Molecular & Cellular Proteomics最新文献

{"title":"N-Glycoproteomics Sample Preparation Using Commercially Available Cellulose Magnetic Particles.","authors":"Ken Hanzawa, Miki Tanaka-Okamoto, Matej Nemcic, Yasuhide Miyamoto, Kazuki Nakajima","doi":"10.1016/j.mcpro.2026.101638","DOIUrl":"10.1016/j.mcpro.2026.101638","url":null,"abstract":"<p><p>Glycopeptide preparation is a critical step in bottom-up glycoproteomics. In this study, a robust method for N-glycopeptide preparation was developed using low-cost, commercially available magnetic particles. These particles function as a solid phase for hydrophilic interaction liquid chromatography (HILIC) to enrich N-glycopeptides from mixtures of N-glycopeptides and non-glycosylated peptides. Two types of magnetic particles, carboxylated polymer beads and cellulose resin, were compared. The latter demonstrated higher efficiency in N-glycopeptide recovery and non-glycopeptide removal. Biological samples often contain impurities such as salts and detergents that reduce efficiency and reproducibility of trypsin digestion and subsequent HILIC purification. To remove these impurities, we combined an optimized HILIC extraction protocol with a single-pot solid-phase-enhanced sample preparation protocol (SP3) for N-glycopeptide enrichment. Blood-derived samples (serum/plasma) were first tested. Compared with in-solution digestion, the method improved digestion efficiency and achieved N-glycopeptide recoveries comparable to those of conventional HILIC solid-phase extraction in a single tube. This method can be used for N-glycopeptide preparation not only from albumin-immunoglobulin-depleted serum but also from tissue extracts. Furthermore, the method has been successfully applied to glycoproteomic analysis of clinical serum and tissue samples from patients with gastric cancer, enabling detection of cancer-related alterations in glycoproteins.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101638"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13579034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Integrated Cardiac Microtissue Proteome Map Extends Therapeutic Remodeling by Nanovesicles.","authors":"Jonathan Lozano, Jarmon G Lees, Jonathon Cross, Taha Aghajanzadeh, Haoyun Fang, Anne M Kong, Ren J Phang, Alice Pébay, Alin Rai, Shiang Y Lim, David W Greening","doi":"10.1016/j.mcpro.2026.101643","DOIUrl":"10.1016/j.mcpro.2026.101643","url":null,"abstract":"<p><p>Human cardiac microtissues are a promising model to study cardiac biology and disease, but their application is constrained by therapeutic remodeling strategies and limited knowledge of their functional protein expression profiles. Here, we define the use of human cardiac microtissue (hCMT) model generated by assembling induced pluripotent stem cell-derived endothelial cells, cardiac fibroblasts, and cardiomyocytes (CMs) to model ischemia-reperfusion injury (IRI) through a model of hypoxia and reoxygenation and nanovesicle (NV)-mediated functional remodeling. Engineered NVs, generated directly from human stem cells, have been shown to influence cardiac tissue and cell repair, and provide a platform for scalable and reproducible cell free-mediated therapy. We show the functional regulation of the hCMT model and define that administration of NVs (from human induced pluripotent stem cell origin) during reoxygenation significantly increase CM survival and preserve contractility function (contractile duration, relaxation time, and relaxation:contraction velocity). We establish NV uptake and transfer with target cells from the hCMT model. Quantitative proteomics was applied to decipher the cell proteome dynamics and molecular mechanisms of IRI in our in vitro model following NV treatment, linked with networks associated with cell survival, energy production, and stress response regulation. Notably, cell type-specific enrichment analysis revealed that NVs drive distinct proteomic remodeling based on their cell origin, where CERA NVs selectively upregulate cytoprotective and structural networks (such as HSP70, MYH6, and XIRP1) within parenchymal CMs, whereas CL2 NVs predominantly suppress non-myocyte activation and extracellular matrix remodeling factors within the endothelial and fibroblast compartments. Our findings provide an advanced human stem cell-based platform to understand underlying mechanisms of IRI and assess cell-free therapeutic cardioprotective strategies.