An integrated cell atlas of the lung in health and disease

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Sikkema, LisaDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany (författare)

An integrated cell atlas of the lung in health and disease

Artikel/kapitelEngelska2023

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Springer Nature,2023
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LIBRIS-ID:oai:DiVA.org:kth-331444
https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-331444URI
https://doi.org/10.1038/s41591-023-02327-2DOI

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QC 20230710
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 + profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.

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Ramírez-Suástegui, CiroDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA, La Jolla (författare)
Strobl, Daniel C.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 (författare)
Gillett, Tessa E.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 (författare)
Zappia, LukeDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Department of Mathematics, Technical University of Munich, Garching, Germany (författare)
Madissoon, EloWellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
Markov, Nikolay S.Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA (författare)
Zaragosi, Laure EmmanuelleInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France (författare)
Ji, YugeDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany (författare)
Ansari, MeshalDepartment 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 (författare)
Arguel, Marie JeanneInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France (författare)
Apperloo, LeonieGroningen 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 (författare)
Banchero, MartinGroningen 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 (författare)
Bécavin, ChristopheInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France (författare)
Berg, MarijnGroningen 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 (författare)
Chichelnitskiy, EvgenyInstitute for Transplant Immunology, Hannover Medical School, Hannover, Germany (författare)
Chung, Mei i.Translational Genomics Research Institute, Phoenix, AZ, USA (författare)
Collin, AntoineInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France; 3IA Côte d’Azur, Nice, France (författare)
Gay, Aurore C.A.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 (författare)
Gote-Schniering, JanineInstitute 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 (författare)
Hooshiar Kashani, BaharakInstitute 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 (författare)
Inecik, KemalDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany (författare)
Jain, ManuDivision of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA (författare)
Kapellos, Theodore S.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 (författare)
Kole, Tessa 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 (författare)
Leroy, SylviePulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, Nice, France (författare)
Mayr, Christoph H.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 (författare)
Oliver, Amanda J.Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
von Papen, MichaelResearch, Development and Innovation, Comma Soft, Bonn, Germany (författare)
Peter, LanceTranslational Genomics Research Institute, Phoenix, AZ, USA (författare)
Taylor, Chase J.Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA (författare)
Walzthoeni, ThomasCore Facility Genomics, Helmholtz Center Munich, Munich, Germany (författare)
Xu, ChuanWellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
Bui, Linh T.Translational Genomics Research Institute, Phoenix, AZ, USA (författare)
De Donno, CarloDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany (författare)
Dony, LeanderDepartment 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 (författare)
Faiz, AlenGroningen 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 (författare)
Guo, MinzheDivision 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 (författare)
Gutierrez, Austin J.Translational Genomics Research Institute, Phoenix, AZ, USA (författare)
Heumos, LukasDepartment 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 (författare)
Huang, NiWellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
Ibarra, Ignacio L.Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany (författare)
Jackson, Nathan D.Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA (författare)
Kadur Lakshminarasimha Murthy, PreetishDepartment of Cell Biology, Duke University School of Medicine, Durham, NC, USA; Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA (författare)
Lotfollahi, MohammadDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
Tabib, TracyDivision of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA (författare)
Talavera-López, CarlosDepartment 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 (författare)
Travaglini, Kyle J.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 (författare)
Wilbrey-Clark, AnnaWellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
Worlock, Kaylee B.Department of Respiratory Medicine, Division of Medicine, University College London, London, UK (författare)
Yoshida, MasahiroDepartment of Respiratory Medicine, Division of Medicine, University College London, London, UK (författare)
Chen, YuexinInstitute 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 (författare)
Hagood, James S.Department of Pediatrics (Pulmonology), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (författare)
Agami, AhmedInstitute 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 (författare)
Horvath, PeterBiological Research Centre, Szeged, Hungary; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland (författare)
Lundeberg, JoakimKTH,Genteknologi(Swepub:kth)u1qkn9kw (författare)
Marquette, Charles HugoPulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, Nice, France (författare)
Pryhuber, GloriaDepartment of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA (författare)
Samakovlis, ChistosLab and Department of Molecular Bioscience, Stockholm University, Stockholm, Sweden (författare)
Sun, XinUniversity of California, San Diego, La Jolla, CA, USA, La Jolla (författare)
Ware, Lorraine B.Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA (författare)
Zhang, KunUniversity of California, San Diego, La Jolla, CA, USA, La Jolla (författare)
van den Berge, MaartenGroningen 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 (författare)
Bossé, YohanInstitut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada (författare)
Desai, Tushar J.Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA (författare)
Eickelberg, OliverDivision of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA (författare)
Kaminski, NaftaliPulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA (författare)
Krasnow, Mark A.Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA (författare)
Lafyatis, RobertDivision of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA (författare)
Nikolic, Marko Z.Department of Respiratory Medicine, Division of Medicine, University College London, London, UK (författare)
Powell, Joseph E.Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia (författare)
Rajagopal, JayarajCenter for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA (författare)
Rojas, MauricioDepartment of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA (författare)
Rozenblatt-Rosen, OritKlarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA (författare)
Seibold, Max A.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 (författare)
Sheppard, DeanDivision of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA (författare)
Shepherd, Douglas P.Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA (författare)
Sin, Don D.Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada (författare)
Timens, WimGroningen 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 (författare)
Tsankov, Alexander M.Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA (författare)
Whitsett, JeffreyDivision of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA (författare)
Xu, YanDivision of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA (författare)
Banovich, Nicholas E.Translational Genomics Research Institute, Phoenix, AZ, USA (författare)
Barbry, PascalInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France; 3IA Côte d’Azur, Nice, France (författare)
Duong, Thu ElizabethDepartment of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA, La Jolla (författare)
Falk, Christine S.Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany (författare)
Meyer, Kerstin B.Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge (författare)
Kropski, Jonathan A.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 (författare)
Pe’er, DanaHoward Hughes Medical Institute, Chevy Chase, MD, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA (författare)
Schiller, Herbert 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 (författare)
Tata, Purushothama RaoDepartment of Cell Biology, Duke University School of Medicine, Durham, NC, USA (författare)
Schultze, Joachim L.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 (författare)
Teichmann, Sara A.Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge; Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK (författare)
Misharin, Alexander V.Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA (författare)
Nawijn, Martijn C.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 (författare)
Luecken, Malte D.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 (författare)
Theis, Fabian J.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 Mathematics, Technical University of Munich, Garching, Germany (författare)
Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, GermanyDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA, La Jolla (creator_code:org_t)

