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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Zheng H, Rao AM, Dermadi D, Toh J, Murphy Jones L, Donato M, Liu Y, Su Y, Dai CL, Kornilov SA, Karagiannis M, Marantos T, Hasin-Brumshtein Y, He YD, Giamarellos-Bourboulis EJ, Heath JR, Khatri P. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021; 54:753-768.e5. [PMID: 33765435 PMCID: PMC7988739 DOI: 10.1016/j.immuni.2021.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
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Affiliation(s)
- Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Jiaying Toh
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Lara Murphy Jones
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA; Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Stanford University, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Yiran Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Cancer Biology program, Stanford University, CA 94305, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Cheng L Dai
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Minas Karagiannis
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | - Theodoros Marantos
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | | | | | | | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA.
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