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101643"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mass Spectrometry-Based De Novo Sequencing of N-Glycosylated Light Chains: Linking Urinary Proteoforms to In Situ Renal Amyloid Deposits.","authors":"Yueyue Zhu, Xin Wang, Xinyue Zhou, Shuang Wang, Peifeng Ji, Zidi Yan, Kai Chen, Xiaojuan Yu, Gang Liu, Li Yang, Yi Liu, Suxia Wang","doi":"10.1016/j.mcpro.2026.101652","DOIUrl":"10.1016/j.mcpro.2026.101652","url":null,"abstract":"<p><p>Systemic immunoglobulin light-chain (AL) amyloidosis is characterized by clonal immunoglobulin-secreting cells that produce a monoclonal light chain prone to misfolding and amyloid fibril formation in tissues. Understanding its molecular basis requires accurate full-length sequencing of amyloidogenic light chains and linkage of circulating light chains to renal deposits. Achieving this is technically challenging because the low abundance and N-glycosylation of amyloidogenic light chains can complicate protein purification and peptide-level sequence analysis. To address these challenges, we implemented a robust analytical pipeline that integrates intact-mass measurement by Q-TOF MS before and after deglycosylation with multi-protease digestion and de novo peptide sequencing to systematically characterize urinary N-glycosylated light chains. Mass shifts observed before and after deglycosylation supported the presence of N-glycosylation, whereas deglycosylated intact masses were used to constrain full-length sequence assembly. The assembled urinary light-chain sequences were subsequently compared with matched renal amyloid proteomes isolated by laser microdissection and analyzed by bottom-up liquid chromatography-tandem mass spectrometry (LC-MS/MS). Enzymatic deglycosylation reduced glycan-induced spectral interference. Eight monoclonal light-chain sequences were assembled from urinary light chains, including five derived from the immunoglobulin kappa variable 1 (IGKV1), two from the immunoglobulin lambda variable 2 (IGLV2), and one from IGKV4. The close agreement between theoretical and experimental intact masses confirmed the accuracy and completeness of sequence assembly. In each renal amyloid proteome, the corresponding urine-derived sequence had the highest score among light-chain identifications of the patient's clinically determined isotype (κ or λ) and showed 87.6% to 100% variable-region peptide coverage. Together, these findings support urinary N-glycosylated monoclonal light chains as the precursor proteins of the corresponding renal amyloid fibrils. In conclusion, we have demonstrated a robust workflow that applies established de novo peptide sequencing to characterize urinary N-glycosylated light chains and trace the corresponding sequences in renal amyloid deposits, with potential applications across light chain-related diseases.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101652"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13635717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148874564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic Alterations of Site-Specific N-Glycoform and Plasma Proteasome Signatures Stratify Chemotherapy Benefit in Pancreatic Ductal Adenocarcinoma.","authors":"Shanying Gui, Yaqiong Zhang, Tao Xia, Jiazi Qian, Zemin Fang, Wenhui Ouyang, Jie Wang, Jie Chen, Xiaojun Ren, Jianxin Lyu, Wei Cui, Hezhi Fang","doi":"10.1016/j.mcpro.2026.101642","DOIUrl":"10.1016/j.mcpro.2026.101642","url":null,"abstract":"<p><p>Pancreatic ductal adenocarcinoma (PDAC) exhibits profound systemic remodeling during chemotherapy, yet how site-specific intact N-glycosylation in plasma is rewired by treatment remains largely undefined. Here, we perform an integrated plasma multi-omics study combining intact N-glycopeptidomics, deep proteomics, and metabolomics in a longitudinal cohort with paired pre- and post-chemotherapy samples and follow-ups (n = 177). Patients were further stratified according to radiographic treatment response. We identified 17,501 intact N-glycopeptides corresponding to 16,754 glycoforms, together with 6045 proteins and 1080 annotated metabolites. Paired analyses revealed extensive chemotherapy-associated changes across all three omics layers. Temporal glycopeptide and protein patterns were consistently enriched for complement, coagulation, extracellular-matrix, proteasome, and immune-related annotations, while oxidative-phosphorylation-related signatures showed relative depletion after treatment. Exploratory comparisons of within-patient changes (Δ = Post - Pre) between patients with partial response (PR) and those with stable or progressive disease highlighted 140 glycoforms, 18 glycosylation sites, and 103 proteins with response-associated patterns. These included coordinated increases in several proteasome-related plasma proteins in the PR group, as well as site- and glycoform-specific changes