Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling

Abstract

IntroductionSARS-CoV-2 infection results in varying disease severity, ranging from asymptomatic infection to severe illness. A detailed understanding of the immune response to SARS-CoV-2 is critical to unravel the causative factors underlying differences in disease severity and to develop optimal vaccines against new SARS-CoV-2 variants.MethodsWe combined single-cell RNA and T cell receptor sequencing with CITE-seq antibodies to characterize the CD8+ T cell response to SARS-CoV-2 infection at high resolution and compared responses between mild and severe COVID-19.ResultsWe observed increased CD8+ T cell exhaustion in severe SARS-CoV-2 infection and identified a population of NK-like, terminally differentiated CD8+ effector T cells characterized by expression of FCGR3A (encoding CD16). Further characterization of NK-like CD8+ T cells revealed heterogeneity among CD16+ NK-like CD8+ T cells and profound differences in cytotoxicity, exhaustion, and NK-like differentiation between mild and severe disease conditions.DiscussionWe propose a model in which differences in the surrounding inflammatory milieu lead to crucial differences in NK-like differentiation of CD8+ effector T cells, ultimately resulting in the appearance of NK-like CD8+ T cell populations of different functionality and pathogenicity. Our in-depth characterization of the CD8+ T cell-mediated response to SARS-CoV-2 infection provides a basis for further investigation of the importance of NK-like CD8+ T cells in COVID-19 severity.

Alterations in the CD56− and CD56+ T Cell Subsets during COVID-19

“…It has been shown earlier that CD8 + cells constitute the majority of the NKT-like subset [17]. Several publications emphasize an increase in CD8 + T cells with more mature phenotype during SARS-CoV-2 infection [14,[18][19][20].…”

Flow cytometry analysis of protein expression using antibody‐derived tags followed by CITE‐Seq

“…Using antibody‐derived tags (ADTs), the abundance of surface protein markers can be quantitatively measured using single‐cell sequencing of the unique oligo barcode of ADT reagents [1]. Downstream analyses provide genomic and proteomic insights and allow identification of rare cell populations [2], deconvolution of cellular heterogeneity [3] and determination of cell differentiation processes [4].…”

“…3) or FlowJo™ (V10.8.1) software. Stain index is calculated by subtracting the median fluorescent intensity (MFI) of the negative population of a given fluorescent channel from the MFI of the positive population, divided by two times the standard deviation of the negative population.…”