Innate lymphoid cells and COVID-19 severity in SARS-CoV-2 infection
- University of Massachusetts Medical School, United States
- Ragon Institute of MGH, MIT and Harvard, United States
- Massachusetts General Hospital, United States
- University of Pennsylvania, United States
- Brigham and Women's Hospital, United States
- Ragon Institute of MGH, MIT, and Harvard, United States
Abstract
Background: Risk of severe COVID-19 increases with age, is greater in males, and is associated with lymphopenia, but not with higher burden of SARS-CoV-2. It is unknown whether effects of age and sex on abundance of specific lymphoid subsets explain these correlations.
Methods: Multiple regression was used to determine the relationship between abundance of specific blood lymphoid cell types, age, sex, requirement for hospitalization, duration of hospitalization, and elevation of blood markers of systemic inflammation, in adults hospitalized for severe COVID-19 (n=40), treated for COVID-19 as outpatients (n=51), and in uninfected controls (n=86), as well as in children with COVID-19 (n=19), recovering from COVID-19 (n=14), MIS-C (n=11), recovering from MIS-C (n=7), and pediatric controls (n=17).
Results: This observational study found that the abundance of innate lymphoid cells (ILCs) decreases more than 7-fold over the human lifespan - T cell subsets decrease less than 2-fold - and is lower in males than in females. After accounting for effects of age and sex, ILCs, but not T cells, were lower in adults hospitalized with COVID-19, independent of lymphopenia. Among SARS-CoV-2-infected adults, the abundance of ILCs, but not of T cells, correlated inversely with odds and duration of hospitalization, and with severity of inflammation. ILCs were also uniquely decreased in pediatric COVID-19 and the numbers of these cells did not recover during follow-up. In contrast, children with MIS-C had depletion of both ILCs and T cells, and both cell types increased during follow-up. In both pediatric COVID-19 and MIS-C, ILC abundance correlated inversely with inflammation. Blood ILC mRNA and phenotype tracked closely with ILCs from lung. Importantly, blood ILCs produced amphiregulin, a protein implicated in disease tolerance and tissue homeostasis. Among controls, the percentage of ILCs that produced amphiregulin was higher in females than in males, and people hospitalized with COVID-19 had a lower percentage of ILCs that produced amphiregulin than did controls.
Conclusions: These results suggest that, by promoting disease tolerance, homeostatic ILCs decrease morbidity and mortality associated with SARS-CoV-2 infection, and that lower ILC abundance contributes to increased COVID-19 severity with age and in males.
Funding: This work was supported in part by the Massachusetts Consortium for Pathogen Readiness and NIH grants R37AI147868, R01AI148784, F30HD100110, 5K08HL143183.
Data availability
All clinical and flow cytometry data generated and analyzed in this article are included in the manuscript and are provided in three spreadsheets titled: "Adult_COVIDandControl_data.xlsx", "Pediatric_ COVID_MISC_andControl_data.xlsx", and "AREG_in_ILCs.xlsx". New Bulk RNA-seq datasets generated here are deposited at: NCBI Gene Expression Omnibus (GEO): GSE168212.
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Systematic analysis of innate lymphoid cells and natural killer cells in context of HIV-1 infectionNCBI Gene Expression Omnibus, GSE168212.
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Group 3 innate lymphoid cells mediate early protective immunity against Mycobacterium tuberculosisNCBI Gene Expression Omnibus, GSE131031.
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Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue SpecificityNCBI Gene Expression Omnibus, GSE126107.
Article and author information
Author details
Noah J Silverstein
Funding
National Institutes of Health (R37AI147868)
- Jeremy Luban
National Institutes of Health (R01AI148784)
- Jeremy Luban
National Institutes of Health (F30HD100110)
- Noah J Silverstein
National Institutes of Health (5K08HL143183)
- Lael M Yonker
Massachusetts Consortium for Pathogen Readiness
- Jeremy Luban
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: As part of a COVID-19 observational study, peripheral blood samples were collected between March 31st and June 3rd of 2020 from 91 adults with SARS-CoV-2 infection, either after admission to Massachusetts General Hospital for the hospitalized cohort, or while at affiliated outpatient clinics for the outpatient cohort. Request for access to coded patient samples was reviewed by the Massachusetts Consortium for Pathogen Readiness (https://masscpr.hms.harvard.edu/) and approved by the University of Massachusetts Medical School IRB (protocol #H00020836). Pediatric participants with COVID-19 or MIS-C were enrolled in the Massachusetts General Hospital Pediatric COVID-19 Biorepository (MGB IRB # 2020P000955). Healthy pediatric controls were enrolled in the Pediatric Biorepository (MGB IRB # 2016P000949). Samples were collected after obtaining consent from the patient if 18 years or older, or from the parent/guardian, plus assent when appropriate.
Copyright
© 2022, Silverstein et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Innate lymphoid cells and COVID-19 severity in SARS-CoV-2 infection
eLife 11:e74681.
https://doi.org/10.7554/eLife.74681
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