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Liu Z, Zheng Q, Li Z, Huang M, Zhong C, Yu R, Jiang R, Dai H, Zhang J, Gu X, Xu Y, Li C, Shan S, Xu F, Hong Y, Ren T. Epithelial stem cells from human small bronchi offer a potential for therapy of idiopathic pulmonary fibrosis. EBioMedicine 2025; 112:105538. [DOI: 10.1016/j.ebiom.2024.105538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2025] Open
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2
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Reynolds SD, Hill CL, Alsudayri A, Stack JT, Shontz KM, Carraro G, Stripp BR, Chiang T. Factor 3 regulates airway engraftment by human bronchial basal cells. Stem Cells Transl Med 2024:szae084. [PMID: 39485996 DOI: 10.1093/stcltm/szae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 09/01/2024] [Indexed: 11/03/2024] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) gene editing and transplantation of CFTR-gene corrected airway basal cells has the potential to cure CF lung disease. Although mouse studies established that cell transplantation was feasible, the engraftment rate was typically low and frequently less than the estimated therapeutic threshold. The purpose of this study was to identify genes and culture conditions that regulate the therapeutic potential of human bronchial basal cells. Factor 3 (F3, Tissue Factor 1) is a component of the extrinsic coagulation pathway and activates a cascade of proteases that convert fibrinogen to fibrin. Based on reports that F3 was necessary for human basal cell survival and adhesion in vitro, the present study evaluated F3 as a potential determinant of therapeutic fitness. The gene expression profile of F3 mRNA-positive human bronchial basal cells was evaluated by scRNAseq and the impact of the lung environment on F3 expression was modeled by varying in vitro culture conditions. F3 necessity for adhesion, proliferation, and differentiation was determined by CRISPR/Cas9 knockout (KO) of the F3 gene. Finally, the impact of F3 manipulation on engraftment was determined by orthotropic co-transplantation of wild-type and F3-KO cells into the airways of immunocompromised mice. In contrast with the hypothesis that F3 increases the therapeutic fitness of basal cells, F3 expression decreased engraftment. These studies guide the ongoing development of cellular therapies by showing that in vitro assessments may not predict therapeutic potential and that the lung milieu influences the functional properties of transplanted bronchial basal cells.
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Affiliation(s)
- Susan D Reynolds
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, OH 43215, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, United States
| | - Cynthia L Hill
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, OH 43215, United States
| | - Alfahdah Alsudayri
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, OH 43215, United States
| | - Jacob T Stack
- Center for Regenerative Medicine, Nationwide Children's Hospital, Columbus, OH 43215, United States
| | - Kimberly M Shontz
- Center for Regenerative Medicine, Nationwide Children's Hospital, Columbus, OH 43215, United States
| | - Gianni Carraro
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Barry R Stripp
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Tendy Chiang
- Center for Regenerative Medicine, Nationwide Children's Hospital, Columbus, OH 43215, United States
- Department of Otolaryngology, Nationwide Children's Hospital, Columbus, OH 43215, United States
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3
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Zhang X, Xu Z, Chen Q, Zhou Z. Notch signaling regulates pulmonary fibrosis. Front Cell Dev Biol 2024; 12:1450038. [PMID: 39450276 PMCID: PMC11499121 DOI: 10.3389/fcell.2024.1450038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 09/23/2024] [Indexed: 10/26/2024] Open
Abstract
Pulmonary fibrosis is a progressive interstitial lung disease associated with aging. The pathogenesis of pulmonary fibrosis remains unclear, however, alveolar epithelial cell injury, myofibroblast activation, and extracellular matrix (ECM) accumulation are recognized as key contributors. Moreover, recent studies have implicated cellular senescence, endothelial-mesenchymal transition (EndMT), and epigenetic modifications in the pathogenesis of fibrotic diseases. Various signaling pathways regulate pulmonary fibrosis, including the TGF-β, Notch, Wnt, Hedgehog, and mTOR pathways. Among these, the TGF-β pathway is extensively studied, while the Notch pathway has emerged as a recent research focus. The Notch pathway influences the fibrotic process by modulating immune cell differentiation (e.g., macrophages, lymphocytes), inhibiting autophagy, and promoting interstitial transformation. Consequently, inhibiting Notch signaling represents a promising approach to mitigating pulmonary fibrosis. In this review, we discuss the role of Notch signaling pathway in pulmonary fibrosis, aiming to offer insights for future therapeutic investigations.
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Affiliation(s)
| | - Zhihao Xu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
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4
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Wang J, Li K, Hao D, Li X, Zhu Y, Yu H, Chen H. Pulmonary fibrosis: pathogenesis and therapeutic strategies. MedComm (Beijing) 2024; 5:e744. [PMID: 39314887 PMCID: PMC11417429 DOI: 10.1002/mco2.744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
Pulmonary fibrosis (PF) is a chronic and progressive lung disease characterized by extensive alterations of cellular fate and function and excessive accumulation of extracellular matrix, leading to lung tissue scarring and impaired respiratory function. Although our understanding of its pathogenesis has increased, effective treatments remain scarce, and fibrotic progression is a major cause of mortality. Recent research has identified various etiological factors, including genetic predispositions, environmental exposures, and lifestyle factors, which contribute to the onset and progression of PF. Nonetheless, the precise mechanisms by which these factors interact to drive fibrosis are not yet fully elucidated. This review thoroughly examines the diverse etiological factors, cellular and molecular mechanisms, and key signaling pathways involved in PF, such as TGF-β, WNT/β-catenin, and PI3K/Akt/mTOR. It also discusses current therapeutic strategies, including antifibrotic agents like pirfenidone and nintedanib, and explores emerging treatments targeting fibrosis and cellular senescence. Emphasizing the need for omni-target approaches to overcome the limitations of current therapies, this review integrates recent findings to enhance our understanding of PF and contribute to the development of more effective prevention and management strategies, ultimately improving patient outcomes.
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Affiliation(s)
- Jianhai Wang
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese MedicineTianjin Institute of Respiratory DiseasesTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - Kuan Li
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - De Hao
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
| | - Xue Li
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - Yu Zhu
- Department of Clinical LaboratoryNankai University Affiliated Third Central HospitalTianjinChina
- Department of Clinical LaboratoryThe Third Central Hospital of TianjinTianjin Key Laboratory of Extracorporeal Life Support for Critical DiseasesArtificial Cell Engineering Technology Research Center of TianjinTianjin Institute of Hepatobiliary DiseaseTianjinChina
| | - Hongzhi Yu
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - Huaiyong Chen
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese MedicineTianjin Institute of Respiratory DiseasesTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
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5
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Li C, Xiao N, Song W, Lam AHC, Liu F, Cui X, Ye Z, Chen Y, Ren P, Cai J, Lee ACY, Chen H, Ou Z, Chan JFW, Yuen KY, Chu H, Zhang AJX. Chronic lung inflammation and CK14+ basal cell proliferation induce persistent alveolar-bronchiolization in SARS-CoV-2-infected hamsters. EBioMedicine 2024; 108:105363. [PMID: 39326207 PMCID: PMC11470415 DOI: 10.1016/j.ebiom.2024.105363] [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: 05/21/2024] [Revised: 09/10/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
BACKGROUND Post-acute sequalae of COVID-19 defines a wide range of ongoing symptoms and conditions long after SARS-CoV-2 infection including respiratory diseases. The histopathological changes in the lung and underlying mechanism remain elusive. METHODS We investigated lung histopathological and transcriptional changes in SARS-CoV-2-infected male hamsters at 7, 14, 42, 84 and 120dpi, and compared with A (H1N1)pdm09 infection. FINDINGS We demonstrated viral residue, inflammatory and fibrotic changes in lung after SARS-CoV-2 but not H1N1 infection. The most prominent histopathological lesion was multifocal alveolar-bronchiolization observed in every SARS-CoV-2 infected hamster (31/31), from 42dpi to 120dpi. Proliferating (Ki67+) CK14+ basal cells accumulated in alveoli adjacent to bronchioles at 7dpi, where they proliferated and differentiated into SCGB1A+ club cell or Tubulin+ ciliated cells forming alveolar-bronchiolization foci. Molecularly, Notch pathway significantly upregulated with intensive Notch3 and Hes1 protein expression in alveolar-bronchiolization foci at 42 and 120dpi, suggesting Notch signaling involving the persistence of alveolar-bronchiolization. This is further demonstrated by spatial transcriptomic analysis. Intriguingly, significant upregulation of some cell-growth promoting pathways and genes such as Tubb4b, Stxbp4, Grb14 and Mlf1 were spatially overlapping with bronchiolization lesion. INTERPRETATION Incomplete resolution of SARS-CoV-2 infection in lung with viral residue, chronic inflammatory and fibrotic damage and alveolar-bronchiolization impaired respiratory function. Aberrant activation of CK14+ basal cells during tissue regeneration led to persistent alveolar-bronchiolization due to sustained Notch signaling. This study advances our understanding of respiratory PASC, sheds light on disease management and highlights the necessity for monitoring disease progression in people with respiratory PASC. FUNDING Funding is listed in the Acknowledgements section.
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Affiliation(s)
- Can Li
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Na Xiao
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Wenchen Song
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Alvin Hiu-Chung Lam
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Feifei Liu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | | | - Zhanhong Ye
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Yanxia Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Jianpiao Cai
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Andrew Chak-Yiu Lee
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Honglin Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.
| | - Anna Jin-Xia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China.
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6
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Liu ZY, Lin LC, Liu ZY, Song K, Tu B, Sun H, Zhou Y, Mao S, Zhang Y, Li R, Yang JJ, Zhao JY, Tao H. N 6-Methyladenosine-mediated phase separation suppresses NOTCH1 expression and promotes mitochondrial fission in diabetic cardiac fibrosis. Cardiovasc Diabetol 2024; 23:347. [PMID: 39342271 PMCID: PMC11439301 DOI: 10.1186/s12933-024-02444-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is crucial for liquid-liquid phase separation in mammals. Increasing evidence indicates that liquid-liquid phase separation in proteins and RNAs affects diabetic cardiomyopathy. However, the molecular mechanism by which m6A-mediated phase separation regulates diabetic cardiac fibrosis remains elusive. METHODS Leptin receptor-deficient mice (db/db), cardiac fibroblast-specific Notch1 conditional knockout (POSTN-Cre × Notch1flox/flox) mice, and Cre mice were used to induce diabetic cardiac fibrosis. Adeno-associated virus 9 carrying cardiac fibroblast-specific periostin (Postn) promoter-driven small hairpin RNA targeting Alkbh5, Ythdf2, or Notch1, and the phase separation inhibitor 1,6-hexanediol were administered to investigate their roles in diabetic cardiac fibrosis. Histological and biochemical analyses were performed to determine how Alkbh5 and Ythdf2 regulate Notch1 expression in diabetic cardiac fibrosis. NOTCH1 was reconstituted in ALKBH5- and YTHDF2-deficient cardiac fibroblasts and mouse hearts to study its effects on mitochondrial fission and diabetic cardiac fibrosis. Heart tissue samples from patients with diabetic cardiomyopathy were used to validate our findings. RESULTS In mice with diabetic cardiac fibrosis, decreased Notch1 expression was accompanied by high m6A mRNA levels and mitochondrial fission. Fibroblast-specific deletion of Notch1 enhanced mitochondrial fission and cardiac fibroblast proliferation and induced diabetic cardiac fibrosis in mice. Notch1 downregulation was associated with Alkbh5-mediated m6A demethylation in the 3'UTR of Notch1 mRNA and elevated m6A mRNA levels. These elevated m6A levels in Notch1 mRNA markedly enhanced YTHDF2 phase separation, increased the recognition of m6A residues in Notch1 mRNA by YTHDF2, and induced Notch1 degradation. Conversely, epitranscriptomic downregulation rescues Notch1 expression, resulting in the opposite effects. Human heart tissues from patients with diabetic cardiomyopathy were used to validate the findings in mice with diabetic cardiac fibrosis. CONCLUSIONS We identified a novel epitranscriptomic mechanism by which m6A-mediated phase separation suppresses Notch1 expression, thereby promoting mitochondrial fission in diabetic cardiac fibrosis. Our findings provide new insights for the development of novel treatment approaches for patients with diabetic cardiac fibrosis.