in complement- and acute-phase-related proteins. Response-associated differences in circulating metabolites further involved pyrimidine-, amino-acid-, and dipeptide-related features. Finally, leakage-controlled nested cross-validation prioritized 11 recurrent N-glycopeptide candidates and yielded modest prognostic discrimination, with a C-index of 0.591 and a 12-months area under the curve of 0.712. Collectively, this study provides a site- and glycoform-resolved view of chemotherapy-associated plasma molecular changes in PDAC and identifies candidate response- and prognosis-related features for future validation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101642"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface Proteomics of Cancer-Derived Extracellular Vesicles Reveals Universal Heat Shock Proteins and Cancer Signatures.","authors":"Leyla Ayse Erozenci, Fenna Feenstra, Sander R Piersma, Thang V Pham, Jianing Liu, Joke Wortel, Jan R T van Weering, Natasja Fj Dits, Guido Jenster, R Jeroen A van Moorselaar, Irene V Bijnsdorp, Connie R Jimenez","doi":"10.1016/j.mcpro.2026.101649","DOIUrl":"10.1016/j.mcpro.2026.101649","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) secreted by cancer cells are a valuable source of noninvasive biomarkers, as they are released into biofluids and reflect the molecular makeup of their cells of origin. To enable direct capture and detection of cancer-derived EVs, detailed knowledge of their surface proteome is essential. Here, we combined mild enzymatic treatment with mass spectrometry to analyze outward-facing proteins of EVs across a panel of 18 cell lines. This approach identified 1094 EV-associated surface proteins, including 144 transmembrane proteins involved in cellular communication and transport. Peptide-level analyses revealed that nearly 50% of multi-pass transmembrane proteins, such as ATP1A1, displayed their intracellular domains on the external EV surface. Out of a core set of 112 EV surface proteins shared across all cancer types, we report a top list of 15 highly abundant EV-surface proteins including ATP1A1, heat shock proteins (HSP)A8 and HSP90AB1 and nuclear proteins linked to EV biogenesis and cancer progression. This comprehensive profiling of EV surface proteomes from diverse cancer types reveals a robust set of pan-cancer EV surface markers with potential for diagnostic analysis.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101649"},"PeriodicalIF":6.3,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nicotinamide Mononucleotide Combined Glucose Counteracts Iron Overload-Induced Mitochondrial Dysfunction in Mice Under Hypobaric Hypoxia.","authors":"Fancheng Tan, Xiaoyun Huang, Xiaoya Mao, Yanyi Wang, Xingyao Wang, Feitai Tang, Xing Chen, Ridong Mao, Xiaoyu Gong, Lin Chen, Li-Jun Di, Shen Zhang, Jun Zeng, Shu-Hai Lin","doi":"10.1016/j.mcpro.2026.101648","DOIUrl":"10.1016/j.mcpro.2026.101648","url":null,"abstract":"<p><p>Extreme high-altitude environment poses severe threats to human health, underscoring the urgent need for effective, safe metabolic interventions. Here, we demonstrate that combined regimen of nicotinamide mononucleotide (NMN) and glucose attenuates tissue injury and prevents body weight loss in mice under hypobaric hypoxia (HH). By leveraging a multi-tissue integrative atlas encompassing metabolome, lipidome, proteome, and phenotypic profiles, we identified HH-induced iron overload and oxidative stress as key pathological drivers. NMN plus glucose supplementation significantly counteracted metabolic disruptions across multiple tissues. Mechanistically, HH-induced, transferrin-inspired iron delivery, causing iron overload and oxidative stress, along with glutathione depletion and lipid peroxidation across multiple tissues. Notably, we observed no significant changes in the protein levels of ferroptotic markers including ACSL4, GPX4, and FSP1, although cannot rule out the possibility of activity alterations of these proteins. Nevertheless, NMN combined with glucose effectively reversed the ferroptosis-associated metabolic alterations and alleviated mitochondrial dysfunction. Collectively, our study provides a systems-level metabolic atlas and reveals that NMN combined glucose mitigates HH-induced multi-organ injury by suppressing ferroptosis through metabolic reprogramming, offering a therapeutic potential for high-altitude hypoxia.