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Yang M, Shulkin N, Gonzalez E, Castillo J, Yan C, Zhang K, Arvanitis L, Borok Z, Wallace WD, Raz D, Torres ETR, Marconett CN. Cell of origin alters myeloid-mediated immunosuppression in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599651. [PMID: 38948812 PMCID: PMC11213232 DOI: 10.1101/2024.06.19.599651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Solid carcinomas are often highly heterogenous cancers, arising from multiple epithelial cells of origin. Yet, how the cell of origin influences the response of the tumor microenvironment is poorly understood. Lung adenocarcinoma (LUAD) arises in the distal alveolar epithelium which is populated primarily by alveolar epithelial type I (AT1) and type II (AT2) cells. It has been previously reported that Gramd2 + AT1 cells can give rise to a histologically-defined LUAD that is distinct in pathology and transcriptomic identity from that arising from Sftpc + AT2 cells1,2. To determine how cells of origin influence the tumor immune microenvironment (TIME) landscape, we comprehensively characterized transcriptomic, molecular, and cellular states within the TIME of Gramd2 + AT1 and Sftpc + AT2-derived LUAD using KRASG12D oncogenic driver mouse models. Myeloid cells within the Gramd2 + AT1-derived LUAD TIME were increased, specifically, immunoreactive monocytes and tumor associated macrophages (TAMs). In contrast, the Sftpc + AT2 LUAD TIME was enriched for Arginase-1+ myeloid derived suppressor cells (MDSC) and TAMs expressing profiles suggestive of immunosuppressive function. Validation of immune infiltration was performed using flow cytometry, and intercellular interaction analysis between the cells of origin and major myeloid cell populations indicated that cell-type specific markers SFTPD in AT2 cells and CAV1 in AT1 cells mediated unique interactions with myeloid cells of the differential immunosuppressive states within each cell of origin mouse model. Taken together, Gramd2 + AT1-derived LUAD presents with an anti-tumor, immunoreactive TIME, while the TIME of Sftpc + AT2-derived LUAD has hallmarks of immunosuppression. This study suggests that LUAD cell of origin influences the composition and suppression status of the TIME landscape and may hold critical implications for patient response to immunotherapy.
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Affiliation(s)
- Minxiao Yang
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
- Department of Translational Genomics, University of Southern California, Los Angeles, CA USA 90089
| | - Noah Shulkin
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
| | - Edgar Gonzalez
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Jonathan Castillo
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
| | - Chunli Yan
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
| | - Keqiang Zhang
- Division of Thoracic Surgery, Department of Surgery, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA USA 92093
| | - W. Dean Wallace
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Dan Raz
- Division of Thoracic Surgery, Department of Surgery, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Evanthia T. Roussos Torres
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Crystal N. Marconett
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
- Department of Translational Genomics, University of Southern California, Los Angeles, CA USA 90089
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2
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Yombo DJK, Ghandikota S, Vemulapalli CP, Singh P, Jegga AG, Hardie WD, Madala SK. SEMA3B inhibits TGFβ-induced extracellular matrix protein production and its reduced levels are associated with a decline in lung function in IPF. Am J Physiol Cell Physiol 2024; 326:C1659-C1668. [PMID: 38646784 PMCID: PMC11371361 DOI: 10.1152/ajpcell.00681.2023] [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: 12/08/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/23/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is marked by the activation of fibroblasts, leading to excessive production and deposition of extracellular matrix (ECM) within the lung parenchyma. Despite the pivotal role of ECM overexpression in IPF, potential negative regulators of ECM production in fibroblasts have yet to be identified. Semaphorin class 3B (SEMA3B), a secreted protein highly expressed in lung tissues, has established roles in axonal guidance and tumor suppression. However, the role of SEMA3B in ECM production by fibroblasts in the pathogenesis of IPF remains unexplored. Here, we show the downregulation of SEMA3B and its cognate binding receptor, neuropilin 1 (NRP1), in IPF lungs compared with healthy controls. Notably, the reduced expression of SEMA3B and NRP1 is associated with a decline in lung function in IPF. The downregulation of SEMA3B and NRP1 transcripts was validated in the lung tissues of patients with IPF, and two alternative mouse models of pulmonary fibrosis. In addition, we show that transforming growth factor-β (TGFβ) functions as a negative regulator of SEMA3B and NRP1 expression in lung fibroblasts. Furthermore, we demonstrate the antifibrotic effects of SEMA3B against TGFβ-induced ECM production in IPF lung fibroblasts. Overall, our findings uncovered a novel role of SEMA3B in the pathogenesis of pulmonary fibrosis and provided novel insights into modulating the SEMA3B-NRP1 axis to attenuate pulmonary fibrosis.NEW & NOTEWORTHY The excessive production and secretion of collagens and other extracellular matrix proteins by fibroblasts lead to the scarring of the lung in severe fibrotic lung diseases. This study unveils an antifibrotic role for semaphorin class 3B (SEMA3B) in the pathogenesis of idiopathic pulmonary fibrosis. SEMA3B functions as an inhibitor of transforming growth factor-β-driven fibroblast activation and reduced levels of SEMA3B and its receptor, neuropilin 1, are associated with decreased lung function in idiopathic pulmonary fibrosis.
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Affiliation(s)
- Dan J K Yombo
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States
| | - Sudhir Ghandikota
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Chanukya P Vemulapalli
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Priyanka Singh
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Anil G Jegga
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - William D Hardie
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States
| | - Satish K Madala
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
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Tanabe I, Ishimori K, Ishikawa S. Development of an in vitro human alveolar epithelial air-liquid interface model using a small molecule inhibitor cocktail. BMC Mol Cell Biol 2024; 25:9. [PMID: 38500038 PMCID: PMC10946194 DOI: 10.1186/s12860-024-00507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The alveolar epithelium is exposed to numerous stimuli, such as chemicals, viruses, and bacteria that cause a variety of pulmonary diseases through inhalation. Alveolar epithelial cells (AECs) cultured in vitro are a valuable tool for studying the impacts of these stimuli and developing therapies for associated diseases. However, maintaining the proliferative capacity of AECs in vitro is challenging. In this study, we used a cocktail of three small molecule inhibitors to cultivate AECs: Y-27632, A-83-01, and CHIR99021 (YAC). These inhibitors reportedly maintain the proliferative capacity of several types of stem/progenitor cells. RESULTS Primary human AECs cultured in medium containing YAC proliferated for more than 50 days (over nine passages) under submerged conditions. YAC-treated AECs were subsequently cultured at the air-liquid interface (ALI) to promote differentiation. YAC-treated AECs on ALI day 7 formed a monolayer of epithelial tissue with strong expression of the surfactant protein-encoding genes SFTPA1, SFTPB, SFTPC, and SFTPD, which are markers for type II AECs (AECIIs). Immunohistochemical analysis revealed that paraffin sections of YAC-treated AECs on ALI day 7 were mainly composed of cells expressing surfactant protein B and prosurfactant protein C. CONCLUSIONS Our results indicate that YAC-containing medium could be useful for expansion of AECIIs, which are recognized as local stem/progenitor cells, in the alveoli.
