanistic and functional studies.

Plasma protein signatures associated with functional outcome heterogeneity in rtPA-treated acute ischemic stroke.

Mechanism of PP2A affecting ubiquitination pathway in spermatogenesis.

Integrated proteomic profiling of aqueous humor reveals CDC42/RHOA-mediated pathogenic mechanisms in nAMD and PDR.

The mouse model of induced sperm DNA damage caused by polystyrene microplastics exhibited distinct transcriptomic and proteomic features.

Proteomic profiling of early-stage non-small cell lung cancer identifies a high-performance protein signature associated with postoperative recurrence.

Identification of diabetic kidney disease biomarkers via iTRAQ plasma proteomics analysis.

Immune checkpoint inhibitors (ICIs) have limited benefit in epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC). However, they are often tried after tumors develop resistance to EGFR tyrosine kinase inhibitors (TKIs). Because EGFR-TKI treatment alters the tumor microenvironment, biomarkers predictive of ICI response are ideally identified post-EGFR-TKI resistance, but obtaining repeat biopsies at this time can be challenging. The purpose of this study was to explore predictive biomarkers for ICI response using plasma samples collected after EGFR-TKI therapy. This retrospective analysis included 28 patients with EGFR-mutant NSCLC treated with an ICI after developing resistance to EGFR-TKI. Plasma samples collected at TKI progression were profiled using an Olink Target 96 immune protein panel to identify differential protein expression. Candidate protein biomarkers were validated by immunohistochemistry in tumor tissue. Durable clinical response (DCB) was defined as patients achieving progression-free survival (PFS) ≥ 6 months during ICI therapy. Of the 28 patients, 6 (21.4%) achieved durable clinical benefit, with PFS ≥ 6 months. Proteomic analysis identified four plasma proteins that differed significantly between DCB and NCB. Gal-9 and GZMH levels were elevated in NCB, whereas IL-4 and IL-6 were elevated in DCB. Notably, PFS was significantly longer in patients with lower Gal-9 and higher IL-4 levels. Plasma-based immune markers measured at the time of TKI resistance may help predict which patients with EGFR-mutant NSCLC will respond to subsequent ICI therapy. Such biomarkers could guide immunotherapy decision-making in this clinically challenging population.

Global environmental change affects organisms, including their physiology. In freshwater ecosystems, where migration is limited, populations often rely on phenotypic plasticity to respond. While transcriptomics has been widely used to study stress responses at the molecular level, less is known about the proteome, which reflects post-transcriptional and post-translational regulation that shapes the resulting phenotype. We conducted the first proteome-level study on the endangered Mira chub, Squalius torgalensis, which inhabits unstable habitats, enduring harsh summers with high temperatures and frequent droughts. We assessed the effect of warming and acidification, independently and combined, on protein expression and phosphorylation in gills and muscle using tandem mass tags labelling proteomics. While both tissues exhibited similar numbers of differentially expressed proteins, the muscle showed more differentially phosphorylated proteins, particularly under warming. We observed four protein differential expression patterns: consistent regulation across all scenarios, opposite response in one scenario, stress prioritisation in response to dominant stressor (warming), and reduced expression in combined compared to single stressors. The latter suggests a buffering mechanism that limits protein-level changes under simultaneous stressors, possibly as an energy-saving mechanism or a consequence of stress overload. A gene set enrichment-like analysis revealed that, despite the presence of distinct regulatory patterns in each tissue and condition, key biological functions like metabolism, gene/protein expression, and immunity were affected by all stressors. Gene/protein expression was the most affected at the phosphoproteome level. Our findings highlight the importance of proteomics and phosphoproteomics studies to understand species' molecular responses to climate change. By identifying key proteins involved in resilience, we pinpointed candidate stress markers for the Mira chub that can be used to assess the impact of environmental changes. Integrating these tools with genomics and ecological modelling could help improve predictive models for climate adaptation and species conservation.

