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Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M. Single-cell multi-omics analysis of the immune response in COVID-19. Nat Med 2021; 27:904-916. [PMID: 33879890 PMCID: PMC8121667 DOI: 10.1038/s41591-021-01329-2] [Citation(s) in RCA: 317] [Impact Index Per Article: 105.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.
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Affiliation(s)
- Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Michael D Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Karsten Bach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Katarzyna Kania
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Bayanne Olabi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Nicola K Wilson
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicole Mende
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Louis C S Gardner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jim McGrath
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Michael W Mather
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Florian Gothe
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kenneth F Baker
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Aidan T Hanrath
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | | | - Andrew S Barr
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Amada Sanchez-Gonzalez
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Eliz Kilich
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Angus de Wilton
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Anita Saigal
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nusayhah Gopee
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Caroline Wilson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- The Innovation Lab Integrated COVID Hub North East, Newcastle Upon Tyne, UK
| | - Paul Coupland
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Stijn van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| | - Hamish W King
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Anthony J Rostron
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Integrated Critical Care Unit, Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Elisa Laurenti
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge Biomedical Campus, Cambridge, UK.
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - Berthold Göttgens
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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