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Januska MN, Walsh MJ. Single-Cell RNA Sequencing Reveals New Basic and Translational Insights in the Cystic Fibrosis Lung. Am J Respir Cell Mol Biol 2023; 68:131-139. [PMID: 36194688 PMCID: PMC9986558 DOI: 10.1165/rcmb.2022-0038tr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/04/2022] [Indexed: 02/03/2023] Open
Abstract
Cystic fibrosis (CF) is a multisystemic, autosomal recessive disorder caused by mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene, with the majority of morbidity and mortality extending from lung disease. Single-cell RNA sequencing (scRNA-seq) has been leveraged in the lung and elsewhere in the body to articulate discrete cell populations, describing cell types, states, and lineages as well as their roles in health and disease. In this translational review, we provide an overview of the current applications of scRNA-seq to the study of the normal and CF lungs, allowing the beginning of a new cellular and molecular narrative of CF lung disease, and we highlight some of the future opportunities to further leverage scRNA-seq and complementary single-cell technologies in the study of CF as we bridge from scientific understanding to clinical application.
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Affiliation(s)
- Megan N. Januska
- Department of Pediatrics
- Department of Genetics and Genomic Sciences, and
| | - Martin J. Walsh
- Department of Pediatrics
- Department of Genetics and Genomic Sciences, and
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; and
- Mount Sinai Center for RNA Biology and Medicine, New York, New York
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52
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Liu D, Xu C, Jiang L, Zhu X. Pulmonary endogenous progenitor stem cell subpopulation: Physiology, pathogenesis, and progress. JOURNAL OF INTENSIVE MEDICINE 2023; 3:38-51. [PMID: 36789358 PMCID: PMC9924023 DOI: 10.1016/j.jointm.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/09/2022] [Accepted: 08/13/2022] [Indexed: 06/18/2023]
Abstract
Lungs are structurally and functionally complex organs consisting of diverse cell types from the proximal to distal axis. They have direct contact with the external environment and are constantly at risk of various injuries. Capable to proliferate and differentiate, pulmonary endogenous progenitor stem cells contribute to the maintenance of lung structure and function both under homeostasis and following injuries. Discovering candidate pulmonary endogenous progenitor stem cell types and underlying regenerative mechanisms provide insights into therapeutic strategy development for lung diseases. In this review, we reveal their compositions, roles in lung disease pathogenesis and injury repair, and the underlying mechanisms. We further underline the advanced progress in research approach and potential therapy for lung regeneration. We also demonstrate the feasibility and prospects of pulmonary endogenous stem cell transplantation for lung disease treatment.
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Affiliation(s)
- Di Liu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Chufan Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Xiaoyan Zhu
- Department of Physiology, Navy Medical University, 800 Xiangyin Road, Shanghai 200433, China
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53
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Yu F, Liu F, Liang X, Duan L, Li Q, Pan G, Ma C, Liu M, Li M, Wang P, Zhao X. iPSC-Derived Airway Epithelial Cells: Progress, Promise, and Challenges. Stem Cells 2023; 41:1-10. [PMID: 36190736 DOI: 10.1093/stmcls/sxac074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/14/2022] [Indexed: 02/02/2023]
Abstract
Induced pluripotent stem cells (iPSCs) generated from somatic cell sources are pluripotent and capable of indefinite expansion in vitro. They provide an unlimited source of cells that can be differentiated into lung progenitor cells for potential clinical use in pulmonary regenerative medicine. This review gives a comprehensive overview of recent progress toward the use of iPSCs to generate proximal and distal airway epithelial cells and mix lung organoids. Furthermore, their potential applications and future challenges for the field are discussed, with a focus on the technological hurdles that must be cleared before stem cell therapeutics can be used for clinical treatment.
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Affiliation(s)
- Fenggang Yu
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Fei Liu
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Xiaohua Liang
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Linwei Duan
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Qiongqiong Li
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Ge Pan
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Chengyao Ma
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Minmin Liu
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Mingyue Li
- Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Peng Wang
- Guangxi Yinfeng Stem Cell Engineering Technology Co., Ltd., Yufeng, Liuzhou, Guangxi Province, People's Republic of China
| | - Xuening Zhao
- Department of Otolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
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54
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Cerro Chiang G, Parimon T. Understanding Interstitial Lung Diseases Associated with Connective Tissue Disease (CTD-ILD): Genetics, Cellular Pathophysiology, and Biologic Drivers. Int J Mol Sci 2023; 24:ijms24032405. [PMID: 36768729 PMCID: PMC9917355 DOI: 10.3390/ijms24032405] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Connective tissue disease-associated interstitial lung disease (CTD-ILD) is a collection of systemic autoimmune disorders resulting in lung interstitial abnormalities or lung fibrosis. CTD-ILD pathogenesis is not well characterized because of disease heterogeneity and lack of pre-clinical models. Some common risk factors are inter-related with idiopathic pulmonary fibrosis, an extensively studied fibrotic lung disease, which includes genetic abnormalities and environmental risk factors. The primary pathogenic mechanism is that these risk factors promote alveolar type II cell dysfunction triggering many downstream profibrotic pathways, including inflammatory cascades, leading to lung fibroblast proliferation and activation, causing abnormal lung remodeling and repairs that result in interstitial pathology and lung fibrosis. In CTD-ILD, dysregulation of regulator pathways in inflammation is a primary culprit. However, confirmatory studies are required. Understanding these pathogenetic mechanisms is necessary for developing and tailoring more targeted therapy and provides newly discovered disease biomarkers for early diagnosis, clinical monitoring, and disease prognostication. This review highlights the central CTD-ILD pathogenesis and biological drivers that facilitate the discovery of disease biomarkers.
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Affiliation(s)
- Giuliana Cerro Chiang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Correspondence:
| | - Tanyalak Parimon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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55
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Xu H, Pan G, Wang J. Repairing Mechanisms for Distal Airway Injuries and Related Targeted Therapeutics for Chronic Lung Diseases. Cell Transplant 2023; 32:9636897231196489. [PMID: 37698245 PMCID: PMC10498699 DOI: 10.1177/09636897231196489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
Chronic lung diseases, such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), involve progressive and irreversible destruction and pathogenic remodeling of airways and have become the leading health care burden worldwide. Pulmonary tissue has extensive capacities to launch injury-responsive repairing programs (IRRPs) to replace the damaged or dead cells upon acute lung injuries. However, the IRRPs are frequently compromised in chronic lung diseases. In this review, we aim to provide an overview of somatic stem cell subpopulations within distal airway epithelium and the underlying mechanisms mediating their self-renewal and trans-differentiation under both physiological and pathological circumstances. We also compared the differences between humans and mice on distal airway structure and stem cell composition. At last, we reviewed the current status and future directions for the development of targeted therapeutics on defective distal airway regeneration and repairment in chronic lung diseases.
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Affiliation(s)
- Huahua Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Guihong Pan
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jun Wang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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56
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Glenn LM, Troy LK, Corte TJ. Novel diagnostic techniques in interstitial lung disease. Front Med (Lausanne) 2023; 10:1174443. [PMID: 37188089 PMCID: PMC10175799 DOI: 10.3389/fmed.2023.1174443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Research into novel diagnostic techniques and targeted therapeutics in interstitial lung disease (ILD) is moving the field toward increased precision and improved patient outcomes. An array of molecular techniques, machine learning approaches and other innovative methods including electronic nose technology and endobronchial optical coherence tomography are promising tools with potential to increase diagnostic accuracy. This review provides a comprehensive overview of the current evidence regarding evolving diagnostic methods in ILD and to consider their future role in routine clinical care.
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Affiliation(s)
- Laura M. Glenn
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
- *Correspondence: Laura M. Glenn,
| | - Lauren K. Troy
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
| | - Tamera J. Corte
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
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57
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Konda B, Mulay A, Yao C, Israely E, Beil S, Huynh CA, Tourtellotte WG, Rampolla R, Chen P, Carraro G, Stripp BR. Cryobanking of Human Distal Lung Epithelial Cells for Preservation of Their Phenotypic and Functional Characteristics. Am J Respir Cell Mol Biol 2022; 67:623-631. [PMID: 36036918 PMCID: PMC12042124 DOI: 10.1165/rcmb.2021-0507ma] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
Abstract
The epithelium lining airspaces of the human lung is maintained by regional stem cells, including basal cells of pseudostratified airways and alveolar type 2 (AT2) pneumocytes of the gas-exchange region. Despite effective techniques for long-term preservation of airway basal cells, procedures for efficient preservation of functional epithelial cell types of the distal gas-exchange region are lacking. Here we detail a method for cryobanking of epithelial cells from either mouse or human lung tissue for preservation of their phenotypic and functional characteristics. Flow cytometric profiling, epithelial organoid-forming efficiency, and single-cell transcriptomic analysis were used to compare cells recovered from cryobanked tissue with those of freshly dissociated tissue. AT2 cells within single-cell suspensions of enzymatically digested cryobanked distal lung tissue retained expression of the pan-epithelial marker CD326 and the AT2 cell surface antigen recognized by monoclonal antibody HT II-280, allowing antibody-mediated enrichment and downstream analysis. Isolated AT2 cells from cryobanked tissue were comparable with those of freshly dissociated tissue both in their single-cell transcriptome and their capacity for in vitro organoid formation in three-dimensional cultures. We conclude that the cryobanking method described herein allows long-term preservation of distal human lung tissue for downstream analysis of lung cell function and molecular phenotype and is ideally suited for the creation of an easily accessible tissue resource for the research community.
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Affiliation(s)
- Bindu Konda
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
| | - Apoorva Mulay
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
| | - Changfu Yao
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
| | - Edo Israely
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
| | - Stephen Beil
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
| | - Carissa A Huynh
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, California
| | | | | | | | - Gianni Carraro
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
| | - Barry R Stripp
- Lung Institute, Department of Medicine
- Regenerative Medicine Institute, and
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58
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Zhou S, Zhu J, Zhou PK, Gu Y. Alveolar type 2 epithelial cell senescence and radiation-induced pulmonary fibrosis. Front Cell Dev Biol 2022; 10:999600. [PMID: 36407111 PMCID: PMC9666897 DOI: 10.3389/fcell.2022.999600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
Radiation-induced pulmonary fibrosis (RIPF) is a chronic and progressive respiratory tract disease characterized by collagen deposition. The pathogenesis of RIPF is still unclear. Type 2 alveolar epithelial cells (AT2), the essential cells that maintain the structure and function of lung tissue, are crucial for developing pulmonary fibrosis. Recent studies indicate the critical role of AT2 cell senescence during the onset and progression of RIPF. In addition, clearance of senescent AT2 cells and treatment with senolytic drugs efficiently improve lung function and radiation-induced pulmonary fibrosis symptoms. These findings indicate that AT2 cell senescence has the potential to contribute significantly to the innovative treatment of fibrotic lung disorders. This review summarizes the current knowledge from basic and clinical research about the mechanism and functions of AT2 cell senescence in RIPF and points to the prospects for clinical treatment by targeting senescent AT2 cells.
