A time-resolved proteomic and prognostic map of COVID-19.

Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK. Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany. Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany. University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK. National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW72AZ, UK; Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London SW7 2AZ, UK. The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK. Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield AL10 9AB, UK; Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow 119435, Russia. Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK. Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria. Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria. Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria. Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria. Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany. Charité Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany. Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany. The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Chalmers Tekniska Högskola, Department of Biology and Biological Engineering, SE-412 96 Gothenburg, Sweden. University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK. University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK. University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK. University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK. University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK; Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod 603105, Russia. Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany. Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany. The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK. Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany. Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK. Electronic address: markus.ralser@charite.de. Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany.

Cell systems. 2021;(8):780-794.e7
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Abstract

COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.