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Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Christoph Muus, Malte D. Luecken, Gokcen Eraslan, Avinash Waghray, Graham Heimberg, Lisa Sikkema, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smilie, Karthik Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, J. Samuel, Allon Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon, Michael S Cuoco, Marie Deprez, David S Fischer, Astrid Gillich, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Alok Jaiswal, Peiyong Jiang, Theodoros Kapellos, Christin S Kuo, Ludvig Larsson, Michael A. Leney-Greene Kyungtae Lim, Monika Litviňuková, Ji Lu, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Charles-Hugo Marquette, Ian Mbano, Alexi Marie McAdams, Ross J Metzger, Ahmad N Nabhan, Sarah K. Nyquist, Jose Ordovas-Montanes, Lolita Penland, Olivier B Poirion, Sergio Poli, CanCan Qi, Daniel Reichart, Ivan Rosas, Jonas Schupp, Rahul Sinha, Rene V Sit, Kamil Slowikowski, Michal Slyper, Neal Smith, Alex Sountoulidis, Maximilian Strunz, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J Travaglini, Nathan R. Tucker, Katherine Vernon, Marc H. Wadsworth, Julia Waldmann, Xiuting Wang, Wenjun Yan, William Zhao, Carly G. K. Ziegler, The NHLBI LungMAP Consortium, and The Human Cell Atlas Lung Biological Network
doi: https://doi.org/10.1101/2020.04.19.049254
Christoph Muus
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
2John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
Malte D. Luecken
3Institute of Computational Biology, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
Gokcen Eraslan
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Avinash Waghray
5Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
6Harvard Stem Cell Institute, Cambridge, MA, USA
Graham Heimberg
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Lisa Sikkema
3Institute of Computational Biology, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
Yoshihiko Kobayashi
7Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
Eeshit Dhaval Vaishnav
8Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA
Ayshwarya Subramanian
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Christopher Smilie
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Karthik Jagadeesh
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Elizabeth Thu Duong
9University of California San Diego
10Department of Pediatrics, Division of Respiratory Medicine
Evgenij Fiskin
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Elena Torlai Triglia
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Meshal Ansari
11Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
12Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
Peiwen Cai
13Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
Brian Lin
14Center for Regenerative Medicine, Massachusetts General Hospital,Boston, MA, USA
6Harvard Stem Cell Institute, Cambridge, MA, USA
Justin Buchanan
15Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093
16Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
Sijia Chen
17Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
Jian Shu
18Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
19Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
Adam L Haber
20Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Hattie Chung
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Daniel T Montoro
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Taylor Adams
21Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
Hananeh Aliee
3Institute of Computational Biology, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
J. Samuel
22Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
Allon Zaneta Andrusivova
23SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
Ilias Angelidis
11Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
Orr Ashenberg
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Kevin Bassler
24Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
Christophe Bécavin
25Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, 06560, France
Inbal Benhar
26Center for Brain Science, Harvard University, Cambridge, MA 02138
27Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
Joseph Bergenstråhle
23SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
Ludvig Bergenstråhle
23SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
Liam Bolt
28Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
Emelie Braun
29Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
Linh T Bui
30Translational Genomics Research Institute, Phoenix, AZ
Mark Chaffin
31Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
Evgeny Chichelnitskiy
32Institute of Transplant Immunology, Hannover Medical School, MHH, Carl-Neuberg Str. 1, 30625 Hannover, Germany, phone +40 511 532 9745; fax +40 511 532 8090; German Center for Infectious Diseases DZIF, TTU-IICH 07.801
Joshua Chiou
33Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA, 92093
Thomas M Conlon
11Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
Michael S Cuoco
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Marie Deprez
25Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, 06560, France
David S Fischer
3Institute of Computational Biology, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
Astrid Gillich
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Joshua Gould
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Minzhe Guo
35Divisions of Pulmonary Biology; Perinatal Institute, Cincinnati Children’s Hospital Medical Center
Austin J Gutierrez
30Translational Genomics Research Institute, Phoenix, AZ
Arun C Habermann
36Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
Tyler Harvey
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Peng He
28Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
Xiaomeng Hou
15Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093
17Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
Lijuan Hu
29Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
Alok Jaiswal
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Peiyong Jiang
37Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
Theodoros Kapellos
24Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
Christin S Kuo
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Ludvig Larsson
23SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
Michael A. Leney-Greene Kyungtae Lim
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
38Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
Monika Litviňuková
39Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
40Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
Ji Lu
37Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
Henrike Maatz
40Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
Elo Madissoon
28Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