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Affiliation(s)
- Shenghui Zhou
- Hengyang Medical College, University of South China, Hengyang, China,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - Jiaojiao Zhu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - Ping-Kun Zhou
- Hengyang Medical College, University of South China, Hengyang, China,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China,*Correspondence: Yongqing Gu, ; Ping-Kun Zhou,
| | - Yongqing Gu
- Hengyang Medical College, University of South China, Hengyang, China,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China,*Correspondence: Yongqing Gu, ; Ping-Kun Zhou,
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59
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Zhou Y, Yang Y, Guo L, Qian J, Ge J, Sinner D, Ding H, Califano A, Cardoso WV. Airway basal cells show regionally distinct potential to undergo metaplastic differentiation. eLife 2022; 11:e80083. [PMID: 36178196 PMCID: PMC9578702 DOI: 10.7554/elife.80083] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/29/2022] [Indexed: 02/07/2023] Open
Abstract
Basal cells are multipotent stem cells of a variety of organs, including the respiratory tract, where they are major components of the airway epithelium. However, it remains unclear how diverse basal cells are and how distinct subpopulations respond to airway challenges. Using single cell RNA-sequencing and functional approaches, we report a significant and previously underappreciated degree of heterogeneity in the basal cell pool, leading to identification of six subpopulations in the adult murine trachea. Among these, we found two major subpopulations, collectively comprising the most uncommitted of all the pools, but with distinct gene expression signatures. Notably, these occupy distinct ventral and dorsal tracheal niches and differ in their ability to self-renew and initiate a program of differentiation in response to environmental perturbations in primary cultures and in mouse injury models in vivo. We found that such heterogeneity is acquired prenatally, when the basal cell pool and local niches are still being established, and depends on the integrity of these niches, as supported by the altered basal cell phenotype of tracheal cartilage-deficient mouse mutants. Finally, we show that features that distinguish these progenitor subpopulations in murine airways are conserved in humans. Together, the data provide novel insights into the origin and impact of basal cell heterogeneity on the establishment of regionally distinct responses of the airway epithelium during injury-repair and in disease conditions.
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Affiliation(s)
- Yizhuo Zhou
- Columbia Center for Human Development, Columbia University Irving Medical CenterNew YorkUnited States
- Department of Medicine, Pulmonary Allergy Critical Care, Columbia University Irving Medical CenterNew YorkUnited States
| | - Ying Yang
- Columbia Center for Human Development, Columbia University Irving Medical CenterNew YorkUnited States
- Department of Genetics and Development, Columbia University Irving Medical CenterNew YorkUnited States
| | - Lihao Guo
- Department of Pharmacy Practice and Science, College of Pharmacy, University of ArizonaTucsonUnited States
| | - Jun Qian
- Columbia Center for Human Development, Columbia University Irving Medical CenterNew YorkUnited States
- Department of Medicine, Pulmonary Allergy Critical Care, Columbia University Irving Medical CenterNew YorkUnited States
| | - Jian Ge
- Columbia Center for Human Development, Columbia University Irving Medical CenterNew YorkUnited States
| | - Debora Sinner
- Neonatology and Pulmonary Biology Perinatal Institute, Cincinnati Children’s Hospital Medical Center and University of Cincinnati, College of MedicineCincinnatiUnited States
| | - Hongxu Ding
- Department of Pharmacy Practice and Science, College of Pharmacy, University of ArizonaTucsonUnited States
| | - Andrea Califano
- Departments of Systems Biology, Biochemistry & Molecular Biophysics, Biomedical Informatics, Medicine; JP Sulzberger Columbia Genome Center; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical CenterNew YorkUnited States
| | - Wellington V Cardoso
- Columbia Center for Human Development, Columbia University Irving Medical CenterNew YorkUnited States
- Department of Medicine, Pulmonary Allergy Critical Care, Columbia University Irving Medical CenterNew YorkUnited States
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60
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Abstract
The mammalian respiratory system or lung is a tree-like branching structure, and the main site of gas exchange with the external environment. Structurally, the lung is broadly classified into the proximal (or conducting) airways and the distal alveolar region, where the gas exchange occurs. In parallel with the respiratory tree, the pulmonary vasculature starts with large pulmonary arteries that subdivide rapidly ending in capillaries adjacent to alveolar structures to enable gas exchange. The NOTCH signalling pathway plays an important role in lung development, differentiation and regeneration post-injury. Signalling via the NOTCH pathway is mediated through activation of four NOTCH receptors (NOTCH1-4), with each receptor capable of regulating unique biological processes. Dysregulation of the NOTCH pathway has been associated with development and pathophysiology of multiple adult acute and chronic lung diseases. This includes accumulating evidence that alteration of NOTCH3 signalling plays an important role in the development and pathogenesis of chronic obstructive pulmonary disease, lung cancer, asthma, idiopathic pulmonary fibrosis and pulmonary arterial hypertension. Herein, we provide a comprehensive summary of the role of NOTCH3 signalling in regulating repair/regeneration of the adult lung, its association with development of lung disease and potential therapeutic strategies to target its signalling activity.
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61
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Stancil IT, Michalski JE, Schwartz DA. An Airway-Centric View of Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2022; 206:410-416. [PMID: 35446237 PMCID: PMC12039158 DOI: 10.1164/rccm.202109-2219pp] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/20/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
| | | | - David A Schwartz
- Department of Medicine and
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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62
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Reynolds SD, Hill CL, Alsudayri A, Lallier SW, Wijeratne S, Tan ZH, Chiang T, Cormet-Boyaka E. Assemblies of JAG1 and JAG2 determine tracheobronchial cell fate in mucosecretory lung disease. JCI Insight 2022; 7:e157380. [PMID: 35819850 PMCID: PMC9462471 DOI: 10.1172/jci.insight.157380] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/06/2022] [Indexed: 11/17/2022] Open
Abstract
Mucosecretory lung disease compromises airway epithelial function and is characterized by goblet cell hyperplasia and ciliated cell hypoplasia. Goblet and ciliated cell types are derived from tracheobronchial stem/progenitor cells via a Notch-dependent mechanism. Although specific arrays of Notch receptors regulate cell fate determination, the function of the ligands Jagged1 (JAG1) and JAG2 is unclear. This study examined JAG1 and JAG2 function using human air-liquid-interface cultures that were treated with γ-secretase complex (GSC) inhibitors, neutralizing peptides/antibodies, or WNT/β-catenin pathway antagonists/agonists. These experiments revealed that JAG1 and JAG2 regulated cell fate determination in the tracheobronchial epithelium; however, their roles did not adhere to simple necessity and sufficiency rules. Biochemical studies indicated that JAG1 and JAG2 underwent posttranslational modifications that resulted in generation of a JAG1 C-terminal peptide and regulated the abundance of full-length JAG2 on the cell surface. GSC and glycogen synthase kinase 3 were implicated in these posttranslational events, but WNT agonist/antagonist studies and RNA-Seq indicated a WNT-independent mechanism. Collectively, these data suggest that posttranslational modifications create distinct assemblies of JAG1 and JAG2, which regulate Notch signal strength and determine the fate of tracheobronchial stem/progenitor cells.
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Affiliation(s)
| | | | | | | | | | - Zheng Hong Tan
- Center for Regenerative Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Tendy Chiang
- Center for Regenerative Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
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63
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Berical A, Lee RE, Lu J, Beermann ML, Le Suer JA, Mithal A, Thomas D, Ranallo N, Peasley M, Stuffer A, Bukis K, Seymour R, Harrington J, Coote K, Valley H, Hurley K, McNally P, Mostoslavsky G, Mahoney J, Randell SH, Hawkins FJ. A multimodal iPSC platform for cystic fibrosis drug testing. Nat Commun 2022; 13:4270. [PMID: 35906215 PMCID: PMC9338271 DOI: 10.1038/s41467-022-31854-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Cystic fibrosis is a monogenic lung disease caused by dysfunction of the cystic fibrosis transmembrane conductance regulator anion channel, resulting in significant morbidity and mortality. The progress in elucidating the role of CFTR using established animal and cell-based models led to the recent discovery of effective modulators for most individuals with CF. However, a subset of individuals with CF do not respond to these modulators and there is an urgent need to develop novel therapeutic strategies. In this study, we generate a panel of airway epithelial cells using induced pluripotent stem cells from individuals with common or rare CFTR variants representative of three distinct classes of CFTR dysfunction. To measure CFTR function we adapt two established in vitro assays for use in induced pluripotent stem cell-derived airway cells. In both a 3-D spheroid assay using forskolin-induced swelling as well as planar cultures composed of polarized mucociliary airway epithelial cells, we detect genotype-specific differences in CFTR baseline function and response to CFTR modulators. These results demonstrate the potential of the human induced pluripotent stem cell platform as a research tool to study CF and in particular accelerate therapeutic development for CF caused by rare variants.
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Affiliation(s)
- Andrew Berical
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Rhianna E Lee
- Marsico Lung Institute and Cystic Fibrosis Research Center, Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Junjie Lu
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | - Mary Lou Beermann
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Jake A Le Suer
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Aditya Mithal
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Dylan Thomas
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Nicole Ranallo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Megan Peasley
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | - Alex Stuffer
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | | | | | | | - Kevin Coote
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | | | - Killian Hurley
- Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin, Ireland
- Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Paul McNally
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Children's Health Ireland, Dublin, Ireland
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - John Mahoney
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | - Scott H Randell
- Marsico Lung Institute and Cystic Fibrosis Research Center, Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA.
- The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA, 02118, USA.
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Mikami S, Miura Y, Kondo S, Sakai K, Nishimura H, Kyoyama H, Moriyama G, Koyama N, Noguchi H, Ohkubo H, Kanazawa S, Uematsu K. Nintedanib induces gene expression changes in the lung of induced-rheumatoid arthritis–associated interstitial lung disease mice. PLoS One 2022; 17:e0270056. [PMID: 35714115 PMCID: PMC9205484 DOI: 10.1371/journal.pone.0270056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/02/2022] [Indexed: 12/15/2022] Open
Abstract
Nintedanib is a multi-tyrosine kinase inhibitor widely used to treat progressive fibrosing interstitial lung diseases because it slows the reduction in forced vital capacity. However, the prognosis for patients treated with nintedanib remains poor. To improve nintedanib treatment, we examined the effects of nintedanib on gene expression in the lungs of induced-rheumatoid arthritis–associated interstitial lung disease model mice, which develop rheumatoid arthritis and subsequent pulmonary fibrosis. Using next-generation sequencing, we identified 27 upregulated and 130 downregulated genes in the lungs of these mice after treatment with nintedanib. The differentially expressed genes included mucin 5B and heat shock protein 70 family genes, which are related to interstitial lung diseases, as well as genes associated with extracellular components, particularly the myocardial architecture, suggesting unanticipated effects of nintedanib. Of the genes upregulated in the nintedanib-treated lung, expression of regulatory factor X2, which is suspected to be involved in cilia movement, and bone morphogenetic protein receptor type 2, which is involved in the pathology of pulmonary hypertension, was detected by immunohistochemistry and RNA in situ hybridization in peripheral airway epithelium and alveolar cells. Thus, the present findings indicate a set of genes whose expression alteration potentially underlies the effects of nintedanib on pulmonary fibrosis. It is expected that these findings will contribute to the development of improved nintedanib strategies for the treatment of progressive fibrosing interstitial lung diseases.
