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Aragam KG, Jiang T, Goel A, Kanoni S, Wolford BN, Atri DS, Weeks EM, Wang M, Hindy G, Zhou W, Grace C, Roselli C, Marston NA, Kamanu FK, Surakka I, Venegas LM, Sherliker P, Koyama S, Ishigaki K, Åsvold BO, Brown MR, Brumpton B, de Vries PS, Giannakopoulou O, Giardoglou P, Gudbjartsson DF, Güldener U, Haider SMI, Helgadottir A, Ibrahim M, Kastrati A, Kessler T, Kyriakou T, Konopka T, Li L, Ma L, Meitinger T, Mucha S, Munz M, Murgia F, Nielsen JB, Nöthen MM, Pang S, Reinberger T, Schnitzler G, Smedley D, Thorleifsson G, von Scheidt M, Ulirsch JC, Arnar DO, Burtt NP, Costanzo MC, Flannick J, Ito K, Jang DK, Kamatani Y, Khera AV, Komuro I, Kullo IJ, Lotta LA, Nelson CP, Roberts R, Thorgeirsson G, Thorsteinsdottir U, Webb TR, Baras A, Björkegren JLM, Boerwinkle E, Dedoussis G, Holm H, Hveem K, Melander O, Morrison AC, Orho-Melander M, Rallidis LS, Ruusalepp A, Sabatine MS, Stefansson K, Zalloua P, Ellinor PT, Farrall M, Danesh J, Ruff CT, Finucane HK, Hopewell JC, Clarke R, Gupta RM, Erdmann J, Samani NJ, Schunkert H, Watkins H, Willer CJ, Deloukas P, Kathiresan S, Butterworth AS. Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants. Nat Genet 2022; 54:1803-1815. [PMID: 36474045 PMCID: PMC9729111 DOI: 10.1038/s41588-022-01233-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/17/2022] [Indexed: 12/12/2022]
Abstract
The discovery of genetic loci associated with complex diseases has outpaced the elucidation of mechanisms of disease pathogenesis. Here we conducted a genome-wide association study (GWAS) for coronary artery disease (CAD) comprising 181,522 cases among 1,165,690 participants of predominantly European ancestry. We detected 241 associations, including 30 new loci. Cross-ancestry meta-analysis with a Japanese GWAS yielded 38 additional new loci. We prioritized likely causal variants using functionally informed fine-mapping, yielding 42 associations with less than five variants in the 95% credible set. Similarity-based clustering suggested roles for early developmental processes, cell cycle signaling and vascular cell migration and proliferation in the pathogenesis of CAD. We prioritized 220 candidate causal genes, combining eight complementary approaches, including 123 supported by three or more approaches. Using CRISPR-Cas9, we experimentally validated the effect of an enhancer in MYO9B, which appears to mediate CAD risk by regulating vascular cell motility. Our analysis identifies and systematically characterizes >250 risk loci for CAD to inform experimental interrogation of putative causal mechanisms for CAD.
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Affiliation(s)
- Krishna G Aragam
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Tao Jiang
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anuj Goel
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Brooke N Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Deepak S Atri
- Cardiovascular Disease Initiative, 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
| | - Elle M Weeks
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Minxian Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - George Hindy
- Department of Population Medicine, Qatar University College of Medicine, Doha, Qatar
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher Grace
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carolina Roselli
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas A Marston
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frederick K Kamanu
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Loreto Muñoz Venegas
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Research Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Paul Sherliker
- Medical Research Council Population Health Research Unit, CTSU-Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Japan
| | - Bjørn O Åsvold
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway.,Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ben Brumpton
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Olga Giannakopoulou
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Panagiota Giardoglou
- Department of Nutrition-Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Ulrich Güldener
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany
| | - Syed M Ijlal Haider
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Research Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | | | - Maysson Ibrahim
- CTSU-Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Adnan Kastrati
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany.,German Research Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | - Thorsten Kessler
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany.,German Research Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | | | - Tomasz Konopka
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ling Li
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany
| | - Lijiang Ma
- Department of Genetics and Genomic Science, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Meitinger
- German Research Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Klinikum Rechts der Isar, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Sören Mucha
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Research Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Matthias Munz
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Research Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Federico Murgia
- CTSU-Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA.,Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Markus M Nöthen
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Shichao Pang
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany
| | - Tobias Reinberger
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Research Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Gavin Schnitzler
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Moritz von Scheidt
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany.,German Research Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jacob C Ulirsch
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | | | | | - David O Arnar
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Internal Medicine, Division of Cardiology, Landspitali-National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Noël P Burtt
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria C Costanzo
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jason Flannick
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Japan