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Affiliation(s)
- Ikuya Tanabe
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Kanae Ishimori
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Shinkichi Ishikawa
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa, 227-8512, Japan.
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4
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Yang M, Shen H, Flodby P, Koss MD, Bassiouni R, Liu Y, Jashashvili T, Neely A, Ogbolu E, Castillo J, Stueve TR, Mullen DJ, Ryan AL, Carpten J, Castaldi A, Wallace WD, Zhou B, Borok Z, Marconett CN. Alveolar type I cells can give rise to KRAS-induced lung adenocarcinoma. Cell Rep 2023; 42:113286. [PMID: 37995179 PMCID: PMC10842735 DOI: 10.1016/j.celrep.2023.113286] [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: 01/26/2023] [Revised: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 11/25/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer and presents clinically with a high degree of biological heterogeneity and distinct clinical outcomes. The current paradigm of LUAD etiology posits alveolar epithelial type II (AT2) cells as the primary cell of origin, while the role of AT1 cells in LUAD oncogenesis remains unknown. Here, we examine oncogenic transformation in mouse Gram-domain containing 2 (Gramd2)+ AT1 cells via oncogenic KRASG12D. Activation of KRASG12D in AT1 cells induces multifocal LUAD, primarily of papillary histology. Furthermore, KRT8+ intermediate cell states were observed in both AT2- and AT1-derived LUAD, but SCGB3A2+, another intermediate cell marker, was primarily associated with AT1 cells, suggesting different mechanisms of tumor evolution. Collectively, our study reveals that Gramd2+ AT1 cells can serve as a cell of origin for LUAD and suggests that distinct subtypes of LUAD based on cell of origin be considered in the development of therapeutics.
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Affiliation(s)
- Minxiao Yang
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA; Department of Surgery, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Hua Shen
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Per Flodby
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael D Koss
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Rania Bassiouni
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Yixin Liu
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90089, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Tea Jashashvili
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Aaron Neely
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA; Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Ezuka Ogbolu
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA
| | - Jonathan Castillo
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA; Department of Surgery, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Theresa Ryan Stueve
- Department of Surgery, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel J Mullen
- Department of Surgery, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy L Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA
| | - John Carpten
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Alessandra Castaldi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - W Dean Wallace
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90089, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Crystal N Marconett
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90089, USA; Department of Surgery, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90089, USA.
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5
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Cheong SS, Luis TC, Stewart M, Hillier R, Hind M, Dean CH. A method for TAT-Cre recombinase-mediated floxed allele modification in ex vivo tissue slices. Dis Model Mech 2023; 16:dmm050267. [PMID: 37828896 PMCID: PMC10629676 DOI: 10.1242/dmm.050267] [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: 04/24/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023] Open
Abstract
Precision-cut lung slices (PCLS) are used for a variety of applications. However, methods to manipulate genes in PCLS are currently limited. We developed a new method, TAT-Cre recombinase-mediated floxed allele modification in tissue slices (TReATS), to induce highly effective and temporally controlled gene deletion or activation in ex vivo PCLS. Treatment of PCLS from Rosa26-flox-stop-flox-EYFP mice with cell-permeant TAT-Cre recombinase induced ubiquitous EYFP protein expression, indicating successful Cre-mediated excision of the upstream loxP-flanked stop sequence. Quantitative real-time PCR confirmed induction of EYFP. We successfully replicated the TReATS method in PCLS from Vangl2flox/flox mice, leading to the deletion of loxP-flanked exon 4 of the Vangl2 gene. Cre-treated Vangl2flox/flox PCLS exhibited cytoskeletal abnormalities, a known phenotype caused by VANGL2 dysfunction. We report a new method that bypasses conventional Cre-Lox breeding, allowing rapid and highly effective gene manipulation in ex vivo tissue models.
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Affiliation(s)
- Sek-Shir Cheong
- National Heart and Lung Institute (NHLI), Imperial College London, London SW7 2AZ, UK
| | - Tiago C. Luis
- Centre for Inflammatory Diseases, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Michelle Stewart
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rosie Hillier
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Matthew Hind
- National Heart and Lung Institute (NHLI), Imperial College London, London SW7 2AZ, UK
- National Institute for Health Research (NIHR) Respiratory Biomedical Research Unit at the Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Charlotte H. Dean
- National Heart and Lung Institute (NHLI), Imperial College London, London SW7 2AZ, UK
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6
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Shen H, Chen W, Liu Y, Castaldi A, Castillo J, Horie M, Flodby P, Sundar S, Li C, Ji Y, Minoo P, Marconett CN, Zhou B, Borok Z. GRAMD2 + alveolar type I cell plasticity facilitates cell state transitions in organoid culture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.560801. [PMID: 37905051 PMCID: PMC10614891 DOI: 10.1101/2023.10.17.560801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Alveolar epithelial regeneration is critical for normal lung function and becomes dysregulated in disease. While alveolar type 2 (AT2) and club cells are known distal lung epithelial progenitors, determining if alveolar epithelial type 1 (AT1) cells also contribute to alveolar regeneration has been hampered by lack of highly specific mouse models labeling AT1 cells. To address this, the Gramd2 CreERT2 transgenic strain was generated and crossed to Rosa mTmG mice. Extensive cellular characterization, including distal lung immunofluorescence and cytospin staining, confirmed that GRAMD2 + AT1 cells are highly enriched for green fluorescent protein (GFP). Interestingly, Gramd2 CreERT2 GFP + cells were able to form organoids in organoid co-culture with Mlg fibroblasts. Temporal scRNAseq revealed that Gramd2 + AT1 cells transition through numerous intermediate lung epithelial cell states including basal, secretory and AT2 cell in organoids while acquiring proliferative capacity. Our results indicate that Gramd2 + AT1 cells are highly plastic suggesting they may contribute to alveolar regeneration.