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Affiliation(s)
- Shintaro Mikami
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Yoko Miura
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Shinji Kondo
- Center for Genome Informatics, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Kosuke Sakai
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Hiroaki Nishimura
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Hiroyuki Kyoyama
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Gaku Moriyama
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Nobuyuki Koyama
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hirotsugu Ohkubo
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Satoshi Kanazawa
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Kazutsugu Uematsu
- Department of Pulmonary Medicine, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
- * E-mail:
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65
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Heinzelmann K, Hu Q, Hu Y, Dobrinskikh E, Ansari M, Melo-Narváez MC, Ulke HM, Leavitt C, Mirita C, Trudeau T, Saal ML, Rice P, Gao B, Janssen WJ, Yang IV, Schiller HB, Vladar EK, Lehmann M, Königshoff M. Single-cell RNA sequencing identifies G-protein coupled receptor 87 as a basal cell marker expressed in distal honeycomb cysts in idiopathic pulmonary fibrosis. Eur Respir J 2022; 59:2102373. [PMID: 35604813 PMCID: PMC9203838 DOI: 10.1183/13993003.02373-2021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/02/2022] [Indexed: 11/15/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a devastating and life-threatening lung disease characterised by epithelial reprogramming and increased extracellular matrix deposition leading to loss of lung function. Prominent histopathological structures in the distal IPF lung include honeycomb cysts in the alveolar space [1]. These are heterogeneous bronchiolised areas that feature clusters of simple epithelium with keratin (KRT)5+ basal-like cells interspersed with pseudostratified epithelium containing differentiated, hyperplastic epithelial cells, as well as aberrant ciliated cells [2–5]. Recent single-cell RNA sequencing studies of whole lungs from IPF and donor tissue revealed cellular subtypes unique to IPF, including basaloid KRT5−/KRT17+ cells present in the distal lung [6–10]. Bronchiolisation and honeycombing are features of IPF. ScRNA sequencing identified GPR87 as a novel marker of basal cells in IPF, enriched in honeycomb cysts. GPR87 overexpression resulted in aberrant airway cell differentiation. https://bit.ly/3i4dXeT
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Affiliation(s)
- Katharina Heinzelmann
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- K. Heinzelmann and Q. Hu contributed equally
| | - Qianjiang Hu
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Division of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- K. Heinzelmann and Q. Hu contributed equally
| | - Yan Hu
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Evgenia Dobrinskikh
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Meshal Ansari
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - M Camila Melo-Narváez
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Henrik M Ulke
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Colton Leavitt
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Carol Mirita
- Eastern Colorado VA Healthcare System, Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
| | - Tammy Trudeau
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maxwell L Saal
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Pamela Rice
- Eastern Colorado VA Healthcare System, Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
| | - Bifeng Gao
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - William J Janssen
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Dept of Medicine, National Jewish Health, Denver, CO, USA
| | - Ivana V Yang
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Eszter K Vladar
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Dept of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mareike Lehmann
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- M. Lehmann and M. Königshoff contributed equally to this article as lead authors and supervised the work
| | - Melanie Königshoff
- Division of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- M. Lehmann and M. Königshoff contributed equally to this article as lead authors and supervised the work
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66
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Carraro G, Stripp BR. Insights gained in the pathology of lung disease through single cell transcriptomics. J Pathol 2022; 257:494-500. [PMID: 35608561 DOI: 10.1002/path.5971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/17/2022] [Indexed: 11/07/2022]
Abstract
The human lung is a relatively quiescent organ in the normal healthy state but contains stem/progenitor cells that contribute to normal tissue maintenance and either repair or remodeling in response to injury and disease. Maintenance or repair lead to proper restoration of functional lung tissue and maintenance of physiological functions, with remodeling resulting in altered structure and function that is typically associated with disease. Knowledge of cell types contributing to lung tissue maintenance and repair/remodeling have largely relied on mouse models of injury-repair and lineage tracing of local progenitors. Therefore, many of the functional alterations underlying remodeling in human lung disease, have remained poorly defined. However, the advent of advanced genomics approaches to define the molecular phenotype of lung cells at single cell resolution has paved the way for rapid advances in our understanding of cell types present within the normal human lung and changes that accompany disease. Here we summarize recent advances in our understanding of disease-related changes in the molecular phenotype of human lung epithelium that have emerged from single-cell transcriptomic studies. We focus attention on emerging concepts of epithelial transitional states that characterize the pathological remodeling that accompanies chronic lung diseases, including idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, cystic fibrosis, and asthma. Concepts arising from these studies are actively evolving and require corroborative studies to improve our understanding of disease mechanisms. Whenever possible we highlight opportunities for providing a unified nomenclature in this rapidly advancing field of research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gianni Carraro
- Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Barry R Stripp
- Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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67
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Zhang M, Guo FR. BSDE: barycenter single-cell differential expression for case-control studies. Bioinformatics 2022; 38:2765-2772. [PMID: 35561165 PMCID: PMC9113363 DOI: 10.1093/bioinformatics/btac171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/14/2022] [Accepted: 03/23/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Single-cell sequencing brings about a revolutionarily high resolution for finding differentially expressed genes (DEGs) by disentangling highly heterogeneous cell tissues. Yet, such analysis is so far mostly focused on comparing between different cell types from the same individual. As single-cell sequencing becomes cheaper and easier to use, an increasing number of datasets from case-control studies are becoming available, which call for new methods for identifying differential expressions between case and control individuals. RESULTS To bridge this gap, we propose barycenter single-cell differential expression (BSDE), a nonparametric method for finding DEGs for case-control studies. Through the use of optimal transportation for aggregating distributions and computing their distances, our method overcomes the restrictive parametric assumptions imposed by standard mixed-effect-modeling approaches. Through simulations, we show that BSDE can accurately detect a variety of differential expressions while maintaining the type-I error at a prescribed level. Further, 1345 and 1568 cell type-specific DEGs are identified by BSDE from datasets on pulmonary fibrosis and multiple sclerosis, among which the top findings are supported by previous results from the literature. AVAILABILITY AND IMPLEMENTATION R package BSDE is freely available from doi.org/10.5281/zenodo.6332254. For real data analysis with the R package, see doi.org/10.5281/zenodo.6332566. These can also be accessed thorough GitHub at github.com/mqzhanglab/BSDE and github.com/mqzhanglab/BSDE_pipeline. The two single-cell sequencing datasets can be download with UCSC cell browser from cells.ucsc.edu/?ds=ms and cells.ucsc.edu/?ds=lung-pf-control. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mengqi Zhang
- Department of Surgery, Perelman Medical School, University of Pennsylvania, Philadelphia, PA 19104, USA
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68
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Wu M, Zhang X, Lin Y, Zeng Y. Roles of airway basal stem cells in lung homeostasis and regenerative medicine. Respir Res 2022; 23:122. [PMID: 35562719 PMCID: PMC9102684 DOI: 10.1186/s12931-022-02042-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/01/2022] [Indexed: 11/10/2022] Open
Abstract
Airway basal stem cells (BSCs) in the proximal airways are recognized as resident stem cells capable of self-renewing and differentiating to virtually every pseudostratified epithelium cell type under steady-state and after acute injury. In homeostasis, BSCs typically maintain a quiescent state. However, when exposed to acute injuries by either physical insults, chemical damage, or pathogen infection, the remaining BSCs increase their proliferation rate apace within the first 24 h and differentiate to restore lung homeostasis. Given the progenitor property of airway BSCs, it is attractive to research their biological characteristics and how they maintain homeostatic airway structure and respond to injury. In this review, we focus on the roles of BSCs in lung homeostasis and regeneration, detail the research progress in the characteristics of airway BSCs, the cellular and molecular signaling communications involved in BSCs-related airway repair and regeneration, and further discuss the in vitro models for airway BSC propagation and their applications in lung regenerative medicine therapy.
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Affiliation(s)
- Meirong Wu
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China
| | - Xiaojing Zhang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China
| | - Yijian Lin
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China
| | - Yiming Zeng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China. .,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China. .,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China.
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69
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Kadur Lakshminarasimha Murthy P, Sontake V, Tata A, Kobayashi Y, Macadlo L, Okuda K, Conchola AS, Nakano S, Gregory S, Miller LA, Spence JR, Engelhardt JF, Boucher RC, Rock JR, Randell SH, Tata PR. Human distal lung maps and lineage hierarchies reveal a bipotent progenitor. Nature 2022; 604:111-119. [PMID: 35355018 PMCID: PMC9169066 DOI: 10.1038/s41586-022-04541-3] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/09/2022] [Indexed: 12/22/2022]
Abstract
Mapping the spatial distribution and molecular identity of constituent cells is essential for understanding tissue dynamics in health and disease. We lack a comprehensive map of human distal airways, including the terminal and respiratory bronchioles (TRBs), which are implicated in respiratory diseases1-4. Here, using spatial transcriptomics and single-cell profiling of microdissected distal airways, we identify molecularly distinct TRB cell types that have not-to our knowledge-been previously characterized. These include airway-associated LGR5+ fibroblasts and TRB-specific alveolar type-0 (AT0) cells and TRB secretory cells (TRB-SCs). Connectome maps and organoid-based co-cultures reveal that LGR5+ fibroblasts form a signalling hub in the airway niche. AT0 cells and TRB-SCs are conserved in primates and emerge dynamically during human lung development. Using a non-human primate model of lung injury, together with human organoids and tissue specimens, we show that alveolar type-2 cells in regenerating lungs transiently acquire an AT0 state from which they can differentiate into either alveolar type-1 cells or TRB-SCs. This differentiation programme is distinct from that identified in the mouse lung5-7. Our study also reveals mechanisms that drive the differentiation of the bipotent AT0 cell state into normal or pathological states. In sum, our findings revise human lung cell maps and lineage trajectories, and implicate an epithelial transitional state in primate lung regeneration and disease.
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Affiliation(s)
| | - Vishwaraj Sontake
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Lauren Macadlo
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ansley S Conchola
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simon Gregory
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Lisa A Miller
- California National Primate Research Center, Davis, CA, USA
- Department of Anatomy, Physiology and Cell biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John F Engelhardt
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason R Rock
- Department of Immunology Discovery, Genentech, South San Francisco, CA, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA.
- Division of Pulmonary Critical Care, Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
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70
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Chakraborty A, Mastalerz M, Ansari M, Schiller HB, Staab-Weijnitz CA. Emerging Roles of Airway Epithelial Cells in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:cells11061050. [PMID: 35326501 PMCID: PMC8947093 DOI: 10.3390/cells11061050] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease with incompletely understood aetiology and limited treatment options. Traditionally, IPF was believed to be mainly caused by repetitive injuries to the alveolar epithelium. Several recent lines of evidence, however, suggest that IPF equally involves an aberrant airway epithelial response, which contributes significantly to disease development and progression. In this review, based on recent clinical, high-resolution imaging, genetic, and single-cell RNA sequencing data, we summarize alterations in airway structure, function, and cell type composition in IPF. We furthermore give a comprehensive overview on the genetic and mechanistic evidence pointing towards an essential role of airway epithelial cells in IPF pathogenesis and describe potentially implicated aberrant epithelial signalling pathways and regulation mechanisms in this context. The collected evidence argues for the investigation of possible therapeutic avenues targeting these processes, which thus represent important future directions of research.
