Clinical proteomics最新文献

{"title":"Proteomic and phosphoproteomic signatures of disease progression in unmutated IGHV chronic lymphocytic leukemia.","authors":"Renee C Tschumper, Neil E Kay, Sameer A Parikh, Kari G Rabe, Partho Sen, Akhilesh Pandey, Richard K Kandasamy, Diane F Jelinek","doi":"10.1186/s12014-026-09607-2","DOIUrl":"https://doi.org/10.1186/s12014-026-09607-2","url":null,"abstract":"<p><strong>Background: </strong>Chronic lymphocytic leukemia (CLL) patients with an unmutated (UM) immunoglobulin heavy chain variable region gene (IGHV) typically have poorer prognosis and require earlier treatment compared to those with mutated IGHV. Nevertheless, disease progression among UM-CLL patients is heterogeneous, with some experiencing stable disease and prolonged time to first treatment (TTFT). Because the cellular proteome directly reflects cell function, comprehensive proteomic and phosphoproteomic profiling may improve prediction of progression of UM-CLL and uncover novel biomarkers.</p><p><strong>Methods: </strong>We applied mass spectrometry-based quantitative proteomics and phosphoproteomics to peripheral blood mononuclear cells from 18 UM‑CLL patients, comparing those with a TTFT of ≤ 2 years (progressive disease) to those with TTFT ≥ 4 years (stable disease).</p><p><strong>Results: </strong>We quantified over 6,300 proteins across all samples. The top 100 differentially expressed proteins clearly distinguished progressive from stable UM-CLL. Phosphoproteomic analysis identified over 15,000 phosphorylation sites across 4,200 proteins, with the top 100 phosphopeptides similarly separating patient groups. Gene set enrichment analysis of proteins up‑regulated in progressive UM‑CLL revealed strong enrichment for RNA processing and ribosome biogenesis, together with mitochondrial translation and oxidative phosphorylation pathways, underscoring dysregulated RNA metabolism and energy production as key features of disease progression.</p><p><strong>Conclusions: </strong>Specific proteins and phosphopeptides identified here, upon further validation, may serve as biomarkers for early intervention in UM‑CLL. More broadly, our study demonstrates the value of integrated proteomic and phosphoproteomic profiling which may lead to refining risk stratification and advancing understanding of the complex biology underlying CLL progression.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative Proteomic and Phosphoproteomic Analysis Reveals Altered Vesicle Transport in Systemic Lupus Erythematosus.","authors":"Lingling Zhou, Yixi Li, Mengyao Wu, Donge Tang, Wei Zhang, Yong Dai","doi":"10.1186/s12014-026-09599-z","DOIUrl":"https://doi.org/10.1186/s12014-026-09599-z","url":null,"abstract":"","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma proteomics of extracellular vesicles identifies key proteins correlating to postoperative atrial fibrillation after coronary artery bypass surgery.","authors":"Huan-Xin Chen, Qin Yang, Guo-Wei He","doi":"10.1186/s12014-026-09606-3","DOIUrl":"https://doi.org/10.1186/s12014-026-09606-3","url":null,"abstract":"","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated serum proteomics and metabolomics reveal an INR-associated multi-omics signature in hepatocellular carcinoma.","authors":"Yuying Cai, Lingna Lyu, Jiayi Ma, Xiaoru Wang, Wenxia Ma, Jiming Yin, Shanshan Wang","doi":"10.1186/s12014-026-09603-6","DOIUrl":"https://doi.org/10.1186/s12014-026-09603-6","url":null,"abstract":"","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147721819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical peptidomics for respiratory diseases: matrices, workflows, and translation towards treatable traits, with a focus on COPD.","authors":"Qingyu Zhou, Yahui Shen","doi":"10.1186/s12014-026-09583-7","DOIUrl":"https://doi.org/10.1186/s12014-026-09583-7","url":null,"abstract":"<p><strong>Background: </strong>Peptidomics is an emerging tool for biomarker discovery. By capturing end products and active peptides generated during protein breakdown, it helps reveal short peptides linked to disease. This narrative review centers on chronic obstructive pulmonary disease (COPD) and synthesizes recent advances in respiratory peptidomics across patient-accessible matrices and laboratory workflows toward treatable-trait translation.