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7
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da Rosa NN, Appel JM, Irioda AC, Mogharbel BF, de Oliveira NB, Perussolo MC, Stricker PEF, Rosa-Fernandes L, Marinho CRF, de Carvalho KAT. Three-Dimensional Bioprinting of an In Vitro Lung Model. Int J Mol Sci 2023; 24:5852. [PMID: 36982923 PMCID: PMC10059924 DOI: 10.3390/ijms24065852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
In December 2019, COVID-19 emerged in China, and in January 2020, the World Health Organization declared a state of international emergency. Within this context, there is a significant search for new drugs to fight the disease and a need for in vitro models for preclinical drug tests. This study aims to develop a 3D lung model. For the execution, Wharton's jelly mesenchymal stem cells (WJ-MSC) were isolated and characterized through flow cytometry and trilineage differentiation. For pulmonary differentiation, the cells were seeded in plates coated with natural functional biopolymer matrix as membrane until spheroid formation, and then the spheroids were cultured with differentiation inductors. The differentiated cells were characterized using immunocytochemistry and RT-PCR, confirming the presence of alveolar type I and II, ciliated, and goblet cells. Then, 3D bioprinting was performed with a sodium alginate and gelatin bioink in an extrusion-based 3D printer. The 3D structure was analyzed, confirming cell viability with a live/dead assay and the expression of lung markers with immunocytochemistry. The results showed that the differentiation of WJ-MSC into lung cells was successful, as well as the bioprinting of these cells in a 3D structure, a promising alternative for in vitro drug testing.
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Affiliation(s)
- Nádia Nascimento da Rosa
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Julia Maurer Appel
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Ana Carolina Irioda
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Bassam Felipe Mogharbel
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Nathalia Barth de Oliveira
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Maiara Carolina Perussolo
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Priscila Elias Ferreira Stricker
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Lívia Rosa-Fernandes
- Experimental Immunoparasitology Laboratory, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (L.R.-F.); (C.R.F.M.)
| | - Cláudio Romero Farias Marinho
- Experimental Immunoparasitology Laboratory, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (L.R.-F.); (C.R.F.M.)
| | - Katherine Athayde Teixeira de Carvalho
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
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8
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Shmarakov IO, Gusarova GA, Islam MN, Marhuenda-Muñoz M, Bhattacharya J, Blaner WS. Retinoids stored locally in the lung are required to attenuate the severity of acute lung injury in male mice. Nat Commun 2023; 14:851. [PMID: 36792627 PMCID: PMC9932169 DOI: 10.1038/s41467-023-36475-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Retinoids are potent transcriptional regulators that act in regulating cell proliferation, differentiation, and other cellular processes. We carried out studies in male mice to establish the importance of local cellular retinoid stores within the lung alveolus for maintaining its health in the face of an acute inflammatory challenge induced by intranasal instillation of lipopolysaccharide. We also undertook single cell RNA sequencing and bioinformatic analyses to identify roles for different alveolar cell populations involved in mediating these retinoid-dependent responses. Here we show that local retinoid stores and uncompromised metabolism and signaling within the lung are required to lessen the severity of an acute inflammatory challenge. Unexpectedly, our data also establish that alveolar cells other than lipofibroblasts, specifically microvascular endothelial and alveolar epithelial cells, are able to take up lipoprotein-transported retinoid and to accumulate cellular retinoid stores that are directly used to respond to an acute inflammatory challenge.
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Affiliation(s)
- Igor O Shmarakov
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.
- Department of Animal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Galina A Gusarova
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Mohammad N Islam
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - María Marhuenda-Muñoz
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Department of Nutrition, Food Science and Gastronomy, School of Pharmacy and Food Sciences and XIA, Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921, Santa Coloma de Gramenet, Spain
| | - Jahar Bhattacharya
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - William S Blaner
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
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9
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Alysandratos KD, Garcia-de-Alba C, Yao C, Pessina P, Huang J, Villacorta-Martin C, Hix OT, Minakin K, Burgess CL, Bawa P, Murthy A, Konda B, Beers MF, Stripp BR, Kim CF, Kotton DN. Culture impact on the transcriptomic programs of primary and iPSC-derived human alveolar type 2 cells. JCI Insight 2023; 8:e158937. [PMID: 36454643 PMCID: PMC9870086 DOI: 10.1172/jci.insight.158937] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Dysfunction of alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli, is implicated in pulmonary disease pathogenesis, highlighting the importance of human in vitro models. However, AEC2-like cells in culture have yet to be directly compared to their in vivo counterparts at single-cell resolution. Here, we performed head-to-head comparisons among the transcriptomes of primary (1°) adult human AEC2s, their cultured progeny, and human induced pluripotent stem cell-derived AEC2s (iAEC2s). We found each population occupied a distinct transcriptomic space with cultured AEC2s (1° and iAEC2s) exhibiting similarities to and differences from freshly purified 1° cells. Across each cell type, we found an inverse relationship between proliferative and maturation states, with preculture 1° AEC2s being most quiescent/mature and iAEC2s being most proliferative/least mature. Cultures of either type of human AEC2s did not generate detectable alveolar type 1 cells in these defined conditions; however, a subset of iAEC2s cocultured with fibroblasts acquired a transitional cell state described in mice and humans to arise during fibrosis or following injury. Hence, we provide direct comparisons of the transcriptomic programs of 1° and engineered AEC2s, 2 in vitro models that can be harnessed to study human lung health and disease.
