{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T10:57:10Z","timestamp":1778410630570,"version":"3.51.4"},"reference-count":37,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Odense University Hospital Research Fund","award":["#A4527"],"award-info":[{"award-number":["#A4527"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Malignant pleural mesothelioma (MPM) is an asbestos-associated, highly aggressive cancer characterized by late-stage diagnosis and poor prognosis. Gold standards for diagnosis are pleural biopsy and cytology of pleural effusion (PE), both of which are limited by low sensitivity and markedly inter-observer variations. Therefore, the assessment of PE biomarkers is considered a viable and objective diagnostic tool for MPM diagnosis. We applied a novel affinity-enrichment mass spectrometry-based proteomics method for explorative analysis of pleural effusions from a prospective cohort of 84 patients referred for thoracoscopy due to clinical suspicion of MPM. Protein biomarkers with a high capability to discriminate MPM from non-MPM patients were identified, and a Random Forest algorithm was applied for building classification models. Immunohistology of pleural biopsies confirmed MPM in 40 patients and ruled out MPM in 44 patients. Proteomic analysis of pleural effusions identified panels of proteins with excellent diagnostic properties (90\u2013100% sensitivities, 89\u201398% specificities, and AUC 0.97\u20130.99) depending on the specific protein combination. Diagnostic proteins associated with cancer growth included galactin-3 binding protein, testican-2, haptoglobin, Beta ig-h3, and protein AMBP. Moreover, we also confirmed previously reported diagnostic accuracies of the MPM markers fibulin-3 and mesothelin measured by two complementary mass spectrometry-based methods. In conclusion, a novel affinity-enrichment mass spectrometry-based proteomics identified panels of proteins in pleural effusion with extraordinary diagnostic accuracies, which are described here for the first time as biomarkers for MPM.<\/jats:p>","DOI":"10.3390\/cancers15030641","type":"journal-article","created":{"date-parts":[[2023,1,20]],"date-time":"2023-01-20T02:52:21Z","timestamp":1674183141000},"page":"641","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Identification of Highly Sensitive Pleural Effusion Protein Biomarkers for Malignant Pleural Mesothelioma by Affinity-Based Quantitative Proteomics"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1480-6550","authenticated-orcid":false,"given":"Nicolai B.","family":"Palstr\u00f8m","sequence":"first","affiliation":[{"name":"Department of Clinical Biochemistry, Odense University Hospital, 5000 Odense, Denmark"},{"name":"Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2277-590X","authenticated-orcid":false,"given":"Martin","family":"Overgaard","sequence":"additional","affiliation":[{"name":"Department of Clinical Biochemistry, Odense University Hospital, 5000 Odense, Denmark"},{"name":"Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Licht","sequence":"additional","affiliation":[{"name":"Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark"},{"name":"Department of Cardiothoracic and Vascular Surgery, Odense University Hospital, 5000 Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7763-3637","authenticated-orcid":false,"given":"Hans C.","family":"Beck","sequence":"additional","affiliation":[{"name":"Department of Clinical Biochemistry, Odense University Hospital, 5000 Odense, Denmark"},{"name":"Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"ref_1","first-page":"491","article-title":"Malignant pleural mesothelioma: An epidemiological perspective","volume":"1","author":"Robinson","year":"2012","journal-title":"Ann. Cardiothorac. Surg."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1146\/annurev-pathol-020712-163942","article-title":"Molecular basis of asbestos-induced lung disease","volume":"8","author":"Liu","year":"2013","journal-title":"Annu. Rev. Pathol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/jcb.24642","article-title":"Malignant mesothelioma: Development to therapy","volume":"115","author":"Thompson","year":"2014","journal-title":"J. Cell. Biochem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/S0140-6736(05)67025-0","article-title":"Malignant mesothelioma","volume":"366","author":"Robinson","year":"2005","journal-title":"Lancet"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"413946","DOI":"10.1155\/2014\/413946","article-title":"Pleural fluid mesothelin as an adjunct to the diagnosis of pleural malignant