A molecular cell atlas of the human lung from single-cell RNA sequencing
Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 – 9 , it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using d...
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| Veröffentlicht in: | Nature (London) Jg. 587; H. 7835; S. 619 - 625 |
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| Hauptverfasser: | , , , , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
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London
Nature Publishing Group UK
26.11.2020
Nature Publishing Group |
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| ISSN: | 0028-0836, 1476-4687, 1476-4687 |
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| Abstract | Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles
1
,
2
,
3
,
4
,
5
,
6
,
7
,
8
–
9
, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.
Expression profiling on 75,000 single cells creates a comprehensive cell atlas of the human lung that includes 41 out of 45 previously known cell types and 14 new ones. |
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| AbstractList | Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles
1
,
2
,
3
,
4
,
5
,
6
,
7
,
8
–
9
, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.
Expression profiling on 75,000 single cells creates a comprehensive cell atlas of the human lung that includes 41 out of 45 previously known cell types and 14 new ones. Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution. Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles , it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution. Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles.sup.1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution. Expression profiling on 75,000 single cells creates a comprehensive cell atlas of the human lung that includes 41 out of 45 previously known cell types and 14 new ones. Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution. Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles.sup.1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution. Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles1–9, it has proven more difficult to systematically identify and localize all molecular types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing (scRNAseq) applied to ~75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, which have allowed us to define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 of 45 previously known cell types or subtypes and 14 new ones. This comprehensive molecular atlas elucidates the biochemical functions of lung cell types and the cell-selective transcription factors and optimal markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signaling interactions including sources and targets of chemokines in immune cell trafficking and expression changes on lung homing; and identifies the cell types directly affected by lung disease genes and respiratory viruses. Comparison to mouse identified 17 molecular types that appear to have been gained or lost during lung evolution and others whose expression profiles have been substantially altered, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution. |
| Audience | Academic |
| Author | Nabhan, Ahmad N. Kuo, Christin S. Weissman, Irving L. Neff, Norma Conley, Stephanie D. Travaglini, Kyle J. Shrager, Joseph B. Quake, Stephen R. Mori, Yasuo Berry, Gerald J. Krasnow, Mark A. Seita, Jun Sit, Rene V. Gillich, Astrid Chang, Stephen Penland, Lolita Sinha, Rahul Metzger, Ross J. |
| AuthorAffiliation | 3 Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA 11 Department of Bioengineering, Stanford University, Stanford, CA, USA 6 Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA, USA 10 Chan Zuckerberg Biohub, San Francisco, CA, USA 8 Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA 1 Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA 4 Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA 5 Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA 9 Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA 2 Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA 7 Department of Pediatrics, Pu |
| AuthorAffiliation_xml | – name: 1 Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA – name: 5 Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA – name: 8 Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA – name: 3 Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA – name: 10 Chan Zuckerberg Biohub, San Francisco, CA, USA – name: 6 Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA, USA – name: 4 Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA – name: 11 Department of Bioengineering, Stanford University, Stanford, CA, USA – name: 7 Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA – name: 9 Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA – name: 2 Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA |