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71
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Wijk SC, Prabhala P, Löfdahl A, Nybom A, Lang S, Brunnström H, Bjermer L, Westergren-Thorsson G, Magnusson M. Ciliated (FOXJ1+) Cells Display Reduced Ferritin Light Chain in the Airways of Idiopathic Pulmonary Fibrosis Patients. Cells 2022; 11:cells11061031. [PMID: 35326483 PMCID: PMC8947470 DOI: 10.3390/cells11061031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
Cell-based therapies hold great promise in re-establishing organ function for many diseases, including untreatable lung diseases such as idiopathic pulmonary fibrosis (IPF). However, many hurdles still remain, in part due to our lack of knowledge about the disease-driving mechanisms that may affect the cellular niche and thereby possibly hinder the function of any transplanted cells by imposing the disease phenotype onto the newly generated progeny. Recent findings have demonstrated increased ciliation of lung cells from IPF patients, but how this affects ciliated cell function and the airway milieu is not well-known. Here, we performed single-cell RNA sequencing on primary ciliated (FOJ1+) cells isolated from IPF patients and from healthy control donors. The sequencing identified multiple biological processes, such as cilium morphogenesis and cell signaling, that were significantly changed between IPF and healthy ciliated cells. Ferritin light chain (FTL) was downregulated in IPF, which suggests that iron metabolism may be affected in the IPF ciliated cells. The RNA expression was confirmed at the protein level with histological localization in lung tissue, prompting future functional assays to reveal the potential role of FTL. Taken together, our data demonstrate the importance of careful analyses in pure cell populations to better understand the IPF disease mechanism.
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Affiliation(s)
- Sofia C. Wijk
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 223 62 Lund, Sweden; (S.C.W.); (P.P.)
| | - Pavan Prabhala
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 223 62 Lund, Sweden; (S.C.W.); (P.P.)
| | - Anna Löfdahl
- Division of Lung Biology, Department of Experimental Medical Science, Lund University, 223 62 Lund, Sweden; (A.L.); (A.N.); (G.W.-T.)
| | - Annika Nybom
- Division of Lung Biology, Department of Experimental Medical Science, Lund University, 223 62 Lund, Sweden; (A.L.); (A.N.); (G.W.-T.)
| | - Stefan Lang
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 223 62 Lund, Sweden;
| | - Hans Brunnström
- Department of Clinical Sciences, Lund University, 223 62 Lund, Sweden;
| | - Leif Bjermer
- Division of Respiratory Medicine and Allergology, Department of Clinical Sciences, Lund University, 223 62 Lund, Sweden;
| | - Gunilla Westergren-Thorsson
- Division of Lung Biology, Department of Experimental Medical Science, Lund University, 223 62 Lund, Sweden; (A.L.); (A.N.); (G.W.-T.)
| | - Mattias Magnusson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 223 62 Lund, Sweden; (S.C.W.); (P.P.)
- Correspondence: ; Tel.: +46-46-222-06-08
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72
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Khan P, Fytianos K, Blumer S, Roux J, Gazdhar A, Savic S, Knudsen L, Jonigk D, Kuehnel MP, Mykoniati S, Tamm M, Geiser T, Hostettler KE. Basal-Like Cell-Conditioned Medium Exerts Anti-Fibrotic Effects In Vitro and In Vivo. Front Bioeng Biotechnol 2022; 10:844119. [PMID: 35350187 PMCID: PMC8957873 DOI: 10.3389/fbioe.2022.844119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/04/2022] [Indexed: 12/15/2022] Open
Abstract
In idiopathic pulmonary fibrosis (IPF), basal-like cells are atypically present in the alveolar region, where they may affect adjacent stromal cells by paracrine mechanisms. We here aimed to confirm the presence of basal-like cells in peripheral IPF lung tissue in vivo, to culture and characterize the cells in vitro, and to investigate their paracrine effects on IPF fibroblasts in vitro and in bleomycin-injured rats in vivo. Basal-like cells are mainly localized in areas of pathological bronchiolization or honeycomb cysts in peripheral IPF lung tissue. Single-cell RNA sequencing (scRNA-seq) demonstrated an overall homogeneity, the expression of the basal cell markers cytokeratin KRT5 and KRT17, and close transcriptomic similarities to basal cells in the majority of cells cultured in vitro. Basal-like cells secreted significant levels of prostaglandin E2 (PGE2), and their conditioned medium (CM) inhibited alpha-smooth muscle actin (α-SMA) and collagen 1A1 (Col1A1) and upregulated matrix metalloproteinase-1 (MMP-1) and hepatocyte growth factor (HGF) by IPF fibroblasts in vitro. The instillation of CM in bleomycin-injured rat lungs resulted in reduced collagen content, improved lung architecture, and reduced α-SMA-positive cells. Our data suggested that basal-like cells may limit aberrant fibroblast activation and differentiation in IPF through paracrine mechanisms.
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Affiliation(s)
- Petra Khan
- Department of Biomedicine and Clinics of Respiratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Kleanthis Fytianos
- Department of Pulmonary Medicine, University Hospital Bern, and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Sabrina Blumer
- Department of Biomedicine and Clinics of Respiratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Julien Roux
- Department of Biomedicine and Clinics of Respiratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Amiq Gazdhar
- Department of Pulmonary Medicine, University Hospital Bern, and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Spasenija Savic
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Lars Knudsen
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Danny Jonigk
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Mark P. Kuehnel
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Sofia Mykoniati
- Department of Internal Medicine, Jura Cantonal Hospital, Delemont, Switzerland
| | - Michael Tamm
- Department of Biomedicine and Clinics of Respiratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Thomas Geiser
- Department of Pulmonary Medicine, University Hospital Bern, and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Katrin E. Hostettler
- Department of Biomedicine and Clinics of Respiratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
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73
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Wang R, Hume AJ, Beermann ML, Simone-Roach C, Lindstrom-Vautrin J, Le Suer J, Huang J, Olejnik J, Villacorta-Martin C, Bullitt E, Hinds A, Ghaedi M, Rollins S, Werder RB, Abo KM, Wilson AA, Mühlberger E, Kotton DN, Hawkins FJ. Human airway lineages derived from pluripotent stem cells reveal the epithelial responses to SARS-CoV-2 infection. Am J Physiol Lung Cell Mol Physiol 2022; 322:L462-L478. [PMID: 35020534 PMCID: PMC8917936 DOI: 10.1152/ajplung.00397.2021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 02/01/2023] Open
Abstract
There is an urgent need to understand how SARS-CoV-2 infects the airway epithelium and in a subset of individuals leads to severe illness or death. Induced pluripotent stem cells (iPSCs) provide a near limitless supply of human cells that can be differentiated into cell types of interest, including airway epithelium, for disease modeling. We present a human iPSC-derived airway epithelial platform, composed of the major airway epithelial cell types, that is permissive to SARS-CoV-2 infection. Subsets of iPSC-airway cells express the SARS-CoV-2 entry factors angiotensin-converting enzyme 2 (ACE2), and transmembrane protease serine 2 (TMPRSS2). Multiciliated cells are the primary initial target of SARS-CoV-2 infection. On infection with SARS-CoV-2, iPSC-airway cells generate robust interferon and inflammatory responses, and treatment with remdesivir or camostat mesylate causes a decrease in viral propagation and entry, respectively. In conclusion, iPSC-derived airway cells provide a physiologically relevant in vitro model system to interrogate the pathogenesis of, and develop treatment strategies for, COVID-19 pneumonia.
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Affiliation(s)
- Ruobing Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
| | - Mary Lou Beermann
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Chantelle Simone-Roach
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Jake Le Suer
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University, Boston, Massachusetts
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Mahboobe Ghaedi
- Research and Early Development Respiratory & Inflammation (R&I), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Stuart Rollins
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts
| | - Finn J Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
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74
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Xie T, Lynn H, Parks WC, Stripp B, Chen P, Jiang D, Noble PW. Abnormal respiratory progenitors in fibrotic lung injury. Stem Cell Res Ther 2022; 13:64. [PMID: 35130980 PMCID: PMC8822870 DOI: 10.1186/s13287-022-02737-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/18/2022] [Indexed: 12/19/2022] Open
Abstract
Recent advances in single-cell RNA sequencing (scRNA-seq) and epithelium lineage labeling have yielded identification of multiple abnormal epithelial progenitor populations during alveolar type 2 (ATII) cell differentiation into alveolar type 1 (ATI) cells during regenerative lung post-fibrotic injury. These abnormal cells include basaloid/basal-like cells, ATII transition cells, and persistent epithelial progenitors (PEPs). These cells occurred and accumulated during the regeneration of distal airway and alveoli in response to both chronic and acute pulmonary injury. Among the alveolar epithelial progenitors, PEPs express a distinct Krt8+ phenotype that is rarely found in intact alveoli. However, post-injury, the Krt8+ phenotype is seen in dysplastic epithelial cells. Fully understanding the characteristics and functions of these newly found, injury-induced abnormal behavioral epithelial progenitors and the signaling pathways regulating their phenotype could potentially point the way to unique therapeutic targets for fibrosing lung diseases. This review summarizes recent advances in understanding these epithelial progenitors as they relate to uncovering regenerative mechanisms.
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Affiliation(s)
- Ting Xie
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Heather Lynn
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - William C Parks
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Barry Stripp
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Peter Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dianhua Jiang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul W Noble
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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75
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Moss BJ, Ryter SW, Rosas IO. Pathogenic Mechanisms Underlying Idiopathic Pulmonary Fibrosis. ANNUAL REVIEW OF PATHOLOGY 2022; 17:515-546. [PMID: 34813355 DOI: 10.1146/annurev-pathol-042320-030240] [Citation(s) in RCA: 361] [Impact Index Per Article: 120.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pathogenesis of idiopathic pulmonary fibrosis (IPF) involves a complex interplay of cell types and signaling pathways. Recurrent alveolar epithelial cell (AEC) injury may occur in the context of predisposing factors (e.g., genetic, environmental, epigenetic, immunologic, and gerontologic), leading to metabolic dysfunction, senescence, aberrant epithelial cell activation, and dysregulated epithelial repair. The dysregulated epithelial cell interacts with mesenchymal, immune, and endothelial cells via multiple signaling mechanisms to trigger fibroblast and myofibroblast activation. Recent single-cell RNA sequencing studies of IPF lungs support the epithelial injury model. These studies have uncovered a novel type of AEC with characteristics of an aberrant basal cell, which may disrupt normal epithelial repair and propagate a profibrotic phenotype. Here, we review the pathogenesis of IPF in the context of novel bioinformatics tools as strategies to discover pathways of disease, cell-specific mechanisms, and cell-cell interactions that propagate the profibrotic niche.