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MESH Headings
- Animals
- Mitochondrial Dynamics
- Receptor, Notch1/metabolism
- Receptor, Notch1/genetics
- Humans
- Fibrosis
- Diabetic Cardiomyopathies/metabolism
- Diabetic Cardiomyopathies/genetics
- Diabetic Cardiomyopathies/pathology
- Diabetic Cardiomyopathies/etiology
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Mice, Knockout
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- Signal Transduction
- Male
- AlkB Homolog 5, RNA Demethylase/metabolism
- AlkB Homolog 5, RNA Demethylase/genetics
- Cells, Cultured
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Disease Models, Animal
- Mice, Inbred C57BL
- Fibroblasts/metabolism
- Fibroblasts/pathology
- Mice
- RNA Processing, Post-Transcriptional
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Phase Separation
- Cell Adhesion Molecules
- Receptors, Leptin
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Affiliation(s)
- Zhi-Yan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Li-Chan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Zhen-Yu Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Kai Song
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Bin Tu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - He Sun
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Yang Zhou
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Sui Mao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Ye Zhang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China
| | - Rui Li
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China.
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China.
| | - Jian-Yuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, People's Republic of China.
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China.
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People's Republic of China.
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7
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Lingamallu SM, Deshpande A, Joy N, Ganeshan K, Ray N, Ladher RK, Taketo MM, Lafkas D, Guha A. Neuroepithelial bodies and terminal bronchioles are niches for distinctive club cells that repair the airways following acute notch inhibition. Cell Rep 2024; 43:114654. [PMID: 39182223 DOI: 10.1016/j.celrep.2024.114654] [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: 01/02/2024] [Revised: 06/05/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024] Open
Abstract
Lower airway club cells (CCs) serve the dual roles of a secretory cell and a stem cell. Here, we probe how the CC fate is regulated. We find that, in response to acute perturbation of Notch signaling, CCs adopt distinct fates. Although the vast majority transdifferentiate into multiciliated cells, a "variant" subpopulation (v-CCs), juxtaposed to neuroepithelial bodies (NEBs; 5%-10%) and located at bronchioalveolar duct junctions (>80%), does not. Instead, v-CCs transition into lineage-ambiguous states but can revert to a CC fate upon restoration of Notch signaling and repopulate the airways with CCs and multiciliated cells. The v-CC response to Notch inhibition is dependent on localized activation of β-catenin in v-CCs. We propose that the CC fate is stabilized by canonical Notch signaling, that airways are susceptible to perturbations to this pathway, and that NEBs/terminal bronchioles comprise niches that modulate CC plasticity via β-catenin activation to facilitate airway repair post Notch inhibition.
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Affiliation(s)
- Sai Manoz Lingamallu
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore 560065, India; Manipal Academy of Higher Education (MAHE), Madhav Nagar, Manipal 576104, India
| | - Aditya Deshpande
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore 560065, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka 560064, Bangalore, India
| | - Neenu Joy
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore 560065, India; SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613401, India
| | - Kirthana Ganeshan
- Immunology Discovery, Genentech Inc., South San Francisco, CA 94080, USA
| | - Neelanjana Ray
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Rajesh Kumar Ladher
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Makoto Mark Taketo
- Colon Cancer Project, Kyoto University Hospital-iACT, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Daniel Lafkas
- Immunology, Infectious Diseases, and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center, Basel, Switzerland
| | - Arjun Guha
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore 560065, India.
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8
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Burgy O, Königshoff M. Teatime: epigallocatechin gallate targets fibroblast-epithelial cell crosstalk to combat lung fibrosis. J Clin Invest 2024; 134:e183970. [PMID: 39286980 PMCID: PMC11405033 DOI: 10.1172/jci183970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Epigallocatechin gallate (EGCG) is a polyphenol plant metabolite abundant in tea that has demonstrated antifibrotic properties in the lung. In this issue of the JCI, Cohen, Brumwell, and colleagues interrogated the mechanistic action of EGCG by investigating lung biopsies of patients with mild interstitial lung disease (ILD) who had undergone EGCG treatment. EGCG targeted the WNT inhibitor SFRP2, which was enriched in fibrotic fibroblasts and acted as a TGF-β target, with paracrine effects leading to pathologic basal metaplasia of alveolar epithelial type 2 cells. This study emphasizes the epithelial-mesenchymal trophic unit as a central signaling hub in lung fibrosis. Understanding and simultaneous targeting of interlinked signaling pathways, such as TGF-β and WNT, paves the road for future treatment options for pulmonary fibrosis.
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Affiliation(s)
- Olivier Burgy
- INSERM U1231, Faculty of Health Sciences, Université de Bourgogne, Dijon, France
- Constitutive Reference Center for Rare Pulmonary Diseases-OrphaLung, University Hospital Dijon-Bourgogne, Dijon, France
| | - Melanie Königshoff
- Center for Lung Aging and Regeneration (CLAR), Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Geriatric Research Education and Clinical Center (GRECC) at the VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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9
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Chilosi M, Piciucchi S, Ravaglia C, Spagnolo P, Sverzellati N, Tomassetti S, Wuyts W, Poletti V. "Alveolar stem cell exhaustion, fibrosis and bronchiolar proliferation" related entities. A narrative review. Pulmonology 2024:S2531-0437(24)00092-8. [PMID: 39277539 DOI: 10.1016/j.pulmoe.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/11/2024] [Accepted: 05/27/2024] [Indexed: 09/17/2024] Open
Affiliation(s)
- M Chilosi
- Department of Medical Specialities/Pulmonology Ospedale GB Morgagni, Forlì I
| | - S Piciucchi
- Department of Radiology, Ospedale GB Morgagni, Forlì I.
| | - C Ravaglia
- Department of Medical Specialities/Pulmonology Ospedale GB Morgagni, Forlì (I); DIMEC, Bologna University, Forlì Campus, Forlì I, Department
| | - P Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - N Sverzellati
- Scienze Radiologiche, Department of Medicine and Surgery, University Hospital Parma, Parma, Italy
| | - S Tomassetti
- Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - W Wuyts
- Pulmonology Department, UZ Leuven, Leuven, Belgium
| | - V Poletti
- Department of Medical Specialities/Pulmonology Ospedale GB Morgagni, Forlì (I); DIMEC, Bologna University, Forlì Campus, Forlì I, Department; Department of Respiratory Diseases & Allergy, Aarhus University, Aarhus, Denmark
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10
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Cheng C, Katoch P, Zhong YP, Higgins CT, Moredock M, Chang MEK, Flory MR, Randell SH, Streeter PR. Identification of a Novel Subset of Human Airway Epithelial Basal Stem Cells. Int J Mol Sci 2024; 25:9863. [PMID: 39337350 PMCID: PMC11432080 DOI: 10.3390/ijms25189863] [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: 08/16/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
The basal cell maintains the airway's respiratory epithelium as the putative resident stem cell. Basal cells are known to self-renew and differentiate into airway ciliated and secretory cells. However, it is not clear if every basal cell functions as a stem cell. To address functional heterogeneity amongst the basal cell population, we developed a novel monoclonal antibody, HLO1-6H5, that identifies a subset of KRT5+ (cytokeratin 5) basal cells. We used HLO1-6H5 and other known basal cell-reactive reagents to isolate viable airway subsets from primary human airway epithelium by Fluorescence Activated Cell Sorting. Isolated primary cell subsets were assessed for the stem cell capabilities of self-renewal and differentiation in the bronchosphere assay, which revealed that bipotent stem cells were, at minimum 3-fold enriched in the HLO1-6H5+ cell subset. Crosslinking-mass spectrometry identified the HLO1-6H5 target as a glycosylated TFRC/CD71 (transferrin receptor) proteoform. The HLO1-6H5 antibody provides a valuable new tool for identifying and isolating a subset of primary human airway basal cells that are substantially enriched for bipotent stem/progenitor cells and reveals TFRC as a defining surface marker for this novel cell subset.
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Affiliation(s)
- Christopher Cheng
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Parul Katoch
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Yong-Ping Zhong
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Claire T. Higgins
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Maria Moredock
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Matthew E. K. Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Mark R. Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Scott H. Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Philip R. Streeter
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
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11
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Ziora D. May Small Airways Dysfunction (SAD) Play a Role in the Idiopathic Pulmonary Fibrosis (IPF) and May SAD Be a Therapeutic Target? Adv Respir Med 2024; 92:348-355. [PMID: 39311112 PMCID: PMC11417804 DOI: 10.3390/arm92050033] [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: 07/31/2024] [Revised: 08/28/2024] [Accepted: 09/05/2024] [Indexed: 09/26/2024]
Abstract
Small airway dysfunction (SAD) is a pathological process that affects the bronchioles and non-cartilaginous airways below 2 mm in diameter. This short review presents a link between SAD and IPF. Pathomorphological changes of small airways in fibrotic lungs are discussed. Additionally, functional abnormalities related to SAD measured by spirometry and oscillometry are presented. The problem of early detection and treatment of SAD as a procedure potentially capable of mitigating fibrosis is mentioned.
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Affiliation(s)
- Dariusz Ziora
- Department of Lung Diseases and Tuberculosis, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-800 Zabrze, Poland;
- Specjalistyczny Gabinet Lekarski, 42-202 Czestochowa, Poland
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12
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Murthy S, Seabold DA, Gautam LK, Caceres AM, Sease R, Calvert BA, Busch S, Neely A, Marconett CN, Ryan AL. Culture Conditions Differentially Regulate the Inflammatory Niche and Cellular Phenotype of Tracheo-Bronchial Basal Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611264. [PMID: 39282256 PMCID: PMC11398510 DOI: 10.1101/2024.09.04.611264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Human bronchial epithelial cells (HBECs) derived from the tracheo-bronchial regions of human airways provide an excellent in vitro model for studying pathological mechanisms and evaluating therapeutics in human airway cells. This cell population comprises a mixed population of basal cells (BCs), the predominant stem cell in airways capable of both self-renewal and functional differentiation. Despite their potential for regenerative medicine, BCs exhibit significant phenotypic variability in culture. To investigate how culture conditions influence BC phenotype and function, we expanded three independent BC isolates in three media, airway epithelial cell growth medium (AECGM), dual-SMAD inhibitor (DSI)-enriched AECGM, and Pneumacult Ex plus (PEx+). Extensive RNA sequencing, immune assays and electrical measurements revealed that PEx+ media significantly drove cell proliferation and a broad pro-inflammatory phenotype in BCs. In contrast, BCs expanded in AECGM, displayed increased expression of structural and extracellular matrix components at high passage. Whereas culture in AECGM increased expression of some cytokines at high passage, DSI suppressed inflammation altogether thus implicating TGF-β in BC inflammatory processes. Differentiation capacity declined with time in culture irrespective of expansion media except for PLUNC expressing secretory cells that were elevated at high passage in AECGM and PEx+ suggestive of an immune modulatory role of PLUNC in BCs. These findings underscore the profound impact of media conditions on inflammatory niche and function of in vitro expanded BCs. The broad pro-inflammatory phenotype driven by PEx+ media, in particular, should be considered in the development of cell-based models for airway diseases and therapeutic application.