| | - Dong-Keun Jang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yoichiro Kamatani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Amit V Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Issei Komuro
- Department of Cardiovascular Medicine, The University of Tokyo, Tokyo, Japan
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Christopher P Nelson
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Glenfield Hospital, Leicester, UK
| | - Robert Roberts
- Cardiovascular Genomics and Genetics, University of Arizona College of Medicin, Phoenix, AZ, USA
| | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Internal Medicine, Division of Cardiology, Landspitali-National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Thomas R Webb
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Glenfield Hospital, Leicester, UK
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Integrated Cardio Metabolic Centre, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden.,Clinical Gene Networks AB, Stockholm, Sweden
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - George Dedoussis
- Department of Nutrition-Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
| | - Kristian Hveem
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway
| | - Olle Melander
- Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Loukianos S Rallidis
- Second Department of Cardiology, Medical School, National and Kapodistrian University of Athens, University General Hospital Attikon, Athens, Greece
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital and Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Marc S Sabatine
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Pierre Zalloua
- Harvard T.H.Chan School of Public Health, Boston, MA, USA.,College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin Farrall
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John Danesh
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,National Institute for Health and Care Research Cambridge Biomedical Research Centre, Cambridge University Hospitals, Cambridge, UK.,The National Institute for Health and Care Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK.,Human Genetics, Wellcome Sanger Institute, Saffron Walden, UK.,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.,British Heart Foundation Centre of Research Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Christian T Ruff
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hilary K Finucane
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jemma C Hopewell
- CTSU-Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Robert Clarke
- CTSU-Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Rajat M Gupta
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, 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
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Research Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Nilesh J Samani
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Heribert Schunkert
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany.,German Research Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | - Hugh Watkins
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Adam S Butterworth
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. .,National Institute for Health and Care Research Cambridge Biomedical Research Centre, Cambridge University Hospitals, Cambridge, UK. .,The National Institute for Health and Care Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK. .,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK. .,British Heart Foundation Centre of Research Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK.
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2
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Weber B, Siddiqi H, Zhou G, Vieira J, Kim A, Rutherford H, Mitre X, Feeley M, Oganezova K, Varshney AS, Bhatt AS, Nauffal V, Atri DS, Blankstein R, Karlson EW, Di Carli M, Baden LR, Bhatt DL, Woolley AE. Relationship Between Myocardial Injury During Index Hospitalization for SARS-CoV-2 Infection and Longer-Term Outcomes. J Am Heart Assoc 2022; 11:e022010. [PMID: 34970914 PMCID: PMC9075193 DOI: 10.1161/jaha.121.022010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/15/2021] [Indexed: 12/15/2022]
Abstract
Background Myocardial injury in patients with COVID-19 is associated with increased mortality during index hospitalization; however, the relationship to long-term sequelae of SARS-CoV-2 is unknown. This study assessed the relationship between myocardial injury (high-sensitivity cardiac troponin T level) during index hospitalization for COVID-19 and longer-term outcomes. Methods and Results This is a prospective cohort of patients who were hospitalized at a single center between March and May 2020 with SARS-CoV-2. Cardiac biomarkers were systematically collected. Outcomes were adjudicated and stratified on the basis of myocardial injury. The study cohort includes 483 patients who had high-sensitivity cardiac troponin T data during their index hospitalization. During index hospitalization, 91 (18.8%) died, 70 (14.4%) had thrombotic complications, and 126 (25.6%) had cardiovascular complications. By 12 months, 107 (22.2%) died. During index hospitalization, 301 (62.3%) had cardiac injury (high-sensitivity cardiac troponin T≧14 ng/L); these patients had 28.6%, 32.2%, and 33.2% mortality during index hospitalization, at 6 months, and at 12 months, respectively, compared with 4.1%, 4.9%, and 4.9% mortality for those with low-level positive troponin and 0%, 0%, and 0% for those with undetectable troponin. Of 392 (81.2%) patients who survived the index hospitalization, 94 (24%) had at least 1 readmission within 12 months, of whom 61 (65%) had myocardial injury during the index hospitalization. Of 377 (96%) patients who were alive and had follow-up after the index hospitalization, 211 (56%) patients had a documented, detailed clinical assessment at 6 months. A total of 78 of 211 (37.0%) had ongoing COVID-19-related symptoms; 34 of 211 (16.1%) had neurocognitive decline, 8 of 211 (3.8%) had increased supplemental oxygen requirements, and 42 of 211 (19.9%) had worsening functional status. Conclusions Myocardial injury during index hospitalization for COVID-19 was associated with increased mortality and may predict who are more likely to have postacute sequelae of COVID-19. Among patients who survived their index hospitalization, the incremental mortality through 12 months was low, even among troponin-positive patients.