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Affiliation(s)
- Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Carolina Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Changfu Yao
- Women’s Guild Lung Institute
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Patrizia Pessina
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jessie Huang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Olivia T. Hix
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Kasey Minakin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Claire L. Burgess
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Aditi Murthy
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, and
- PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bindu Konda
- Women’s Guild Lung Institute
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michael F. Beers
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, and
- PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Barry R. Stripp
- Women’s Guild Lung Institute
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carla F. Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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10
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Duong TE, Wu Y, Sos BC, Dong W, Limaye S, Rivier LH, Myers G, Hagood JS, Zhang K. A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. CELL GENOMICS 2022; 2:100108. [PMID: 35434692 PMCID: PMC9012447 DOI: 10.1016/j.xgen.2022.100108] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 05/05/2021] [Accepted: 02/02/2022] [Indexed: 04/14/2023]
Abstract
Ex-utero regulation of the lungs' responses to breathing air and continued alveolar development shape adult respiratory health. Applying single-cell transposome hypersensitive site sequencing (scTHS-seq) to over 80,000 cells, we assembled the first regulatory atlas of postnatal human and mouse lung alveolar development. We defined regulatory modules and elucidated new mechanistic insights directing alveolar septation, including alveolar type 1 and myofibroblast cell signaling and differentiation, and a unique human matrix fibroblast population. Incorporating GWAS, we mapped lung function causal variants to myofibroblasts and identified a pathogenic regulatory unit linked to lineage marker FGF18, demonstrating the utility of chromatin accessibility data to uncover disease mechanism targets. Our regulatory map and analysis model provide valuable new resources to investigate age-dependent and species-specific control of critical developmental processes. Furthermore, these resources complement existing atlas efforts to advance our understanding of lung health and disease across the human lifespan.
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Affiliation(s)
- Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yan Wu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Brandon Chin Sos
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Weixiu Dong
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Siddharth Limaye
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Lauraine H. Rivier
- Department of Pediatrics, Division of Pediatric Pulmonology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Greg Myers
- Department of Pediatrics, Division of Pediatric Pulmonology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James S. Hagood
- Department of Pediatrics, Division of Pediatric Pulmonology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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11
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Diacofotaki A, Loriot A, De Smet C. Identification of Tissue-Specific Gene Clusters Induced by DNA Demethylation in Lung Adenocarcinoma: More Than Germline Genes. Cancers (Basel) 2022; 14:cancers14041007. [PMID: 35205751 PMCID: PMC8870412 DOI: 10.3390/cancers14041007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Loss of DNA methylation is often observed in human tumors, but how this epigenetic alteration impacts the transcriptome of cancer cells remains largely undefined. So far, DNA hypomethylation in tumors has been associated with aberrant activation of a germline-specific gene expression program. Here, we exploited transcriptomic and methylomic datasets of lung adenocarcinoma to investigate the possibility that other gene expression programs also become ectopically activated in hypomethylated tumors. Remarkably, we found that DNA hypomethylation in lung adenocarcinoma is associated with ectopic activation of not only germline-specific genes, but also gene clusters displaying specific expression in the gastrointestinal tract, or in stratified epithelia. Interestingly, expression of genes in this latter group was of prognostic value. Together, our study brings novel insight into the transcriptomic changes associated with DNA hypomethylation in tumors, and is an incentive to explore the value of hypomethylated DNA sequences as cancer biomarkers. Abstract Genome-wide loss of DNA methylation is commonly observed in human cancers, but its impact on the tumor transcriptome remains ill-defined. Previous studies demonstrated that this epigenetic alteration causes aberrant activation of a germline-specific gene expression program. Here, we examined if DNA hypomethylation in tumors also leads to de-repression of gene clusters with other tissue specificities. To this end, we explored transcriptomic and methylomic datasets from human lung adenocarcinoma (LUAD) cell lines, normal lung, and lung alveolar type II cells, considered as the origin of LUAD. Interestingly, DNA demethylation in LUAD cell lines was associated with activation of not only germline-specific (CG) genes, but also gene clusters displaying specific expression in the gastrointestinal tract (GI), or in stratified epithelia (SE). Consistently, genes from all three clusters showed highly specific patterns of promoter methylation among normal tissues and cell types, and were generally sensitive to induction by a DNA demethylating agent. Analysis of TCGA datasets confirmed that demethylation and activation of CG, GI and SE genes also occurs in vivo in LUAD tumor tissues, in association with global genome hypomethylation. For genes of the GI cluster, we demonstrated that HNF4A is a necessary factor for transcriptional activation following promoter demethylation. Interestingly, expression of several SE genes, in particular FAM83A, correlated with both tumor grade and reduced patient survival. Together, our study uncovers novel cell-type specific gene clusters that become aberrantly activated in LUAD tumors in association with genome-wide hypomethylation.
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Affiliation(s)
- Anna Diacofotaki
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (A.D.); (A.L.)
| | - Axelle Loriot
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (A.D.); (A.L.)
- Group of Computational Biology and Bioinformatics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Charles De Smet
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (A.D.); (A.L.)
- Correspondence:
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12
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Zhou B, Stueve TR, Mihalakakos EA, Miao L, Mullen D, Wang Y, Liu Y, Luo J, Tran E, Siegmund KD, Lynch SK, Ryan AL, Offringa IA, Borok Z, Marconett CN. Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity. BMC Genomics 2021; 22:906. [PMID: 34922464 PMCID: PMC8684104 DOI: 10.1186/s12864-021-08152-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Disruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide. Elucidating underlying disease pathogenesis requires a mechanistic molecular understanding of AEC differentiation. Previous studies have focused on changes of individual transcription factors, and to date no study has comprehensively characterized the dynamic, global epigenomic alterations that facilitate this critical differentiation process in humans. RESULTS We comprehensively profiled the epigenomic states of human AECs during type 2 to type 1-like cell differentiation, including the methylome and chromatin functional domains, and integrated this with transcriptome-wide RNA expression data. Enhancer regions were drastically altered during AEC differentiation. Transcription factor binding analysis within enhancer regions revealed diverse interactive networks with enrichment for many transcription factors, including NKX2-1 and FOXA family members, as well as transcription factors with less well characterized roles in AEC differentiation, such as members of the MEF2, TEAD, and AP1 families. Additionally, associations among transcription factors changed during differentiation, implicating a complex network of heterotrimeric complex switching in driving differentiation. Integration of AEC enhancer states with the catalog of enhancer elements in the Roadmap Epigenomics Mapping Consortium and Encyclopedia of DNA Elements (ENCODE) revealed that AECs have similar epigenomic structures to other profiled epithelial cell types, including human mammary epithelial cells (HMECs), with NKX2-1 serving as a distinguishing feature of distal lung differentiation. CONCLUSIONS Enhancer regions are hotspots of epigenomic alteration that regulate AEC differentiation. Furthermore, the differentiation process is regulated by dynamic networks of transcription factors acting in concert, rather than individually. These findings provide a roadmap for understanding the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases that may be therapeutically amenable.