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Affiliation(s)
- Shubha Murthy
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Denise A. Seabold
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Lalit K. Gautam
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Adrian M. Caceres
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Rosemary Sease
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA
| | - Ben A. Calvert
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
| | - Shana Busch
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
| | - Aaron Neely
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Crystal N. Marconett
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Amy L. Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA
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13
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Ruysseveldt E, Steelant B, Wils T, Cremer J, Bullens DMA, Hellings PW, Martens K. The nasal basal cell population shifts toward a diseased phenotype with impaired barrier formation capacity in allergic rhinitis. J Allergy Clin Immunol 2024; 154:631-643. [PMID: 38705259 DOI: 10.1016/j.jaci.2024.04.021] [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: 12/21/2023] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND The integrity of the airway epithelium is guarded by the airway basal cells that serve as progenitor cells and restore wounds in case of injury. Basal cells are a heterogenous population, and specific changes in their behavior are associated with chronic barrier disruption-mechanisms that have not been studied in detail in allergic rhinitis (AR). OBJECTIVE We aimed to study basal cell subtypes in AR and healthy controls. METHODS Single-cell RNA sequencing (scRNA-Seq) of the nasal epithelium was performed on nonallergic and house dust mite-allergic AR patients to reveal basal cell diversity and to identify allergy-related alterations. Flow cytometry, immunofluorescence staining, and in vitro experiments using primary basal cells were performed to confirm phenotypic findings at the protein level and functionally. RESULTS The scRNA-Seq, flow cytometry, and immunofluorescence staining revealed that basal cells are abundantly and heterogeneously present in the nasal epithelium, suggesting specialized subtypes. The total basal cell fraction within the epithelium in AR is increased compared to controls. scRNA-Seq demonstrated that potentially beneficial basal cells are missing in AR epithelium, while an activated population of allergy-associated basal cells is more dominantly present. Furthermore, our in vitro proliferation, wound healing assay and air-liquid interface cultures show that AR-associated basal cells have altered progenitor capacity compared to nonallergic basal cells. CONCLUSIONS The nasal basal cell population is abundant and diverse, and it shifts toward a diseased state in AR. The absence of potentially protective subtypes and the rise of a proinflammatory population suggest that basal cells are important players in maintaining epithelial barrier defects in AR.
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Affiliation(s)
- Emma Ruysseveldt
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium.
| | - Brecht Steelant
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Tine Wils
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Jonathan Cremer
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Dominique M A Bullens
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Clinical Department of Paediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Peter W Hellings
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Clinical Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium; Upper Airways Research Laboratory, University of Ghent, Ghent, Belgium
| | - Katleen Martens
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
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14
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Adegunsoye A, Kropski JA, Behr J, Blackwell TS, Corte TJ, Cottin V, Glanville AR, Glassberg MK, Griese M, Hunninghake GM, Johannson KA, Keane MP, Kim JS, Kolb M, Maher TM, Oldham JM, Podolanczuk AJ, Rosas IO, Martinez FJ, Noth I, Schwartz DA. Genetics and Genomics of Pulmonary Fibrosis: Charting the Molecular Landscape and Shaping Precision Medicine. Am J Respir Crit Care Med 2024; 210:401-423. [PMID: 38573068 PMCID: PMC11351799 DOI: 10.1164/rccm.202401-0238so] [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: 01/29/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024] Open
Abstract
Recent genetic and genomic advancements have elucidated the complex etiology of idiopathic pulmonary fibrosis (IPF) and other progressive fibrotic interstitial lung diseases (ILDs), emphasizing the contribution of heritable factors. This state-of-the-art review synthesizes evidence on significant genetic contributors to pulmonary fibrosis (PF), including rare genetic variants and common SNPs. The MUC5B promoter variant is unusual, a common SNP that markedly elevates the risk of early and established PF. We address the utility of genetic variation in enhancing understanding of disease pathogenesis and clinical phenotypes, improving disease definitions, and informing prognosis and treatment response. Critical research gaps are highlighted, particularly the underrepresentation of non-European ancestries in PF genetic studies and the exploration of PF phenotypes beyond usual interstitial pneumonia/IPF. We discuss the role of telomere length, often critically short in PF, and its link to progression and mortality, underscoring the genetic complexity involving telomere biology genes (TERT, TERC) and others like SFTPC and MUC5B. In addition, we address the potential of gene-by-environment interactions to modulate disease manifestation, advocating for precision medicine in PF. Insights from gene expression profiling studies and multiomic analyses highlight the promise for understanding disease pathogenesis and offer new approaches to clinical care, therapeutic drug development, and biomarker discovery. Finally, we discuss the ethical, legal, and social implications of genomic research and therapies in PF, stressing the need for sound practices and informed clinical genetic discussions. Looking forward, we advocate for comprehensive genetic testing panels and polygenic risk scores to improve the management of PF and related ILDs across diverse populations.
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Affiliation(s)
- Ayodeji Adegunsoye
- Pulmonary/Critical Care, and
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Juergen Behr
- Department of Medicine V, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Comprehensive Pneumology Center Munich, member of the German Center for Lung Research (DZL), Munich, Germany
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Tamera J. Corte
- Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, New South Wales, Australia
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Vincent Cottin
- National Reference Center for Rare Pulmonary Diseases (OrphaLung), Louis Pradel Hospital, Hospices Civils de Lyon, ERN-LUNG (European Reference Network on Rare Respiratory Diseases), Lyon, France
- Claude Bernard University Lyon, Lyon, France
| | - Allan R. Glanville
- Lung Transplant Unit, St. Vincent’s Hospital Sydney, Sydney, New South Wales, Australia
| | - Marilyn K. Glassberg
- Department of Medicine, Loyola Chicago Stritch School of Medicine, Chicago, Illinois
| | - Matthias Griese
- Department of Pediatric Pneumology, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, German Center for Lung Research, Munich, Germany
| | - Gary M. Hunninghake
- Harvard Medical School, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - Michael P. Keane
- Department of Respiratory Medicine, St. Vincent’s University Hospital and School of Medicine, University College Dublin, Dublin, Ireland
| | - John S. Kim
- Department of Medicine, School of Medicine, and
| | - Martin Kolb
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Toby M. Maher
- Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | | | | | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - David A. Schwartz
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
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15
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Jin C, Chen Y, Wang Y, Li J, Liang J, Zheng S, Zhang L, Li Q, Wang Y, Ling F, Li Y, Zheng Y, Nie Q, Feng Q, Wang J, Yang H. Single-cell RNA sequencing reveals special basal cells and fibroblasts in idiopathic pulmonary fibrosis. Sci Rep 2024; 14:15778. [PMID: 38982264 PMCID: PMC11233624 DOI: 10.1038/s41598-024-66947-5] [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: 03/30/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most predominant type of idiopathic interstitial pneumonia and has an increasing incidence, poor prognosis, and unclear pathogenesis. In order to investigate the molecular mechanisms underlying IPF further, we performed single-cell RNA sequencing analysis on three healthy controls and five IPF lung tissue samples. The results revealed a significant shift in epithelial cells (ECs) phenotypes in IPF, which may be attributed to the differentiation of alveolar type 2 cells to basal cells. In addition, several previously unrecognized basal cell subtypes were preliminarily identified, including extracellular matrix basal cells, which were increased in the IPF group. We identified a special population of fibroblasts that highly expressed extracellular matrix-related genes, POSTN, CTHRC1, COL3A1, COL5A2, and COL12A1. We propose that the close interaction between ECs and fibroblasts through ligand-receptor pairs may have a critical function in IPF development. Collectively, these outcomes provide innovative perspectives on the complexity and diversity of basal cells and fibroblasts in IPF and contribute to the understanding of possible mechanisms in pathological lung fibrosis.
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Affiliation(s)
- Chengji Jin
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yahong Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yujie Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Jia Li
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Jin Liang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Shaomao Zheng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Lipeng Zhang
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiaoyu Li
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Yongchao Wang
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, 211800, China
| | - Fayu Ling
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yongjie Li
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yu Zheng
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiuli Nie
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiong Feng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Jing Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China.
- NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, 571199, China.
| | - Huiling Yang
- School of Pharmacy, Guangdong Medical University, Dongguan, 523808, China.
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16
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Thangam T, Parthasarathy K, Supraja K, Haribalaji V, Sounderrajan V, Rao SS, Jayaraj S. Lung Organoids: Systematic Review of Recent Advancements and its Future Perspectives. Tissue Eng Regen Med 2024; 21:653-671. [PMID: 38466362 PMCID: PMC11187038 DOI: 10.1007/s13770-024-00628-2] [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: 07/25/2023] [Revised: 01/06/2024] [Accepted: 01/23/2024] [Indexed: 03/13/2024] Open
Abstract
Organoids are essentially an in vitro (lab-grown) three-dimensional tissue culture system model that meticulously replicates the structure and physiology of human organs. A few of the present applications of organoids are in the basic biological research area, molecular medicine and pharmaceutical drug testing. Organoids are crucial in connecting the gap between animal models and human clinical trials during the drug discovery process, which significantly lowers the time duration and cost associated with each stage of testing. Likewise, they can be used to understand cell-to-cell interactions, a crucial aspect of tissue biology and regeneration, and to model disease pathogenesis at various stages of the disease. Lung organoids can be utilized to explore numerous pathophysiological activities of a lung since they share similarities with its function. Researchers have been trying to recreate the complex nature of the lung by developing various "Lung organoids" models.This article is a systematic review of various developments of lung organoids and their potential progenitors. It also covers the in-depth applications of lung organoids for the advancement of translational research. The review discusses the methodologies to establish different types of lung organoids for studying the regenerative capability of the respiratory system and comprehending various respiratory diseases.Respiratory diseases are among the most common worldwide, and the growing burden must be addressed instantaneously. Lung organoids along with diverse bio-engineering tools and technologies will serve as a novel model for studying the pathophysiology of various respiratory diseases and for drug screening purposes.
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Affiliation(s)
- T Thangam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, 600119, India
| | - Krupakar Parthasarathy
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, 600119, India.
| | - K Supraja
- Medway Hospitals, No 2/26, 1st Main Road, Kodambakkam, Chennai, Tamil Nadu, 600024, India
| | - V Haribalaji
- VivagenDx, No. 28, Venkateswara Nagar, 100 Feet Bypass Road, Velachery, Chennai, Tamil Nadu, 600042, India
| | - Vignesh Sounderrajan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, 600119, India
| | - Sudhanarayani S Rao
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, 600119, India
| | - Sakthivel Jayaraj
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, 600119, India
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17
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Xie T, Liang J, Stripp B, Noble PW. Cell-cell interactions and communication dynamics in lung fibrosis. CHINESE MEDICAL JOURNAL PULMONARY AND CRITICAL CARE MEDICINE 2024; 2:63-71. [PMID: 39169931 PMCID: PMC11332853 DOI: 10.1016/j.pccm.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Indexed: 08/23/2024]
Abstract
Cell-cell interactions are essential components of coordinated cell function in lung homeostasis. Lung diseases involve altered cell-cell interactions and communication between different cell types, as well as between subsets of cells of the same type. The identification and understanding of intercellular signaling in lung fibrosis offer insights into the molecular mechanisms underlying these interactions and their implications in the development and progression of lung fibrosis. A comprehensive cell atlas of the human lung, established with the facilitation of single-cell RNA transcriptomic analysis, has enabled the inference of intercellular communications using ligand-receptor databases. In this review, we provide a comprehensive overview of the modified cell-cell communications in lung fibrosis. We highlight the intricate interactions among the major cell types within the lung and their contributions to fibrogenesis. The insights presented in this review will contribute to a better understanding of the molecular mechanisms underlying lung fibrosis and may guide future research efforts in developing targeted therapies for this debilitating disease.
