Journal Article

Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19

Chen, Liang, Zhang, Dawei, You, Maojun, Gao, Yanan, Qin, En-Qiang, Zhao, Peng, Chen, Zhu, Davis, Mark M., Yang, Pengyuan

2021

Overview

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection often causes severe complications and even death. However, asymptomatic infection has also been reported, highlighting the difference in immune responses among individuals. Here we performed single-cell chromatin accessibility and T cell-receptor analyses of peripheral blood mononuclear cells collected from individuals convalescing from COVID-19 and healthy donors. Chromatin remodelling was observed in both innate and adaptive immune cells in the individuals convalescing from COVID-19. Compared with healthy donors, recovered individuals contained abundant TBET-enriched CD16 + and IRF1-enriched CD14 + monocytes with sequential trained and activated epigenomic states. The B-cell lineage in recovered individuals exhibited an accelerated developmental programme from immature B cells to antibody-producing plasma cells. Finally, an integrated analysis of single-cell T cell-receptor clonality with the chromatin accessibility landscape revealed the expansion of putative SARS-CoV-2-specific CD8 + T cells with epigenomic profiles that promote the differentiation of effector or memory cells. Overall, our data suggest that immune cells of individuals convalescing from COVID-19 exhibit global remodelling of the chromatin accessibility landscape, indicative of the establishment of immunological memory. You et al. report single-cell ATAC-seq profiles of periphery immune cells from patients recovered from COVID-19, which reveals a global remodelling of the chromatin accessibility that may contribute to immune memory formation.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 45/23 / 45/77 / 631/208/212/177 / 631/250/1619 / 631/250/256 / 631/337/100/1701 / Accessibility / Adaptive Immunity / Adolescent / Adult / Aged / Analysis / Antibodies / Asymptomatic infection / B-Lymphocytes - immunology / B-Lymphocytes - metabolism / B-Lymphocytes - virology / Biomedical and Life Sciences / Cancer Research / Case-Control Studies / CD14 antigen / CD16 antigen / CD8 antigen / CD8-Positive T-Lymphocytes - immunology / CD8-Positive T-Lymphocytes - metabolism / CD8-Positive T-Lymphocytes - virology / Cell Biology / Cell Differentiation / Cell lineage / Chromatin Assembly and Disassembly / Chromatin remodeling / Coronaviruses / COVID-19 / COVID-19 - genetics / COVID-19 - immunology / COVID-19 - metabolism / COVID-19 - virology / Developmental Biology / Effector cells / Epigenesis, Genetic / Epigenomics / Female / Gene Expression Profiling / Genes, T-Cell Receptor / Host-Pathogen Interactions / Humans / Immune system / Immunity / Immunity (Disease) / Immunity, Innate / Immunologic Memory / Immunological memory / Immunology / Interferon regulatory factor 1 / Leukocytes (mononuclear) / Life Sciences / Lymphocyte Subsets - immunology / Lymphocyte Subsets - metabolism / Lymphocyte Subsets - virology / Lymphocytes / Lymphocytes B / Lymphocytes T / Male / Memory cells / Middle Aged / Monocytes / Monocytes - immunology / Monocytes - metabolism / Monocytes - virology / Peripheral blood mononuclear cells / Plasma cells / Receptors / Resource / Respiratory diseases / SARS-CoV-2 - immunology / SARS-CoV-2 - pathogenicity / Severe acute respiratory syndrome coronavirus 2 / Single-Cell Analysis / Stem Cells / Viral diseases / Young Adult