{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T05:25:35Z","timestamp":1767677135963,"version":"3.48.0"},"reference-count":53,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,4]],"date-time":"2026-01-04T00:00:00Z","timestamp":1767484800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010193","name":"Madigan Army Medical Center","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100010193","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Department of Clinical Investigation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteomes"],"abstract":"<jats:p>Background: Despite existing proteomics studies of other cell types, a comprehensive proteome of mesothelial cells has not been characterized. This study establishes a crucial baseline proteome for mesothelial cells to better understand their fundamental bioprocesses in healthy and injured states. Methods: Using mass spectrometry-based shotgun proteomics, we characterized the cellular fraction (CF) and conditioned medium (CM) proteomes of mesothelial cell line MeT-5A. The datasets were analyzed for Gene Ontology (GO) terms and canonical pathway enrichments to identify biological themes. Results: Our analysis identified 5087 protein groups, including 1532 shared proteins, 3122 unique to the CF and 433 exclusive to the CM. GO annotation revealed distinct functional enrichment profiles, reflecting the differing roles of intracellular and secreted proteins. While intracellular proteins were linked to core cellular functions, the extracellular proteome was enriched for signaling and cell-to-cell interaction pathways. The proteins shared by both compartments provided an integrated view of the molecular coordination between the cellular and extracellular environments. Conclusions: This study provides the first comprehensive baseline proteome for mesothelial cells and their secreted medium, offering a vital resource for future investigations into the mesothelium, particularly in the context of disease or injury.<\/jats:p>","DOI":"10.3390\/proteomes14010002","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T10:03:48Z","timestamp":1767607428000},"page":"2","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Proteomics and Bioinformatics Profiles of Human Mesothelial Cell Line MeT-5A"],"prefix":"10.3390","volume":"14","author":[{"given":"Rachel L.","family":"Watkin","sequence":"first","affiliation":[{"name":"Department of OB\/GYN, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Avedis A.","family":"Kazanjian","sequence":"additional","affiliation":[{"name":"Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9764-0188","authenticated-orcid":false,"given":"Jennifer R.","family":"Damicis","sequence":"additional","affiliation":[{"name":"Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth","family":"Yohannes","sequence":"additional","affiliation":[{"name":"Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s42003-018-0180-x","article-title":"Mesothelial to mesenchyme transition as a major developmental and pathological player in trunk organs and their cavities","volume":"1","author":"Koopmans","year":"2018","journal-title":"Commun. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1046\/j.1440-1843.2002.00404.x","article-title":"Mesothelial cells: Their structure, function and role in serosal repair","volume":"7","author":"Mutsaers","year":"2002","journal-title":"Respirology"},{"key":"ref_3","first-page":"520","article-title":"Source of peritoneal proteoglycans. Human peritoneal mesothelial cells synthesize and secrete mainly small dermatan sulfate proteoglycans","volume":"146","author":"Yung","year":"1995","journal-title":"Am. J. Pathol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1164\/ajrccm.158.3.9801097","article-title":"Talc-induced expression of C-C and C-X-C chemokines and intercellular adhesion molecule-1 in mesothelial cells","volume":"158","author":"Nasreen","year":"1998","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4206","DOI":"10.1128\/iai.63.10.4206-4209.1995","article-title":"Interleukin-8 production by human mesothelial cells after direct stimulation with staphylococci","volume":"63","author":"Visser","year":"1995","journal-title":"Infect. Immun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1515\/pp-2016-0009","article-title":"Diverse properties of the mesothelial cells in health and disease","volume":"1","author":"Kawanishi","year":"2016","journal-title":"Pleura Peritoneum"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.coi.2020.04.005","article-title":"Mesothelial cells regulate immune responses in health and disease: Role for immunotherapy in malignant mesothelioma","volume":"64","author":"Mutsaers","year":"2020","journal-title":"Curr. Opin. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1002\/(SICI)1096-9896(199611)180:3<333::AID-PATH659>3.0.CO;2-Y","article-title":"Changes in the concentration of microvilli on the free surface of healing mesothelium are associated with alterations in surface membrane charge","volume":"180","author":"Mutsaers","year":"1996","journal-title":"J. Pathol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.ccm.2005.12.003","article-title":"Pleural fibrosis","volume":"27","author":"Jantz","year":"2006","journal-title":"Clin. Chest Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/path.1711510309","article-title":"Role of macrophages in mesothelial healing","volume":"151","author":"Fotev","year":"1987","journal-title":"J. Pathol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1016\/j.molmed.2025.03.014","article-title":"Mesothelial and immune cells interplay in the tumor microenvironment","volume":"31","author":"Sheng","year":"2025","journal-title":"Trends Mol. Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4161\/spmg.19885","article-title":"Cell lines: Valuable tools or useless artifacts","volume":"2","author":"Kaur","year":"2012","journal-title":"Spermatogenesis"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Voloshin, N., Tyurin-Kuzmin, P., Karagyaur, M., Akopyan, Z., and Kulebyakin, K. (2023). Practical Use of Immortalized Cells in Medicine: Current Advances and Future Perspectives. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241612716"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Chalak, M., Hesaraki, M., Mirbahari, S.N., Yeganeh, M., Abdi, S., Rajabi, S., and Hemmatzadeh, F. (2024). Cell Immortality: In Vitro Effective Techniques to Achieve and Investigate Its Applications and Challenges. Life, 14.","DOI":"10.3390\/life14030417"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1074\/mcp.M800258-MCP200","article-title":"Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions","volume":"8","author":"Pan","year":"2009","journal-title":"Mol. Cell Proteom."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/j.ccell.2022.06.010","article-title":"Pan-cancer proteomic map of 949 human cell lines","volume":"40","author":"Goncalves","year":"2022","journal-title":"Cancer Cell"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2019.12.023","article-title":"Quantitative Proteomics of the Cancer Cell Line Encyclopedia","volume":"180","author":"Nusinow","year":"2020","journal-title":"Cell"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1016\/S0002-9440(10)63739-X","article-title":"Proteomic analysis of exosomes secreted by human mesothelioma cells","volume":"164","author":"Hegmans","year":"2004","journal-title":"Am. J. Pathol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1080\/14789450.2023.2174851","article-title":"Proteomic study of mesothelial and endothelial cross-talk: Key lessons","volume":"19","author":"Sacnun","year":"2022","journal-title":"Expert. Rev. Proteom."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nmeth.1322","article-title":"Universal sample preparation method for proteome analysis","volume":"6","author":"Wisniewski","year":"2009","journal-title":"Nat. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"8980","DOI":"10.1038\/s41598-019-44962-1","article-title":"The human tubal lavage proteome reveals biological processes that may govern the pathology of hydrosalpinx","volume":"9","author":"Yohannes","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Yohannes, E., Ippolito, D.L., Damicis, J.R., Dornisch, E.M., Leonard, K.M., Napolitano, P.G., and Ieronimakis, N. (2022). Longitudinal Proteomic Analysis of Plasma across Healthy Pregnancies Reveals Indicators of Gestational Age. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23137076"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"166747","DOI":"10.1016\/j.jmb.2020.166747","article-title":"FunRich enables enrichment analysis of OMICs datasets","volume":"433","author":"Fonseka","year":"2021","journal-title":"J. Mol. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1477-5956-11-5","article-title":"On protein abundance distributions in complex mixtures","volume":"11","author":"Koziol","year":"2013","journal-title":"Proteome Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"37606","DOI":"10.1038\/srep37606","article-title":"Quantitative secretomic analysis of pancreatic cancer cells in serum-containing conditioned medium","volume":"6","author":"Liu","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Nakamura, R., Nakajima, D., Sato, H., Endo, Y., Ohara, O., and Kawashima, Y. (2021). A Simple Method for In-Depth Proteome Analysis of Mammalian Cell Culture Conditioned Media Containing Fetal Bovine Serum. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22052565"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Didiasova, M., Schaefer, L., and Wygrecka, M. (2019). When Place Matters: Shuttling of Enolase-1 Across Cellular Compartments. Front. Cell Dev. Biol., 7.","DOI":"10.3389\/fcell.2019.00061"},{"key":"ref_28","first-page":"156795","article-title":"alpha-Enolase, a multifunctional protein: Its role on pathophysiological situations","volume":"2012","year":"2012","journal-title":"J. Biomed. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1038\/s41419-020-03179-1","article-title":"Exosome-derived ENO1 regulates integrin alpha6beta4 expression and promotes hepatocellular carcinoma growth and metastasis","volume":"11","author":"Jiang","year":"2020","journal-title":"Cell Death Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"365","DOI":"10.4049\/jimmunol.1102073","article-title":"alpha-Enolase expressed on the surfaces of monocytes and macrophages induces robust synovial inflammation in rheumatoid arthritis","volume":"189","author":"Bae","year":"2012","journal-title":"J. Immunol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.omto.2021.12.026","article-title":"ENO1 and Cancer","volume":"24","author":"Huang","year":"2022","journal-title":"Mol. Ther. Oncolytics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.copbio.2010.06.004","article-title":"Pathways of unconventional protein secretion","volume":"21","author":"Nickel","year":"2010","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Maricchiolo, E., Panfili, E., Pompa, A., De Marchis, F., Bellucci, M., and Pallotta, M.T. (2022). Unconventional Pathways of Protein Secretion: Mammals vs. Plants. Front. Cell Dev. Biol., 10.","DOI":"10.3389\/fcell.2022.895853"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/s41419-025-07749-z","article-title":"Tumor exosomal circPTBP3 drives gastric cancer peritoneal metastasis via mesothelial-mesenchymal transition","volume":"16","author":"Dong","year":"2025","journal-title":"Cell Death Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"56855","DOI":"10.18632\/oncotarget.10869","article-title":"Tumor exosome-mediated promotion of adhesion to mesothelial cells in gastric cancer cells","volume":"7","author":"Arita","year":"2016","journal-title":"Oncotarget"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Pascual-Anton, L., Cardenes, B., Sainz de la Cuesta, R., Gonzalez-Cortijo, L., Lopez-Cabrera, M., Cabanas, C., and Sandoval, P. (2021). Mesothelial-to-Mesenchymal Transition and Exosomes in Peritoneal Metastasis of Ovarian Cancer. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222111496"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Mutsaers, S.E., Birnie, K., Lansley, S., Herrick, S.E., Lim, C.B., and Prele, C.M. (2015). Mesothelial cells in tissue repair and fibrosis. Front. Pharmacol., 6.","DOI":"10.3389\/fphar.2015.00113"},{"key":"ref_38","first-page":"547","article-title":"Role of mesothelial and submesothelial stromal cells in matrix remodeling following pleural injury","volume":"142","author":"Davila","year":"1993","journal-title":"Am. J. Pathol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.yjmcc.2016.01.011","article-title":"Extracellular matrix-mediated cellular communication in the heart","volume":"91","author":"Schafer","year":"2016","journal-title":"J. Mol. Cell Cardiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1007\/s43032-021-00595-2","article-title":"Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology","volume":"28","author":"Priyanka","year":"2021","journal-title":"Reprod. Sci."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Rose, A., Schraegle, S.J., Stahlberg, E.A., and Meier, I. (2005). Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control. BMC Evol. Biol., 5.","DOI":"10.1186\/1471-2148-5-66"},{"key":"ref_42","first-page":"615","article-title":"The endoplasmic reticulum-gateway of the secretory pathway","volume":"11","author":"Vitale","year":"1999","journal-title":"Plant Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"8301","DOI":"10.1038\/s41467-023-43931-7","article-title":"Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding","volume":"14","author":"Yamada","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Piperigkou, Z., Mangani, S., Koletsis, N.E., Koutsakis, C., Mastronikolis, N.S., Franchi, M., and Karamanos, N.K. (2025). Principal mechanisms of extracellular matrix-mediated cell-cell communication in physiological and tumor microenvironments. FEBS J.","DOI":"10.1111\/febs.70207"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s12964-017-0177-y","article-title":"The role of JAK-STAT signaling pathway and its regulators in the fate of T helper cells","volume":"15","author":"Seif","year":"2017","journal-title":"Cell Commun. Signal"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Hu, Q., Bian, Q., Rong, D., Wang, L., Song, J., Huang, H.S., Zeng, J., Mei, J., and Wang, P.Y. (2023). JAK\/STAT pathway: Extracellular signals, diseases, immunity, and therapeutic regimens. Front. Bioeng. Biotechnol., 11.","DOI":"10.3389\/fbioe.2023.1110765"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.cytogfr.2023.05.001","article-title":"The role of Extracellular Vesicles in glycolytic and lipid metabolic reprogramming of cancer cells: Consequences for drug resistance","volume":"73","author":"Polonia","year":"2023","journal-title":"Cytokine Growth Factor. Rev."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.cca.2018.10.044","article-title":"Extracellular vesicles and energy metabolism","volume":"488","year":"2019","journal-title":"Clin. Chim. Acta"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.semcancer.2019.02.004","article-title":"Ras and exosome signaling","volume":"54","author":"Sexton","year":"2019","journal-title":"Semin. Cancer Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1074\/mcp.O116.064188","article-title":"Extracellular Protein Phosphorylation, the Neglected Side of the Modification","volume":"16","author":"Klement","year":"2017","journal-title":"Mol. Cell Proteom."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1016\/j.cell.2015.05.028","article-title":"A Single Kinase Generates the Majority of the Secreted Phosphoproteome","volume":"161","author":"Tagliabracci","year":"2015","journal-title":"Cell"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e58184","DOI":"10.7554\/eLife.58184","article-title":"The role of extracellular matrix phosphorylation on energy dissipation in bone","volume":"9","author":"Bailey","year":"2020","journal-title":"Elife"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e2200287","DOI":"10.1002\/pmic.202200287","article-title":"Integrating intracellular and extracellular proteomic profiling for in-depth investigations of cellular communication in a model of prostate cancer","volume":"23","author":"Miles","year":"2023","journal-title":"Proteomics"}],"container-title":["Proteomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-7382\/14\/1\/2\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T05:14:09Z","timestamp":1767676449000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-7382\/14\/1\/2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,4]]},"references-count":53,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["proteomes14010002"],"URL":"https:\/\/doi.org\/10.3390\/proteomes14010002","relation":{},"ISSN":["2227-7382"],"issn-type":[{"type":"electronic","value":"2227-7382"}],"subject":[],"published":{"date-parts":[[2026,1,4]]}}}