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Affiliation(s)
- Brittany Weber
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Hasan Siddiqi
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Guohai Zhou
- Center for Clinical InvestigationBrigham and Women's HospitalBostonMA
| | - Jefferson Vieira
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Andy Kim
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
| | - Henry Rutherford
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
| | - Xhoi Mitre
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
| | - Monica Feeley
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
| | - Karina Oganezova
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
| | - Anubodh S. Varshney
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Ankeet S. Bhatt
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Victor Nauffal
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Deepak S. Atri
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Ron Blankstein
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Elizabeth W. Karlson
- Division of Rheumatology, Inflammation, and ImmunityBrigham and Women’s Hospital Harvard Medical SchoolBostonMA
| | - Marcelo Di Carli
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
| | - Deepak L. Bhatt
- Division of Cardiovascular MedicineDepartment of Medicine, Heart and Vascular CenterBrigham and Women’s HospitalHarvard Medical SchoolBostonMA
| | - Ann E. Woolley
- Division of Infectious Diseases, Brigham and Women’s HospitalBostonMA
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3
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Atri DS, Lee-Kim VS, Vellarikkal SK, Sias-Garcia O, Yanamandala M, Schniztler GR, Gupta RM. CRISPR-Cas9 Genome Editing of Primary Human Vascular Cells In Vitro. Curr Protoc 2021; 1:e291. [PMID: 34748284 PMCID: PMC8580244 DOI: 10.1002/cpz1.291] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/12/2022]
Abstract
Genome editing of primary human cells with CRISPR-Cas9 is a powerful tool to study gene function. For many cell types, there are efficient protocols for editing with optimized plasmids for Cas9 and sgRNA expression. Vascular cells, however, remain refractory to plasmid-based delivery of CRISPR machinery for in vitro genome editing due to low transfection efficiency, poor expression of the Cas9 machinery, and toxic effects of the selection antibiotics. Here, we describe a method for high-efficiency editing of primary human vascular cells in vitro using nucleofection for direct delivery of sgRNA:Cas9-NLS ribonucleoprotein complexes. This method is more rapid and its high editing efficiency eliminates the need for additional selection steps. The edited cells can be employed in diverse applications, such as gene expression measurement or functional assays to assess various genetic perturbation effects in vitro. This method proves effective in vascular cells that are refractory to standard genome manipulation techniques using viral plasmid delivery. We anticipate that this technique will be applied to other non-vascular cell types that face similar barriers to efficient genome editing. © 2021 Wiley Periodicals LLC. Basic Protocol: CRISPR-Cas9 genome editing of primary human vascular cells in vitro.
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Affiliation(s)
- Deepak S. Atri
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
| | - Vivian S. Lee-Kim
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
| | - Shamsudheen K. Vellarikkal
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
| | - Oscar Sias-Garcia
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
| | - Mounica Yanamandala
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
| | - Gavin R. Schniztler
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
| | - Rajat M. Gupta
- Division of Cardiovascular Medicine and Department of Genetics, Brigham & Women’s Hospital, Boston MA
- Broad Institute of MIT and Harvard, Cambridge MA
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4
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Wang M, Lee-Kim VS, Atri DS, Elowe NH, Yu J, Garvie CW, Won HH, Hadaya JE, MacDonald BT, Trindade K, Melander O, Rader DJ, Natarajan P, Kathiresan S, Kaushik VK, Khera AV, Gupta RM. Rare, Damaging DNA Variants in CORIN and Risk of Coronary Artery Disease: Insights From Functional Genomics and Large-Scale Sequencing Analyses. Circ Genom Precis Med 2021; 14:e003399. [PMID: 34592835 DOI: 10.1161/circgen.121.003399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Corin is a protease expressed in cardiomyocytes that plays a key role in salt handling and intravascular volume homeostasis via activation of natriuretic peptides. It is unknown if Corin loss-of-function (LOF) is causally associated with risk of coronary artery disease (CAD). METHODS We analyzed all coding CORIN variants in an Italian case-control study of CAD. We functionally tested all 64 rare missense mutations in Western Blot and Mass Spectroscopy assays for proatrial natriuretic peptide cleavage. An expanded rare variant association analysis for Corin LOF mutations was conducted in whole exome sequencing data from 37 799 CAD cases and 212 184 controls. RESULTS We observed LOF variants in CORIN in 8 of 1803 (0.4%) CAD cases versus 0 of 1725 controls (P, 0.007). Of 64 rare missense variants profiled, 21 (33%) demonstrated <30% of wild-type activity and were deemed damaging in the 2 functional assays for Corin activity. In a rare variant association study that aggregated rare LOF and functionally validated damaging missense variants from the Italian study, we observed no association with CAD-21 of 1803 CAD cases versus 12 of 1725 controls with adjusted odds ratio of 1.61 ([95% CI, 0.79-3.29]; P=0.17). In the expanded sequencing dataset, there was no relationship between rare LOF variants with CAD was also observed (odds ratio, 1.15 [95% CI, 0.89-1.49]; P=0.30). Consistent with the genetic analysis, we observed no relationship between circulating Corin concentrations with incident CAD events among 4744 participants of a prospective cohort study-sex-stratified hazard ratio per SD increment of 0.96 ([95% CI, 0.87-1.07], P=0.48). CONCLUSIONS Functional testing of missense mutations improved the accuracy of rare variant association analysis. Despite compelling pathophysiology and a preliminary observation suggesting association, we observed no relationship between rare damaging variants in CORIN or circulating Corin concentrations with risk of CAD.
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Affiliation(s)
- Minxian Wang
- Program in Medical and Population Genetics (M.W., J.E.H., P.N., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Center for Genomic Medicine (M.W., P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston
