An integrated cell atlas of the lung in health and disease.


Journal

Nature medicine
ISSN: 1546-170X
Titre abrégé: Nat Med
Pays: United States
ID NLM: 9502015

Informations de publication

Date de publication:
Jun 2023
Historique:
received: 10 03 2022
accepted: 30 03 2023
medline: 26 6 2023
pubmed: 9 6 2023
entrez: 8 6 2023
Statut: ppublish

Résumé

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1

Identifiants

pubmed: 37291214
doi: 10.1038/s41591-023-02327-2
pii: 10.1038/s41591-023-02327-2
pmc: PMC10287567
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1563-1577

Subventions

Organisme : NHLBI NIH HHS
ID : R01 HL153375
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL127349
Pays : United States
Organisme : NHLBI NIH HHS
ID : U54 HL165443
Pays : United States
Organisme : NHLBI NIH HHS
ID : P01 HL107202
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL148856
Pays : United States
Organisme : NHLBI NIH HHS
ID : R21 HL156124
Pays : United States
Organisme : NIA NIH HHS
ID : U54 AG075931
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : R01 HL146557
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL123766
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL148861
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL141852
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES034350
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL126176
Pays : United States
Organisme : NHLBI NIH HHS
ID : R21 HL161760
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL145372
Pays : United States
Organisme : NIA NIH HHS
ID : P01 AG049665
Pays : United States
Organisme : NICHD NIH HHS
ID : K12 HD105271
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI135964
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL142568
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL153312
Pays : United States
Organisme : NIA NIH HHS
ID : U54 AG079754
Pays : United States
Organisme : NHLBI NIH HHS
ID : R56 HL157632
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL158139
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL135156
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL153045
Pays : United States
Organisme : NHLBI NIH HHS
ID : U54 HL145608
Pays : United States
Organisme : NIAMS NIH HHS
ID : P50 AR060780
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL128439
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL146519
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL117004
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL068702
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL145567
Pays : United States
Organisme : NHLBI NIH HHS
ID : P01 HL132821
Pays : United States
Organisme : Medical Research Council
ID : MR/R015635/1
Pays : United Kingdom
Organisme : NIMHD NIH HHS
ID : R01 MD010443
Pays : United States

Investigateurs

Yuexin Chen (Y)
James S Hagood (JS)
Ahmed Agami (A)
Peter Horvath (P)
Joakim Lundeberg (J)
Charles-Hugo Marquette (CH)
Gloria Pryhuber (G)
Chistos Samakovlis (C)
Xin Sun (X)
Lorraine B Ware (LB)
Kun Zhang (K)

Informations de copyright

© 2023. The Author(s).

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Auteurs

Lisa Sikkema (L)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
TUM School of Life Sciences, Technical University of Munich, Munich, Germany.

Ciro Ramírez-Suástegui (C)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.

Daniel C Strobl (DC)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany.

Tessa E Gillett (TE)

Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands.
Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Luke Zappia (L)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Department of Mathematics, Technical University of Munich, Garching, Germany.

Elo Madissoon (E)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Nikolay S Markov (NS)

Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.

Laure-Emmanuelle Zaragosi (LE)

Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.

Yuge Ji (Y)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
TUM School of Life Sciences, Technical University of Munich, Munich, Germany.

Meshal Ansari (M)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.

Marie-Jeanne Arguel (MJ)

Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.

Leonie Apperloo (L)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Martin Banchero (M)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Christophe Bécavin (C)

Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.

Marijn Berg (M)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Evgeny Chichelnitskiy (E)

Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany.

Mei-I Chung (MI)

Translational Genomics Research Institute, Phoenix, AZ, USA.

Antoine Collin (A)

Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.
3IA Côte d'Azur, Nice, France.

Aurore C A Gay (ACA)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Janine Gote-Schniering (J)

Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.

Baharak Hooshiar Kashani (B)

Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.

Kemal Inecik (K)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
TUM School of Life Sciences, Technical University of Munich, Munich, Germany.