| Author_xml | – sequence: 1 givenname: Kyle J. orcidid: 0000-0003-3164-6448 surname: Travaglini fullname: Travaglini, Kyle J. organization: Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine – sequence: 2 givenname: Ahmad N. surname: Nabhan fullname: Nabhan, Ahmad N. organization: Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Genentech – sequence: 3 givenname: Lolita surname: Penland fullname: Penland, Lolita organization: Chan Zuckerberg Biohub, Calico Life Sciences – sequence: 4 givenname: Rahul surname: Sinha fullname: Sinha, Rahul organization: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Department of Pathology, Stanford University School of Medicine – sequence: 5 givenname: Astrid orcidid: 0000-0002-7016-0494 surname: Gillich fullname: Gillich, Astrid organization: Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine – sequence: 6 givenname: Rene V. surname: Sit fullname: Sit, Rene V. organization: Chan Zuckerberg Biohub – sequence: 7 givenname: Stephen orcidid: 0000-0001-7385-075X surname: Chang fullname: Chang, Stephen organization: Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine – sequence: 8 givenname: Stephanie D. surname: Conley fullname: Conley, Stephanie D. organization: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Department of Pathology, Stanford University School of Medicine – sequence: 9 givenname: Yasuo surname: Mori fullname: Mori, Yasuo organization: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Department of Pathology, Stanford University School of Medicine, Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science – sequence: 10 givenname: Jun surname: Seita fullname: Seita, Jun organization: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Department of Pathology, Stanford University School of Medicine, Medical Sciences Innovation Hub Program – sequence: 11 givenname: Gerald J. surname: Berry fullname: Berry, Gerald J. organization: Department of Pathology, Stanford University School of Medicine – sequence: 12 givenname: Joseph B. surname: Shrager fullname: Shrager, Joseph B. organization: Department of Cardiothoracic Surgery, Stanford University School of Medicine – sequence: 13 givenname: Ross J. orcidid: 0000-0003-0069-4949 surname: Metzger fullname: Metzger, Ross J. organization: Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine – sequence: 14 givenname: Christin S. surname: Kuo fullname: Kuo, Christin S. organization: Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine – sequence: 15 givenname: Norma orcidid: 0000-0001-7141-5420 surname: Neff fullname: Neff, Norma organization: Chan Zuckerberg Biohub – sequence: 16 givenname: Irving L. orcidid: 0000-0002-9077-7467 surname: Weissman fullname: Weissman, Irving L. organization: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Department of Pathology, Stanford University School of Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford Cancer Institute, Stanford University School of Medicine – sequence: 17 givenname: Stephen R. orcidid: 0000-0002-1613-0809 surname: Quake fullname: Quake, Stephen R. email: steve@czbiohub.org organization: Chan Zuckerberg Biohub, Department of Bioengineering, Stanford University – sequence: 18 givenname: Mark A. orcidid: 0000-0002-1976-5471 surname: Krasnow fullname: Krasnow, Mark A. email: krasnow@stanford.edu organization: Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33208946$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | The Author(s), under exclusive licence to Springer Nature Limited 2020 COPYRIGHT 2020 Nature Publishing Group Copyright Nature Publishing Group Nov 26, 2020 |
| Copyright_xml | – notice: The Author(s), under exclusive licence to Springer Nature Limited 2020 – notice: COPYRIGHT 2020 Nature Publishing Group – notice: Copyright Nature Publishing Group Nov 26, 2020 |
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| DOI | 10.1038/s41586-020-2922-4 |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Present address: Calico Life Sciences, South San Francisco, CA USA (L.P.). Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan (Y.S.). Medical Sciences Innovation Hub Program, RIKEN, Japan (J.S.). K.J.T., A.N.N., L.P., R.S., A.G., C.S.K., R.J.M., and M.A.K. conceived the project and designed the lung and blood cell isolation strategy, J.B.S. and C.S.K. designed clinical protocols, reviewed clinical histories and coordinated patient care teams to obtain profiled tissues, G.B. provided expert clinical evaluation and micrographs of donor tissue histology, K.J.T., A.N.N., R.S., and A.G. processed tissue to single cell suspensions, K.J.T., A.N.N., L.P. A.G., R.S., S.D.C. sorted cells for SS2, A.N.N., L.P., S.C., and R.V.S. prepared sequencing libraries, and K.J.T., R.V.S. and L.P. processed and aligned sequencing data. R.S., J.S., and Y.M. performed and supervised bulk mRNA sequencing on defined immune populations. K.J.T., A.N.N., R.S. A.G., and R.J.M. provided tissue expertise and annotated cell types. K.J.T., A.N.N., and M.A.K. designed and implemented bioinformatic methods and interpreted results. K.J.T., A.N.N., and A.G. performed follow up stains. M.A.K., S.R.Q., N.F.N., I.L.W., C.S.K., and R.J.M. supervised and supported the work. K.J.T., A.N.N., and M.A.K. wrote the manuscript, and all authors reviewed and edited the manuscript. These authors contributed equally and will list themselves first on their CVs. Author Contributions |
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, it has been... Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles , it has been difficult to systematically identify and... Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles.sup.1-9, it has been difficult to systematically... Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify... Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles1–9, it has proven more difficult to systematically... |
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| Title | A molecular cell atlas of the human lung from single-cell RNA sequencing |
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