| | - Vivian S Lee-Kim
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Divisions of Genetics and Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (V.S.L.-K., D.S.A.)
| | - Deepak S Atri
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Divisions of Genetics and Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (V.S.L.-K., D.S.A.)
| | - Nadine H Elowe
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - John Yu
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Colin W Garvie
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Gyeonggi, South Korea (H.-H.W.)
| | - Joseph E Hadaya
- Program in Medical and Population Genetics (M.W., J.E.H., P.N., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Bryan T MacDonald
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kevin Trindade
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.T., D.J.R.)
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Skåne, Sweden (O.M.).,Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden (O.M.)
| | - Daniel J Rader
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.T., D.J.R.)
| | - Pradeep Natarajan
- Program in Medical and Population Genetics (M.W., J.E.H., P.N., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Center for Genomic Medicine (M.W., P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston.,Division of Cardiology (P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston
| | - Sekar Kathiresan
- Center for Genomic Medicine (M.W., P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston.,Division of Cardiology (P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston.,Verve Therapeutics, Cambridge, MA (S.K.)
| | - Virendar K Kaushik
- Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Amit V Khera
- Program in Medical and Population Genetics (M.W., J.E.H., P.N., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Center for Genomic Medicine (M.W., P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston.,Division of Cardiology (P.N., S.K., A.V.K.), Massachusetts General Hospital, Boston
| | - Rajat M Gupta
- Program in Medical and Population Genetics (M.W., J.E.H., P.N., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA.,Cardiovascular Disease Initiative (M.W., V.S.L.-K., D.S.A., N.H.E., J.Y., C.W.G., B.T.M., P.N., V.K.K., A.V.K., R.M.G.), Broad Institute of MIT and Harvard, Cambridge, MA
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5
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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 CB, 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: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Harvard Medical School, Boston, MA 02115, USA,Massachusetts Institute of Technology, Cambridge, MA
02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public
Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Division of Infectious Diseases, Department of Medicine,
Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki,
Finland,Analytical & Translational Genetics Unit,
Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Systems Biology, Harvard Medical School,
Boston, MA 02115, USA,FAS Center for Systems Biology, Department of Organismic
and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
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 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical
Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Genetics and BASE Initiative, Stanford
University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109,
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
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki,
Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115,Harvard-MIT Division of Health Sciences and Technology,
Cambridge MA,Department of Pathology, Harvard Medical School, Boston,
MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA,Center for Regenerative Medicine, Massachusetts General
Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, 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 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public
Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of
MIT and Harvard, Cambridge, MA
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston,
MA 02115, USA,Department of Molecular Biology and Center for
Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
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
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138,Wyss Institute for Biologically Inspired Engineering,
Harvard University,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 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY,Herbert Irving Comprehensive Cancer Center, Columbia
University Irving Medical Center, New York, NY,Program for Mathematical Genomics, Columbia University
Irving Medical Center, New York, NY
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA,Harvard Medical School, Boston, MA 02115, USA,Harvard Stem Cell Institute, Cambridge, MA, USA,Program in Computational & Systems Biology,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Program in Immunology, Harvard Medical School, Boston, MA
02115, USA,Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
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6
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Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun HJ. A neutrophil activation signature predicts critical illness and mortality in COVID-19. Blood Adv 2021; 5:1164-1177. [PMID: 33635335 PMCID: PMC7908851 DOI: 10.1182/bloodadvances.2020003568] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/13/2021] [Indexed: 12/29/2022] Open
Abstract
Pathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling of plasma from cross-sectional and longitudinal cohorts of hospitalized patients with COVID-19 and analyzed clinical data from our health system database of more than 3300 patients. Using a machine learning algorithm, we identified a prominent signature of neutrophil activation, including resistin, lipocalin-2, hepatocyte growth factor, interleukin-8, and granulocyte colony-stimulating factor, which were the strongest predictors of critical illness. Evidence of neutrophil activation was present on the first day of hospitalization in patients who would only later require transfer to the intensive care unit, thus preceding the onset of critical illness and predicting increased mortality. In the health system database, early elevations in developing and mature neutrophil counts also predicted higher mortality rates. Altogether, these data suggest a central role for neutrophil activation in the pathogenesis of severe COVID-19 and identify molecular markers that distinguish patients at risk of future clinical decompensation.