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Affiliation(s)
- Ting Xie
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jiurong Liang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Barry Stripp
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W. Noble
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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18
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Luo L, Zhang W, You S, Cui X, Tu H, Yi Q, Wu J, Liu O. The role of epithelial cells in fibrosis: Mechanisms and treatment. Pharmacol Res 2024; 202:107144. [PMID: 38484858 DOI: 10.1016/j.phrs.2024.107144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/19/2024] [Accepted: 03/12/2024] [Indexed: 03/19/2024]
Abstract
Fibrosis is a pathological process that affects multiple organs and is considered one of the major causes of morbidity and mortality in multiple diseases, resulting in an enormous disease burden. Current studies have focused on fibroblasts and myofibroblasts, which directly lead to imbalance in generation and degradation of extracellular matrix (ECM). In recent years, an increasing number of studies have focused on the role of epithelial cells in fibrosis. In some cases, epithelial cells are first exposed to external physicochemical stimuli that may directly drive collagen accumulation in the mesenchyme. In other cases, the source of stimulation is mainly immune cells and some cytokines, and epithelial cells are similarly altered in the process. In this review, we will focus on the multiple dynamic alterations involved in epithelial cells after injury and during fibrogenesis, discuss the association among them, and summarize some therapies targeting changed epithelial cells. Especially, epithelial mesenchymal transition (EMT) is the key central step, which is closely linked to other biological behaviors. Meanwhile, we think studies on disruption of epithelial barrier, epithelial cell death and altered basal stem cell populations and stemness in fibrosis are not appreciated. We believe that therapies targeted epithelial cells can prevent the progress of fibrosis, but not reverse it. The epithelial cell targeting therapies will provide a wonderful preventive and delaying action.
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Affiliation(s)
- Liuyi Luo
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China
| | - Wei Zhang
- Department of Oral Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Siyao You
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China
| | - Xinyan Cui
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China
| | - Hua Tu
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China
| | - Qiao Yi
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China
| | - Jianjun Wu
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China.
| | - Ousheng Liu
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China.
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19
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Ramananda Y, Naren AP, Arora K. Functional Consequences of CFTR Interactions in Cystic Fibrosis. Int J Mol Sci 2024; 25:3384. [PMID: 38542363 PMCID: PMC10970640 DOI: 10.3390/ijms25063384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 09/01/2024] Open
Abstract
Cystic fibrosis (CF) is a fatal autosomal recessive disorder caused by the loss of function mutations within a single gene for the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). CFTR is a chloride channel that regulates ion and fluid transport across various epithelia. The discovery of CFTR as the CF gene and its cloning in 1989, coupled with extensive research that went into the understanding of the underlying biological mechanisms of CF, have led to the development of revolutionary therapies in CF that we see today. The highly effective modulator therapies have increased the survival rates of CF patients and shifted the epidemiological landscape and disease prognosis. However, the differential effect of modulators among CF patients and the presence of non-responders and ineligible patients underscore the need to develop specialized and customized therapies for a significant number of patients. Recent advances in the understanding of the CFTR structure, its expression, and defined cellular compositions will aid in developing more precise therapies. As the lifespan of CF patients continues to increase, it is becoming critical to clinically address the extra-pulmonary manifestations of CF disease to improve the quality of life of the patients. In-depth analysis of the molecular signature of different CF organs at the transcriptional and post-transcriptional levels is rapidly advancing and will help address the etiological causes and variability of CF among patients and develop precision medicine in CF. In this review, we will provide an overview of CF disease, leading to the discovery and characterization of CFTR and the development of CFTR modulators. The later sections of the review will delve into the key findings derived from single-molecule and single-cell-level analyses of CFTR, followed by an exploration of disease-relevant protein complexes of CFTR that may ultimately define the etiological course of CF disease.
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Affiliation(s)
- Yashaswini Ramananda
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anjaparavanda P. Naren
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kavisha Arora
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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20
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Rouhani MJ, Janes SM, Kim CF. Epithelial stem and progenitor cells of the upper airway. Cells Dev 2024; 177:203905. [PMID: 38355015 DOI: 10.1016/j.cdev.2024.203905] [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: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
The upper airway acts as a conduit for the passage of air to the respiratory system and is implicated in several chronic diseases. Whilst the cell biology of the distal respiratory system has been described in great detail, less is known about the proximal upper airway. In this review, we describe the relevant anatomy of the upper airway and discuss the literature detailing the identification and roles of the progenitor cells of these regions.
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Affiliation(s)
- Maral J Rouhani
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Carla F Kim
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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21
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Chu CY, Kim SY, Pryhuber GS, Mariani TJ, McGraw MD. Single-cell resolution of human airway epithelial cells exposed to bronchiolitis obliterans-associated chemicals. Am J Physiol Lung Cell Mol Physiol 2024; 326:L135-L148. [PMID: 38084407 PMCID: PMC11279737 DOI: 10.1152/ajplung.00304.2023] [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: 09/25/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 01/24/2024] Open
Abstract
Bronchiolitis obliterans (BO) is a fibrotic lung disease characterized by progressive luminal narrowing and obliteration of the small airways. In the nontransplant population, inhalation exposure to certain chemicals is associated with BO; however, the mechanisms contributing to disease induction remain poorly understood. This study's objective was to use single-cell RNA sequencing for the identification of transcriptomic signatures common to primary human airway epithelial cells after chemical exposure to BO-associated chemicals-diacetyl or nitrogen mustard-to help explain BO induction. Primary airway epithelial cells were cultured at air-liquid interface and exposed to diacetyl, nitrogen mustard, or control vapors. Cultures were dissociated and sequenced for single-cell RNA. Differential gene expression and functional pathway analyses were compared across exposures. In total, 75,663 single cells were captured and sequenced from all exposure conditions. Unbiased clustering identified 11 discrete phenotypes, including 5 basal, 2 ciliated, and 2 secretory cell clusters. With chemical exposure, the proportion of cells assigned to keratin 5+ basal cells decreased, whereas the proportion of cells aligned to secretory cell clusters increased compared with control exposures. Functional pathway analysis identified interferon signaling and antigen processing/presentation as pathways commonly upregulated after diacetyl or nitrogen mustard exposure in a ciliated cell cluster. Conversely, the response of airway basal cells differed significantly with upregulation of the unfolded protein response in diacetyl-exposed basal cells, not seen in nitrogen mustard-exposed cultures. These new insights provide early identification of airway epithelial signatures common to BO-associated chemical exposures.NEW & NOTEWORTHY Bronchiolitis obliterans (BO) is a devastating fibrotic lung disease of the small airways, or bronchioles. This original manuscript uses single-cell RNA sequencing for identifying common signatures of chemically exposed airway epithelial cells in BO induction. Chemical exposure reduced the proportion of keratin 5+ basal cells while increasing the proportion of keratin 4+ suprabasal cells. Functional pathways contributory to these shifts differed significantly across exposures. These new results highlight similarities and differences in BO induction across exposures.
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Affiliation(s)
- Chin-Yi Chu
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - So-Young Kim
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew D McGraw
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
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22
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Mohan S, Hakami MA, Dailah HG, Khalid A, Najmi A, Zoghebi K, Halawi MA, Alotaibi TM. From inflammation to metastasis: The central role of miR-155 in modulating NF-κB in cancer. Pathol Res Pract 2024; 253:154962. [PMID: 38006837 DOI: 10.1016/j.prp.2023.154962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023]
Abstract
Cancer is a multifaceted, complex disease characterized by unchecked cell growth, genetic mutations, and dysregulated signalling pathways. These factors eventually cause evasion of apoptosis, sustained angiogenesis, tissue invasion, and metastasis, which makes it difficult for targeted therapeutic interventions to be effective. MicroRNAs (miRNAs) are essential gene expression regulators linked to several biological processes, including cancer and inflammation. The NF-κB signalling pathway, a critical regulator of inflammatory reactions and oncogenesis, has identified miR-155 as a significant participant in its modulation. An intricate network of transcription factors known as the NF-κB pathway regulates the expression of genes related to inflammation, cell survival, and immunological responses. The NF-κB pathway's dysregulation contributes to many cancer types' development, progression, and therapeutic resistance. In numerous cancer models, the well-studied miRNA miR-155 has been identified as a crucial regulator of NF-κB signalling. The p65 subunit and regulatory molecules like IκB are among the primary targets that miR-155 directly targets to alter NF-κB activity. The molecular processes by which miR-155 affects the NF-κB pathway are discussed in this paper. It also emphasizes the miR-155's direct and indirect interactions with important NF-κB cascade elements to control the expression of NF-κB subunits. We also investigate how miR-155 affects NF-κB downstream effectors in cancer, including inflammatory cytokines and anti-apoptotic proteins.
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Affiliation(s)
- Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia; School of Health Sciences, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India; Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al, Quwayiyah, Shaqra University, Riyadh, Saudi Arabia.
| | - Hamad Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Maryam A Halawi
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
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23
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Blumhagen RZ, Kurche JS, Cool CD, Walts AD, Heinz D, Fingerlin TE, Yang IV, Schwartz DA. Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis. Respir Res 2023; 24:287. [PMID: 37978501 PMCID: PMC10655274 DOI: 10.1186/s12931-023-02572-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/21/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these pathologically heterogeneous regions of the IPF lung is critical to understanding the distribution and extent of fibrotic lung disease and identifying potential therapeutic targets. Application of a spatial transcriptomics platform would provide more detailed spatial resolution of transcriptional signals compared to previous single cell or bulk RNA-Seq studies. METHODS We performed spatial transcriptomics using GeoMx Nanostring Digital Spatial Profiling on formalin-fixed paraffin-embedded (FFPE) tissue from 32 IPF and 12 control subjects and identified 231 regions of interest (ROIs). We compared normal-appearing lung parenchyma and airways between IPF and controls with histologically normal lung tissue, as well as histologically distinct regions within IPF (normal-appearing lung parenchyma, transition zones containing fibroblastic foci, areas of dense fibrosis, and honeycomb epithelium metaplasia). RESULTS We identified 254 differentially expressed genes (DEGs) between IPF and controls in histologically normal-appearing regions of lung parenchyma; pathway analysis identified disease processes such as EIF2 signaling (important for cap-dependent mRNA translation), epithelial adherens junction signaling, HIF1α signaling, and integrin signaling. Within IPF, we identified 173 DEGs between transition and normal-appearing lung parenchyma and 198 DEGs between dense fibrosis and normal lung parenchyma; pathways dysregulated in both transition and dense fibrotic areas include EIF2 signaling pathway activation (upstream of endoplasmic reticulum (ER) stress proteins ATF4 and CHOP) and wound healing signaling pathway deactivation. Through cell deconvolution of transcriptome data and immunofluorescence staining, we confirmed loss of alveolar parenchymal signals (AGER, SFTPB, SFTPC), gain of secretory cell markers (SCGB3A2, MUC5B) as well as dysregulation of the upstream regulator ATF4, in histologically normal-appearing tissue in IPF. CONCLUSIONS Our findings demonstrate that histologically normal-appearing regions from the IPF lung are transcriptionally distinct when compared to similar lung tissue from controls with histologically normal lung tissue, and that transition zones and areas of dense fibrosis within the IPF lung demonstrate activation of ER stress and deactivation of wound healing pathways.
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Affiliation(s)
- Rachel Z Blumhagen
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Office M222D, Denver, CO, 80206, USA.