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Affiliation(s)
- B Zhou
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - T R Stueve
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - E A Mihalakakos
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - L Miao
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - D Mullen
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Y Wang
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Y Liu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - J Luo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - E Tran
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - K D Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - S K Lynch
- Department of Engineering, Test Manufacturing Group, MAXIM Integrated Products, Sunnyvale, CA, 95134, USA
| | - A L Ryan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - I A Offringa
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Z Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - C N Marconett
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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13
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Chen XY, Feng PH, Han CL, Jheng YT, Wu CD, Chou HC, Chen YY, Wu SM, Lee KY, Kuo HP, Chung KF, Hsiao TC, Chen KY, Ho SC, Chang TY, Chuang HC. Alveolar epithelial inter-alpha-trypsin inhibitor heavy chain 4 deficiency associated with senescence-regulated apoptosis by air pollution. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 278:116863. [PMID: 33735794 DOI: 10.1016/j.envpol.2021.116863] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/16/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
Inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) is a type II acute-phase protein; however, the role of pulmonary ITIH4 after exposure to air pollution remains unclear. In this study, we investigated the role of ITIH4 in the lungs in response to air pollution. ITIH4 expression in bronchoalveolar lavage fluid (BAL) of 47 healthy human subjects and of Sprague-Dawley rats whole-body exposed to air pollution was determined, and the underlying antiapoptotic and matrix-stabilizing pathways in alveolar epithelial A549 cells induced by diesel exhaust particles (DEPs) as well as ITIH4-knockdown were investigated. We found that an interquartile range (IQR) increase in PM2.5 was associated with a decrease of 2.673 ng/mL in ITIH4, an increase of 1.104 pg/mL of 8-isoprostane, and an increase of 6.918 pg/mL of interleukin (IL)-6 in human BAL. In rats, increases in 8-isoprostane, IL-6, and p53 and a decrease in sirtuin-1 (Sirt1) in the lungs and decreases in ITIH4 in the BAL, lungs, and serum were observed after PM2.5 and gaseous exposure. ITIH4 levels in lung lysates were correlated with levels in BAL samples (r = 0.377, p < 0.01), whereas ITIH4 levels in BAL were correlated with IL-6 levels (r = -0.420, p < 0.01). ITIH4 expression was significantly reduced in alveolar epithelial A549 cells by DEP in a dose-dependent manner. A decrease in Sirt1 and increases in phosphorylated extracellular signal-regulated kinase (p-ERK) and caspase-3 were observed after DEP exposure and ITIH4-knockdown. In conclusion, air pollution decreased ITIH4 expression in the lungs, which was associated with alveolar epithelial cell senescence and apoptosis. ITIH4 could be a vital protein in regulating alveolar cell destruction and its inhibition after exposure to air pollution.
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Affiliation(s)
- Xiao-Yue Chen
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Teng Jheng
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Chih-Da Wu
- Department of Geomatics, National Cheng Kung University, Tainan, Taiwan; National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Hsiu-Chu Chou
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Ying Chen
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Han-Pin Kuo
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ta-Chih Hsiao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Taiwan
| | - Kuan-Yuan Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shu-Chuan Ho
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Ta-Yuan Chang
- Department of Occupational Safety and Health, College of Public Health, China Medical University, Taichung, Taiwan
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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14
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Kanagaki S, Suezawa T, Moriguchi K, Nakao K, Toyomoto M, Yamamoto Y, Murakami K, Hagiwara M, Gotoh S. Hydroxypropyl Cyclodextrin Improves Amiodarone-induced Aberrant Lipid Homeostasis of Alveolar Cells. Am J Respir Cell Mol Biol 2021; 64:504-514. [PMID: 33493427 DOI: 10.1165/rcmb.2020-0119oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alveolar epithelial type II (AT2) cells secrete pulmonary surfactant via lamellar bodies (LBs). Abnormalities in LBs are associated with pulmonary disorders, including fibrosis. However, high-content screening (HCS) for LB abnormalities is limited by the lack of understanding of AT2 cell functions. In the present study, we have developed LB cells harboring LB-like organelles that secrete surfactant proteins. These cells were more similar to AT2 cells than to parental A549 cells. LB cells recapitulated amiodarone (AMD)-induced LB enlargement, similar to AT2 cells of patients exposed to AMD. To reverse AMD-induced LB abnormalities, we performed HCS of approved drugs and identified 2-hydroxypropyl-β-cyclodextrin (HPβCD), a cyclic oligosaccharide, as a potential therapeutic agent. A transcriptome analysis revealed that HPβCD modulates lipid homeostasis. In addition, HPβCD inhibited AMD-induced LB abnormalities in human induced pluripotent stem cell-derived AT2 cells. Our results demonstrate that LB cells are useful for HCS and suggest that HPβCD is a candidate therapeutic agent for AMD-induced interstitial pneumonia.