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Affiliation(s)
- Benjamin J Moss
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
| | - Stefan W Ryter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
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76
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Mei Q, Liu Z, Zuo H, Yang Z, Qu J. Idiopathic Pulmonary Fibrosis: An Update on Pathogenesis. Front Pharmacol 2022; 12:797292. [PMID: 35126134 PMCID: PMC8807692 DOI: 10.3389/fphar.2021.797292] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, lethal fibrotic lung disease that occurs primarily in middle-aged and elderly adults. It is a major cause of morbidity and mortality. With an increase in life expectancy, the economic burden of IPF is expected to continuously rise in the near future. Although the exact pathophysiological mechanisms underlying IPF remain not known. Significant progress has been made in our understanding of the pathogenesis of this devastating disease in last decade. The current paradigm assumes that IPF results from sustained or repetitive lung epithelial injury and subsequent activation of fibroblasts and myofibroblast differentiation. Persistent myofibroblast phenotype contributes to excessive deposition of the extracellular matrix (ECM) and aberrant lung repair, leading to tissue scar formation, distortion of the alveolar structure, and irreversible loss of lung function. Treatments of patients with IPF by pirfenidone and nintedanib have shown significant reduction of lung function decline and slowing of disease progression in patients with IPF. However, these drugs do not cure the disease. In this review, we discuss recent advances on the pathogenesis of IPF and highlight the development of novel therapeutic strategies against the disease.
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Affiliation(s)
| | | | | | | | - Jing Qu
- *Correspondence: Zhenhua Yang, ; Jing Qu,
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77
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Human alveolar type 2 epithelium transdifferentiates into metaplastic KRT5 + basal cells. Nat Cell Biol 2021; 24:10-23. [PMID: 34969962 PMCID: PMC8761168 DOI: 10.1038/s41556-021-00809-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/04/2021] [Indexed: 01/06/2023]
Abstract
Loss of alveolar type 2 cells (AEC2s) and ectopic appearance of basal cells in the alveoli characterize severe lung injuries such as idiopathic pulmonary fibrosis (IPF). Here we demonstrate that human alveolar type 2 cells (hAEC2s), unlike murine AEC2s, transdifferentiate into basal cells in response to fibrotic signaling in the lung mesenchyme in vitro and in vivo. Single cell analysis of normal hAEC2s and mesenchymal cells in organoid co-cultures revealed the emergence of pathologic fibroblasts and basloid cells previously described in IPF. TGFβ1 and anti-BMP signaling in the organoids promoted transdifferentiation. Trajectory and histologic analyses of both hAEC2-derived organoids and IPF epithelium indicated hAEC2s transdifferentiate into basal cells through alveolar-basal intermediates (ABIs) that accumulate in proximity to pathologic CTHRC1high/TGFB1high fibroblasts. Our study indicates that hAEC2-loss and expansion of alveolar metaplastic basal cells in severe human lung injuries are causally connected through a hAEC2-basal cell lineage trajectory driven by aberrant mesenchyme.
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78
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Ghosh M, Hill CL, Alsudayri A, Lallier SW, Hayes D, Wijeratne S, Tan ZH, Chiang T, Mahoney JE, Carraro G, Stripp BR, Reynolds SD. Repeated injury promotes tracheobronchial tissue stem cell attrition. Stem Cells Transl Med 2021; 10:1696-1713. [PMID: 34546001 PMCID: PMC8641087 DOI: 10.1002/sctm.21-0032] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/20/2022] Open
Abstract
Chronic lung disease has been attributed to stem cell aging and/or exhaustion. We investigated these mechanisms using mouse and human tracheobronchial tissue-specific stem cells (TSC). In mouse, chromatin labeling and flow cytometry demonstrated that naphthalene (NA) injury activated a subset of TSC. These activated TSC continued to proliferate after the epithelium was repaired and a clone study demonstrated that ~96% of activated TSC underwent terminal differentiation. Despite TSC attrition, epithelial repair after a second NA injury was normal. The second injury accelerated proliferation of previously activated TSC and a nucleotide-label retention study indicated that the second injury recruited TSC that were quiescent during the first injury. These mouse studies indicate that (a) injury causes selective activation of the TSC pool; (b) activated TSC are predisposed to further proliferation; and (c) the activated state leads to terminal differentiation. In human TSC, repeated proliferation also led to terminal differentiation and depleted the TSC pool. A clone study identified long- and short-lived TSC and showed that short-lived TSC clones had significantly shorter telomeres than their long-lived counterparts. The TSC pool was significantly depleted in dyskeratosis congenita donors, who harbor mutations in telomere biology genes. The remaining TSC had short telomeres and short lifespans. Collectively, the mouse and human studies support a model in which epithelial injury increases the biological age of the responding TSC. When applied to chronic lung disease, this model suggests that repeated injury accelerates the biological aging process resulting in abnormal repair and disease initiation.
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Affiliation(s)
- Moumita Ghosh
- Department of MedicineUniversity of Colorado‐DenverDenverColoradoUSA
| | - Cynthia L. Hill
- Center for Perinatal ResearchNationwide Children's HospitalColumbusOhioUSA
| | - Alfahdah Alsudayri
- Center for Perinatal ResearchNationwide Children's HospitalColumbusOhioUSA
| | - Scott W. Lallier
- Center for Perinatal ResearchNationwide Children's HospitalColumbusOhioUSA
| | - Don Hayes
- Department of PediatricsThe Ohio State University College of MedicineColumbusOhioUSA
| | - Saranga Wijeratne
- Department of PediatricsThe Ohio State University College of MedicineColumbusOhioUSA
| | - Zhang Hong Tan
- Center for Regenerative MedicineNationwide Children's HospitalColumbusOhioUSA
| | - Tendy Chiang
- Center for Regenerative MedicineNationwide Children's HospitalColumbusOhioUSA
| | - John E. Mahoney
- Cystic Fibrosis Foundation TherapeuticsLexingtonMassachusettsUSA
- Cystic Fibrosis FoundationBethesdaMarylandUSA
| | - Gianni Carraro
- Department of Medicine, Cedars‐Sinai Medical CenterLung and Regenerative Medicine InstitutesLos AngelesCaliforniaUSA
| | - Barry R. Stripp
- Department of Medicine, Cedars‐Sinai Medical CenterLung and Regenerative Medicine InstitutesLos AngelesCaliforniaUSA
| | - Susan D. Reynolds
- Center for Perinatal ResearchNationwide Children's HospitalColumbusOhioUSA
- Department of PediatricsThe Ohio State University College of MedicineColumbusOhioUSA
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79
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Cell-Type-Specific Profibrotic Scores across Multi-Organ Systems Predict Cancer Prognosis. Cancers (Basel) 2021; 13:cancers13236024. [PMID: 34885134 PMCID: PMC8656778 DOI: 10.3390/cancers13236024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Fibrosis is a major player and contributor in the tumor microenvironment. Profibrotic changes precede the early development and establishment of a variety of human diseases, such as fibrosis and cancer. Being able to measure such early signals at the single cell level is critically useful for identifying new mechanisms and potential drug targets for a wide range of diseases. This study was designed to computationally identify profibrotic cell populations using single-cell transcriptomic data and to identify gene signatures that could predict cancer prognosis. Abstract Fibrosis is a major cause of mortality. Key profibrotic mechanisms are common pathways involved in tumorigenesis. Characterizing the profibrotic phenotype will help reveal the underlying mechanisms of early development and progression of a variety of human diseases, such as fibrosis and cancer. Fibroblasts have been center stage in response to various stimuli, such as viral infections. However, a comprehensive catalog of cell types involved in this process is currently lacking. Here, we deployed single-cell transcriptomic data across multi-organ systems (i.e., heart, kidney, liver, and lung) to identify novel profibrotic cell populations based on ECM pathway activity at single-cell resolution. In addition to fibroblasts, we also reported that epithelial, endothelial, myeloid, natural killer T, and secretory cells, as well as proximal convoluted tubule cells of the nephron, were significantly actively involved. Cell-type-specific gene signatures were enriched in viral infection pathways, enhanced glycolysis, and carcinogenesis, among others; they were validated using independent datasets in this study. By projecting the signatures into bulk TCGA tumor samples, we could predict prognosis in the patients using profibrotic scores. Our profibrotic cellular phenotype is useful for identifying new mechanisms and potential drug targets at the cell-type level for a wide range of diseases involved in ECM pathway activation.
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80
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The NOTCH3 Downstream Target HEYL Is Required for Efficient Human Airway Basal Cell Differentiation. Cells 2021; 10:cells10113215. [PMID: 34831437 PMCID: PMC8620267 DOI: 10.3390/cells10113215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Abstract
Basal cells (BCs) are stem/progenitor cells of the mucociliary airway epithelium, and their differentiation is orchestrated by the NOTCH signaling pathway. NOTCH3 receptor signaling regulates BC to club cell differentiation; however, the downstream responses that regulate this process are unknown. Overexpression of the active NOTCH3 intracellular domain (NICD3) in primary human bronchial epithelial cells (HBECs) on in vitro air–liquid interface culture promoted club cell differentiation. Bulk RNA-seq analysis identified 692 NICD3-responsive genes, including the classical NOTCH target HEYL, which increased in response to NICD3 and positively correlated with SCGB1A1 (club cell marker) expression. siRNA knockdown of HEYL decreased tight junction formation and cell proliferation. Further, HEYL knockdown reduced club, goblet and ciliated cell differentiation. In addition, we observed decreased expression of HEYL in HBECs from donors with chronic obstructive pulmonary disease (COPD) vs. normal donors which correlates with the impaired differentiation capacity of COPD cells. Finally, overexpression of HEYL in COPD HBECs promoted differentiation into club, goblet and ciliated cells, suggesting the impaired capacity of COPD cells to generate a normal airway epithelium is a reversible phenotype that can be regulated by HEYL. Overall, our data identify the NOTCH3 downstream target HEYL as a key regulator of airway epithelial differentiation.
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81
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Smoking shifts human small airway epithelium club cells toward a lesser differentiated population. NPJ Genom Med 2021; 6:73. [PMID: 34497273 PMCID: PMC8426481 DOI: 10.1038/s41525-021-00237-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
The club cell, a small airway epithelial (SAE) cell, plays a central role in human lung host defense. We hypothesized that subpopulations of club cells with distinct functions may exist. The SAE of healthy nonsmokers and healthy cigarette smokers were evaluated by single-cell RNA sequencing, and unsupervised clustering revealed subpopulations of SCGCB1A1+KRT5loMUC5AC- club cells. Club cell heterogeneity was supported by evaluations of SAE tissue sections, brushed SAE cells, and in vitro air-liquid interface cultures. Three subpopulations included: (1) progenitor; (2) proliferating; and (3) effector club cells. The progenitor club cell population expressed high levels of mitochondrial, ribosomal proteins, and KRT5 relative to other club cell populations and included a differentiation branch point leading to mucous cell production. The small proliferating population expressed high levels of cyclins and proliferation markers. The effector club cell cluster expressed genes related to host defense, xenobiotic metabolism, and barrier functions associated with club cell function. Comparison of smokers vs. nonsmokers demonstrated that smoking limited the extent of differentiation of all three subclusters and altered SAM pointed domain-containing Ets transcription factor (SPDEF)-regulated transcription in the effector cell population leading to a change in the location of the branch point for mucous cell production, a potential explanation for the concomitant reduction in effector club cells and increase in mucous cells in smokers. These observations provide insights into both the makeup of human SAE club cell subpopulations and the smoking-induced changes in club cell biology.
