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Leung JM, Wu MJ, Kheradpour P, Chen C, Drake KA, Tong G, Ridaura VK, Zisser HC, Conrad WA, Hudson N, Allen J, Welberry C, Parsy-Kowalska C, Macdonald I, Tapson VF, Moy JN, deFilippi CR, Rosas IO, Basit M, Krishnan JA, Parthasarathy S, Prabhakar BS, Salvatore M, Kim CC. Early immune factors associated with the development of post-acute sequelae of SARS-CoV-2 infection in hospitalized and non-hospitalized individuals. Front Immunol 2024; 15:1348041. [PMID: 38318183 PMCID: PMC10838987 DOI: 10.3389/fimmu.2024.1348041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Background Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to post-acute sequelae of SARS-CoV-2 (PASC) that can persist for weeks to years following initial viral infection. Clinical manifestations of PASC are heterogeneous and often involve multiple organs. While many hypotheses have been made on the mechanisms of PASC and its associated symptoms, the acute biological drivers of PASC are still unknown. Methods We enrolled 494 patients with COVID-19 at their initial presentation to a hospital or clinic and followed them longitudinally to determine their development of PASC. From 341 patients, we conducted multi-omic profiling on peripheral blood samples collected shortly after study enrollment to investigate early immune signatures associated with the development of PASC. Results During the first week of COVID-19, we observed a large number of differences in the immune profile of individuals who were hospitalized for COVID-19 compared to those individuals with COVID-19 who were not hospitalized. Differences between individuals who did or did not later develop PASC were, in comparison, more limited, but included significant differences in autoantibodies and in epigenetic and transcriptional signatures in double-negative 1 B cells, in particular. Conclusions We found that early immune indicators of incident PASC were nuanced, with significant molecular signals manifesting predominantly in double-negative B cells, compared with the robust differences associated with hospitalization during acute COVID-19. The emerging acute differences in B cell phenotypes, especially in double-negative 1 B cells, in PASC patients highlight a potentially important role of these cells in the development of PASC.
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Affiliation(s)
| | - Michelle J. Wu
- Verily Life Sciences, South San Francisco, CA, United States
| | | | - Chen Chen
- Verily Life Sciences, South San Francisco, CA, United States
| | | | - Gary Tong
- Verily Life Sciences, South San Francisco, CA, United States
| | | | | | - William A. Conrad
- Providence Little Company of Mary Medical Center Torrance, Torrance, CA, United States
| | | | - Jared Allen
- Oncimmune Limited, Nottingham, United Kingdom
| | | | | | | | - Victor F. Tapson
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - James N. Moy
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | | | - Ivan O. Rosas
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Mujeeb Basit
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jerry A. Krishnan
- Breathe Chicago Center, University of Illinois Chicago, Chicago, IL, United States
| | - Sairam Parthasarathy
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, University of Arizona, Tucson, AZ, United States
| | - Bellur S. Prabhakar
- Department of Microbiology and Immunology, University of Illinois - College of Medicine, Chicago, IL, United States
| | - Mirella Salvatore
- Department of Medicine and Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, United States
| | - Charles C. Kim
- Verily Life Sciences, South San Francisco, CA, United States
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Drake KA, Talantov D, Tong GJ, Lin JT, Verheijden S, Katz S, Leung JM, Yuen B, Krishna V, Wu MJ, Sutherland AM, Short SA, Kheradpour P, Mumbach MR, Franz KM, Trifonov V, Lucas MV, Merson J, Kim CC. Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors. Clin Immunol 2023; 256:109808. [PMID: 37852344 DOI: 10.1016/j.clim.2023.109808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
We sought to better understand the immune response during the immediate post-diagnosis phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. In lymphocytes, the CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. These early stage observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. BACKGROUND: Much of the literature on immune response post-SARS-CoV-2 infection has been in the acute and post-acute phases of infection. TRANSLATIONAL SIGNIFICANCE: We found differences at early time points of infection in approximately 160 participants. We compared multi-omic signatures in immune cells between individuals progressing to needing more significant medical intervention and non-progressors. We observed widespread evidence of a state of increased inflammation associated with progression, supported by a range of epigenomic, transcriptomic, and proteomic signatures. The signatures we identified support other findings at later time points and serve as the basis for prognostic biomarker development or to inform interventional strategies.
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Affiliation(s)
- Katherine A Drake
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Dimitri Talantov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Gary J Tong
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Jack T Lin
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Samuel Katz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Benjamin Yuen
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vinod Krishna
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Michelle J Wu
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Sarah A Short
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Pouya Kheradpour
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Maxwell R Mumbach
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Kate M Franz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vladimir Trifonov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Molly V Lucas
- Janssen Research & Development, LLC, NJ, United States of America
| | - James Merson
- Janssen Research & Development, LLC, San Francisco, CA, United States of America
| | - Charles C Kim
- Verily Life Sciences, South San Francisco, CA, United States of America.
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