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Affiliation(s)
- Shuhei Kanagaki
- Department of Drug Discovery for Lung Diseases and.,Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Takahiro Suezawa
- Department of Drug Discovery for Lung Diseases and.,Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Keita Moriguchi
- Department of Drug Discovery for Lung Diseases and.,Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Kazuhisa Nakao
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Masayasu Toyomoto
- Department of Drug Discovery for Lung Diseases and.,Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; and
| | | | - Koji Murakami
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; and
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15
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Margaroli C, Benson P, Sharma NS, Madison MC, Robison SW, Arora N, Ton K, Liang Y, Zhang L, Patel RP, Gaggar A. Spatial mapping of SARS-CoV-2 and H1N1 lung injury identifies differential transcriptional signatures. Cell Rep Med 2021; 2:100242. [PMID: 33778787 PMCID: PMC7985929 DOI: 10.1016/j.xcrm.2021.100242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/16/2020] [Accepted: 03/16/2021] [Indexed: 12/17/2022]
Abstract
Severe SARS-CoV-2 infection often leads to the development of acute respiratory distress syndrome (ARDS), with profound pulmonary patho-histological changes post-mortem. It is not clear whether ARDS from SARS-CoV-2 is similar to that observed in influenza H1N1, another common viral cause of lung injury. Here, we analyze specific ARDS regions of interest utilizing a spatial transcriptomic platform on autopsy-derived lung tissue from patients with SARS-CoV-2 (n = 3), H1N1 (n = 3), and a dual infected individual (n = 1). Enhanced gene signatures in alveolar epithelium, vascular tissue, and lung macrophages identify not only increased regional coagulopathy but also increased extracellular remodeling, alternative macrophage activation, and squamous metaplasia of type II pneumocytes in SARS-CoV-2. Both the H1N1 and dual-infected transcriptome demonstrated an enhanced antiviral response compared to SARS-CoV-2. Our results uncover regional transcriptional changes related to tissue damage/remodeling, altered cellular phenotype, and vascular injury active in SARS-CoV-2 and present therapeutic targets for COVID-19-related ARDS.
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Affiliation(s)
- Camilla Margaroli
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul Benson
- Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nirmal S. Sharma
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Matthew C. Madison
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarah W. Robison
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nitin Arora
- Department of Pediatrics, Division of Neonatology University of Alabama at Birmingham and Children’s Hospital of Alabama, Birmingham, AL, USA
| | - Kathy Ton
- Nanostring Technologies Inc., Seattle, WA, USA
| | - Yan Liang
- Nanostring Technologies Inc., Seattle, WA, USA
| | - Liang Zhang
- Nanostring Technologies Inc., Seattle, WA, USA
| | - Rakesh P. Patel
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pathology, Division of Molecular & Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amit Gaggar
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
- Birmingham VA Medical Center, Birmingham, AL, USA
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16
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Tan W, Zhang B, Liu X, Zhang C, Liu J, Miao Q. Interleukin-33-Dependent Accumulation of Regulatory T Cells Mediates Pulmonary Epithelial Regeneration During Acute Respiratory Distress Syndrome. Front Immunol 2021; 12:653803. [PMID: 33936076 PMCID: PMC8082076 DOI: 10.3389/fimmu.2021.653803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/09/2021] [Indexed: 01/17/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) triggered mostly by infection, is a syndrome that involves respiratory failure. ARDS induces strong local infiltration of regulatory T cells (Treg cells) in the lungs, and Treg cells were recently highlighted as being related to the repair of various tissue. However, at present, there is still a lack of adequate evidence showing the impact of Treg cells on pulmonary regeneration during ARDS. Here, we verified that Treg cells are strongly induced in ARDS mice and Treg depletion results in impaired lung repair. Moreover, Treg cells show high expression of ST2, a cellular receptor for the tissue alarmin IL-33, which is strongly upregulated in the lung during ARDS. In addition, we demonstrated that IL-33 signaling is crucial for Treg cell accumulation, and ST2-blocked mice show a decrease in the Treg cell population. Critically, transfer of exogenous IL-33 into Treg depleted mice restored Treg cells and facilitated lung regeneration by promoting alveolar type II cell (AEC2) recovery in ARDS, with elevated neutrophils infiltration and upregulated TGF-β1 release. These results emphasized the importance of IL-33 in accelerating the expansion of pulmonary Treg cells and promoting their activity to mediate pulmonary epithelial regeneration during ARDS in a TGF-β1-dependent manner.
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Affiliation(s)
- Wen Tan
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Bohan Zhang
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinpei Liu
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chaoji Zhang
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianzhou Liu
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Miao
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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17
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Kanagaki S, Ikeo S, Suezawa T, Yamamoto Y, Seki M, Hirai T, Hagiwara M, Suzuki Y, Gotoh S. Directed induction of alveolar type I cells derived from pluripotent stem cells via Wnt signaling inhibition. Stem Cells 2020; 39:156-169. [PMID: 33241896 PMCID: PMC7898721 DOI: 10.1002/stem.3302] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/31/2020] [Indexed: 12/17/2022]
Abstract
Alveologenesis is a developmental step involving the expansion of the lung surface area which is essential for gas exchange. The gas exchange process is mediated by alveolar type I (AT1) cells, which are known to be differentiated from alveolar type II (AT2) or bipotent cells. Due to the difficulty of isolating and culturing primary AT1 cells, the mechanism underlying their differentiation is not completely understood. We performed single‐cell RNA sequencing (scRNA‐seq) of fibroblast‐dependent alveolar organoids (FD‐AOs), including human induced pluripotent stem cell (hiPSC)‐derived epithelial cells and fetal lung fibroblasts, and identified hiPSC‐derived AT1 (iAT1) cells. A comparison of the FD‐AOs and fibroblast‐free alveolar organoids showed that iAT1 cells were mainly present in the FD‐AOs. Importantly, the transcriptomes of iAT1 cells were remarkably similar to those of primary AT1 cells. Additionally, XAV‐939, a tankyrase inhibitor, increased iAT1 cells in passaged FD‐AOs, suggesting that these cells were differentiated from hiPSC‐derived AT2 (iAT2) cells through the inhibition of canonical Wnt signaling. Consequently, our scRNA‐seq data allowed us to define iAT1 cells and identify FD‐AOs as a useful model for investigating the mechanism underlying human AT1 cell differentiation from AT2 cells in vitro.
