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Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell 2023; 186:3882-3902.e24. [PMID: 37597510 PMCID: PMC10638861 DOI: 10.1016/j.cell.2023.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/21/2023]
Abstract
Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.
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Affiliation(s)
- Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Siddhartha Sharma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Simon A Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paoline Laurent
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Lucinda Paddock
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Emin Onur Karakaslar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinay K Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Jim K Yee
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Minh Y Mays
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alexia Martinez de Paz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dughan Ahimovic
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Victor Ramos
- The Rockefeller University, New York, NY 10065, USA
| | | | - Erik Nielsen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Ling Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Alisha Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lexi Robbins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Karissa L Weidman
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sabrina Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - He S Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David R Price
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Louise Leyre
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Junbum Kim
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Northwell Health, Greenvale, NY 11548, USA
| | | | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Virginia Pascual
- Department of Pediatrics, Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Rachel E Niec
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; The Rockefeller University, New York, NY 10065, USA
| | - Franck J Barrat
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA; HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lindsay Lief
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA.
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