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Feyaerts D, Hédou J, Gillard J, Chen H, Tsai ES, Peterson LS, Ando K, Manohar M, Do E, Dhondalay GKR, Fitzpatrick J, Artandi M, Chang I, Snow TT, Chinthrajah RS, Warren CM, Wittman R, Meyerowitz JG, Ganio EA, Stelzer IA, Han X, Verdonk F, Gaudillière DK, Mukherjee N, Tsai AS, Rumer KK, Jacobsen DR, Bjornson-Hooper ZB, Jiang S, Saavedra SF, Valdés Ferrer SI, Kelly JD, Furman D, Aghaeepour N, Angst MS, Boyd SD, Pinsky BA, Nolan GP, Nadeau KC, Gaudillière B, McIlwain DR. Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19. Cell Rep Med 2022; 3:100680. [PMID: 35839768 PMCID: PMC9238057 DOI: 10.1016/j.xcrm.2022.100680] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/25/2022] [Accepted: 06/14/2022] [Indexed: 02/06/2023]
Abstract
The biological determinants underlying the range of coronavirus 2019 (COVID-19) clinical manifestations are not fully understood. Here, over 1,400 plasma proteins and 2,600 single-cell immune features comprising cell phenotype, endogenous signaling activity, and signaling responses to inflammatory ligands are cross-sectionally assessed in peripheral blood from 97 patients with mild, moderate, and severe COVID-19 and 40 uninfected patients. Using an integrated computational approach to analyze the combined plasma and single-cell proteomic data, we identify and independently validate a multi-variate model classifying COVID-19 severity (multi-class area under the curve [AUC]training = 0.799, p = 4.2e-6; multi-class AUCvalidation = 0.773, p = 7.7e-6). Examination of informative model features reveals biological signatures of COVID-19 severity, including the dysregulation of JAK/STAT, MAPK/mTOR, and nuclear factor κB (NF-κB) immune signaling networks in addition to recapitulating known hallmarks of COVID-19. These results provide a set of early determinants of COVID-19 severity that may point to therapeutic targets for prevention and/or treatment of COVID-19 progression.
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Affiliation(s)
- Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julien Hédou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua Gillard
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Han Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eileen S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura S Peterson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - Evan Do
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - Gopal K R Dhondalay
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jessica Fitzpatrick
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - Maja Artandi
- Department of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Iris Chang
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - Theo T Snow
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - R Sharon Chinthrajah
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher M Warren
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA
| | - Richard Wittman
- Department of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin G Meyerowitz
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ina A Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaoyuan Han
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Sciences, University of the Pacific, Arthur A. Dugoni School of Dentistry, San Francisco, CA, USA
| | - Franck Verdonk
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dyani K Gaudillière
- Division of Plastic & Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Nilanjan Mukherjee
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kristen K Rumer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Danielle R Jacobsen
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Zachary B Bjornson-Hooper
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sizun Jiang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sergio Fragoso Saavedra
- Departamento de Neurología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico; Plan de Estudios Combinados en Medicina (MD/PhD Program), Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sergio Iván Valdés Ferrer
- Departamento de Neurología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA; Institute for Global Health Sciences, UCSF, San Francisco, CA, USA; F.I. Proctor Foundation, UCSF, San Francisco, CA, USA
| | - David Furman
- Buck Artificial Intelligence Platform, Buck Institute for Research on Aging, Novato, CA, USA; Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA; Austral Institute for Applied Artificial Intelligence, Institute for Research in Translational Medicine (IIMT), Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Scott D Boyd
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Kari C Nadeau
- Sean N Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - David R McIlwain
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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