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
- Medical Service, Rocky Mountain Regional Veterans Administration Medical Center, 1700 N Wheeling St, Aurora, CO, 80045, USA
| | - Carlyne D Cool
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
- Department of Medicine, National Jewish Health, 1400 Jackson St, Denver, CO, 80206, USA
| | - Avram D Walts
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
| | - David Heinz
- Pathology Laboratory, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Office M222D, Denver, CO, 80206, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
- Medical Service, Rocky Mountain Regional Veterans Administration Medical Center, 1700 N Wheeling St, Aurora, CO, 80045, USA
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24
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Luo Z, Ji L, Liu H, Sun Y, Zhao C, Xu X, Gu X, Ai X, Yang C. Inhalation Lenalidomide-Loaded Liposome for Bleomycin-Induced Pulmonary Fibrosis Improvement. AAPS PharmSciTech 2023; 24:235. [PMID: 37973629 DOI: 10.1208/s12249-023-02690-w] [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: 07/14/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, fibrotic interstitial lung disease with unclear etiology and increasing prevalence. Pulmonary administration can make the drug directly reach the lung lesion location and reduce systemic toxic and side effects. The effectiveness of lenalidomide (Len) liposomal lung delivery in idiopathic pulmonary fibrosis was investigated. Len liposomes (Len-Lip) were prepared from soybean lecithin, cholesterol (Chol), and medicine in different weight ratios by thin film hydration method. The Len-Lip were spherical in shape with an average size of 226.7 ± 1.389 nm. The liposomes with a higher negative zeta potential of around - 34 mV, which was conducive to improving stability by repelling each other. The drug loading and encapsulation rate were 2.42 ± 0.07% and 85.47 ± 2.42%. Len-Lip had little toxicity at the cellular level and were well taken up by cells. At bleomycin-induced pulmonary fibrosis model mice, inhalation Len-Lip could improve lung function and decrease lung hydroxyproline contents, and alleviate pulmonary fibrosis state. Inhalation Len-Lip provided a reference for the treatment of idiopathic pulmonary fibrosis.
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Affiliation(s)
- Zhilin Luo
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Liyuan Ji
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China
| | - Hongting Liu
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Yao Sun
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Conglu Zhao
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Xiang Xu
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Xiaoting Gu
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China.
| | - Xiaoyu Ai
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China.
| | - Cheng Yang
- College of Pharmacy, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin, 300350, China.
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25
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Luo W, Gu Y, Fu S, Wang J, Zhang J, Wang Y. Emerging opportunities to treat idiopathic pulmonary fibrosis: Design, discovery, and optimizations of small-molecule drugs targeting fibrogenic pathways. Eur J Med Chem 2023; 260:115762. [PMID: 37683364 DOI: 10.1016/j.ejmech.2023.115762] [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: 06/30/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common fibrotic form of idiopathic diffuse lung disease. Due to limited treatment options, IPF patients suffer from poor survival. About ten years ago, Pirfenidone (Shionogi, 2008; InterMune, 2011) and Nintedanib (Boehringer Ingelheim, 2014) were approved, greatly changing the direction of IPF drug design. However, limited efficacy and side effects indicate that neither can reverse the process of IPF. With insights into the occurrence of IPF, novel targets and agents have been proposed, which have fundamentally changed the treatment of IPF. With the next-generation agents, targeting pro-fibrotic pathways in the epithelial-injury model offers a promising approach. Besides, several next-generation IPF drugs have entered phase II/III clinical trials with encouraging results. Due to the rising IPF treatment requirements, there is an urgent need to completely summarize the mechanisms, targets, problems, and drug design strategies over the past ten years. In this review, we summarize known mechanisms, target types, drug design, and novel technologies of IPF drug discovery, aiming to provide insights into the future development and clinical application of next-generation IPF drugs.
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Affiliation(s)
- Wenxin Luo
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yilin Gu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Siyu Fu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Jifa Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
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26
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Hewitt RJ, Puttur F, Gaboriau DCA, Fercoq F, Fresquet M, Traves WJ, Yates LL, Walker SA, Molyneaux PL, Kemp SV, Nicholson AG, Rice A, Roberts E, Lennon R, Carlin LM, Byrne AJ, Maher TM, Lloyd CM. Lung extracellular matrix modulates KRT5 + basal cell activity in pulmonary fibrosis. Nat Commun 2023; 14:6039. [PMID: 37758700 PMCID: PMC10533905 DOI: 10.1038/s41467-023-41621-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Aberrant expansion of KRT5+ basal cells in the distal lung accompanies progressive alveolar epithelial cell loss and tissue remodelling during fibrogenesis in idiopathic pulmonary fibrosis (IPF). The mechanisms determining activity of KRT5+ cells in IPF have not been delineated. Here, we reveal a potential mechanism by which KRT5+ cells migrate within the fibrotic lung, navigating regional differences in collagen topography. In vitro, KRT5+ cell migratory characteristics and expression of remodelling genes are modulated by extracellular matrix (ECM) composition and organisation. Mass spectrometry- based proteomics revealed compositional differences in ECM components secreted by primary human lung fibroblasts (HLF) from IPF patients compared to controls. Over-expression of ECM glycoprotein, Secreted Protein Acidic and Cysteine Rich (SPARC) in the IPF HLF matrix restricts KRT5+ cell migration in vitro. Together, our findings demonstrate how changes to the ECM in IPF directly influence KRT5+ cell behaviour and function contributing to remodelling events in the fibrotic niche.
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Affiliation(s)
- Richard J Hewitt
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Franz Puttur
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | | | - Maryline Fresquet
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - William J Traves
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Laura L Yates
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Simone A Walker
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Philip L Molyneaux
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Samuel V Kemp
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, City Campus, Hucknall Road, Nottingham, NG5 1PB, UK
| | - Andrew G Nicholson
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Alexandra Rice
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Edward Roberts
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Leo M Carlin
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Adam J Byrne
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Keck Medicine of USC, 1510 San Pablo Street, Los Angeles, CA, 90033, USA
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK.
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27
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Beppu AK, Zhao J, Yao C, Carraro G, Israely E, Coelho AL, Drake K, Hogaboam CM, Parks WC, Kolls JK, Stripp BR. Epithelial plasticity and innate immune activation promote lung tissue remodeling following respiratory viral infection. Nat Commun 2023; 14:5814. [PMID: 37726288 PMCID: PMC10509177 DOI: 10.1038/s41467-023-41387-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/02/2023] [Indexed: 09/21/2023] Open
Abstract
Epithelial plasticity has been suggested in lungs of mice following genetic depletion of stem cells but is of unknown physiological relevance. Viral infection and chronic lung disease share similar pathological features of stem cell loss in alveoli, basal cell (BC) hyperplasia in small airways, and innate immune activation, that contribute to epithelial remodeling and loss of lung function. We show that a subset of distal airway secretory cells, intralobar serous (IS) cells, are activated to assume BC fates following influenza virus infection. Injury-induced hyperplastic BC (hBC) differ from pre-existing BC by high expression of IL-22Ra1 and undergo IL-22-dependent expansion for colonization of injured alveoli. Resolution of virus-elicited inflammation results in BC to IS re-differentiation in repopulated alveoli, and increased local expression of protective antimicrobial factors, but fails to restore normal alveolar epithelium responsible for gas exchange.
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Affiliation(s)
- Andrew K Beppu
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Juanjuan Zhao
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Changfu Yao
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Gianni Carraro
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Edo Israely
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Anna Lucia Coelho
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Katherine Drake
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Cory M Hogaboam
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - William C Parks
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jay K Kolls
- Tulane Center for Translational Research in Infection and Inflammation, School of Medicine, New Orleans, LA, 70112, USA
| | - Barry R Stripp
- Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Department of Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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Gentemann L, Donath S, Seidler AE, Patyk L, Buettner M, Heisterkamp A, Kalies S. Mimicking acute airway tissue damage using femtosecond laser nanosurgery in airway organoids. Front Cell Dev Biol 2023; 11:1268621. [PMID: 37745302 PMCID: PMC10514509 DOI: 10.3389/fcell.2023.1268621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
Airway organoids derived from adult murine epithelial cells represent a complex 3D in vitro system mimicking the airway epithelial tissue's native cell composition and physiological properties. In combination with a precise damage induction via femtosecond laser-based nanosurgery, this model might allow for the examination of intra- and intercellular dynamics in the course of repair processes with a high spatio-temporal resolution, which can hardly be reached using in vivo approaches. For characterization of the organoids' response to single or multiple-cell ablation, we first analyzed overall organoid survival and found that airway organoids were capable of efficiently repairing damage induced by femtosecond laser-based ablation of a single to ten cells within 24 h. An EdU staining assay further revealed a steady proliferative potential of airway organoid cells. Especially in the case of ablation of five cells, proliferation was enhanced within the first 4 h upon damage induction, whereas ablation of ten cells was followed by a slight decrease in proliferation within this time frame. Analyzing individual trajectories of single cells within airway organoids, we found an increased migratory behavior in cells within close proximity to the ablation site following the ablation of ten, but not five cells. Bulk RNA sequencing and subsequent enrichment analysis revealed the differential expression of sets of genes involved in the regulation of epithelial repair, distinct signaling pathway activities such as Notch signaling, as well as cell migration after laser-based ablation. Together, our findings demonstrate that organoid repair upon ablation of ten cells involves key processes by which native airway epithelial wound healing is regulated. This marks the herein presented in vitro damage model suitable to study repair processes following localized airway injury, thereby posing a novel approach to gain insights into the mechanisms driving epithelial repair on a single-cell level.
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Affiliation(s)
- Lara Gentemann
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development, Hannover, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover, Germany
| | - Sören Donath
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development, Hannover, Germany
| | - Anna E. Seidler
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development, Hannover, Germany
| | - Lara Patyk
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development, Hannover, Germany
| | - Manuela Buettner
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Alexander Heisterkamp
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development, Hannover, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover, Germany
- German Center for Lung Research (DZL), Gießen, Germany
| | - Stefan Kalies
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development, Hannover, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover, Germany
- German Center for Lung Research (DZL), Gießen, Germany
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29
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Wang S, Shan S, Zhang J, Liu Z, Gu X, Hong Y, He H, Ren T. Airway epithelium regeneration by photoactivated basal cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 245:112732. [PMID: 37290293 DOI: 10.1016/j.jphotobiol.2023.112732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 04/27/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
The airway epithelium is the footstone to maintain the structure and functions of lung, in which resident basal cells (BCs) maintain homeostasis and functional regeneration of epithelial barrier in response to injury. In recent clinical researches, transplanting BCs has shown great inspiring achievements in therapy of various lung diseases. In this study, we report a noninvasive optical method to activate BCs for airway epithelium regeneration in vivo by fast scanning of focused femtosecond laser on BCs of airway epithelium to active Ca2+ signaling and subsequent ERK and Wnt pathways. The photoactivated BCs present high proliferative capacity and maintain high pluripotency, which enables them to plant in the injured airway epithelium and differentiate to club cells for regeneration of epithelium. This optical method can also work in situ to activate localized BCs in airway tissue. Therefore, our results provide a powerful technology for noninvasive BC activation in stem-cell therapy of lung diseases.
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Affiliation(s)
- Shaoyang Wang
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China; School of Biomedical Engineering, Hainan University, 58 Renmin Avenue, 570228, Haikou, China; School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, 200030 Shanghai, China
| | - Shan Shan
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China
| | - Jingyuan Zhang
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China; School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, 200030 Shanghai, China
| | - Zeyu Liu
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China
| | - Xiaohua Gu
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China
| | - Yue Hong
- Stem Cell Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China; School of Life Sciences, Hainan University, 58 Renmin Avenue, 570228 Haikou, China.
| | - Hao He
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, 200030 Shanghai, China.
| | - Tao Ren
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, 200233 Shanghai, China; Shanghai Key Laboratory of Sleep Disordered Breathing, 600 Yishan Road, 200233 Shanghai, China.