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Affiliation(s)
- Shuhei Kanagaki
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Ikeo
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Suezawa
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Yamamoto
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shimpei Gotoh
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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18
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Horie M, Castaldi A, Sunohara M, Wang H, Ji Y, Liu Y, Li F, Wilkinson TA, Hung L, Shen H, Kage H, Offringa IA, Marconett CN, Flodby P, Zhou B, Borok Z. Integrated Single-Cell RNA-Sequencing Analysis of Aquaporin 5-Expressing Mouse Lung Epithelial Cells Identifies GPRC5A as a Novel Validated Type I Cell Surface Marker. Cells 2020; 9:cells9112460. [PMID: 33187367 PMCID: PMC7697677 DOI: 10.3390/cells9112460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/01/2022] Open
Abstract
Molecular and functional characterization of alveolar epithelial type I (AT1) cells has been challenging due to difficulty in isolating sufficient numbers of viable cells. Here we performed single-cell RNA-sequencing (scRNA-seq) of tdTomato+ cells from lungs of AT1 cell-specific Aqp5-Cre-IRES-DsRed (ACID);R26tdTomato reporter mice. Following enzymatic digestion, CD31-CD45-E-cadherin+tdTomato+ cells were subjected to fluorescence-activated cell sorting (FACS) followed by scRNA-seq. Cell identity was confirmed by immunofluorescence using cell type-specific antibodies. After quality control, 92 cells were analyzed. Most cells expressed ‘conventional’ AT1 cell markers (Aqp5, Pdpn, Hopx, Ager), with heterogeneous expression within this population. The remaining cells expressed AT2, club, basal or ciliated cell markers. Integration with public datasets identified three robust AT1 cell- and lung-enriched genes, Ager, Rtkn2 and Gprc5a, that were conserved across species. GPRC5A co-localized with HOPX and was not expressed in AT2 or airway cells in mouse, rat and human lung. GPRC5A co-localized with AQP5 but not pro-SPC or CC10 in mouse lung epithelial cell cytospins. We enriched mouse AT1 cells to perform molecular phenotyping using scRNA-seq. Further characterization of putative AT1 cell-enriched genes revealed GPRC5A as a conserved AT1 cell surface marker that may be useful for AT1 cell isolation.
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Affiliation(s)
- Masafumi Horie
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Alessandra Castaldi
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Mitsuhiro Sunohara
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
- Division for Health Service Promotion, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hongjun Wang
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Yanbin Ji
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Yixin Liu
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Fan Li
- Single-Cell, Sequencing, and CyTOF Core (SC2), Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (F.L.); (T.A.W.); (L.H.)
| | - Thomas A. Wilkinson
- Single-Cell, Sequencing, and CyTOF Core (SC2), Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (F.L.); (T.A.W.); (L.H.)
| | - Long Hung
- Single-Cell, Sequencing, and CyTOF Core (SC2), Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (F.L.); (T.A.W.); (L.H.)
| | - Hua Shen
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Hidenori Kage
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
| | - Ite A. Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (I.A.O.); (C.N.M.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (I.A.O.); (C.N.M.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Per Flodby
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Beiyun Zhou
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zea Borok
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Correspondence: ; Tel.: +323-409-7184; Fax: +323-226-2738
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19
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Kunisaki SM, Jiang G, Biancotti JC, Ho KKY, Dye BR, Liu AP, Spence JR. Human induced pluripotent stem cell-derived lung organoids in an ex vivo model of the congenital diaphragmatic hernia fetal lung. Stem Cells Transl Med 2020; 10:98-114. [PMID: 32949227 PMCID: PMC7780804 DOI: 10.1002/sctm.20-0199] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/03/2020] [Accepted: 08/09/2020] [Indexed: 01/06/2023] Open
Abstract
Three‐dimensional lung organoids (LOs) derived from pluripotent stem cells have the potential to enhance our understanding of disease mechanisms and to enable novel therapeutic approaches in neonates with pulmonary disorders. We established a reproducible ex vivo model of lung development using transgene‐free human induced pluripotent stem cells generated from fetuses and infants with Bochdalek congenital diaphragmatic hernia (CDH), a polygenic disorder associated with fetal lung compression and pulmonary hypoplasia at birth. Molecular and cellular comparisons of CDH LOs revealed impaired generation of NKX2.1+ progenitors, type II alveolar epithelial cells, and PDGFRα+ myofibroblasts. We then subjected these LOs to disease relevant mechanical cues through ex vivo compression and observed significant changes in genes associated with pulmonary progenitors, alveolar epithelial cells, and mesenchymal fibroblasts. Collectively, these data suggest both primary cell‐intrinsic and secondary mechanical causes of CDH lung hypoplasia and support the use of this stem cell‐based approach for disease modeling in CDH.
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Affiliation(s)
- Shaun M Kunisaki
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Guihua Jiang
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Juan C Biancotti
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kenneth K Y Ho
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Briana R Dye
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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20
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Finn J, Sottoriva K, Pajcini KV, Kitajewski JK, Chen C, Zhang W, Malik AB, Liu Y. Dlk1-Mediated Temporal Regulation of Notch Signaling Is Required for Differentiation of Alveolar Type II to Type I Cells during Repair. Cell Rep 2020; 26:2942-2954.e5. [PMID: 30865885 PMCID: PMC6464111 DOI: 10.1016/j.celrep.2019.02.046] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 01/15/2019] [Accepted: 02/12/2019] [Indexed: 01/26/2023] Open
Abstract
Lung alveolar type I cells (AT1) and alveolar type II cells (AT2) regulate the structural integrity and function of alveoli. AT1, covering ∼95% of the surface area, are responsible for gas exchange, whereas AT2 serve multiple functions, including alveolar repair through proliferation and differentiation into AT1. However, the signaling mechanisms for alveolar repair remain unclear. Here, we demonstrate, in Pseudomonas aeruginosa-induced acute lung injury in mice, that non-canonical Notch ligand Dlk1 (delta-like 1 homolog) is essential for AT2-to-AT1 differentiation. Notch signaling was activated in AT2 at the onset of repair but later suppressed by Dlk1. Deletion of Dlk1 in AT2 induced persistent Notch activation, resulting in stalled transition to AT1 and accumulation of an intermediate cell population that expressed low levels of both AT1 and AT2 markers. Thus, Dlk1 expression leads to precisely timed inhibition of Notch signaling and activates AT2-to-AT1 differentiation, leading to alveolar repair.
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Affiliation(s)
- Johanna Finn
- Department of Pharmacology, The University of Illinois College of Medicine, Chicago, IL 60612, USA; The Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Kilian Sottoriva
- Department of Pharmacology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Kostandin V Pajcini
- Department of Pharmacology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jan K Kitajewski
- Department of Physiology and Biophysics, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Chang Chen
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Asrar B Malik
- Department of Pharmacology, The University of Illinois College of Medicine, Chicago, IL 60612, USA; The Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Yuru Liu
- Department of Pharmacology, The University of Illinois College of Medicine, Chicago, IL 60612, USA; The Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA.
