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

Introduction

SARS-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.

Methods

We 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.

Results

We 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.

Discussion

We 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.

Identification of a distinct NK-like hepatic T-cell population activated by NKG2C in a TCR-independent manner

BACKGROUND & AIMS

The liver provides a unique niche of lymphocytes enriched with a large proportion of innate-like T cells. However, the heterogeneity and functional characteristics of the hepatic T-cell population remain to be fully elucidated.

METHODS

We obtained liver sinusoidal mononuclear cells from the liver perfusate of healthy donors and recipients with HBV-associated chronic liver disease (CLD) during liver transplantation. We performed a CITE-seq analysis of liver sinusoidal CD45⁺ cells in combination with T cell receptor (TCR)-seq and flow cytometry to examine the phenotypes and functions of liver sinusoidal CD8⁺ T cells.

RESULTS

We identified a distinct CD56^hiCD161^-CD8⁺ T-cell population characterized by natural killer (NK)-related gene expression and a uniquely restricted TCR repertoire. The frequency of these cells among the liver sinusoidal CD8⁺ T-cell population was significantly increased in patients with HBV-associated CLD. Although CD56^hiCD161^-CD8⁺ T cells exhibit weak responsiveness to TCR stimulation, CD56^hiCD161^-CD8⁺ T cells highly expressed various NK receptors, including CD94, killer immunoglobulin-like receptors, and NKG2C, and exerted NKG2C-mediated NK-like effector functions even in the absence of TCR stimulation. In addition, CD56^hiCD161^-CD8⁺ T cells highly respond to innate cytokines, such as IL-12/18 and IL-15, in the absence of TCR stimulation. We validated the results from liver sinusoidal CD8⁺ T cells using intrahepatic CD8⁺ T cells obtained from liver tissues.

CONCLUSIONS

In summary, the current study found a distinct CD56^hiCD161^-CD8⁺ T-cell population characterized by NK-like activation via TCR-independent NKG2C ligation. Further studies are required to elucidate the roles of liver sinusoidal CD56^hiCD161^-CD8⁺ T cells in immune responses to microbial pathogens or liver immunopathology.

LAY SUMMARY

The role of different immune cell populations in the liver is becoming an area of increasing interest. Herein, we identified a distinct T-cell population that had features similar to those of natural killer (NK) cells - a type of innate immune cell. This distinct population was expanded in the livers of patients with chronic liver disease and could thus have pathogenic relevance.