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Strunz M, Simon LM, Ansari M, Kathiriya JJ, Angelidis I, Mayr CH, Tsidiridis G, Lange M, Mattner LF, Yee M, Ogar P, Sengupta A, Kukhtevich I, Schneider R, Zhao Z, Voss C, Stoeger T, Neumann JHL, Hilgendorff A, Behr J, O'Reilly M, Lehmann M, Burgstaller G, Königshoff M, Chapman HA, Theis FJ, Schiller HB. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis. Nat Commun 2020; 11:3559. [PMID: 32678092 PMCID: PMC7366678 DOI: 10.1038/s41467-020-17358-3] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/24/2020] [Indexed: 12/22/2022] Open
Abstract
The cell type specific sequences of transcriptional programs during lung regeneration have remained elusive. Using time-series single cell RNA-seq of the bleomycin lung injury model, we resolved transcriptional dynamics for 28 cell types. Trajectory modeling together with lineage tracing revealed that airway and alveolar stem cells converge on a unique Krt8 + transitional stem cell state during alveolar regeneration. These cells have squamous morphology, feature p53 and NFkB activation and display transcriptional features of cellular senescence. The Krt8+ state appears in several independent models of lung injury and persists in human lung fibrosis, creating a distinct cell-cell communication network with mesenchyme and macrophages during repair. We generated a model of gene regulatory programs leading to Krt8+ transitional cells and their terminal differentiation to alveolar type-1 cells. We propose that in lung fibrosis, perturbed molecular checkpoints on the way to terminal differentiation can cause aberrant persistence of regenerative intermediate stem cell states.
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Affiliation(s)
- Maximilian Strunz
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Lukas M Simon
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, USA
| | - Meshal Ansari
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Jaymin J Kathiriya
- Biomedical Center, University of California San Francisco, San Francisco, CA, USA
| | - Ilias Angelidis
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Christoph H Mayr
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - George Tsidiridis
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Marius Lange
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
| | - Laura F Mattner
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Min Yee
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Paulina Ogar
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Arunima Sengupta
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Igor Kukhtevich
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Munich, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Munich, Germany
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, USA
| | - Carola Voss
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Tobias Stoeger
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Jens H L Neumann
- Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Anne Hilgendorff
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
- Member of the German Center for Lung Research (DZL), Center for Comprehensive Developmental Care (CDeCLMU), Department of Neonatology, Perinatal Center Grosshadern, Hospital of the Ludwig-Maximilians University (LMU), Munich, Germany
| | - Jürgen Behr
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
- Member of the German Center for Lung Research (DZL), Department of Internal Medicine V, Ludwig Maximilians University Hospital (LMU) Munich, Munich, Germany
- Asklepios Fachkliniken in Munich-Gauting, Munich, Germany
| | - Michael O'Reilly
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Mareike Lehmann
- Comprehensive Pneumology Center (CPC), Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Melanie Königshoff
- Comprehensive Pneumology Center (CPC), Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- University of Colorado, Department of Pulmonary Sciences and Critical Care Medicine, Denver, CO, USA
| | - Harold A Chapman
- Biomedical Center, University of California San Francisco, San Francisco, CA, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany.
- Department of Mathematics, Technische Universität München, Munich, Germany.
| | - Herbert B Schiller
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany.
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Raredon MSB, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Single-cell connectomic analysis of adult mammalian lungs. SCIENCE ADVANCES 2019; 5:eaaw3851. [PMID: 31840053 PMCID: PMC6892628 DOI: 10.1126/sciadv.aaw3851] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 09/18/2019] [Indexed: 05/17/2023]
Abstract
Efforts to decipher chronic lung disease and to reconstitute functional lung tissue through regenerative medicine have been hampered by an incomplete understanding of cell-cell interactions governing tissue homeostasis. Because the structure of mammalian lungs is highly conserved at the histologic level, we hypothesized that there are evolutionarily conserved homeostatic mechanisms that keep the fine architecture of the lung in balance. We have leveraged single-cell RNA sequencing techniques to identify conserved patterns of cell-cell cross-talk in adult mammalian lungs, analyzing mouse, rat, pig, and human pulmonary tissues. Specific stereotyped functional roles for each cell type in the distal lung are observed, with alveolar type I cells having a major role in the regulation of tissue homeostasis. This paper provides a systems-level portrait of signaling between alveolar cell populations. These methods may be applicable to other organs, providing a roadmap for identifying key pathways governing pathophysiology and informing regenerative efforts.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Taylor Sterling Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
| | - Yasir Suhail
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jonas Christian Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
| | - Sergio Poli
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nir Neumark
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Katherine L. Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Allison Marie Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
| | - Yifan Yuan
- Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Corey Horien
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA
| | - George Linderman
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
- Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
| | - Alexander J. Engler
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
| | - Daniel J. Boffa
- Thoracic Surgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yuval Kluger
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
- Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Ivan O. Rosas
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
- Corresponding author. (N.K.); (L.E.N.)
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
- Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
- Corresponding author. (N.K.); (L.E.N.)
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