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82
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Cooney AL, Thurman AL, McCray PB, Pezzulo AA, Sinn PL. Lentiviral vectors transduce lung stem cells without disrupting plasticity. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:293-301. [PMID: 34458011 PMCID: PMC8379527 DOI: 10.1016/j.omtn.2021.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/09/2021] [Indexed: 11/19/2022]
Abstract
Life-long expression of a gene therapy agent likely requires targeting stem cells. Here we ask the question: does viral vector transduction or ectopic expression of a therapeutic transgene preclude airway stem cell function? We used a lentiviral vector containing a GFP or cystic fibrosis transmembrane conductance regulator (CFTR) transgene to transduce primary airway basal cells from human cystic fibrosis (CF) or non-CF lung donors and monitored expression and function after differentiation. Ussing chamber measurements confirmed CFTR-dependent chloride channel activity in CF donor cells. Immunostaining, quantitative real-time PCR, and single-cell sequencing analysis of cell-type markers indicated that vector transduction or CFTR expression does not alter the formation of pseudostratified, fully differentiated epithelial cell cultures or cell type distribution. These results have important implications for use of gene addition or gene editing strategies as life-long curative approaches for lung genetic diseases.
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Affiliation(s)
- Ashley L. Cooney
- Stead Family Department of Pediatrics, The University of Iowa, Department of Pediatrics, 169 Newton RD, 6320 PBDB, Iowa City, IA 52242, USA
- Pappajohn Biomedical Institute and the Center for Gene Therapy, The University of Iowa, Iowa City, IA 52242, USA
| | - Andrew L. Thurman
- Pappajohn Biomedical Institute and the Center for Gene Therapy, The University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, The University of Iowa, Department of Pediatrics, 169 Newton RD, 6320 PBDB, Iowa City, IA 52242, USA
- Pappajohn Biomedical Institute and the Center for Gene Therapy, The University of Iowa, Iowa City, IA 52242, USA
| | - Alejandro A. Pezzulo
- Pappajohn Biomedical Institute and the Center for Gene Therapy, The University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Patrick L. Sinn
- Stead Family Department of Pediatrics, The University of Iowa, Department of Pediatrics, 169 Newton RD, 6320 PBDB, Iowa City, IA 52242, USA
- Pappajohn Biomedical Institute and the Center for Gene Therapy, The University of Iowa, Iowa City, IA 52242, USA
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83
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Podolanczuk AJ, Wong AW, Saito S, Lasky JA, Ryerson CJ, Eickelberg O. Update in Interstitial Lung Disease 2020. Am J Respir Crit Care Med 2021; 203:1343-1352. [PMID: 33835899 DOI: 10.1164/rccm.202103-0559up] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Anna J Podolanczuk
- Division of Pulmonary and Critical Care, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Alyson W Wong
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Shigeki Saito
- Section of Pulmonary Disease, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, Louisiana; and
| | - Joseph A Lasky
- Section of Pulmonary Disease, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, Louisiana; and
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Oliver Eickelberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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84
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Wijk SC, Prabhala P, Michaliková B, Sommarin M, Doyle A, Lang S, Kanzenbach K, Tufvesson E, Lindstedt S, Leigh ND, Karlsson G, Bjermer L, Westergren-Thorsson G, Magnusson M. Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2021; 65:103-113. [PMID: 33789072 DOI: 10.1165/rcmb.2020-0464oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Airway basal cells are crucial for regeneration of the human lung airway epithelium and are believed to be important contributors to chronic obstructive pulmonary disease (COPD) and other lung disorders. To reveal how basal cells contribute to disease and to discover novel therapeutic targets, these basal cells need to be further characterized. In this study, we optimized a flow cytometry-based cell sorting protocol for primary human airway basal cells dependent on cell size and NGFR (nerve-growth factor receptor) expression. The basal cell population was found to be molecularly and functionally heterogeneous, in contrast to cultured basal cells. In addition, significant differences were found, such as KRT14 expression exclusively existing in cultured cells. Also, colony-forming capacity was significantly increased in cultured cells showing a clonal enrichment in vitro. Next, by single-cell RNA sequencing on primary basal cells from healthy donors and patients with Global Initiative for Chronic Obstructive Lung Disease stage IV COPD, the gene expression revealed a continuum ranging from healthy basal cell signatures to diseased basal cell phenotypes. We identified several upregulated genes that may indicate COPD, such as stress response-related genes GADD45B and AHSA1, together with with genes involved in the response to hypoxia, such as CITED2 and SOD1. Taken together, the presence of healthy basal cells in stage IV COPD demonstrates the potential for regeneration through the discovery of novel therapeutic targets. In addition, we show the importance of studying primary basal cells when investigating disease mechanisms as well as for developing future cell-based therapies in the human lung.
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Affiliation(s)
- Sofia C Wijk
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center
| | - Pavan Prabhala
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center
| | | | | | - Alexander Doyle
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center
| | - Stefan Lang
- Division of Molecular Hematology, Lund Stem Cell Center
| | - Karina Kanzenbach
- Division of Respiratory Medicine and Allergology, Department of Clinical Sciences
| | - Ellen Tufvesson
- Division of Respiratory Medicine and Allergology, Department of Clinical Sciences
| | - Sandra Lindstedt
- Department of Cardiothoracic Surgery, Skåne University Hospital, and
| | - Nicholas D Leigh
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
| | | | - Leif Bjermer
- Division of Respiratory Medicine and Allergology, Department of Clinical Sciences
| | | | - Mattias Magnusson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center
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85
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Hynds RE, Zacharias WJ, Nikolić MZ, Königshoff M, Eickelberg O, Gosens R, de Coppi P, Janes SM, Morrisey E, Clevers H, Ryan AL, Stripp BR, Sun X, Kim CF, Lin QS. National Heart, Lung, and Blood Institute and Building Respiratory Epithelium and Tissue for Health (BREATH) Consortium Workshop Report: Moving Forward in Lung Regeneration. Am J Respir Cell Mol Biol 2021; 65:22-29. [PMID: 33625958 PMCID: PMC8320125 DOI: 10.1165/rcmb.2020-0397ws] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The National Heart, Lung, and Blood Institute of the National Institutes of Health, together with the Longfonds BREATH consortium, convened a working group to review the field of lung regeneration and suggest avenues for future research. The meeting took place on May 22, 2019, at the American Thoracic Society 2019 conference in Dallas, Texas, United States, and brought together investigators studying lung development, adult stem-cell biology, induced pluripotent stem cells, biomaterials, and respiratory disease. The purpose of the working group was 1) to examine the present status of basic science approaches to tackling lung disease and promoting lung regeneration in patients and 2) to determine priorities for future research in the field.
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Affiliation(s)
- Robert E. Hynds
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, and
- Division of Medicine, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - William J. Zacharias
- Division of Pulmonary Biology, Department of Pediatrics, Cincinnati Children’s Hospital–College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Marko Z. Nikolić
- Division of Medicine, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Melanie Königshoff
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lung Repair and Regeneration Research Unit, Comprehensive Pneumology Center, Helmholtz Zentrum München, Munich, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Reinoud Gosens
- Department of Molecular Pharmacology and
- Groningen Research Institute for Asthma and Chronic Obstructive Pulmonary Disease, University of Groningen, Groningen, the Netherlands
| | - Paolo de Coppi
- Stem Cell and Regenerative Medicine Section, National Institute for Health Research Great Ormond Street Hospital Biomedical Research Centre–University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Sam M. Janes
- Division of Medicine, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Edward Morrisey
- Department of Medicine
- Department of Cell and Developmental Biology
- Lung Biology Institute, University of Pennsylvania–Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences–University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Amy L. Ryan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Hastings Center for Pulmonary Research, and
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California
| | - Barry R. Stripp
- Lung Institute and
- Board of Governors Regenerative Medicine Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Xin Sun
- Department of Pediatrics and
- Department of Biological Sciences, University of California San Diego, San Diego, California
| | - Carla F. Kim
- Division of Hematology/Oncology and
- Division of Respiratory Disease, Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Harvard University, Boston, Massachusetts
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; and
| | - Qing S. Lin
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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86
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Carlier FM, de Fays C, Pilette C. Epithelial Barrier Dysfunction in Chronic Respiratory Diseases. Front Physiol 2021; 12:691227. [PMID: 34248677 PMCID: PMC8264588 DOI: 10.3389/fphys.2021.691227] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022] Open
Abstract
Mucosal surfaces are lined by epithelial cells, which provide a complex and adaptive module that ensures first-line defense against external toxics, irritants, antigens, and pathogens. The underlying mechanisms of host protection encompass multiple physical, chemical, and immune pathways. In the lung, inhaled agents continually challenge the airway epithelial barrier, which is altered in chronic diseases such as chronic obstructive pulmonary disease, asthma, cystic fibrosis, or pulmonary fibrosis. In this review, we describe the epithelial barrier abnormalities that are observed in such disorders and summarize current knowledge on the mechanisms driving impaired barrier function, which could represent targets of future therapeutic approaches.
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Affiliation(s)
- François M. Carlier
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
- Department of Pneumology and Lung Transplant, Centre Hospitalier Universitaire UCL Namur, Yvoir, Belgium
| | - Charlotte de Fays
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Charles Pilette
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
- Department of Pneumology, Cliniques universitaires St-Luc, Brussels, Belgium
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87
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Yao C, Bora SA, Chen P, Goodridge HS, Gharib SA. Sample processing and single cell RNA-sequencing of peripheral blood immune cells from COVID-19 patients. STAR Protoc 2021; 2:100582. [PMID: 34002169 PMCID: PMC8114807 DOI: 10.1016/j.xpro.2021.100582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) allows in-depth assessment of transcriptional changes in immune cells of patients with COVID-19. However, collecting, processing, and analyzing samples from patients with COVID-19 pose many challenges because blood samples may contain infectious virus, identification of immune cell subtypes can be difficult, and biological interpretation of analytical results is complex. To address these issues, we describe a protocol for sample processing, sorting, methanol fixation, and scRNA-seq analysis of PBMCs from frozen buffy coat samples from patients with COVID-19. For complete details on the use and execution of this protocol, please refer to (Yao et al., 2021).
