{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T16:09:00Z","timestamp":1768838940130,"version":"3.49.0"},"posted":{"date-parts":[[2026,1,13]]},"group-title":"Respiratory Medicine","reference-count":80,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T00:00:00Z","timestamp":1768262400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,1,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Community-acquired pneumonia is a major cause of morbidity and mortality globally. Specific molecular endotypes are currently not well defined and different viral or bacterial pathogens may trigger specific host responses and pathogenic mechanisms. We performed longitudinal proteomic profiling of bronchoalveolar lavage fluid and plasma from bacterial, influenza and SARS-COV-2 driven pneumonia. Our analysis revealed highly pneumonia type specific proteomic signatures, including COVID-19 specific antibodies locally produced in the lung. These antibodies showed biased immunoglobulin V-domain usage, linked to a\n                  <jats:italic>CD69<\/jats:italic>\n                  \/\n                  <jats:italic>CD83<\/jats:italic>\n                  plasma cell state associated with disease severity and degree of autoimmunity. Using mass spectrometry driven autoantibody profiling in two independent COVID-19 cohorts, we identified 177 putative autoantibodies targeting extracellular matrix, nuclear, and immune-related proteins. Of note, temporal changes in autoantibody profiles correlated with clinical markers of inflammation, organ dysfunction, and duration of hospitalization. These findings highlight the autoimmune aspects of COVID-19 and provide potential biomarkers and therapeutic targets to help improve patient outcomes.\n                <\/jats:p>","DOI":"10.64898\/2026.01.12.26343938","type":"posted-content","created":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T05:35:28Z","timestamp":1768368928000},"source":"Crossref","is-referenced-by-count":0,"title":["Longitudinal clinical proteomics reveals pneumonia type-specific protein biomarkers and autoantibodies"],"prefix":"10.64898","author":[{"given":"Anna","family":"Semenova","sequence":"first","affiliation":[{"name":"Research Unit for Precision Regenerative Medicine, Helmholtz Munich, Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taylor A.","family":"Poor","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes B.","family":"M\u00fcller-Reif","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sai Rama Sridatta","family":"Prakki","sequence":"additional","affiliation":[{"name":"Research Unit for Precision Regenerative Medicine, Helmholtz Munich, Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), Munich, Germany"},{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phillip","family":"Geyer","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany"},{"name":"OmicEra Diagnostics GmbH, Planegg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"M\u00fcck-H\u00e4usl","sequence":"additional","affiliation":[{"name":"Research Unit for Precision Regenerative Medicine, Helmholtz Munich, Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lesca M.","family":"Holdt","sequence":"additional","affiliation":[{"name":"Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Teupser","sequence":"additional","affiliation":[{"name":"Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Mann","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali \u00d6.","family":"Yildirim","sequence":"additional","affiliation":[{"name":"Institute of Lung Health and Immunity, Helmholtz Munich, Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), Munich, Germany"},{"name":"Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard G.","family":"Wunderink","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander V.","family":"Misharin","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ben D.","family":"Singer","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G.R. Scott","family":"Budinger","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Theodore S.","family":"Kapellos","sequence":"additional","affiliation":[{"name":"Institute of Lung Health and Immunity, Helmholtz Munich, Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), Munich, Germany"},{"name":"Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herbert B.","family":"Schiller","sequence":"additional","affiliation":[{"name":"Research Unit for Precision Regenerative Medicine, Helmholtz Munich, Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), Munich, Germany"},{"name":"Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026011607400566000_2026.01.12.26343938v1.1","doi-asserted-by":"publisher","DOI":"10.46234\/ccdcw2023.013"},{"key":"2026011607400566000_2026.01.12.26343938v1.2","unstructured":"Sattar SBA , Nguyen AD , Sharma S. 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