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30
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Dudchenko O, Ordovas-Montanes J, Bingle CD. Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing. Biochem J 2023; 480:921-939. [PMID: 37410389 PMCID: PMC10422933 DOI: 10.1042/bcj20220572] [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: 11/19/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Standalone and consortia-led single-cell atlases of healthy and diseased human airways generated with single-cell RNA-sequencing (scRNA-seq) have ushered in a new era in respiratory research. Numerous discoveries, including the pulmonary ionocyte, potentially novel cell fates, and a diversity of cell states among common and rare epithelial cell types have highlighted the extent of cellular heterogeneity and plasticity in the respiratory tract. scRNA-seq has also played a pivotal role in our understanding of host-virus interactions in coronavirus disease 2019 (COVID-19). However, as our ability to generate large quantities of scRNA-seq data increases, along with a growing number of scRNA-seq protocols and data analysis methods, new challenges related to the contextualisation and downstream applications of insights are arising. Here, we review the fundamental concept of cellular identity from the perspective of single-cell transcriptomics in the respiratory context, drawing attention to the need to generate reference annotations and to standardise the terminology used in literature. Findings about airway epithelial cell types, states and fates obtained from scRNA-seq experiments are compared and contrasted with information accumulated through the use of conventional methods. This review attempts to discuss major opportunities and to outline some of the key limitations of the modern-day scRNA-seq that need to be addressed to enable efficient and meaningful integration of scRNA-seq data from different platforms and studies, with each other as well as with data from other high-throughput sequencing-based genomic, transcriptomic and epigenetic analyses.
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Affiliation(s)
- Oleksandr Dudchenko
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, South Yorkshire, U.K
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, U.S.A
- Programme in Immunology, Harvard Medical School, Boston, MA, U.S.A
| | - Colin D. Bingle
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, South Yorkshire, U.K
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31
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Marega M, El-Merhie N, Gökyildirim MY, Orth V, Bellusci S, Chao CM. Stem/Progenitor Cells and Related Therapy in Bronchopulmonary Dysplasia. Int J Mol Sci 2023; 24:11229. [PMID: 37446407 DOI: 10.3390/ijms241311229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/18/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a chronic lung disease commonly seen in preterm infants, and is triggered by infection, mechanical ventilation, and oxygen toxicity. Among other problems, lifelong limitations in lung function and impaired psychomotor development may result. Despite major advances in understanding the disease pathologies, successful interventions are still limited to only a few drug therapies with a restricted therapeutic benefit, and which sometimes have significant side effects. As a more promising therapeutic option, mesenchymal stem cells (MSCs) have been in focus for several years due to their anti-inflammatory effects and their secretion of growth and development promoting factors. Preclinical studies provide evidence in that MSCs have the potential to contribute to the repair of lung injuries. This review provides an overview of MSCs, and other stem/progenitor cells present in the lung, their identifying characteristics, and their differentiation potential, including cytokine/growth factor involvement. Furthermore, animal studies and clinical trials using stem cells or their secretome are reviewed. To bring MSC-based therapeutic options further to clinical use, standardized protocols are needed, and upcoming side effects must be critically evaluated. To fill these gaps of knowledge, the MSCs' behavior and the effects of their secretome have to be examined in more (pre-) clinical studies, from which only few have been designed to date.
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Affiliation(s)
- Manuela Marega
- German Center for Lung Research (DZL), Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Justus Liebig University Giessen, 35392 Giessen, Germany
- Department of Pediatrics, Centre for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
| | - Natalia El-Merhie
- Institute for Lung Health (ILH), Member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Mira Y Gökyildirim
- Department of Pediatrics, University Medical Center Rostock, University of Rostock, 18057 Rostock, Germany
| | - Valerie Orth
- Department of Pediatrics, Centre for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
| | - Saverio Bellusci
- German Center for Lung Research (DZL), Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Cho-Ming Chao
- German Center for Lung Research (DZL), Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Justus Liebig University Giessen, 35392 Giessen, Germany
- Department of Pediatrics, Centre for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
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Liang J, Huang G, Liu X, Liu N, Taghavifar F, Dai K, Yao C, Deng N, Wang Y, Chen P, Hogaboam C, Stripp BR, Parks WC, Noble PW, Jiang D. Reciprocal interactions between alveolar progenitor dysfunction and aging promote lung fibrosis. eLife 2023; 12:e85415. [PMID: 37314162 PMCID: PMC10292844 DOI: 10.7554/elife.85415] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/13/2023] [Indexed: 06/15/2023] Open
Abstract
Aging is a critical risk factor in idiopathic pulmonary fibrosis (IPF). Dysfunction and loss of type 2 alveolar epithelial cells (AEC2s) with failed regeneration is a seminal causal event in the pathogenesis of IPF, although the precise mechanisms for their regenerative failure and demise remain unclear. To systematically examine the genomic program changes of AEC2s in aging and after lung injury, we performed unbiased single-cell RNA-seq analyses of lung epithelial cells from uninjured or bleomycin-injured young and old mice, as well as from lungs of IPF patients and healthy donors. We identified three AEC2 subsets based on their gene signatures. Subset AEC2-1 mainly exist in uninjured lungs, while subsets AEC2-2 and AEC2-3 emerged in injured lungs and increased with aging. Functionally, AEC2 subsets are correlated with progenitor cell renewal. Aging enhanced the expression of the genes related to inflammation, stress responses, senescence, and apoptosis. Interestingly, lung injury increased aging-related gene expression in AEC2s even in young mice. The synergistic effects of aging and injury contributed to impaired AEC2 recovery in aged mouse lungs after injury. In addition, we also identified three subsets of AEC2s from human lungs that formed three similar subsets to mouse AEC2s. IPF AEC2s showed a similar genomic signature to AEC2 subsets from bleomycin-injured old mouse lungs. Taken together, we identified synergistic effects of aging and AEC2 injury in transcriptomic and functional analyses that promoted fibrosis. This study provides new insights into the interactions between aging and lung injury with interesting overlap with diseased IPF AEC2 cells.
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Affiliation(s)
- Jiurong Liang
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Guanling Huang
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Xue Liu
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Ningshan Liu
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Forough Taghavifar
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Kristy Dai
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Changfu Yao
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Nan Deng
- Genomics Core, Cedars-Sinai Medical Centerlos AngelesUnited States
| | - Yizhou Wang
- Genomics Core, Cedars-Sinai Medical Centerlos AngelesUnited States
| | - Peter Chen
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Cory Hogaboam
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Barry R Stripp
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - William C Parks
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
- Department of Biomedical Sciences, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Paul W Noble
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Dianhua Jiang
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical CenterLos AngelesUnited States
- Department of Biomedical Sciences, Cedars-Sinai Medical CenterLos AngelesUnited States
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33
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Wang X, Hallen NR, Lee M, Samuchiwal S, Ye Q, Buchheit KM, Maxfield AZ, Roditi RE, Bergmark RW, Bhattacharyya N, Ryan T, Gakpo D, Raychaudhuri S, Dwyer D, Laidlaw TM, Boyce JA, Gutierrez-Arcelus M, Barrett NA. Type 2 inflammation drives an airway basal stem cell program through insulin receptor substrate signaling. J Allergy Clin Immunol 2023; 151:1536-1549. [PMID: 36804595 PMCID: PMC10784786 DOI: 10.1016/j.jaci.2023.01.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/17/2023] [Accepted: 01/26/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND Chronic rhinosinusitis with nasal polyposis (CRSwNP) is a type 2 (T2) inflammatory disease associated with an increased number of airway basal cells (BCs). Recent studies have identified transcriptionally distinct BCs, but the molecular pathways that support or inhibit human BC proliferation and differentiation are largely unknown. OBJECTIVE We sought to determine the role of T2 cytokines in regulating airway BCs. METHODS Single-cell and bulk RNA sequencing of sinus and lung airway epithelial cells was analyzed. Human sinus BCs were stimulated with IL-4 and IL-13 in the presence and absence of inhibitors of IL-4R signaling. Confocal analysis of human sinus tissue and murine airway was performed. Murine BC subsets were sorted for RNA sequencing and functional assays. Fate labeling was performed in a murine model of tracheal injury and regeneration. RESULTS Two subsets of BCs were found in human and murine respiratory mucosa distinguished by the expression of basal cell adhesion molecule (BCAM). BCAM expression identifies airway stem cells among P63+KRT5+NGFR+ BCs. In the sinonasal mucosa, BCAMhi BCs expressing TSLP, IL33, CCL26, and the canonical BC transcription factor TP63 are increased in patients with CRSwNP. In cultured BCs, IL-4/IL-13 increases the expression of BCAM and TP63 through an insulin receptor substrate-dependent signaling pathway that is increased in CRSwNP. CONCLUSIONS These findings establish BCAM as a marker of airway stem cells among the BC pool and demonstrate that airway epithelial remodeling in T2 inflammation extends beyond goblet cell metaplasia to the support of a BC stem state poised to perpetuate inflammation.
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Affiliation(s)
- Xin Wang
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Nils R Hallen
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Minkyu Lee
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Sachin Samuchiwal
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Qihua Ye
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Kathleen M Buchheit
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Alice Z Maxfield
- Department of Otolaryngology, Head and Neck Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Rachel E Roditi
- Department of Otolaryngology, Head and Neck Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Regan W Bergmark
- Department of Otolaryngology, Head and Neck Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Neil Bhattacharyya
- Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Boston, Mass
| | - Tessa Ryan
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Deb Gakpo
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, Mass; Divisions of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Mass; Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Dan Dwyer
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Tanya M Laidlaw
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Joshua A Boyce
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass
| | - Maria Gutierrez-Arcelus
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Mass; Division of Immunology, Boston Children's Hospital, Boston, Mass
| | - Nora A Barrett
- Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass.
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Li X, Gibson G, Qiu P. Gene representation in scRNA-seq is correlated with common motifs at the 3' end of transcripts. FRONTIERS IN BIOINFORMATICS 2023; 3:1120290. [PMID: 37255988 PMCID: PMC10226423 DOI: 10.3389/fbinf.2023.1120290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
One important characteristic of single-cell RNA sequencing (scRNA-seq) data is its high sparsity, where the gene-cell count data matrix contains high proportion of zeros. The sparsity has motivated widespread discussions on dropouts and missing data, as well as imputation algorithms of scRNA-seq analysis. Here, we aim to investigate whether there exist genes that are more prone to be under-detected in scRNA-seq, and if yes, what commonalities those genes may share. From public data sources, we gathered paired bulk RNA-seq and scRNA-seq data from 53 human samples, which were generated in diverse biological contexts. We derived pseudo-bulk gene expression by averaging the scRNA-seq data across cells. Comparisons of the paired bulk and pseudo-bulk gene expression profiles revealed that there indeed exists a collection of genes that are frequently under-detected in scRNA-seq compared to bulk RNA-seq. This result was robust to randomization when unpaired bulk and pseudo-bulk gene expression profiles were compared. We performed motif search to the last 350 bp of the identified genes, and observed an enrichment of poly(T) motif. The poly(T) motif toward the tails of those genes may be able to form hairpin structures with the poly(A) tails of their mRNA transcripts, making it difficult for their mRNA transcripts to be captured during scRNA-seq library preparation, which is a mechanistic conjecture of why certain genes may be more prone to be under-detected in scRNA-seq.