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Affiliation(s)
- Changfu Yao
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephanie A. Bora
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Peter Chen
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Helen S. Goodridge
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sina A. Gharib
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98109, USA
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88
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Parimon T, Hohmann MS, Yao C. Cellular Senescence: Pathogenic Mechanisms in Lung Fibrosis. Int J Mol Sci 2021; 22:6214. [PMID: 34207528 PMCID: PMC8227105 DOI: 10.3390/ijms22126214] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
Pulmonary fibrosis is a chronic and fatal lung disease that significantly impacts the aging population globally. To date, anti-fibrotic, immunosuppressive, and other adjunct therapy demonstrate limited efficacies. Advancing our understanding of the pathogenic mechanisms of lung fibrosis will provide a future path for the cure. Cellular senescence has gained substantial interest in recent decades due to the increased incidence of fibroproliferative lung diseases in the older age group. Furthermore, the pathologic state of cellular senescence that includes maladaptive tissue repair, decreased regeneration, and chronic inflammation resembles key features of progressive lung fibrosis. This review describes regulatory pathways of cellular senescence and discusses the current knowledge on the senescence of critical cellular players of lung fibrosis, including epithelial cells (alveolar type 2 cells, basal cells, etc.), fibroblasts, and immune cells, their phenotypic changes, and the cellular and molecular mechanisms by which these cells contribute to the pathogenesis of pulmonary fibrosis. A few challenges in the field include establishing appropriate in vivo experimental models and identifying senescence-targeted signaling molecules and specific therapies to target senescent cells, known collectively as "senolytic" or "senotherapeutic" agents.
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Affiliation(s)
- Tanyalak Parimon
- Cedars-Sinai Medical Center, Department of Medicine, Women’s Guild Lung Institute, Los Angeles, CA 90048, USA
- Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Miriam S. Hohmann
- Cedars-Sinai Medical Center, Department of Medicine, Women’s Guild Lung Institute, Los Angeles, CA 90048, USA
| | - Changfu Yao
- Cedars-Sinai Medical Center, Department of Medicine, Women’s Guild Lung Institute, Los Angeles, CA 90048, USA
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89
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Orr JC, Hynds RE. Stem Cell-derived Respiratory Epithelial Cell Cultures as Human Disease Models. Am J Respir Cell Mol Biol 2021; 64:657-668. [PMID: 33428856 PMCID: PMC8456877 DOI: 10.1165/rcmb.2020-0440tr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Advances in stem cell biology and the understanding of factors that determine lung stem cell self-renewal have enabled long-term in vitro culture of human lung cells derived from airway basal and alveolar type II cells. Improved capability to expand and study primary cells long term, including in clonal cultures that are recently derived from a single cell, will allow experiments that address fundamental questions about lung homeostasis and repair, as well as translational questions in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and lung cancer research. Here, we provide a brief history of postnatal lung epithelial cell culture and describe recent methodological advances. We further discuss the applications of primary cultures in defining "normal" epithelium, in modeling lung disease, and in future cell therapies.
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Affiliation(s)
- Jessica C Orr
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, and
| | - Robert E Hynds
- UCL Cancer Institute, University College London, London, United Kingdom
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90
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Lehmann M, Königshoff M. Regenerative Medicine and the Hope for a Cure. Clin Chest Med 2021; 42:365-373. [PMID: 34024411 PMCID: PMC11283847 DOI: 10.1016/j.ccm.2021.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Current therapeutic strategies have succeeded in slowing down the progression of idiopathic pulmonary fibrosis (IPF). Emerging evidence highlights IPF as a disease of aging and impaired regeneration. Novel antiaging and regenerative medicine approaches hold promise to be able to reverse disease and might present hope for a cure. Research focusing on a deeper understanding of lung stem cell populations and how these are regulated and altered in fibrotic disease continues to drive the field, and accompanied by earlier diagnosis, the adaptation of clinically relevant models and readouts for regeneration of diseased lung, ultimately paves the way for translation into clinics.
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Affiliation(s)
- Mareike Lehmann
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, German Center of Lung Research (DZL), Max-Lebsche-Platz 31, München 81377, Germany
| | - Melanie Königshoff
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, German Center of Lung Research (DZL), Max-Lebsche-Platz 31, München 81377, Germany; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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91
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Busch SM, Lorenzana Z, Ryan AL. Implications for Extracellular Matrix Interactions With Human Lung Basal Stem Cells in Lung Development, Disease, and Airway Modeling. Front Pharmacol 2021; 12:645858. [PMID: 34054525 PMCID: PMC8149957 DOI: 10.3389/fphar.2021.645858] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
The extracellular matrix (ECM) is not simply a quiescent scaffold. This three-dimensional network of extracellular macromolecules provides structural, mechanical, and biochemical support for the cells of the lung. Throughout life, the ECM forms a critical component of the pulmonary stem cell niche. Basal cells (BCs), the primary stem cells of the airways capable of differentiating to all luminal cell types, reside in close proximity to the basolateral ECM. Studying BC-ECM interactions is important for the development of therapies for chronic lung diseases in which ECM alterations are accompanied by an apparent loss of the lung's regenerative capacity. The complexity and importance of the native ECM in the regulation of BCs is highlighted as we have yet to create an in vitro culture model that is capable of supporting the long-term expansion of multipotent BCs. The interactions between the pulmonary ECM and BCs are, therefore, a vital component for understanding the mechanisms regulating BC stemness during health and disease. If we are able to replicate these interactions in airway models, we could significantly improve our ability to maintain basal cell stemness ex vivo for use in in vitro models and with prospects for cellular therapies. Furthermore, successful, and sustained airway regeneration in an aged or diseased lung by small molecules, novel compounds or via cellular therapy will rely upon both manipulation of the airway stem cells and their immediate niche within the lung. This review will focus on the current understanding of how the pulmonary ECM regulates the basal stem cell function, how this relationship changes in chronic disease, and how replicating native conditions poses challenges for ex vivo cell culture.
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Affiliation(s)
- Shana M. Busch
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Zareeb Lorenzana
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Amy L. Ryan
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, United States
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92
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Thurman AL, Ratcliff JA, Chimenti MS, Pezzulo AA. Differential gene expression analysis for multi-subject single cell RNA sequencing studies with aggregateBioVar. Bioinformatics 2021; 37:3243-3251. [PMID: 33970215 PMCID: PMC8504643 DOI: 10.1093/bioinformatics/btab337] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 04/07/2021] [Accepted: 04/30/2021] [Indexed: 11/14/2022] Open
Abstract
Motivation Single-cell RNA-sequencing (scRNA-seq) provides more granular biological information than bulk RNA-sequencing; bulk RNA sequencing remains popular due to lower costs which allows processing more biological replicates and design more powerful studies. As scRNA-seq costs have decreased, collecting data from more than one biological replicate has become more feasible, but careful modeling of different layers of biological variation remains challenging for many users. Here, we propose a statistical model for scRNA-seq gene counts, describe a simple method for estimating model parameters and show that failing to account for additional biological variation in scRNA-seq studies can inflate false discovery rates (FDRs) of statistical tests. Results First, in a simulation study, we show that when the gene expression distribution of a population of cells varies between subjects, a naïve approach to differential expression analysis will inflate the FDR. We then compare multiple differential expression testing methods on scRNA-seq datasets from human samples and from animal models. These analyses suggest that a naïve approach to differential expression testing could lead to many false discoveries; in contrast, an approach based on pseudobulk counts has better FDR control. Availability and implementation A software package, aggregateBioVar, is freely available on Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/aggregateBioVar.html) to accommodate compatibility with upstream and downstream methods in scRNA-seq data analysis pipelines. Supplementary information Raw gene-by-cell count matrices for pig scRNA-seq data are available as GEO accession GSE150211. Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew L Thurman
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- To whom correspondence should be addressed. or
| | - Jason A Ratcliff
- Iowa Institute of Human Genetics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alejandro A Pezzulo
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- To whom correspondence should be addressed. or
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93
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Mulay A, Konda B, Garcia G, Yao C, Beil S, Villalba JM, Koziol C, Sen C, Purkayastha A, Kolls JK, Pociask DA, Pessina P, de Aja JS, Garcia-de-Alba C, Kim CF, Gomperts B, Arumugaswami V, Stripp BR. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery. Cell Rep 2021; 35:109055. [PMID: 33905739 PMCID: PMC8043574 DOI: 10.1016/j.celrep.2021.109055] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/09/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic caused by severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Although infection initiates in the proximal airways, severe and sometimes fatal symptoms of the disease are caused by infection of the alveolar type 2 (AT2) cells of the distal lung and associated inflammation. In this study, we develop primary human lung epithelial infection models to understand initial responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface (ALI) cultures of proximal airway epithelium and alveosphere cultures of distal lung AT2 cells are readily infected by SARS-CoV-2, leading to an epithelial cell-autonomous proinflammatory response with increased expression of interferon signaling genes. Studies to validate the efficacy of selected candidate COVID-19 drugs confirm that remdesivir strongly suppresses viral infection/replication. We provide a relevant platform for study of COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and emergent respiratory pathogens.
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Affiliation(s)
- Apoorva Mulay
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bindu Konda
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Changfu Yao
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephen Beil
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jaquelyn M Villalba
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; California State University, Long Beach, CA, USA
| | - Colin Koziol
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chandani Sen
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Arunima Purkayastha
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jay K Kolls
- Tulane School of Medicine, New Orleans, LA 70112, USA
| | | | - Patrizia Pessina
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Julio Sainz de Aja
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Carolina Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brigitte Gomperts
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad, Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA; Eli and Edythe Broad, Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
| | - Barry R Stripp
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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94
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Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition. Nat Med 2021; 27:806-814. [PMID: 33958799 PMCID: PMC9009537 DOI: 10.1038/s41591-021-01332-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
Cystic fibrosis (CF) is a lethal autosomal recessive disorder that afflicts more than 70,000 people. People with CF experience multi-organ dysfunction resulting from aberrant electrolyte transport across polarized epithelia due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CF-related lung disease is by far the most important determinant of morbidity and mortality. Here we report results from a multi-institute consortium in which single-cell transcriptomics were applied to define disease-related changes by comparing the proximal airway of CF donors (n = 19) undergoing transplantation for end-stage lung disease with that of previously healthy lung donors (n = 19). Disease-dependent differences observed include an overabundance of epithelial cells transitioning to specialized ciliated and secretory cell subsets coupled with an unexpected decrease in cycling basal cells. Our study yields a molecular atlas of the proximal airway epithelium that will provide insights for the development of new targeted therapies for CF airway disease.
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95
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Nathan S, Zhang H, Andreoli M, Leopold PL, Crystal RG. CREB-dependent LPA-induced signaling initiates a pro-fibrotic feedback loop between small airway basal cells and fibroblasts. Respir Res 2021; 22:97. [PMID: 33794877 PMCID: PMC8015171 DOI: 10.1186/s12931-021-01677-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/04/2021] [Indexed: 01/20/2023] Open
Abstract
Background Lysophosphatidic acid (LPA), generated extracellularly by the action of autotaxin and phospholipase A2, functions through LPA receptors (LPARs) or sphingosine-1-phosphate receptors (S1PRs) to induce pro-fibrotic signaling in the lower respiratory tract of patients with idiopathic pulmonary fibrosis (IPF). We hypothesized that LPA induces changes in small airway epithelial (SAE) basal cells (BC) that create cross-talk between the BC and normal human lung fibroblasts (NHLF), enhancing myofibroblast formation. Methods To assess LPA-induced signaling, BC were treated with LPA for 2.5 min and cell lysates were analyzed by phosphokinase array and Western blot. To assess transcriptional changes, BC were treated with LPA for 3 h and harvested for collection and analysis of RNA by quantitative polymerase chain reaction (qPCR). To assess signaling protein production and function, BC were washed thoroughly after LPA treatment and incubated for 24 h before collection for protein analysis by ELISA or functional analysis by transfer of conditioned medium to NHLF cultures. Transcription, protein production, and proliferation of NHLF were assessed. Results LPA treatment induced signaling by cAMP response element-binding protein (CREB), extracellular signal-related kinases 1 and 2 (Erk1/2), and epithelial growth factor receptor (EGFR) resulting in elevated expression of connective tissue growth factor (CTGF), endothelin-1 (EDN1/ET-1 protein), and platelet derived growth factor B (PDGFB) at the mRNA and protein levels. The conditioned medium from LPA-treated BC induced NHLF proliferation and increased NHLF expression of collagen I (COL1A1), smooth muscle actin (ACTA2), and autotaxin (ENPP2) at the mRNA and protein levels. Increased autotaxin secretion from NHLF correlated with increased LPA in the NHLF culture medium. Inhibition of CREB signaling blocked LPA-induced changes in BC transcription and translation as well as the pro-fibrotic effects of the conditioned medium on NHLF. Conclusion Inhibition of CREB signaling may represent a novel target for alleviating the LPA-induced pro-fibrotic feedback loop between SAE BC and NHLF. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-021-01677-0.