Lira Mamanova
28Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
Kasidet Manakongtreecheep
41Broad Institute of MIT and Harvard, Cambridge, MA, USA
42Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
43Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
Charles-Hugo Marquette
44Université Côte d’Azur, CHU de Nice, FHU OncoAge, CNRS, Inserm, IRCAN team 3, Pulmonology Department, Nice, 06000, France
Ian Mbano
45Africa Health Research Institute, Durban, South Africa
Alexi Marie McAdams
46Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
Ross J Metzger
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Ahmad N Nabhan
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Sarah K. Nyquist
47Computational and Systems Biology, CSAIL, Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
Jose Ordovas-Montanes
48Division of Gastroenterology Boston Children’s Hospital; Program in Immunology Harvard Medical School; Harvard Stem Cell Institute; Broad Institute of MIT and Harvard
Lolita Penland
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Olivier B Poirion
15Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093
16Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
Sergio Poli
21Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
CanCan Qi
49Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
50GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
Daniel Reichart
51Department of Genetics, Harvard Medical School, Boston, MA, United States
52Department of Cardiology, University Heart&Vascular Center, University of Hamburg, Hamburg, Germany
Ivan Rosas
21Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
Jonas Schupp
21Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
Rahul Sinha
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Rene V Sit
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Kamil Slowikowski
41Broad Institute of MIT and Harvard, Cambridge, MA, USA
42Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
43Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
Michal Slyper
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Neal Smith
41Broad Institute of MIT and Harvard, Cambridge, MA, USA
42Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
43Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
Alex Sountoulidis
53Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute
Maximilian Strunz
11Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
Dawei Sun
38Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
Carlos Talavera-López
39Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
Peng Tan
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Jessica Tantivit
41Broad Institute of MIT and Harvard, Cambridge, MA, USA
42Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
43Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
Kyle J Travaglini
34Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
Nathan R. Tucker
31Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
54Masonic Medical Research Institute, Utica, NY, USA 13501
Katherine Vernon
55Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
18Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Marc H. Wadsworth
56Institute for Medical Engineering and Science, Department of Chemistry & Koch Institute for Integrative Cancer Research, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
Julia Waldmann
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
Xiuting Wang
13Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
Wenjun Yan
26Center for Brain Science, Harvard University, Cambridge, MA 02138
27Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
William Zhao
13Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
Carly G. K. Ziegler
57Harvard-MIT Health Sciences and Technology, Institute for Medical Engineering and Science, Koch Institute for Integrative Cancer Research, MIT; Broad Institute of MIT and Harvard; Ragon Institute of MGH, MIT and Harvard
- For correspondence: lung@humancellatlas.org hca@humancellatlas.org
Article usage
Posted April 20, 2020.
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Christoph Muus, Malte D. Luecken, Gokcen Eraslan, Avinash Waghray, Graham Heimberg, Lisa Sikkema, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smilie, Karthik Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, J. Samuel, Allon Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon, Michael S Cuoco, Marie Deprez, David S Fischer, Astrid Gillich, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Alok Jaiswal, Peiyong Jiang, Theodoros Kapellos, Christin S Kuo, Ludvig Larsson, Michael A. Leney-Greene Kyungtae Lim, Monika Litviňuková, Ji Lu, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Charles-Hugo Marquette, Ian Mbano, Alexi Marie McAdams, Ross J Metzger, Ahmad N Nabhan, Sarah K. Nyquist, Jose Ordovas-Montanes, Lolita Penland, Olivier B Poirion, Sergio Poli, CanCan Qi, Daniel Reichart, Ivan Rosas, Jonas Schupp, Rahul Sinha, Rene V Sit, Kamil Slowikowski, Michal Slyper, Neal Smith, Alex Sountoulidis, Maximilian Strunz, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J Travaglini, Nathan R. Tucker, Katherine Vernon, Marc H. Wadsworth, Julia Waldmann, Xiuting Wang, Wenjun Yan, William Zhao, Carly G. K. Ziegler, The NHLBI LungMAP Consortium, and The Human Cell Atlas Lung Biological Network
bioRxiv 2020.04.19.049254; doi: https://doi.org/10.1101/2020.04.19.049254
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Christoph Muus, Malte D. Luecken, Gokcen Eraslan, Avinash Waghray, Graham Heimberg, Lisa Sikkema, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smilie, Karthik Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, J. Samuel, Allon Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon, Michael S Cuoco, Marie Deprez, David S Fischer, Astrid Gillich, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Alok Jaiswal, Peiyong Jiang, Theodoros Kapellos, Christin S Kuo, Ludvig Larsson, Michael A. Leney-Greene Kyungtae Lim, Monika Litviňuková, Ji Lu, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Charles-Hugo Marquette, Ian Mbano, Alexi Marie McAdams, Ross J Metzger, Ahmad N Nabhan, Sarah K. Nyquist, Jose Ordovas-Montanes, Lolita Penland, Olivier B Poirion, Sergio Poli, CanCan Qi, Daniel Reichart, Ivan Rosas, Jonas Schupp, Rahul Sinha, Rene V Sit, Kamil Slowikowski, Michal Slyper, Neal Smith, Alex Sountoulidis, Maximilian Strunz, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J Travaglini, Nathan R. Tucker, Katherine Vernon, Marc H. Wadsworth, Julia Waldmann, Xiuting Wang, Wenjun Yan, William Zhao, Carly G. K. Ziegler, The NHLBI LungMAP Consortium, and The Human Cell Atlas Lung Biological Network
bioRxiv 2020.04.19.049254; doi: https://doi.org/10.1101/2020.04.19.049254
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