Manu Jain (M)

Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.

Theodore S Kapellos (TS)

Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.

Tessa M Kole (TM)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Sylvie Leroy (S)

Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.

Christoph H Mayr (CH)

Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.

Amanda J Oliver (AJ)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Michael von Papen (M)

Research, Development and Innovation, Comma Soft, Bonn, Germany.

Lance Peter (L)

Translational Genomics Research Institute, Phoenix, AZ, USA.

Chase J Taylor (CJ)

Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.

Thomas Walzthoeni (T)

Core Facility Genomics, Helmholtz Center Munich, Munich, Germany.

Chuan Xu (C)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Linh T Bui (LT)

Translational Genomics Research Institute, Phoenix, AZ, USA.

Carlo De Donno (C)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.

Leander Dony (L)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany.

Alen Faiz (A)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia.

Minzhe Guo (M)

Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US.

Austin J Gutierrez (AJ)

Translational Genomics Research Institute, Phoenix, AZ, USA.

Lukas Heumos (L)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.

Ni Huang (N)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Ignacio L Ibarra (IL)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.

Nathan D Jackson (ND)

Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.

Preetish Kadur Lakshminarasimha Murthy (P)

Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA.

Mohammad Lotfollahi (M)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Tracy Tabib (T)

Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.

Carlos Talavera-López (C)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany.

Kyle J Travaglini (KJ)

Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Allen Institute for Brain Science, Seattle, WA, USA.

Anna Wilbrey-Clark (A)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Kaylee B Worlock (KB)

Department of Respiratory Medicine, Division of Medicine, University College London, London, UK.

Masahiro Yoshida (M)

Department of Respiratory Medicine, Division of Medicine, University College London, London, UK.

Maarten van den Berge (M)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Yohan Bossé (Y)

Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada.

Tushar J Desai (TJ)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Oliver Eickelberg (O)

Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA.

Naftali Kaminski (N)

Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.

Mark A Krasnow (MA)

Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.

Robert Lafyatis (R)

Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.

Marko Z Nikolic (MZ)

Department of Respiratory Medicine, Division of Medicine, University College London, London, UK.

Joseph E Powell (JE)

Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.

Jayaraj Rajagopal (J)

Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA.

Mauricio Rojas (M)

Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA.

Orit Rozenblatt-Rosen (O)

Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA.

Max A Seibold (MA)

Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
Department of Pediatrics, National Jewish Health, Denver, CO, USA.
Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA.

Dean Sheppard (D)

Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA.

Douglas P Shepherd (DP)

Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA.

Don D Sin (DD)

Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.

Wim Timens (W)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Alexander M Tsankov (AM)

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Jeffrey Whitsett (J)

Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.

Yan Xu (Y)

Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.

Nicholas E Banovich (NE)

Translational Genomics Research Institute, Phoenix, AZ, USA.

Pascal Barbry (P)

Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.
3IA Côte d'Azur, Nice, France.

Thu Elizabeth Duong (TE)

Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA.

Christine S Falk (CS)

Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany.

Kerstin B Meyer (KB)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Jonathan A Kropski (JA)

Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.

Dana Pe'er (D)

Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Herbert B Schiller (HB)

Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.

Purushothama Rao Tata (PR)

Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.

Joachim L Schultze (JL)

Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany.

Sara A Teichmann (SA)

Wellcome Sanger Institute, Hinxton, Cambridge, UK.
Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.

Alexander V Misharin (AV)

Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.

Martijn C Nawijn (MC)

Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Malte D Luecken (MD)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany. malte.luecken@helmholtz-munich.de.
Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany. malte.luecken@helmholtz-munich.de.

Fabian J Theis (FJ)

Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany. fabian.theis@helmholtz-munich.de.
TUM School of Life Sciences, Technical University of Munich, Munich, Germany. fabian.theis@helmholtz-munich.de.
Department of Mathematics, Technical University of Munich, Garching, Germany. fabian.theis@helmholtz-munich.de.

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