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101648"},"PeriodicalIF":6.3,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13626794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Insights Into Human Induced Regulatory T Cells: The Role of LPXN and CD160 in Immune Suppression.","authors":"Kedar Batkulwar, Syed Bilal Ahmad Andrabi, Roosa Kattelus, Tanja Buchacher, Ilona Arnkil, Inna Starskaia, Omid Rasool, Robert Moulder, Riitta Lahesmaa","doi":"10.1016/j.mcpro.2026.101644","DOIUrl":"10.1016/j.mcpro.2026.101644","url":null,"abstract":"<p><p>Regulatory T cells (Treg) play a central role in maintaining immune homeostasis, and the implementation of in vitro induced Treg cells (iTreg) to control immune function has significant potential in clinical medicine. The clinical application of iTreg has been limited by their poor stability. To better define the molecular characteristics of human iTreg, we performed a data-independent acquisition proteomics, detecting over 8000 proteins and providing a quantitative comparison of their relative levels in iTreg and activated Th0 cells. Consistent with the known molecular characteristics of Treg, several Treg signature proteins, including FOXP3, IKZF4, IL2RA, CTLA4, PD-1, IKZF3, LAG3, RUNX1 and hypermethylated in cancer 1, were identified and validated using Tier two targeted SRM and/or qRT-PCR. Notably, Leupaxin level was upregulated during Treg cell differentiation. Functional studies demonstrated that LPXN-deficient cells showed impaired expression of Treg protein markers FOXP3, IKZF4 and IKZF3 and impaired suppression of effector T cells. In addition, we identified a distinct CD160⁺ iTreg subpopulation characterized by a distinct proteomic signature as compared to CD160^- iTreg. Together, these findings provide a high-resolution proteomic landscape of human iTreg and identified a novel role of LPXN in the development and suppressive activity of iTreg.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101644"},"PeriodicalIF":6.3,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13627119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Analyses of Early Versus Advanced Primary Open-Angle Glaucoma Uncover Biochemical Signatures Associated With Disease Staging.","authors":"Tianwei Ellen Zhou, David J Mathew, Karen Wigg, Darren Chan, Jenny Wanyu Zhang, Carmen Balian, Irfan N Kherani, Matthew B Schlenker, Igor Jurisica, Jeremy M Sivak","doi":"10.1016/j.mcpro.2026.101625","DOIUrl":"10.1016/j.mcpro.2026.101625","url":null,"abstract":"<p><p>Primary open-angle glaucoma (POAG) is a leading cause of blindness, yet the biochemical mechanisms underlying disease progression remain poorly understood. This study characterized aqueous humor (AH) across early and advanced stages of POAG using large-scale proteomics. AH samples were collected from patients with mild POAG, advanced POAG, and non-glaucomatous controls in this prospective cross-sectional study. Profiling of 8000 proteins was performed using an antibody array. Hierarchical clustering, principal component analysis (PCA), Gene Ontology (GO), and pathway enrichment analyses were performed to identify differentially expressed proteins, biological processes, and molecular functions associated with disease stages. Top differential proteins were also correlated with key clinical parameters. Proteomic signatures demonstrated distinct clustering between control and glaucoma patients, with progressive shifts from mild to advanced stages. Comparisons between control and each glaucoma group revealed significant enrichment in pathways related to wound healing, extracellular matrix (ECM) remodeling, and immune responses. Notably, distinct proinflammatory and immune proteins and pathways were enriched when comparing mild to advanced POAG stages. Finally, the top differential AH proteins correlated with multiple clinical endpoints, including intraocular pressure and a variety of retinal outcomes. This signature revealed a tight network associated with disease stage, oriented on immune cell migration and function, and identifying soluble TRPC6 as a novel biomarker. To our knowledge this is the first study to compare large scale proteomic analysis of AH from patients with POAG across disease stages, suggesting new mechanisms underlying glaucoma progression.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101625"},"PeriodicalIF":6.