Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8+ T cells

A Kusnadi, C Ramírez-Suástegui, V Fajardo… - Science …, 2021 - science.org
A Kusnadi, C Ramírez-Suástegui, V Fajardo, SJ Chee, BJ Meckiff, H Simon, E Pelosi…
Science immunology, 2021science.org
The molecular properties of CD8+ T cells that respond to SARS-CoV-2 infection are not fully
known. Here, we report on the single-cell transcriptomes of> 80,000 virus-reactive CD8+ T
cells, obtained using a modified antigen-reactive T cell enrichment assay, from 39 patients
with COVID-19 and 10 healthy participants. Patients with COVID-19 were segregated into
two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was
“exhausted” or “non-exhausted.” SARS-CoV-2–reactive cells in the exhausted subset were …
The molecular properties of CD8+ T cells that respond to SARS-CoV-2 infection are not fully known. Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified antigen-reactive T cell enrichment assay, from 39 patients with COVID-19 and 10 healthy participants. Patients with COVID-19 were segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was “exhausted” or “non-exhausted.” SARS-CoV-2–reactive cells in the exhausted subset were increased in frequency and displayed lesser cytotoxicity and inflammatory features in patients with COVID-19 experiencing mild compared with severe illness. In contrast, SARS-CoV-2–reactive cells in the dominant nonexhausted subset from patients with severe disease showed enrichment of transcripts linked to costimulation, prosurvival NF-κB signaling, and antiapoptotic pathways, suggesting the generation of robust CD8+ T cell memory responses in patients with severe COVID-19 illness. CD8+ T cells reactive to influenza and respiratory syncytial virus from healthy participants displayed polyfunctional features and enhanced glycolysis. Cells with such features were largely absent in SARS-CoV-2–reactive cells from both patients with COVID-19 and healthy controls nonexposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2.
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