Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19
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 an...
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| Veröffentlicht in: | Nature cell biology 2021-06, Vol.23 (6), p.620-630 |
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| creator | You, Maojun Chen, Liang Zhang, Dawei Zhao, Peng Chen, Zhu Qin, En-Qiang Gao, Yanan Davis, Mark M. Yang, Pengyuan |
| description | 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. |
| doi_str_mv | 10.1038/s41556-021-00690-1 |
| format | Article |
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+
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.</description><identifier>ISSN: 1465-7392</identifier><identifier>EISSN: 1476-4679</identifier><identifier>DOI: 10.1038/s41556-021-00690-1</identifier><identifier>PMID: 34108657</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><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</subject><ispartof>Nature cell biology, 2021-06, Vol.23 (6), p.620-630</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Limited 2021</rights><rights>COPYRIGHT 2021 Nature Publishing Group</rights><rights>The Author(s), under exclusive licence to Springer Nature Limited 2021.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c575t-8912565a1672a3c4eb9e9a45ede174d56de4d44ea68a17407a0334afdbcfb08e3</citedby><cites>FETCH-LOGICAL-c575t-8912565a1672a3c4eb9e9a45ede174d56de4d44ea68a17407a0334afdbcfb08e3</cites><orcidid>0000-0001-6868-657X ; 0000-0001-6665-9068 ; 0000-0003-1040-5987</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34108657$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>You, Maojun</creatorcontrib><creatorcontrib>Chen, Liang</creatorcontrib><creatorcontrib>Zhang, Dawei</creatorcontrib><creatorcontrib>Zhao, Peng</creatorcontrib><creatorcontrib>Chen, Zhu</creatorcontrib><creatorcontrib>Qin, En-Qiang</creatorcontrib><creatorcontrib>Gao, Yanan</creatorcontrib><creatorcontrib>Davis, Mark M.</creatorcontrib><creatorcontrib>Yang, Pengyuan</creatorcontrib><title>Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19</title><title>Nature cell biology</title><addtitle>Nat Cell Biol</addtitle><addtitle>Nat Cell Biol</addtitle><description>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.</description><subject>45/23</subject><subject>45/77</subject><subject>631/208/212/177</subject><subject>631/250/1619</subject><subject>631/250/256</subject><subject>631/337/100/1701</subject><subject>Accessibility</subject><subject>Adaptive Immunity</subject><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Analysis</subject><subject>Antibodies</subject><subject>Asymptomatic infection</subject><subject>B-Lymphocytes - immunology</subject><subject>B-Lymphocytes - metabolism</subject><subject>B-Lymphocytes - virology</subject><subject>Biomedical and Life Sciences</subject><subject>Cancer Research</subject><subject>Case-Control Studies</subject><subject>CD14 antigen</subject><subject>CD16 antigen</subject><subject>CD8 antigen</subject><subject>CD8-Positive T-Lymphocytes - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature cell biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>You, Maojun</au><au>Chen, Liang</au><au>Zhang, Dawei</au><au>Zhao, Peng</au><au>Chen, Zhu</au><au>Qin, En-Qiang</au><au>Gao, Yanan</au><au>Davis, Mark M.</au><au>Yang, Pengyuan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19</atitle><jtitle>Nature cell biology</jtitle><stitle>Nat Cell Biol</stitle><addtitle>Nat Cell Biol</addtitle><date>2021-06-01</date><risdate>2021</risdate><volume>23</volume><issue>6</issue><spage>620</spage><epage>630</epage><pages>620-630</pages><issn>1465-7392</issn><eissn>1476-4679</eissn><abstract>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.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>34108657</pmid><doi>10.1038/s41556-021-00690-1</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0001-6868-657X</orcidid><orcidid>https://orcid.org/0000-0001-6665-9068</orcidid><orcidid>https://orcid.org/0000-0003-1040-5987</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Nature cell biology, 2021-06, Vol.23 (6), p.620-630 |
| issn | 1465-7392 1476-4679 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_9105401 |
| source | MEDLINE; Nature; Alma/SFX Local Collection |
| subjects | 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 |
| title | Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19 |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-27T03%3A32%3A43IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Single-cell%20epigenomic%20landscape%20of%20peripheral%20immune%20cells%20reveals%20establishment%20of%20trained%20immunity%20in%20individuals%20convalescing%20from%20COVID-19&rft.jtitle=Nature%20cell%20biology&rft.au=You,%20Maojun&rft.date=2021-06-01&rft.volume=23&rft.issue=6&rft.spage=620&rft.epage=630&rft.pages=620-630&rft.issn=1465-7392&rft.eissn=1476-4679&rft_id=info:doi/10.1038/s41556-021-00690-1&rft_dat=%3Cgale_pubme%3EA664723361%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2539398971&rft_id=info:pmid/34108657&rft_galeid=A664723361&rfr_iscdi=true |