Neurodegenerative disorders such as Alzheimer's disease (AD) and Lewy body disease (LBD) are typically diagnosed after irreversible pathology has developed. Aging, the strongest risk factor, drives molecular changes that predispose the brain to synaptic dysfunction and proteinopathy. Glycosylation and extracellular matrix (ECM) remodeling represent underexplored mechanisms linking aging to neurodegeneration, opening avenues for biomarker discovery, yet mass spectrometry-based glycoproteomics and glycomics studies remain limited. Here, we optimized an on-slide tissue digestion workflow for integrated glycome and proteome profiling from 5-mm brain regions from mice and humans using liquid chromatography data-independent acquisition-tandem mass spectrometry (LC-DIA-MS/MS). This workflow was applied to whole brains from age- and sex-stratified wild-type mice (n = 12) and to human postmortem prefrontal cortex tissue from individuals (n = 14) with brainstem- (n = 8) or limbic-predominant (n = 6) LBD, with or without AD co-pathology. DIA substantially increased protein, glycosylated protein, and ECM coverage by two- to threefold relative to traditional data-dependent acquisition (DDA), while library-free DIA searches further improved detection of low-abundance or region-specific proteins. In aged mouse brains, we observed increased levels of synapse-related proteins-including SYNPR, ZNT3, and HPCA-and enrichment of glutamatergic and postsynaptic pathways, reflecting age-associated synaptic remodeling. Glycomics revealed subtle shifts in the sulfation of chondroitin sulfate (CS) disaccharides with age. In human samples, AD-LBD brainstem tissue exhibited significantly reduced unsulfated, 4-O-sulfated, and total CS levels, along with differential expression of ECM, glycosylated, and mitochondrial proteins, and enrichment of mitochondrial pathways compared with LBD brainstem and AD-LBD limbic tissues. These findings indicate that AD co-pathology exerts a region-specific influence on the proteomic and glycomic landscape of LBD. Collectively, this study establishes a robust DIA-based on-slide digestion platform for high-resolution spatial glycomics and proteomics from minimal tissue, revealing aging- and pathology-specific molecular alterations relevant to neurodegeneration and providing a framework for biomarker discovery.

Abstract Objectives We investigated the correlation between abalone quality characteristics and proteomic profiles in liquid nitrogen freezing (LNF) vs. slow freezing (SF) to reveal potential mechanisms of their quality change. Materials and Methods Using a combination of quality characteristics analysis and 4D-DIA quantitative proteomics, we compared the effects of LNF and SF on abalone quality. We further analyzed changes in differentially expressed proteins (DEPs) after 30 d of frozen storage and established the correlations with key quality characteristics. Results Compared with SF, the LNF treatment significantly delayed abalone quality deterioration. After 150 d, the total volatile basic nitrogen increase was reduced by 40.82%, drip loss by 40.43%, and cooking loss by 36.23%. Hardness and springiness declines were lowered by 51.56% and 34.48%, and the L* value decrease was reduced by 27.58%, effectively preserving color and texture. The DEPs were predominantly identified as binding proteins and metabolic enzymes, and were found to be involved in cytoskeletal organization, cellular metabolic regulation, muscle contraction, and signal transduction. Abalone quality characteristics were influenced by these DEPs, including MYO6, FLNA, MYH6, BLNK, ELMO1, STOM, RHOA, ALDO, INDO, and ALPK. Notably, PRDX5 showed strong correlations with multiple quality characteristics, suggesting its potential as a quality marker for frozen abalone. Conclusions This study clarifies, from a proteomic perspective, the molecular basis for the superiority of LNF over SF method, providing a theoretical foundation for optimizing freezing processes and quality preservation in abalone.

Molecular weight (MW) of rice starch molecules initially increased and then decreased during grain filling, while concurrently the molecular size of amylopectin (AP) decreased (from 173.5 to ∼110 nm) and its MW increased. These dynamic structural changes may be linked to changes in starch granule-associated proteins (SGAPs) during starch synthesis. Label-free quantitative proteomics of SGAPs identified 286 differentially expressed proteins (DEPs) between early/midfilling but only seven DEPs between mid/late-filling stages. Key findings include: (1) Direct synthesis/Modification: Co-increased abundances of debranching and branching enzymes, coupled with reduced granule-bound starch synthase, correlated with a more uniform AP structure, smaller size, and higher MW. (2) Indirect effects: Reduced SGAPs for glycolysis versus highly expressed SGAPs for lipid metabolism, tubulin, and ribosomal proteins during early filling suggest an enhanced starch synthesis rate, intracellular transport, and protein translation function in the amyloplast. This study provides detailed SGAPs proteomics data identifying specific enzymes modulating starch granule structure during development.