mesothelioma","volume":"2014","author":"Creaney","year":"2014","journal-title":"Dis. Markers"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1200\/JCO.2011.39.6671","article-title":"Serum mesothelin for diagnosing malignant pleural mesothelioma: An individual patient data meta-analysis","volume":"30","author":"Hollevoet","year":"2012","journal-title":"J. Clin. Oncol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1056\/NEJMoa1115050","article-title":"Fibulin-3 as a blood and effusion biomarker for pleural mesothelioma","volume":"367","author":"Pass","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"13030","DOI":"10.18632\/oncotarget.14712","article-title":"Diagnostic and prognostic utilities of humoral fibulin-3 in malignant pleural mesothelioma: Evidence from a meta-analysis","volume":"8","author":"Pei","year":"2017","journal-title":"Oncotarget"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/bjc.2015.470","article-title":"A proteomics-based approach identifies secreted protein acidic and rich in cysteine as a prognostic biomarker in malignant pleural mesothelioma","volume":"114","author":"Kao","year":"2016","journal-title":"Br. J. Cancer"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Palstrom, N.B., Rasmussen, L.M., and Beck, H.C. (2020). Affinity Capture Enrichment versus Affinity Depletion: A Comparison of Strategies for Increasing Coverage of Low-Abundant Human Plasma Proteins. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21165903"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Andersen, L.C., Palstrom, N.B., Diederichsen, A., Lindholt, J.S., Rasmussen, L.M., and Beck, H.C. (2021). Determining Plasma Protein Variation Parameters as a Prerequisite for Biomarker Studies-A TMT-Based LC-MSMS Proteome Investigation. Proteomes, 9.","DOI":"10.3390\/proteomes9040047"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1002\/prca.201400070","article-title":"Total and isoform-specific quantitative assessment of circulating fibulin-1 using selected reaction monitoring MS and time-resolved immunofluorometry","volume":"9","author":"Overgaard","year":"2015","journal-title":"Proteom. Clin. Appl."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3325","DOI":"10.1021\/acs.jproteome.8b00594","article-title":"Spectral Library Search Improves Assignment of TMT Labeled MS\/MS Spectra","volume":"17","author":"Shen","year":"2018","journal-title":"J. Proteome Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: An open source document editor for creating and analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1097\/SHK.0000000000001595","article-title":"STEMI, Cardiogenic Shock, and Mortality in Patients Admitted for Acute Angiography: Associations and Predictions from Plasma Proteome Data","volume":"55","author":"Debrabant","year":"2021","journal-title":"Shock"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1007\/978-1-4939-9744-2_13","article-title":"Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets","volume":"2051","author":"Palstrom","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1373\/clinchem.2017.282665","article-title":"Proteomic Discovery and Validation of the Confounding Effect of Heparin Administration on the Analysis of Candidate Cardiovascular Biomarkers","volume":"64","author":"Beck","year":"2018","journal-title":"Clin. Chem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1136\/thoraxjnl-2014-205205","article-title":"Comparison of fibulin-3 and mesothelin as markers in malignant mesothelioma","volume":"69","author":"Creaney","year":"2014","journal-title":"Thorax"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1038\/bjc.2015.286","article-title":"Fibulin-3 levels in malignant pleural mesothelioma are associated with prognosis but not diagnosis","volume":"113","author":"Kirschner","year":"2015","journal-title":"Br. J. Cancer"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/s12967-015-0503-3","article-title":"Enhanced expression of cohesin loading factor NIPBL confers poor prognosis and chemotherapy resistance in non-small cell lung cancer","volume":"13","author":"Xu","year":"2015","journal-title":"J. Transl. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"10461","DOI":"10.3390\/ijms130810461","article-title":"Transforming growth Factor-Beta-Induced Protein (TGFBI)\/(betaig-H3): A matrix protein with dual functions in ovarian cancer","volume":"13","author":"Ween","year":"2012","journal-title":"Int. J. Mol. