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IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques

View ORCID ProfileChristine E. Nelson, Taylor W. Foreman, Keith D. Kauffman, Shunsuke Sakai, Joel D. Fleegle, Felipe Gomez, NIAID/DIR Tuberculosis Imaging Program, Cyril Le Nouën, Xueqiao Liu, Tracey L. Burdette, Nicole L. Garza, Bernard A. P. Lafont, Kelsie Brooks, View ORCID ProfileCecilia S. Lindestam Arlehamn, Daniela Weiskopf, Alessandro Sette, Heather D. Hickman, Ursula J. Buchholz, Reed F. Johnson, Jason M. Brenchley, Laura E. Via, Daniel L. Barber
doi: https://doi.org/10.1101/2022.09.13.507852
Christine E. Nelson
1T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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  • ORCID record for Christine E. Nelson
Taylor W. Foreman
1T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Keith D. Kauffman
1T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Shunsuke Sakai
1T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Joel D. Fleegle
2Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Felipe Gomez
2Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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2Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
Cyril Le Nouën
3RNA Viruses Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Xueqiao Liu
3RNA Viruses Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Tracey L. Burdette
4SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.
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Nicole L. Garza
4SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.
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Bernard A. P. Lafont
4SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.
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Kelsie Brooks
5Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Cecilia S. Lindestam Arlehamn
6Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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  • ORCID record for Cecilia S. Lindestam Arlehamn
Daniela Weiskopf
6Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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Alessandro Sette
6Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
7Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA.
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Heather D. Hickman
8Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Ursula J. Buchholz
3RNA Viruses Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Reed F. Johnson
4SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.
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Jason M. Brenchley
5Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Laura E. Via
9Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
10Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Observatory, South Africa.
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Daniel L. Barber
1T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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  • For correspondence: barberd@niaid.nih.gov
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ABSTRACT

The pro- and anti-inflammatory pathways that determine the balance of inflammation and viral control during SARS-CoV-2 infection are not well understood. Here we examine the roles of IFNγ and IL-10 in regulating inflammation, immune cell responses and viral replication during SARS-CoV-2 infection of rhesus macaques. IFNγ blockade tended to decrease lung inflammation based on 18FDG-PET/CT imaging but had no major impact on innate lymphocytes, neutralizing antibodies, or antigen-specific T cells. In contrast, IL-10 blockade transiently increased lung inflammation and enhanced accumulation of virus-specific T cells in the lower airways. However, IL-10 blockade also inhibited the differentiation of virus-specific T cells into airway CD69+CD103+ TRM cells. While virus-specific T cells were undetectable in the nasal mucosa of all groups, IL-10 blockade similarly reduced the frequency of total TRM cells in the nasal mucosa. Neither cytokine blockade substantially affected viral load and infection ultimately resolved. Thus, in the macaque model of mild COVID-19, the pro- and anti-inflammatory effects of IFNγ and IL-10 have no major role in control of viral replication. However, IL-10 has a key role in suppressing the accumulation of SARS-CoV-2-specific T cells in the lower airways, while also promoting TRM at respiratory mucosal surfaces.

Competing Interest Statement

Alessandro Sette is a consultant for Gritstone Bio, Flow Pharma, Moderna, AstraZeneca, Qiagen, Avalia, Fortress, Gilead, Sanofi, Merck, RiverVest, MedaCorp, Turnstone, NA Vaccine Institute, Gerson Lehrman Group and Guggenheim. LJI has filed for patent protection for various aspects of T cell epitope and vaccine design work. All other authors have no competing interests to disclose.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 13, 2022.
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IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques
Christine E. Nelson, Taylor W. Foreman, Keith D. Kauffman, Shunsuke Sakai, Joel D. Fleegle, Felipe Gomez, NIAID/DIR Tuberculosis Imaging Program, Cyril Le Nouën, Xueqiao Liu, Tracey L. Burdette, Nicole L. Garza, Bernard A. P. Lafont, Kelsie Brooks, Cecilia S. Lindestam Arlehamn, Daniela Weiskopf, Alessandro Sette, Heather D. Hickman, Ursula J. Buchholz, Reed F. Johnson, Jason M. Brenchley, Laura E. Via, Daniel L. Barber
bioRxiv 2022.09.13.507852; doi: https://doi.org/10.1101/2022.09.13.507852
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IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques
Christine E. Nelson, Taylor W. Foreman, Keith D. Kauffman, Shunsuke Sakai, Joel D. Fleegle, Felipe Gomez, NIAID/DIR Tuberculosis Imaging Program, Cyril Le Nouën, Xueqiao Liu, Tracey L. Burdette, Nicole L. Garza, Bernard A. P. Lafont, Kelsie Brooks, Cecilia S. Lindestam Arlehamn, Daniela Weiskopf, Alessandro Sette, Heather D. Hickman, Ursula J. Buchholz, Reed F. Johnson, Jason M. Brenchley, Laura E. Via, Daniel L. Barber
bioRxiv 2022.09.13.507852; doi: https://doi.org/10.1101/2022.09.13.507852

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