Colorectal cancer (CRC) incidence is increasing in many low- and middle-income countries, including Egypt, partly due to urbanization and lifestyle changes. Metaproteomic approaches remain underutilized in these settings. In this study, we applied fecal metaproteomics in Egyptian CRC patients to characterize disease-associated protein expression patterns, explore host-microbiota functional interactions, and identify metabolic pathways that are altered in the CRC gut environment. Stool samples from 10 CRC patients and 10 healthy controls were analyzed. A total of 441 differentially expressed proteins (DEPs) were identified, of which 406 were consensus proteins overlapping across fold-change analysis, Wilcoxon testing, and PLS-DA. Differential microbial protein expression was primarily associated with core metabolic functions, including carbohydrate, amino acid, and nucleotide transport. Notably, proteins from Segatella copri were markedly suppressed in CRC patients. Functional analysis revealed upregulation of microbial proteins related to DPP-4 and cysteine metabolism, suggesting a possible role of microbiome-derived enzymes in colorectal cancer-associated metabolic and immune modulation, without direct evidence of host translocation.

Chronic social isolation stress (CSIS) is a well-established preclinical model for studying stress-induced neurobiological changes and their effects on behavior and brain function in depression. The prefrontal cortex (PFC), a brain region essential for emotional regulation, cognitive control, and social interactions, is particularly susceptible to stress. While CSIS exposure triggers molecular and behavioral changes characteristic of depression-like behavior, a subset of animals displays a resilient phenotype, maintaining normal neurobiological and behavioral function despite experiencing adverse conditions. Understanding the molecular differences between resilient and susceptible phenotypes is crucial for identifying biomarkers and developing novel therapeutic targets for depression. Mass spectrometry-based proteomics, combined with bioinformatics approaches, provides a powerful tool for exploring these complex cellular processes. This review focuses on proteomic changes in cytosolic and synaptosome-enriched fractions of the PFC in adult male rats following CSIS exposure, with particular emphasis on differences between resilient and susceptible animals. We summarize findings of differential protein expression across multiple biological systems, including energy metabolism, cytoskeletal organization, cellular stress defense mechanisms, neurotransmitter regulation, and synaptic function. Additionally, we present protein predictors of resilience to CSIS identified through machine learning-based analyses, highlighting potential pathways for preventing and mitigating depression-like outcomes followingCSIS.

Plasma proteomic profiling of 92 individuals with Post-Acute Sequelae of SARS-CoV-2 infection (PASC), assessed a mean of 34 months after acute infection, revealed a distinct inflammatory signature. Using proximity extension assay technology, 358 proteins were quantified, identifying 26 differentially expressed proteins (DEPs) in PASC: 23 upregulated and 3 downregulated. The most upregulated proteins were Oncostatin M (OSM) and IL-1 receptor antagonist (IL1RN). Additional increases were observed in IL-6, IL-12B, IL-2, CCL22, CSF3, CSF1, and HLA-DRA, as well as proteins involved in tissue remodeling and angiogenesis such as ANGPTL2 and TGFA. Random forest analysis confirmed IL1RN, OSM, ANGPTL2, HLA-DRA, and CLEC4A as strong discriminators between patients and controls. Gene set enrichment analysis demonstrated activation of multiple immune pathways, including Inflammatory Response, TNF-α/NF-κB signaling, IL-6/JAK/STAT3, IL-2/STAT5, and Allograft Rejection, indicating persistent activation of innate and adaptive immunity. STRING network analysis highlighted a tightly connected cytokine-driven inflammatory module. Plasma spike protein levels did not differ between patients and controls, suggesting that PASC-related inflammation may persist independently of ongoing viral replication. Overall, the findings indicate a consistent low-grade inflammatory state in PASC without evidence for distinct biological subtypes.