</p><p><strong>Main body: </strong>We conducted a structured literature search of PubMed, Embase, and Web of Science (January 2000-September 2025, with emphasis on the most recent five years), prioritizing mass-spectrometry-based discovery and targeted verification in human biospecimens. We distinguish clinical endogenous peptidomics, immunopeptidomics, and degradomics as complementary approaches in respiratory disease. Six representative peptide classes were compared across pre-analytical handling, enrichment strategies, and MS identification, building an evidence map for COPD, asthma, lung cancer, and pulmonary fibrosis. Using this map, we discuss matrix-technology fit and recurrent biological signals-airway inflammation, extracellular matrix turnover, and host-pathogen interaction-that show promise for disease subtyping and early diagnosis. For translation, we outline a stepwise pathway: (i) harmonized sampling and internal-standard-driven quality control; (ii) transparent modeling with calibration and decision-curve analysis; and (iii) multicenter external validation. We further consider integration with proteomics and breathomics, emerging peptide-drug leads, and open sharing of data and code to improve reproducibility and transferability.</p><p><strong>Conclusions: </strong>Peptidomics is poised to contribute clinically actionable biomarker panels in respiratory disease, with near-term opportunities in COPD phenotyping and exacerbation risk assessment using sputum and blood. Broad adoption will depend on standardized pre-analytics, feasible targeted assays in routine laboratories, robust external validation, and transparent model calibration.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147688730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational proteomics to enhance personalized treatment of COVID-19 and Long COVID.","authors":"Debasis Sahu, Logan R Van Nynatten, David Tweddell, Mark Daley, Douglas D Fraser","doi":"10.1186/s12014-026-09601-8","DOIUrl":"10.1186/s12014-026-09601-8","url":null,"abstract":"","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13154495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147632691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma exosome proteomics in different glucose statuses: a cross-sectional study on type 2 diabetes pathogenesis.","authors":"Yuxiang Liu, Haijian Guo, Mingma Li, Jinshui Xu, Yu Liu, Kaicheng Sun, Evan Yi-Wen Yu, Zilin Sun, Bei Wang","doi":"10.1186/s12014-026-09600-9","DOIUrl":"https://doi.org/10.1186/s12014-026-09600-9","url":null,"abstract":"<p><strong>Background: </strong>The pathogenesis of type 2 diabetes (T2DM) remained to be fully understood. Meanwhile, exosome have shown its potential to further advance diabetes research as a rich source of biomarkers. This study aims to explore the proteomic profiles of circulating plasma exosomes in individuals with varying glucose statuses and offer potentially new perspective on the pathogenesis of T2DM.</p><p><strong>Methods: </strong>Participants with different glucose status were recruited according to the diagnostic criteria of the American diabetes association. Plasma exosomes were collected and went through data independent acquisition mass spectrometry quantitative proteomics analysis. Differential proteins identified through pairwise group comparisons underwent further analysis like protein-protein interaction (PPI) and gene ontology (GO) to reveal their functions and interactions.</p><p><strong>Results: </strong>A total of 75 participants (25 euglycemia; 25 prediabetes; 25 diabetes) were included in this study. Principal coordinates analysis showed that the proteomic patterns of exosomes in groups with prediabetes and diabetes exhibited certain similarities, contrasting with those in euglycemic individuals. From pairwise differential protein comparison, 32 proteins were selected for PPI and functional analysis, of which 7 were deemed significant within the network. GO annotations highlighted a close link between immunity and T2DM. Local STRING clustering, Reactome and KEGG pathway analysis all indicated great significance of complement and coagulation cascades.</p><p><strong>Conclusion: </strong>The proteomic patterns of exosomes in groups with different glucose levels exhibited that even before overt diabetes manifests, the circulating exosome cargo signals immune and coagulatory activation distinct from normal physiology.