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Affiliation(s)
- Shyam Nathan
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Haijun Zhang
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Mirko Andreoli
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Philip L Leopold
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
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96
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Lafkas D. Cigarette Smoke-induced Effects on Airway Basal Cells: Taking It Up a NOTCH. Am J Respir Cell Mol Biol 2021; 64:397-398. [PMID: 33596396 PMCID: PMC8008797 DOI: 10.1165/rcmb.2021-0041ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Daniel Lafkas
- Department of Immunology Discovery Genentech, Inc. South San Francisco, California
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97
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Bodas M, Moore AR, Subramaniyan B, Georgescu C, Wren JD, Freeman WM, Brown BR, Metcalf JP, Walters MS. Cigarette Smoke Activates NOTCH3 to Promote Goblet Cell Differentiation in Human Airway Epithelial Cells. Am J Respir Cell Mol Biol 2021; 64:426-440. [PMID: 33444514 PMCID: PMC8008804 DOI: 10.1165/rcmb.2020-0302oc] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death in the United States and is primarily caused by cigarette smoking. Increased numbers of mucus-producing secretory ("goblet") cells, defined as goblet cell metaplasia or hyperplasia (GCMH), contributes significantly to COPD pathophysiology. The objective of this study was to determine whether NOTCH signaling regulates goblet cell differentiation in response to cigarette smoke. Primary human bronchial epithelial cells (HBECs) from nonsmokers and smokers with COPD were differentiated in vitro on air-liquid interface and exposed to cigarette smoke extract (CSE) for 7 days. NOTCH signaling activity was modulated using 1) the NOTCH/γ-secretase inhibitor dibenzazepine (DBZ), 2) lentiviral overexpression of the NICD3 (NOTCH3-intracellular domain), or 3) NOTCH3-specific siRNA. Cell differentiation and response to CSE were evaluated by quantitative PCR, Western blotting, immunostaining, and RNA sequencing. We found that CSE exposure of nonsmoker airway epithelium induced goblet cell differentiation characteristic of GCMH. Treatment with DBZ suppressed CSE-dependent induction of goblet cell differentiation. Furthermore, CSE induced NOTCH3 activation, as revealed by increased NOTCH3 nuclear localization and elevated NICD3 protein levels. Overexpression of NICD3 increased the expression of goblet cell-associated genes SPDEF and MUC5AC, whereas NOTCH3 knockdown suppressed CSE-mediated induction of SPDEF and MUC5AC. Finally, CSE exposure of COPD airway epithelium induced goblet cell differentiation in a NOTCH3-dependent manner. These results identify NOTCH3 activation as one of the important mechanisms by which cigarette smoke induces goblet cell differentiation, thus providing a novel potential strategy to control GCMH-related pathologies in smokers and patients with COPD.
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Affiliation(s)
- Manish Bodas
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; and
| | - Andrew R. Moore
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; and
| | - Bharathiraja Subramaniyan
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; and
| | - Constantin Georgescu
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Jonathan D. Wren
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Willard M. Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Brent R. Brown
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; and
| | - Jordan P. Metcalf
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; and
| | - Matthew S. Walters
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; and
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98
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Liu G, Philp AM, Corte T, Travis MA, Schilter H, Hansbro NG, Burns CJ, Eapen MS, Sohal SS, Burgess JK, Hansbro PM. Therapeutic targets in lung tissue remodelling and fibrosis. Pharmacol Ther 2021; 225:107839. [PMID: 33774068 DOI: 10.1016/j.pharmthera.2021.107839] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Structural changes involving tissue remodelling and fibrosis are major features of many pulmonary diseases, including asthma, chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Abnormal deposition of extracellular matrix (ECM) proteins is a key factor in the development of tissue remodelling that results in symptoms and impaired lung function in these diseases. Tissue remodelling in the lungs is complex and differs between compartments. Some pathways are common but tissue remodelling around the airways and in the parenchyma have different morphologies. Hence it is critical to evaluate both common fibrotic pathways and those that are specific to different compartments; thereby expanding the understanding of the pathogenesis of fibrosis and remodelling in the airways and parenchyma in asthma, COPD and IPF with a view to developing therapeutic strategies for each. Here we review the current understanding of remodelling features and underlying mechanisms in these major respiratory diseases. The differences and similarities of remodelling are used to highlight potential common therapeutic targets and strategies. One central pathway in remodelling processes involves transforming growth factor (TGF)-β induced fibroblast activation and myofibroblast differentiation that increases ECM production. The current treatments and clinical trials targeting remodelling are described, as well as potential future directions. These endeavours are indicative of the renewed effort and optimism for drug discovery targeting tissue remodelling and fibrosis.
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Affiliation(s)
- Gang Liu
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Ashleigh M Philp
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia; St Vincent's Medical School, UNSW Medicine, UNSW, Sydney, NSW, Australia
| | - Tamera Corte
- Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mark A Travis
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, United Kingdom
| | - Heidi Schilter
- Pharmaxis Ltd, 20 Rodborough Road, Frenchs Forest, Sydney, NSW, Australia
| | - Nicole G Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Chris J Burns
- Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mathew S Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Sukhwinder S Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Janette K Burgess
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Department of Pathology and Medical Biology, Groningen, The Netherlands; Woolcock Institute of Medical Research, Discipline of Pharmacology, The University of Sydney, Sydney, NSW, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia.
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99
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Allan KM, Farrow N, Donnelley M, Jaffe A, Waters SA. Treatment of Cystic Fibrosis: From Gene- to Cell-Based Therapies. Front Pharmacol 2021; 12:639475. [PMID: 33796025 PMCID: PMC8007963 DOI: 10.3389/fphar.2021.639475] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/11/2022] Open
Abstract
Prognosis of patients with cystic fibrosis (CF) varies extensively despite recent advances in targeted therapies that improve CF transmembrane conductance regulator (CFTR) function. Despite being a multi-organ disease, extensive lung tissue destruction remains the major cause of morbidity and mortality. Progress towards a curative treatment strategy that implements a CFTR gene addition-technology to the patients’ lungs has been slow and not yet developed beyond clinical trials. Improved delivery vectors are needed to overcome the body’s defense system and ensure an efficient and consistent clinical response before gene therapy is suitable for clinical care. Cell-based therapy–which relies on functional modification of allogenic or autologous cells ex vivo, prior to transplantation into the patient–is now a therapeutic reality for various diseases. For CF, pioneering research has demonstrated proof-of-principle for allogenic transplantation of cultured human airway stem cells into mouse airways. However, applying a cell-based therapy to the human airways has distinct challenges. We review CF gene therapies using viral and non-viral delivery strategies and discuss current advances towards autologous cell-based therapies. Progress towards identification, correction, and expansion of a suitable regenerative cell, as well as refinement of pre-cell transplant lung conditioning protocols is discussed.
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Affiliation(s)
- Katelin M Allan
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, Australia
| | - Nigel Farrow
- Respiratory and Sleep Medicine, Women's and Children's Health Network, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Martin Donnelley
- Respiratory and Sleep Medicine, Women's and Children's Health Network, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, Australia
| | - Shafagh A Waters
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, Australia
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100
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Yao C, Guan X, Carraro G, Parimon T, Liu X, Huang G, Mulay A, Soukiasian HJ, David G, Weigt SS, Belperio JA, Chen P, Jiang D, Noble PW, Stripp BR. Senescence of Alveolar Type 2 Cells Drives Progressive Pulmonary Fibrosis. Am J Respir Crit Care Med 2021; 203:707-717. [PMID: 32991815 PMCID: PMC7958503 DOI: 10.1164/rccm.202004-1274oc] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is an insidious and fatal interstitial lung disease associated with declining pulmonary function. Accelerated aging, loss of epithelial progenitor cell function and/or numbers, and cellular senescence are implicated in the pathogenies of IPF.Objectives: We sought to investigate the role of alveolar type 2 (AT2) cellular senescence in initiation and/or progression of pulmonary fibrosis and therapeutic potential of targeting senescence-related pathways and senescent cells.Methods: Epithelial cells of 9 control donor proximal and distal lung tissues and 11 IPF fibrotic lung tissues were profiled by single-cell RNA sequencing to assesses the contribution of epithelial cells to the senescent cell fraction for IPF. A novel mouse model of conditional AT2 cell senescence was generated to study the role of cellular senescence in pulmonary fibrosis.Measurements and Main Results: We show that AT2 cells isolated from IPF lung tissue exhibit characteristic transcriptomic features of cellular senescence. We used conditional loss of Sin3a in adult mouse AT2 cells to initiate a program of p53-dependent cellular senescence, AT2 cell depletion, and spontaneous, progressive pulmonary fibrosis. We establish that senescence rather than loss of AT2 cells promotes progressive fibrosis and show that either genetic or pharmacologic interventions targeting p53 activation or senescence block fibrogenesis.Conclusions: Senescence of AT2 cells is sufficient to drive progressive pulmonary fibrosis. Early attenuation of senescence-related pathways and elimination of senescent cells are promising therapeutic approaches to prevent pulmonary fibrosis.
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Affiliation(s)
- Changfu Yao
- Women’s Guild Lung Institute, Department of Medicine
- The Board of Governors Regenerative Medicine Institute, Department of Biomedical Sciences, and
| | | | | | | | - Xue Liu
- Women’s Guild Lung Institute, Department of Medicine
| | | | - Apoorva Mulay
- Women’s Guild Lung Institute, Department of Medicine
| | - Harmik J. Soukiasian
- Division of Thoracic Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York University, New York, New York; and
| | - Stephen S. Weigt
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - John A. Belperio
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Peter Chen
- Women’s Guild Lung Institute, Department of Medicine
| | - Dianhua Jiang
- Women’s Guild Lung Institute, Department of Medicine
| | - Paul W. Noble
- Women’s Guild Lung Institute, Department of Medicine
| | - Barry R. Stripp
- Women’s Guild Lung Institute, Department of Medicine
- The Board of Governors Regenerative Medicine Institute, Department of Biomedical Sciences, and
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