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Palma Medina LM, Babačić H, Dzidic M, Parke Å, Garcia M, Maleki KT, Unge C, Lourda M, Kvedaraite E, Chen P, Muvva JR, Cornillet M, Emgård J, Moll K, Michaëlsson J, Flodström-Tullberg M, Brighenti S, Buggert M, Mjösberg J, Malmberg KJ, Sandberg JK, Gredmark-Russ S, Rooyackers O, Svensson M, Chambers BJ, Eriksson LI, Pernemalm M, Björkström NK, Aleman S, Ljunggren HG, Klingström J, Strålin K, Norrby-Teglund A. Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia. Respir Res 2023; 24:62. [PMID: 36829233 PMCID: PMC9950694 DOI: 10.1186/s12931-023-02364-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND COVID-19 remains a major public health challenge, requiring the development of tools to improve diagnosis and inform therapeutic decisions. As dysregulated inflammation and coagulation responses have been implicated in the pathophysiology of COVID-19 and sepsis, we studied their plasma proteome profiles to delineate similarities from specific features. METHODS We measured 276 plasma proteins involved in Inflammation, organ damage, immune response and coagulation in healthy controls, COVID-19 patients during acute and convalescence phase, and sepsis patients; the latter included (i) community-acquired pneumonia (CAP) caused by Influenza, (ii) bacterial CAP, (iii) non-pneumonia sepsis, and (iv) septic shock patients. RESULTS We identified a core response to infection consisting of 42 proteins altered in both COVID-19 and sepsis, although higher levels of cytokine storm-associated proteins were evident in sepsis. Furthermore, microbiologic etiology and clinical endotypes were linked to unique signatures. Finally, through machine learning, we identified biomarkers, such as TRIM21, PTN and CASP8, that accurately differentiated COVID-19 from CAP-sepsis with higher accuracy than standard clinical markers. CONCLUSIONS This study extends the understanding of host responses underlying sepsis and COVID-19, indicating varying disease mechanisms with unique signatures. These diagnostic and severity signatures are candidates for the development of personalized management of COVID-19 and sepsis.
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Affiliation(s)
- Laura M. Palma Medina
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Haris Babačić
- grid.4714.60000 0004 1937 0626Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Majda Dzidic
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Åsa Parke
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Marina Garcia
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Kimia T. Maleki
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Christian Unge
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Functional Area of Emergency Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Magda Lourda
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden ,grid.4714.60000 0004 1937 0626Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Egle Kvedaraite
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Puran Chen
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Jagadeeswara Rao Muvva
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Martin Cornillet
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Johanna Emgård
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Kirsten Moll
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | | | - Jakob Michaëlsson
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Malin Flodström-Tullberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Susanna Brighenti
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Marcus Buggert
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Jenny Mjösberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Karl-Johan Malmberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Johan K. Sandberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Sara Gredmark-Russ
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden ,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Olav Rooyackers
- grid.24381.3c0000 0000 9241 5705Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden ,grid.4714.60000 0004 1937 0626Division for Anesthesiology and Intensive Care, Department of Clinical Interventions and Technology CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Svensson
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Benedict J. Chambers
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Lars I. Eriksson
- grid.24381.3c0000 0000 9241 5705Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pernemalm
- grid.4714.60000 0004 1937 0626Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Niklas K. Björkström
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Soo Aleman
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Jonas Klingström
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Kristoffer Strålin
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Norrby-Teglund
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden.
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Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med 2021; 2:100287. [PMID: 33969320 PMCID: PMC8091031 DOI: 10.1016/j.xcrm.2021.100287] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
Mechanisms underlying severe coronavirus disease 2019 (COVID-19) disease remain poorly understood. We analyze several thousand plasma proteins longitudinally in 306 COVID-19 patients and 78 symptomatic controls, uncovering immune and non-immune proteins linked to COVID-19. Deconvolution of our plasma proteome data using published scRNA-seq datasets reveals contributions from circulating immune and tissue cells. Sixteen percent of patients display reduced inflammation yet comparably poor outcomes. Comparison of patients who died to severely ill survivors identifies dynamic immune-cell-derived and tissue-associated proteins associated with survival, including exocrine pancreatic proteases. Using derived tissue-specific and cell-type-specific intracellular death signatures, cellular angiotensin-converting enzyme 2 (ACE2) expression, and our data, we infer whether organ damage resulted from direct or indirect effects of infection. We propose a model in which interactions among myeloid, epithelial, and T cells drive tissue damage. These datasets provide important insights and a rich resource for analysis of mechanisms of severe COVID-19 disease.
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Affiliation(s)
- Michael R. Filbin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexis M. Schneider
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle R. Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Matteo Gentili
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Bánk G. Fenyves
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Semmelweis University, Budapest, Hungary
| | - Nicole C. Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna L.K. Gonye
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Irena Gushterova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K. Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M. Lilley
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L. Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D. Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N. McKaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C. Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F. Thomas
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert E. Gerszten
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- CardioVascular Institute, Department of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Graham S. Heimberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Paul J. Hoover
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - David J. Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian Lin
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Debby Ngo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Miguel Reyes
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S. Smillie
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas E. Wood
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Amanda S. Zajac
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | | | - Roby P. Bhattacharyya
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marcia B. Goldberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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