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21
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Donati Y, Blaskovic S, Ruchonnet-Métrailler I, Lascano Maillard J, Barazzone-Argiroffo C. Simultaneous isolation of endothelial and alveolar epithelial type I and type II cells during mouse lung development in the absence of a transgenic reporter. Am J Physiol Lung Cell Mol Physiol 2020; 318:L619-L630. [PMID: 32022591 DOI: 10.1152/ajplung.00227.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mouse lung developmental maturation and final alveolarization phase begin at birth. During this dynamic process, alveolar cells modify their morphology and anchorage to the extracellular matrix. In particular, alveolar epithelial cell (AEC) type I undergo cytoplasmic flattening and folding to ensure alveoli lining. We developed FACS conditions for simultaneous isolation of alveolar epithelial and endothelial cells in the absence of specific reporters during the early and middle alveolar phase. We evidenced for the first time a pool of extractable epithelial cell populations expressing high levels of podoplanin at postnatal day (pnd)2, and we confirmed by RT-qPCR that these cells are already differentiated but still immature AEC type I. Maturation causes a decrease in isolation yields, reflecting the morphological changes that these cell populations are undergoing. Moreover, we find that major histocompatibility complex II (MHCII), reported as a good marker of AEC type II, is poorly expressed at pnd2 but highly present at pnd8. Combined experiments using LysoTracker and MHCII demonstrate the de novo acquisition of MCHII in AEC type II during lung alveolarization. The lung endothelial populations exhibit FACS signatures from vascular and lymphatic compartments. They can be concomitantly followed throughout alveolar development and were obtained with a noticeable increased yield at the last studied time point (pnd16). Our results provide new insights into early lung alveolar cell isolation feasibility and represent a valuable tool for pure AEC type I preparation as well as further in vitro two- and three-dimensional studies.
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Affiliation(s)
- Yves Donati
- Department of Pediatrics, Gynecology, and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sanja Blaskovic
- Department of Pediatrics, Gynecology, and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Isabelle Ruchonnet-Métrailler
- Department of Pediatrics, Gynecology, and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Constance Barazzone-Argiroffo
- Department of Pediatrics, Gynecology, and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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22
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Abstract
The epithelial lining of the lung is often the first point of interaction between the host and inhaled pathogens, allergens and medications. Epithelial cells are therefore the main focus of studies which aim to shed light on host-pathogen interactions, to dissect the mechanisms of local host immunity and study toxicology. If these studies are not to be conducted exclusively in vivo, it is imperative that in vitro models are developed with a high in vitro- in vivo correlation. We describe here a co-culture model of the bovine alveolus, designed to overcome some of the limitations encountered with mono-culture and live animal models. Our system includes bovine pulmonary arterial endothelial cells (BPAECs) seeded onto a permeable membrane in 24 well Transwell format. The BPAECs are overlaid with immortalised bovine alveolar type II epithelial cells and cultured at air-liquid interface for 14 days before use; in our case to study host-mycobacterial interactions. Characterisation of novel cell lines and the co-culture model have provided compelling evidence that immortalised bovine alveolar type II cells are an authentic substitute for primary alveolar type II cells and their co-culture with BPAECs provides a physiologically relevant in vitro model of the bovine alveolus. The co-culture model may be used to study dynamic intracellular and extracellular host-pathogen interactions, using proteomics, genomics, live cell imaging, in-cell ELISA and confocal microscopy. The model presented in this article enables other researchers to establish an in vitro model of the bovine alveolus that is easy to set up, malleable and serves as a comparable alternative to in vivo models, whilst allowing study of early host-pathogen interactions, currently not feasible in vivo. The model therefore achieves one of the 3Rs objectives in that it replaces the use of animals in research of bovine respiratory diseases.
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Affiliation(s)
- Diane Lee
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK
| | - Mark Chambers
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK
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23
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Riemondy KA, Jansing NL, Jiang P, Redente EF, Gillen AE, Fu R, Miller AJ, Spence JR, Gerber AN, Hesselberth JR, Zemans RL. Single cell RNA sequencing identifies TGFβ as a key regenerative cue following LPS-induced lung injury. JCI Insight 2019; 5:123637. [PMID: 30913038 PMCID: PMC6538357 DOI: 10.1172/jci.insight.123637] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Many lung diseases result from a failure of efficient regeneration of damaged alveolar epithelial cells (AECs) after lung injury. During regeneration, AEC2s proliferate to replace lost cells, after which proliferation halts and some AEC2s transdifferentiate into AEC1s to restore normal alveolar structure and function. Although the mechanisms underlying AEC2 proliferation have been studied, the mechanisms responsible for halting proliferation and inducing transdifferentiation are poorly understood. To identify candidate signaling pathways responsible for halting proliferation and inducing transdifferentiation, we performed single cell RNA sequencing on AEC2s during regeneration in a murine model of lung injury induced by intratracheal LPS. Unsupervised clustering revealed distinct subpopulations of regenerating AEC2s: proliferating, cell cycle arrest, and transdifferentiating. Gene expression analysis of these transitional subpopulations revealed that TGFβ signaling was highly upregulated in the cell cycle arrest subpopulation and relatively downregulated in transdifferentiating cells. In cultured AEC2s, TGFβ was necessary for cell cycle arrest but impeded transdifferentiation. We conclude that during regeneration after LPS-induced lung injury, TGFβ is a critical signal halting AEC2 proliferation but must be inactivated to allow transdifferentiation. This study provides insight into the molecular mechanisms regulating alveolar regeneration and the pathogenesis of diseases resulting from a failure of regeneration.
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Affiliation(s)
- Kent A. Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Nicole L. Jansing
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Peng Jiang
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth F. Redente
- Program in Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Austin E. Gillen
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alyssa J. Miller
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony N. Gerber
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Jay R. Hesselberth
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rachel L. Zemans
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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24
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O'Reilly MA. Giving New Identities to Alveolar Epithelial Type I Cells. Am J Respir Cell Mol Biol 2018; 56:277-278. [PMID: 28248135 DOI: 10.1165/rcmb.2016-0383ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Michael A O'Reilly
- 1 Department of Pediatrics School of Medicine and Dentistry The University of Rochester Rochester, New York
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