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1177\/09603271211017324","article-title":"The usefulness of biomarkers in diagnosis of asbestos-induced malignant pleural mesothelioma","volume":"40","author":"Meteroglu","year":"2021","journal-title":"Hum. Exp. Toxicol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1002\/prca.201300052","article-title":"Comparative proteomic analysis of malignant pleural mesothelioma evidences an altered expression of nuclear lamin and filament-related proteins","volume":"8","author":"Giusti","year":"2014","journal-title":"Proteom. Clin. Appl."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"23798","DOI":"10.1002\/jcp.28948","article-title":"Proteomics analysis of human serum of patients with non-small-cell lung cancer reveals proteins as diagnostic biomarker candidates","volume":"234","author":"Boccellino","year":"2019","journal-title":"J. Cell. Physiol."},{"key":"ref_25","first-page":"3080","article-title":"Gene expression profiling of malignant mesothelioma","volume":"9","author":"Singhal","year":"2003","journal-title":"Clin. Cancer Res."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Lin, T.Y., Yang, C.H., Chou, H.C., Cheng, C.M., Liu, Y.W., Wang, J.Y., Huang, L.R., Tsai, S.F., Huang, S.F., and Chen, Y.R. (2022). EGFR Mutation-Harboring Lung Cancer Cells Produce CLEC11A with Endothelial Trophic and Tumor-Promoting Activities. Cancers, 14.","DOI":"10.3390\/cancers14051356"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Cordeiro, Y.G., Mulder, L.M., van Zeijl, R.J.M., Paskoski, L.B., van Veelen, P., de Ru, A., Strefezzi, R.F., Heijs, B., and Fukumasu, H. (2021). Proteomic Analysis Identifies FNDC1, A1BG, and Antigen Processing Proteins Associated with Tumor Heterogeneity and Malignancy in a Canine Model of Breast Cancer. Cancers, 13.","DOI":"10.3390\/cancers13235901"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e1537427","DOI":"10.1080\/2162402X.2018.1537427","article-title":"Versican modulates tumor-associated macrophage properties to stimulate mesothelioma growth","volume":"8","author":"Pappas","year":"2019","journal-title":"Oncoimmunology"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1080\/08941939.2019.1672839","article-title":"COL11A1 Was Involved in Cell Proliferation, Apoptosis and Migration in Non-Small Cell Lung Cancer Cells","volume":"34","author":"Tu","year":"2021","journal-title":"J. Investig. Surg."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s12935-022-02622-x","article-title":"Thrombospondin-2 acts as a bridge between tumor extracellular matrix and immune infiltration in pancreatic and stomach adenocarcinomas: An integrative pan-cancer analysis","volume":"22","author":"Liao","year":"2022","journal-title":"Cancer Cell Int."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.21873\/anticanres.11460","article-title":"Comparison of the Diagnostic Performance of Fibulin-3 and Mesothelin in Patients with Pleural Effusions from Malignant Mesothelioma","volume":"37","author":"Battolla","year":"2017","journal-title":"Anticancer Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"210057","DOI":"10.1183\/16000617.0057-2021","article-title":"Clinical utility of diagnostic biomarkers in malignant pleural mesothelioma: A systematic review and meta-analysis","volume":"30","author":"Schillebeeckx","year":"2021","journal-title":"Eur. Respir. Rev."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/S0009-9120(00)00157-0","article-title":"Use of tumor markers for differential diagnosis of mesothelioma and secondary pleural malignancies","volume":"33","author":"Fuhrman","year":"2000","journal-title":"Clin. Biochem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"363","DOI":"10.7314\/APJCP.2014.15.1.363","article-title":"CEA, AFP, CA125, CA153 and CA199 in malignant pleural effusions predict the cause","volume":"15","author":"Wang","year":"2014","journal-title":"Asian Pac. J. Cancer Prev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1007\/s12032-013-0543-6","article-title":"Diagnostic value of mesothelin in pleural fluids: Comparison with CYFRA 21-1 and CEA","volume":"30","author":"Filiberti","year":"2013","journal-title":"Med. Oncol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S0169-5002(00)00153-7","article-title":"Diagnostic value of CEA, CA 15-3, CA 19-9, CYFRA 21-1, NSE and TSA assay in pleural effusions","volume":"31","author":"Alatas","year":"2001","journal-title":"Lung Cancer"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Otoshi, T., Kataoka, Y., Ikegaki, S., Saito, E., Matsumoto, H., Kaku, S., Shimada, M., and Hirabayashi, M. (2017). Pleural effusion biomarkers and computed tomography findings in diagnosing malignant pleural mesothelioma: A retrospective study in a single center. 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