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Affiliation(s)
| | | | - Jason D Bishai
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT
| | - George Goshua
- Section of Hematology, Department of Internal Medicine
| | | | - Michael Simonov
- Clinical and Translational Research Accelerator, Department of Internal Medicine
- Department of Dermatology, and
| | - C-Hong Chang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Hanming Zhang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Marcus Shallow
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Parveen Bahel
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Kent Owusu
- Department of Pharmacy, Yale New Haven Health System, New Haven, CT
| | - Yu Yamamoto
- Clinical and Translational Research Accelerator, Department of Internal Medicine
| | - Tanima Arora
- Clinical and Translational Research Accelerator, Department of Internal Medicine
| | - Deepak S Atri
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA; and
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine
| | - Jennifer Kwan
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Christine H Won
- Section of Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, and
| | - Charles Dela Cruz
- Section of Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, and
| | - Christina Price
- Section of Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Jonathan Koff
- Section of Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, and
| | - Brett A King
- Section of Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Henry M Rinder
- Section of Hematology, Department of Internal Medicine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - F Perry Wilson
- Clinical and Translational Research Accelerator, Department of Internal Medicine
| | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | | | | | - David van Dijk
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Alfred I Lee
- Section of Hematology, Department of Internal Medicine
| | - Hyung J Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
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7
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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, 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, Jane-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, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2. bioRxiv 2021:2021.02.25.430130. [PMID: 33655247 PMCID: PMC7924267 DOI: 10.1101/2021.02.25.430130] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.
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Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Asa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Zohar Bloom-Ackerman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, 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 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics and BASE Initiative, Stanford University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109, 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
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Judit Jane-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Cambridge MA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 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 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, 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
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
- Wyss Institute for Biologically Inspired Engineering, Harvard University
- 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 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
- Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
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8
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Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun H. A neutrophil activation signature predicts critical illness and mortality in COVID-19. medRxiv 2020. [PMID: 32908988 DOI: 10.1101/2020.09.01.20183897] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling of plasma from cross-sectional and longitudinal cohorts of hospitalized patients with COVID-19 and analyzed clinical data from our health system database of over 3,300 patients. Using a machine learning algorithm, we identified a prominent signature of neutrophil activation, including resistin, lipocalin-2, HGF, IL-8, and G-CSF, as the strongest predictors of critical illness. Neutrophil activation was present on the first day of hospitalization in patients who would only later require transfer to the intensive care unit, thus preceding the onset of critical illness and predicting increased mortality. In the health system database, early elevations in developing and mature neutrophil counts also predicted higher mortality rates. Altogether, we define an essential role for neutrophil activation in the pathogenesis of severe COVID-19 and identify molecular neutrophil markers that distinguish patients at risk of future clinical decompensation.
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Atri DS, Tsao AL, Yu PB, Berry NC. ST-Segment Elevation Myocardial Infarction Due to Right Coronary Artery Compression by Cardiac Synovial Sarcoma. JACC Cardiovasc Interv 2019; 12:e145-e147. [PMID: 31422086 DOI: 10.1016/j.jcin.2019.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/14/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Deepak S Atri
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Allison L Tsao
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Paul B Yu
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Natalia C Berry
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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