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Affiliation(s)
- Xinling Li
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Greg Gibson
- School of Biological Sciences, and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peng Qiu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
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35
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Bian F, Lan YW, Zhao S, Deng Z, Shukla S, Acharya A, Donovan J, Le T, Milewski D, Bacchetta M, Hozain AE, Tipograf Y, Chen YW, Xu Y, Shi D, Kalinichenko VV, Kalin TV. Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling. Nat Commun 2023; 14:2560. [PMID: 37137915 PMCID: PMC10156846 DOI: 10.1038/s41467-023-38177-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Pulmonary fibrosis results from dysregulated lung repair and involves multiple cell types. The role of endothelial cells (EC) in lung fibrosis is poorly understood. Using single cell RNA-sequencing we identified endothelial transcription factors involved in lung fibrogenesis, including FOXF1, SMAD6, ETV6 and LEF1. Focusing on FOXF1, we found that FOXF1 is decreased in EC within human idiopathic pulmonary fibrosis (IPF) and mouse bleomycin-injured lungs. Endothelial-specific Foxf1 inhibition in mice increased collagen depositions, promoted lung inflammation, and impaired R-Ras signaling. In vitro, FOXF1-deficient EC increased proliferation, invasion and activation of human lung fibroblasts, and stimulated macrophage migration by secreting IL-6, TNFα, CCL2 and CXCL1. FOXF1 inhibited TNFα and CCL2 through direct transcriptional activation of Rras gene promoter. Transgenic overexpression or endothelial-specific nanoparticle delivery of Foxf1 cDNA decreased pulmonary fibrosis in bleomycin-injured mice. Nanoparticle delivery of FOXF1 cDNA can be considered for future therapies in IPF.
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Affiliation(s)
- Fenghua Bian
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Ying-Wei Lan
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Shuyang Zhao
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Zicheng Deng
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- The Materials Science and Engineering Program, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Samriddhi Shukla
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Anusha Acharya
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Johnny Donovan
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Tien Le
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - David Milewski
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Matthew Bacchetta
- Departments of Thoracic and Cardiac Surgery, Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ahmed Emad Hozain
- Department of Surgery, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Yuliya Tipograf
- Department of Surgery, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Ya-Wen Chen
- Department of Cell, Developmental, and Regenerative Biology, Department of Otolaryngology, Institute for Airway Sciences, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Xu
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Donglu Shi
- The Materials Science and Engineering Program, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Vladimir V Kalinichenko
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tanya V Kalin
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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36
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Wang R, Simone-Roach C, Lindstrom-Vautrin J, Wang F, Rollins S, Bawa PS, Lu J, Tang Y, Beermann ML, Schlaeger T, Mahoney J, Rowe SM, Hawkins FJ, Kotton DN. De Novo Generation of Pulmonary Ionocytes from Normal and Cystic Fibrosis Human Induced Pluripotent Stem Cells. Am J Respir Crit Care Med 2023; 207:1249-1253. [PMID: 36857488 PMCID: PMC10161739 DOI: 10.1164/rccm.202205-1010le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Affiliation(s)
- Ruobing Wang
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Chantelle Simone-Roach
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
| | - Stuart Rollins
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Pushpinder Singh Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
| | - Junjie Lu
- Cystic Fibrosis Foundation Therapeutics Laboratories, Lexington, Massachusetts
| | - Yang Tang
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mary Lou Beermann
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine and
| | | | - John Mahoney
- Cystic Fibrosis Foundation Therapeutics Laboratories, Lexington, Massachusetts
| | - Steven M. Rowe
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Finn J. Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine and
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine and
- Department of Pathology & Laboratory Medicine, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts; and
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37
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Morishita R, Suzuki T, Mukherjee P, Abd El-Sadek I, Lim Y, Lichtenegger A, Makita S, Tomita K, Yamamoto Y, Nagamoto T, Yasuno Y. Label-free intratissue activity imaging of alveolar organoids with dynamic optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:2333-2351. [PMID: 37206117 PMCID: PMC10191660 DOI: 10.1364/boe.488097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
An organoid is a three-dimensional (3D) in vitro cell culture emulating human organs. We applied 3D dynamic optical coherence tomography (DOCT) to visualize the intratissue and intracellular activities of human induced pluripotent stem cells (hiPSCs)-derived alveolar organoids in normal and fibrosis models. 3D DOCT data were acquired with an 840-nm spectral domain optical coherence tomography with axial and lateral resolutions of 3.8 µm (in tissue) and 4.9 µm, respectively. The DOCT images were obtained by the logarithmic-intensity-variance (LIV) algorithm, which is sensitive to the signal fluctuation magnitude. The LIV images revealed cystic structures surrounded by high-LIV borders and mesh-like structures with low LIV. The former may be alveoli with a highly dynamics epithelium, while the latter may be fibroblasts. The LIV images also demonstrated the abnormal repair of the alveolar epithelium.
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Affiliation(s)
- Rion Morishita
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Toshio Suzuki
- Department of Medical Oncology, Faculty of
Medicine,
University of
Tsukuba, Ibaraki 305-8575, Japan
- HiLung Inc.,
Kyoto, Japan
| | - Pradipta Mukherjee
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Ibrahim Abd El-Sadek
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Department of Physics, Faculty of Science,
Damietta University, New Damietta City
34517, Damietta, Egypt
| | - Yiheng Lim
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Antonia Lichtenegger
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Center for Medical Physics and Biomedical
Engineering, Medical University of Vienna,
Währinger Gürtel 18-20, 4L, 1090, Vienna, Austria
| | - Shuichi Makita
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Kiriko Tomita
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | | | | | - Yoshiaki Yasuno
- Computational Optics Group,
University of
Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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38
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Herrera JA, Dingle LA, Monetero MA, Venkateswaran RV, Blaikley JF, Granato F, Pearson S, Lawless C, Thornton DJ. Morphologically intact airways in lung fibrosis have an abnormal proteome. Respir Res 2023; 24:99. [PMID: 37005656 PMCID: PMC10066954 DOI: 10.1186/s12931-023-02400-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/16/2023] [Indexed: 04/04/2023] Open
Abstract
Honeycombing is a histological pattern consistent with Usual Interstitial Pneumonia (UIP). Honeycombing refers to cystic airways located at sites of dense fibrosis with marked mucus accumulation. Utilizing laser capture microdissection coupled mass spectrometry (LCM-MS), we interrogated the fibrotic honeycomb airway cells and fibrotic uninvolved airway cells (distant from honeycomb airways and morphologically intact) in specimens from 10 patients with UIP. Non-fibrotic airway cell specimens from 6 patients served as controls. Furthermore, we performed LCM-MS on the mucus plugs found in 6 patients with UIP and 6 patients with mucinous adenocarcinoma. The mass spectrometry data were subject to both qualitative and quantitative analysis and validated by immunohistochemistry. Surprisingly, fibrotic uninvolved airway cells share a similar protein profile to honeycomb airway cells, showing deregulation of the slit and roundabout receptor (Slit and Robo) pathway as the strongest category. We find that (BPI) fold-containing family B member 1 (BPIFB1) is the most significantly increased secretome-associated protein in UIP, whereas Mucin-5AC (MUC5AC) is the most significantly increased in mucinous adenocarcinoma. We conclude that fibrotic uninvolved airway cells share pathological features with fibrotic honeycomb airway cells. In addition, fibrotic honeycomb airway cells are enriched in mucin biogenesis proteins with a marked derangement in proteins essential for ciliogenesis. This unbiased spatial proteomic approach generates novel and testable hypotheses to decipher fibrosis progression.
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Affiliation(s)
- Jeremy A Herrera
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK.
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK.
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Lewis A Dingle
- Blond McIndoe Laboratories, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - M Angeles Monetero
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Rajamiyer V Venkateswaran
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - John F Blaikley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Felice Granato
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Stella Pearson
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - Craig Lawless
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - David J Thornton
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
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39
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Verleden SE, Vanstapel A, Jacob J, Goos T, Hendriks J, Ceulemans LJ, Van Raemdonck DE, De Sadeleer L, Vos R, Kwakkel-van Erp JM, Neyrinck AP, Verleden GM, Boone MN, Janssens W, Wauters E, Weynand B, Jonigk DD, Verschakelen J, Wuyts WA. Radiologic and Histologic Correlates of Early Interstitial Lung Changes in Explanted Lungs. Radiology 2023; 307:e221145. [PMID: 36537894 PMCID: PMC7614383 DOI: 10.1148/radiol.221145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/13/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
Background Interstitial lung abnormalities (ILAs) reflect imaging features on lung CT scans that are compatible with (early) interstitial lung disease. Despite accumulating evidence regarding the incidence, risk factors, and prognosis of ILAs, the histopathologic correlates of ILAs remain elusive. Purpose To determine the correlation between radiologic and histopathologic findings in CT-defined ILAs in human lung explants. Materials and Methods Explanted lungs or lobes from participants with radiologically documented ILAs were prospectively collected from 2010 to 2021. These specimens were air-inflated, frozen, and scanned with CT and micro-CT (spatial resolution of 0.7 mm and 90 μm, respectively). Subsequently, the lungs were cut and sampled with core biopsies. At least five samples per lung underwent micro-CT and subsequent histopathologic assessment with semiquantitative remodeling scorings. Based on area-specific radiologic scoring, the association between radiologic and histopathologic findings was assessed. Results Eight lung explants from six donors (median age at explantation, 71 years [range, 60-83 years]; four men) were included (unused donor lungs, n = 4; pre-emptive lobectomy for oncologic indications, n = 2). Ex vivo CT demonstrated ground-glass opacification, reticulation, and bronchiectasis. Micro-CT and histopathologic examination demonstrated that lung abnormalities were frequently paraseptal and associated with fibrosis and lymphocytic inflammation. The histopathologic results showed varying degrees of fibrosis in areas that appeared normal on CT scans. Regions of reticulation on CT scans generally had greater fibrosis at histopathologic analysis. Vasculopathy and bronchiectasis were also often present at histopathologic examination of lungs with ILAs. Fully developed fibroblastic foci were rarely observed. Conclusion This study demonstrated direct histologic correlates of CT-defined interstitial lung abnormalities. © RSNA, 2022 Supplemental material is available for this article. See also the editorial by Jeudy in this issue.
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Affiliation(s)
- Stijn E. Verleden
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Arno Vanstapel
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Joseph Jacob
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Tinne Goos
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Jeroen Hendriks
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Laurens J. Ceulemans
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Dirk E. Van Raemdonck
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Laurens De Sadeleer
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Robin Vos
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Johanna M. Kwakkel-van Erp
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Arne P. Neyrinck
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Geert M. Verleden
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Matthieu N. Boone
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Wim Janssens
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Els Wauters
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Birgit Weynand
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Danny D. Jonigk
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Johny Verschakelen
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Wim A. Wuyts
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
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40
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Yang J, Liang C, Liu L, Wang L, Yu G. High-Fat Diet Related Lung Fibrosis-Epigenetic Regulation Matters. Biomolecules 2023; 13:biom13030558. [PMID: 36979493 PMCID: PMC10046645 DOI: 10.3390/biom13030558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Pulmonary fibrosis (PF) is an interstitial lung disease characterized by the destruction of the pulmonary parenchyma caused by excessive extracellular matrix deposition. Despite the well-known etiological factors such as senescence, aberrant epithelial cell and fibroblast activation, and chronic inflammation, PF has recently been recognized as a metabolic disease and abnormal lipid signature was observed both in serum and bronchoalveolar lavage fluid (BALF) of PF patients and mice PF model. Clinically, observational studies suggest a significant link between high-fat diet (HFD) and PF as manifested by high intake of saturated fatty acids (SFAs) and meat increases the risk of PF and mice lung fibrosis. However, the possible mechanisms between HFD and PF remain unclear. In the current review we emphasize the diversity effects of the epigenetic dysregulation induced by HFD on the fibrotic factors such as epithelial cell injury, abnormal fibroblast activation and chronic inflammation. Finally, we discuss the potential ways for patients to improve their conditions and emphasize the prospect of targeted therapy based on epigenetic regulation for scientific researchers or drug developers.
