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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021; 595:107-113. [PMID: 33915569 PMCID: PMC8919505 DOI: 10.1038/s41586-021-03570-8] [Citation(s) in RCA: 476] [Impact Index Per Article: 158.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]
Abstract
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.
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Affiliation(s)
- Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carly G K Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen J Fleming
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Karthik A Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kushal K Dey
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yered H Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Barkas
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
| | - Yury V Popov
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Siddharth S Raju
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Linus T-Y Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, Boston, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Victoria M Tran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shamsudheen K Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | | | - Deepak S Atri
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Olga R Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics and BASE Initiative, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, Boston, MA, USA
| | - Donna M Fitzgerald
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robin Fropf
- NanoString Technologies Inc, Seattle, WA, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John Grzyb
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel E McLoughlin
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Liuliu Pan
- NanoString Technologies Inc, Seattle, WA, USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, Boston, MA, USA
| | - Carmel Pe'er
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Christopher J Pinto
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Marty Ross
- NanoString Technologies Inc, Seattle, WA, USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajat M Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Winston Hide
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alkes L Price
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Donald E Ingber
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Gordon Jiang
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA.
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA.
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Health Sciences & Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA.
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Immunology, Harvard Medical School, Boston, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Genentech, South San Francisco, CA, USA.
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