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Ingår i:Nature Medicine: Springer Nature29:6, s. 1563-15771078-89561546-170X

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Av författaren/redakt...: Sikkema, Lisa; Ramírez-Suástegu ...; Strobl, Daniel C ...; Gillett, Tessa E ...; Zappia, Luke; Madissoon, Elo; visa fler...; Markov, Nikolay ...; Zaragosi, Laure ...; Ji, Yuge; Ansari, Meshal; Arguel, Marie Je ...; Apperloo, Leonie; Banchero, Martin; Bécavin, Christo ...; Berg, Marijn; Chichelnitskiy, ...; Chung, Mei i.; Collin, Antoine; Gay, Aurore C.A.; Gote-Schniering, ...; Hooshiar Kashani ...; Inecik, Kemal; Jain, Manu; Kapellos, Theodo ...; Kole, Tessa M.; Leroy, Sylvie; Mayr, Christoph ...; Oliver, Amanda J ...; von Papen, Micha ...; Peter, Lance; Taylor, Chase J.; Walzthoeni, Thom ...; Xu, Chuan; Bui, Linh T.; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austi ...; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio ...; Jackson, Nathan ...; Kadur Lakshminar ...; Lotfollahi, Moha ...; Tabib, Tracy; Talavera-López, ...; Travaglini, Kyle ...; Wilbrey-Clark, A ...; Worlock, Kaylee ...; Yoshida, Masahir ...; Chen, Yuexin; Hagood, James S.; Agami, Ahmed; Horvath, Peter; Lundeberg, Joaki ...; Marquette, Charl ...; Pryhuber, Gloria; Samakovlis, Chis ...; Sun, Xin; Ware, Lorraine B ...; Zhang, Kun; van den Berge, M ...; Bossé, Yohan; Desai, Tushar J.; Eickelberg, Oliv ...; Kaminski, Naftal ...; Krasnow, Mark A.; Lafyatis, Robert; Nikolic, Marko Z ...; Powell, Joseph E ...; Rajagopal, Jayar ...; Rojas, Mauricio; Rozenblatt-Rosen ...; Seibold, Max A.; Sheppard, Dean; Shepherd, Dougla ...; Sin, Don D.; Timens, Wim; Tsankov, Alexand ...; Whitsett, Jeffre ...; Xu, Yan; Banovich, Nichol ...; Barbry, Pascal; Duong, Thu Eliza ...; Falk, Christine ...; Meyer, Kerstin B ...; Kropski, Jonatha ...; Pe’er, Dana; Schiller, Herber ...; Tata, Purushotha ...; Schultze, Joachi ...; Teichmann, Sara ...; Misharin, Alexan ...; Nawijn, Martijn ...; Luecken, Malte D ...; Theis, Fabian J.; visa färre...

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