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147493597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative enrichment of amyloid precursors refines mass spectrometry-based amyloidosis diagnosis.","authors":"Sylvaine Di Tommaso, Bertrand Chauveau, Cyril Dourthe, Jean-William Dupuy, Frédéric Saltel, Brigitte Le Bail, Anne-Aurélie Raymond","doi":"10.1186/s12014-026-09598-0","DOIUrl":"10.1186/s12014-026-09598-0","url":null,"abstract":"<p><strong>Introduction: </strong>Amyloidosis typing is crucial to determine the best therapeutic strategy for patients. Since conventional histological techniques often fail, the identification of amyloid precursors by mass spectrometry has become the new standard. However, without quantification, selecting the amyloid precursor from proteins that may be ubiquitous under non-pathological conditions can be equivocal. Therefore, we quantified protein enrichment in amyloid deposits to improve amyloidosis typing.</p><p><strong>Methods: </strong>Protein enrichment was measured by extracted ion chromatogram-based label-free quantification by comparing a microdissected amyloid area to a non-amyloid area. We assessed the discrimination ability of candidate precursors with this approach compared to the two practiced identification methods.</p><p><strong>Results: </strong>As a proof of concept, we selected 9 cases including the most common amyloidosis subtypes, 6 typed by immunohistochemistry and 3 inconclusive by immunohistochemistry. Proteins associated with amyloid deposits were identified in all samples, confirming the pathology. Where the routine clinical mass spectrometric identification techniques allowed unambiguous conclusions for 3 of 9 cases, quantification of the enrichment ratio in amyloid deposits allowed unambiguous precursor selection in all cases.</p><p><strong>Conclusion: </strong>Quantification of precursor enrichment in amyloid deposits is a promising optimization for amyloidosis typing, which should be studied in larger cohorts. Incorporated into routine clinical processes, it could improve patient care in difficult diagnostic situations.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13107715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics of human duodenum in pre-diabetes and type 2 diabetes reveals potential novel therapeutic targets for aetiology and therapeutics.","authors":"Beatriz D G Alves, Paula Monteiro, Pedro C Martins, José Braga, Rune Matthiesen, José Flávio G Videira, Inês G Mollet","doi":"10.1186/s12014-026-09595-3","DOIUrl":"10.1186/s12014-026-09595-3","url":null,"abstract":"","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13104399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147467287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of human kallikrein 6 in the cerebrospinal fluid of patients with progressive and non-progressive alzheimer's disease: correlation with other biomarkers.","authors":"Miyo K Chatanaka, Antoninus Soosaipillai, Amanda Cano, Adelina Orellana, Mercè Boada, Ioannis Prassas, Xavier Morató, Eleftherios P Diamandis","doi":"10.1186/s12014-025-09577-x","DOIUrl":"10.1186/s12014-025-09577-x","url":null,"abstract":"<p><strong>Background: </strong>Alzheimer's disease (AD) biomarkers in plasma and cerebrospinal fluid (CSF) are useful for disease diagnosis, prognosis, risk assessment and monitoring therapy response, as well as for uncovering altered disease pathways. Previously, we and others cloned a novel gene, KLK6, which encodes a serine protease of the kallikrein family. The protein (hK6) is highly expressed in the brain, spinal cord and cerebellum.</p><p><strong>Methods: </strong>To examine the correlation of hK6 concentration in CSF with various clinicopathological variables in AD, we used a quantitative ELISA system. The variables examined included patient age, sex, MMSE score, APOE status, amyloid β 1-42 (Αβ1-42), phosphorylated Tau 181 (p-Tau181), total Tau (t-Tau). Previously, using a cohort of Swedish and Norwegian patients, we established a positive correlation between CSF hK6 and age as well as the levels of core AD biomarkers in four groups of patients (cognitively normal, MCI without progression to AD, MCI with progression to AD within 2 years and AD dementia). In this investigation, our goal was to validate these previous data with a large and independent patient cohort from Spain.</p><p><strong>Results: </strong>We found that CSF hK6 is minimally or not affected by patient age and sex, but it significantly correlates with MMSE score and CSF Aβ1-42, p-Tau1811 and t-Tau.</p><p><strong>Conclusions: </strong>We conclude that these correlations further support our previous findings and suggest that hK6 may be an additional biomarker for AD and may play some role in the pathogenesis of AD.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13104293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}