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ASAP-ID: Proximity Labelling With Small Tags.","authors":"Ruohua Lyu, Kiersten M Ruff, Catherine S Palmer, Alejandra E Ramirez, Angelique R Ormsby, Daniel J Scott, Rohit V Pappu, Diana Stojanovski, David A Stroud, Danny M Hatters","doi":"10.1016/j.mcpro.2026.101616","DOIUrl":"10.1016/j.mcpro.2026.101616","url":null,"abstract":"<p><p>Biotinylation-based proximity labelling methods are valuable for discovering protein-protein interactions within cellular systems. However, one limitation of these approaches is that most require fusing the target protein with the enzyme that biotinylates nearby proteins (i.e., TurboID or APEX2), which risks sterically disrupting the protein's native function. Here, we present a method designed to reduce the steric impact of these fusions and offer greater flexibility in labelling modalities. The method, Antibody and Small-tag Assembly on Proteins for Interaction Detection (ASAP-ID), involves a bipartite system. Target proteins are fused to a small peptide antigen that recruits TurboID or APEX2 fused to an antibody directed to the antigen. Using two different antigen/antibody systems (SunTag and MoonTag), we show that ASAP-ID can specifically label human Lamin A in cells. The method works when the target protein and nanobody are co-expressed together in cis (ASAP-ID^IC). We also demonstrate that the approach works when the antibody fusion is added in trans to fixed cells post-expression (ASAP-ID^IT). ASAP-ID^IT identified more than 448 known and previously undescribed potential interactors of lamin. We further used ASAP-ID^IT to study how ALS-mutant profilin one affected its interactome. The method identified proteins involved in protein quality control that correlated with aggregation propensity. Moreover, the different mutants showed variation in the cellular location where aggregates formed. ASAP-ID^IT revealed preferences for mitochondrial proteins for the two profilin mutants that tend to aggregate in the cytoplasm, C71G and M114T, and nuclear proteins for a mutant more prone to nuclear aggregation. These findings position ASAP-ID as a powerful addition to the proximity labelling toolkit, capable of probing subtle differences in interactomes in a less invasive manner.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101616"},"PeriodicalIF":6.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13430183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148339267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Urinary Proteomics Identifies ADAMDEC1 as a Non-invasive Biomarker of Unstable Carotid Atherosclerotic Plaques.","authors":"Tian Yu, Qi Qin, Yumei Zhou, Mei Zhang, Qiujuan Zhang, Shilun Yang, Yinzhong Ma, Baofeng Xu, Rui Liu","doi":"10.1016/j.mcpro.2026.101624","DOIUrl":"10.1016/j.mcpro.2026.101624","url":null,"abstract":"<p><p>Rupture of vulnerable carotid atherosclerotic plaques (CAPs) is a major precipitating cause of ischemic stroke. Current imaging-based risk stratification is useful for anatomical and structural assessment, but it does not readily provide noninvasive access to plaque-associated molecular information. Here, we aimed to identify and validate a noninvasive urinary biomarker of CAP instability and to explore its biological relevance. We employed a multi-stage study design integrating untargeted urinary proteomics data-independent acquisition mass spectrometry in a discovery cohort of 179 patients with systematic interrogation of plaque tissue proteomic and transcriptomic datasets. Candidate proteins were further evaluated by ELISA in an independent cohort of 225 individuals, including patients with stable or unstable CAPs and healthy controls. Cellular and tissue-level analyses included single-cell RNA sequencing re-analysis, human plaque validation by immunohistochemistry, western blotting, and immunofluorescence, as well as in vitro macrophage phenotypic assays. Urinary proteomic profiling identified 227 shared differential proteins associated with plaque instability. In the independent validation cohort, urinary ADAM-Like Decysin 1 (ADAMDEC1) was confirmed as a candidate urinary marker, showing a stepwise increase from healthy controls to stable and unstable CAPs. Urinary ADAMDEC1 showed robust discriminatory performance for unstable plaques (AUC = 0.882, 95% CI 0.822-0.941). Higher urinary ADAMDEC1 levels were associated with symptomatic status and plaque vulnerability features, while higher intraplaque ADAMDEC1 expression was associated with adverse cerebrovascular outcomes. Single-cell and human plaque analyses showed that ADAMDEC1 was enriched in inflammatory macrophage-associated plaque regions, and in vitro assays supported an association between ADAMDEC1 and pro-inflammatory macrophage polarization. Urinary ADAMDEC1 is a noninvasive biomarker associated with carotid plaque instability. Integrated tissue, single-cell, and macrophage assays support a link between ADAMDEC1 and macrophage-associated inflammatory features in vulnerable plaques.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101624"},"PeriodicalIF":6.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13486800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}