Genetic and infectious factors shaping population variation in human immune responses to SARS-CoV-2 – COVID-19-POPCELL

We propose to study, using single-cell technologies, the factors that shape immune response variation of peripheral blood mononuclear cells from healthy individuals of different ancestry. Specifically, our aims are: 1) to analyze the immune response to SARS-CoV-2 infection in 200 individuals of African and European descent, using single-cell RNA sequencing (scRNA-seq); 2) to identify regulatory regions that respond to environmental infectious cues and contribute to the priming of the immune response to SARS-CoV-2, using single-cell Assay for Transposase Accessible Chromatin sequencing (scATAC-seq), and 3) to assess the contribution of host genetics factors to the cell-type specific regulation of the immune response to SARS-CoV-2, through the mapping of expression quantitative trait loci (eQTLs).

We have shown that while stimulation with SARS-CoV-2 does not induce a productive infection in PBMCs after 6 or 24 hours, cells are well capable to respond to SARS-CoV-2. Moreover, while the responses of B, T and NK cells are very similar between virus, involving a modulus of genes stimulated by interferons (ISGs; e.g., ISG15, ISG20, MX1, OAS3), the nature of the myeloid response is more virus-dependent. While the response of myeloid cells to IAV is characterized by a stronger induction of ISG (i.e. genes stimulated by interferon), that induced by SARS-CoV-2 mainly involves proinflammatory cytokines (IL1B, IL6, CXCL8 and TNFAIP6). Thereby, the fact that our data capture the transition from an antiviral response to a proinflammatory response, characteristic of SARS-CoV-2 infection, confirms our choice of PBMCs as a system to model this response.

If this kinetics is not intended to be a population study, with 8 individuals we have enough statistical power to detect around 1000 differentially expressed genes, in at least one cell type, time point or condition, between the cells from individuals of European and African origin. Among these genes we find IFITM3, important mediator of the antiviral response, which is much less expressed in the cells of European origin in all cell types and conditions. Nevertheless, while in NK cells the difference in expression of IFITM3 between populations is constant between conditions, it is significantly accentuated after stimulation in CD4 + T cells. Thus, our data reveal population differences that are only apparent upon viral challenge.

Our study should identify key cellular players of the immune response to SARS-CoV-2 as well as host genetic variants and molecular mechanisms underlying differences in the cellular responses between individuals of different ancestry. Altogether, this project will improve our understanding of how host genetics, ancestry, and environmental factors concur to shape the diversity of the human immune response to SARSCoV-2. It will also help to understand the causal mechanisms at play of COVID-19 susceptibility/severity loci identified through genome-wide association studies, and facilitate the translation of these studies into novel preventive and therapeutic strategies.

Mary B O'Neill, Yann Aquino, Aurelie Bixiaux, Zhi Li, Sarah Merkling, Julien Pothlichet, Helene Quach, Nikaia Smith, Darragh Duffy, Valentina Libri, Milena Hasan, Shen-Ying Zhang, Qian Zhang, Laurent Abel, Jean-Laurent Casanova, Nadia Naffakh, Maxime Rotival, Lluis Quintana- Murci. Population Differences in Epigenetic and Transcriptional Responses to
Challenge by RNA viruses at the Single-Cell Level. Biology of Genomes 2021, Cold Spring Harbor Laboratories, New York, USA

Yann Aquino, Mary B O'Neill, Aurelie Bixiaux, Zhi Li, Sarah Merkling, Julien Pothlichet, Helene Quach, Nikaia Smith, Darragh Duffy, Valentina Libri, Milena Hasan, Shen-Ying Zhang, Qian Zhang, Laurent Abel, Jean-Laurent Casanova, Nadia Naffakh, Maxime Rotival, Lluis Quintana-Murci. A single-cell view of the innate immune response to influenza A virus and
SARS-CoV-2 across human populations. Pasteur-Rockefeller Online Retreat 2021

The homeostatic immunological dialogue requires a constant balance between pro- and anti-inflammatory signals. Under normal circumstances, this balance is maintained by tightly regulated networks of signaling cascades and cytokine-mediated cell-cell interactions. However, there is increasing evidence to suggest that such immune equilibrium state differs among individuals and populations. The present proposal aims to characterize the variability of the human immune responses to SARS-CoV-2, the agent of the recent world pandemic of COVID-19, at the cellular and population levels. Indeed, increasing epidemiological evidence indicates that populations from different ethnic background present differential severity of COVID-19. While access to care, health disparities and pre-existing comorbidities may explain a proportion of such marked variability, host genetic factors and past infectious exposure may also play a role, and demand further investigation. Therefore, we hypothesize that: (i) the architecture of the immune response differs between individuals and populations; (ii) both heritable (ancestry-related host genetics) and non-heritable factors (e.g. infectious history and epigenetic priming) contribute to these differences; and (iii) alterations of immune responses contribute to the observed inequalities in susceptibility to, and severity of, COVID-19 between individuals and populations. To test these hypotheses, we propose to study, using single-cell technologies, the factors that shape immune response variation of peripheral blood mononuclear cells from healthy individuals of different ancestry. Specifically, our aims are: 1) to analyze the immune response to SARS-CoV-2 infection in 200 individuals of African and European descent, using single-cell RNA sequencing (scRNA-seq); 2) to identify regulatory regions that respond to environmental infectious cues and contribute to the priming of the immune response to SARS-CoV-2, using single-cell Assay for Transposase Accessible Chromatin sequencing (scATAC-seq), and 3) to assess the contribution of host genetics factors to the cell-type specific regulation of the immune response to SARS-CoV-2, through the mapping of expression quantitative trait loci (eQTLs). In doing so, this study should identify key cellular players of the immune response to SARS-CoV-2 as well as host genetic variants and molecular mechanisms underlying differences in the cellular responses between individuals of different ancestry. Altogether, this project will improve our understanding of how host genetics, ancestry, and environmental factors concur to shape the diversity of the human immune response to SARS-CoV-2. It will also help to understand the causal mechanisms at play of COVID-19 susceptibility/severity loci identified through genome-wide association studies, and facilitate the translation of these studies into novel preventive and therapeutic strategies.