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Affiliation(s)
- Juntang Yang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Chenxi Liang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Lulu Liu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Lan Wang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
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41
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Huang G, Liang J, Huang K, Liu X, Taghavifar F, Yao C, Parimon T, Liu N, Dai K, Aziz A, Wang Y, Waldron RT, Mou H, Stripp B, Noble PW, Jiang D. Basal Cell-derived WNT7A Promotes Fibrogenesis at the Fibrotic Niche in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2023; 68:302-313. [PMID: 36318668 PMCID: PMC9989475 DOI: 10.1165/rcmb.2022-0074oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/01/2022] [Indexed: 12/25/2022] Open
Abstract
Loss of epithelial integrity, bronchiolarization, and fibroblast activation are key characteristics of idiopathic pulmonary fibrosis (IPF). Prolonged accumulation of basal-like cells in IPF may impact the fibrotic niche to promote fibrogenesis. To investigate their role in IPF, basal cells were isolated from IPF explant and healthy donor lung tissues. Single-cell RNA sequencing was used to assess differentially expressed genes in basal cells. Basal cell and niche interaction was demonstrated with the sLP-mCherry niche labeling system. Luminex assays were used to assess cytokines secreted by basal cells. The role of basal cells in fibroblast activation was studied. Three-dimensional organoid culture assays were used to interrogate basal cell effects on AEC2 (type 2 alveolar epithelial cell) renewal capacity. Perturbation was used to investigate WNT7A function in vitro and in a repetitive bleomycin model in vivo. We found that WNT7A is highly and specifically expressed in basal-like cells. Proteins secreted by basal cells can be captured by neighboring fibroblasts and AEC2s. Basal cells or basal cell-conditioned media activate fibroblasts through WNT7A. Basal cell-derived WNT7A inhibits AEC2 progenitor cell renewal in three-dimensional organoid cultures. Neutralizing antibodies against WNT7A or a small molecule inhibitor of Frizzled signaling abolished basal cell-induced fibroblast activation and attenuated lung fibrosis in mice. In summary, basal cells and basal cell-derived WNT7A are key components of the fibrotic niche, providing a unique non-stem cell function of basal cells in IPF progression and a novel targeting strategy for IPF.
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Affiliation(s)
| | | | - Kevin Huang
- Division of Pulmonary, Women's Guild Lung Institute
| | - Xue Liu
- Division of Pulmonary, Women's Guild Lung Institute
| | | | - Changfu Yao
- Division of Pulmonary, Women's Guild Lung Institute
- The Board of Governors Regenerative Medicine Institute
| | | | - Ningshan Liu
- Division of Pulmonary, Women's Guild Lung Institute
| | - Kristy Dai
- Division of Pulmonary, Women's Guild Lung Institute
| | - Adam Aziz
- Division of Pulmonary, Women's Guild Lung Institute
| | | | | | - Hongmei Mou
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Barry Stripp
- Division of Pulmonary, Women's Guild Lung Institute
- The Board of Governors Regenerative Medicine Institute
| | - Paul W Noble
- Division of Pulmonary, Women's Guild Lung Institute
| | - Dianhua Jiang
- Division of Pulmonary, Women's Guild Lung Institute
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California; and
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42
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Königshoff M, Eickelberg O. Listen to the WNT; It Talks: WNT7A Drives Epithelial-Mesenchymal Cross-Talk within the Fibrotic Niche in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2023; 68:239-240. [PMID: 36525670 PMCID: PMC9989476 DOI: 10.1165/rcmb.2022-0479ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Melanie Königshoff
- Division of Pulmonary, Allergy and Critical Care Medicine University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy and Critical Care Medicine University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
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43
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Abstract
The human lung cellular portfolio, traditionally characterized by cellular morphology and individual markers, is highly diverse, with over 40 cell types and a complex branching structure highly adapted for agile airflow and gas exchange. While constant during adulthood, lung cellular content changes in response to exposure, injury, and infection. Some changes are temporary, but others are persistent, leading to structural changes and progressive lung disease. The recent advance of single-cell profiling technologies allows an unprecedented level of detail and scale to cellular measurements, leading to the rise of comprehensive cell atlas styles of reporting. In this review, we chronical the rise of cell atlases and explore their contributions to human lung biology in health and disease.
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Affiliation(s)
- Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA;
| | - Arnaud Marlier
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA;
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Januska MN, Walsh MJ. Single-Cell RNA Sequencing Reveals New Basic and Translational Insights in the Cystic Fibrosis Lung. Am J Respir Cell Mol Biol 2023; 68:131-139. [PMID: 36194688 PMCID: PMC9986558 DOI: 10.1165/rcmb.2022-0038tr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/04/2022] [Indexed: 02/03/2023] Open
Abstract
Cystic fibrosis (CF) is a multisystemic, autosomal recessive disorder caused by mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene, with the majority of morbidity and mortality extending from lung disease. Single-cell RNA sequencing (scRNA-seq) has been leveraged in the lung and elsewhere in the body to articulate discrete cell populations, describing cell types, states, and lineages as well as their roles in health and disease. In this translational review, we provide an overview of the current applications of scRNA-seq to the study of the normal and CF lungs, allowing the beginning of a new cellular and molecular narrative of CF lung disease, and we highlight some of the future opportunities to further leverage scRNA-seq and complementary single-cell technologies in the study of CF as we bridge from scientific understanding to clinical application.
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Affiliation(s)
- Megan N. Januska
- Department of Pediatrics
- Department of Genetics and Genomic Sciences, and
| | - Martin J. Walsh
- Department of Pediatrics
- Department of Genetics and Genomic Sciences, and
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; and
- Mount Sinai Center for RNA Biology and Medicine, New York, New York
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Liu D, Xu C, Jiang L, Zhu X. Pulmonary endogenous progenitor stem cell subpopulation: Physiology, pathogenesis, and progress. JOURNAL OF INTENSIVE MEDICINE 2023; 3:38-51. [PMID: 36789358 PMCID: PMC9924023 DOI: 10.1016/j.jointm.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/09/2022] [Accepted: 08/13/2022] [Indexed: 06/18/2023]
Abstract
Lungs are structurally and functionally complex organs consisting of diverse cell types from the proximal to distal axis. They have direct contact with the external environment and are constantly at risk of various injuries. Capable to proliferate and differentiate, pulmonary endogenous progenitor stem cells contribute to the maintenance of lung structure and function both under homeostasis and following injuries. Discovering candidate pulmonary endogenous progenitor stem cell types and underlying regenerative mechanisms provide insights into therapeutic strategy development for lung diseases. In this review, we reveal their compositions, roles in lung disease pathogenesis and injury repair, and the underlying mechanisms. We further underline the advanced progress in research approach and potential therapy for lung regeneration. We also demonstrate the feasibility and prospects of pulmonary endogenous stem cell transplantation for lung disease treatment.
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Affiliation(s)
- Di Liu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Chufan Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Xiaoyan Zhu
- Department of Physiology, Navy Medical University, 800 Xiangyin Road, Shanghai 200433, China
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Yu F, Liu F, Liang X, Duan L, Li Q, Pan G, Ma C, Liu M, Li M, Wang P, Zhao X. iPSC-Derived Airway Epithelial Cells: Progress, Promise, and Challenges. Stem Cells 2023; 41:1-10. [PMID: 36190736 DOI: 10.1093/stmcls/sxac074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/14/2022] [Indexed: 02/02/2023]
Abstract
Induced pluripotent stem cells (iPSCs) generated from somatic cell sources are pluripotent and capable of indefinite expansion in vitro. They provide an unlimited source of cells that can be differentiated into lung progenitor cells for potential clinical use in pulmonary regenerative medicine. This review gives a comprehensive overview of recent progress toward the use of iPSCs to generate proximal and distal airway epithelial cells and mix lung organoids. Furthermore, their potential applications and future challenges for the field are discussed, with a focus on the technological hurdles that must be cleared before stem cell therapeutics can be used for clinical treatment.
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Affiliation(s)
- Fenggang Yu
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Fei Liu
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Xiaohua Liang
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Linwei Duan
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Qiongqiong Li
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Ge Pan
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Chengyao Ma
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Minmin Liu
- Life Sciences Institute, Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Mingyue Li
- Yinfeng Biological Group, Ltd., Jinan, Shandong Province, People's Republic of China
| | - Peng Wang
- Guangxi Yinfeng Stem Cell Engineering Technology Co., Ltd., Yufeng, Liuzhou, Guangxi Province, People's Republic of China
| | - Xuening Zhao
- Department of Otolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
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47
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Cerro Chiang G, Parimon T. Understanding Interstitial Lung Diseases Associated with Connective Tissue Disease (CTD-ILD): Genetics, Cellular Pathophysiology, and Biologic Drivers. Int J Mol Sci 2023; 24:ijms24032405. [PMID: 36768729 PMCID: PMC9917355 DOI: 10.3390/ijms24032405] [Citation(s) in RCA: 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: 12/24/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Connective tissue disease-associated interstitial lung disease (CTD-ILD) is a collection of systemic autoimmune disorders resulting in lung interstitial abnormalities or lung fibrosis. CTD-ILD pathogenesis is not well characterized because of disease heterogeneity and lack of pre-clinical models. Some common risk factors are inter-related with idiopathic pulmonary fibrosis, an extensively studied fibrotic lung disease, which includes genetic abnormalities and environmental risk factors. The primary pathogenic mechanism is that these risk factors promote alveolar type II cell dysfunction triggering many downstream profibrotic pathways, including inflammatory cascades, leading to lung fibroblast proliferation and activation, causing abnormal lung remodeling and repairs that result in interstitial pathology and lung fibrosis. In CTD-ILD, dysregulation of regulator pathways in inflammation is a primary culprit. However, confirmatory studies are required. Understanding these pathogenetic mechanisms is necessary for developing and tailoring more targeted therapy and provides newly discovered disease biomarkers for early diagnosis, clinical monitoring, and disease prognostication. This review highlights the central CTD-ILD pathogenesis and biological drivers that facilitate the discovery of disease biomarkers.
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Affiliation(s)
- Giuliana Cerro Chiang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Correspondence:
| | - Tanyalak Parimon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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48
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Xu H, Pan G, Wang J. Repairing Mechanisms for Distal Airway Injuries and Related Targeted Therapeutics for Chronic Lung Diseases. Cell Transplant 2023; 32:9636897231196489. [PMID: 37698245 PMCID: PMC10498699 DOI: 10.1177/09636897231196489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
Chronic lung diseases, such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), involve progressive and irreversible destruction and pathogenic remodeling of airways and have become the leading health care burden worldwide. Pulmonary tissue has extensive capacities to launch injury-responsive repairing programs (IRRPs) to replace the damaged or dead cells upon acute lung injuries. However, the IRRPs are frequently compromised in chronic lung diseases. In this review, we aim to provide an overview of somatic stem cell subpopulations within distal airway epithelium and the underlying mechanisms mediating their self-renewal and trans-differentiation under both physiological and pathological circumstances. We also compared the differences between humans and mice on distal airway structure and stem cell composition. At last, we reviewed the current status and future directions for the development of targeted therapeutics on defective distal airway regeneration and repairment in chronic lung diseases.
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Affiliation(s)
- Huahua Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Guihong Pan
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jun Wang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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49
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Glenn LM, Troy LK, Corte TJ. Novel diagnostic techniques in interstitial lung disease. Front Med (Lausanne) 2023; 10:1174443. [PMID: 37188089 PMCID: PMC10175799 DOI: 10.3389/fmed.2023.1174443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Research into novel diagnostic techniques and targeted therapeutics in interstitial lung disease (ILD) is moving the field toward increased precision and improved patient outcomes. An array of molecular techniques, machine learning approaches and other innovative methods including electronic nose technology and endobronchial optical coherence tomography are promising tools with potential to increase diagnostic accuracy. This review provides a comprehensive overview of the current evidence regarding evolving diagnostic methods in ILD and to consider their future role in routine clinical care.
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Affiliation(s)
- Laura M. Glenn
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
- *Correspondence: Laura M. Glenn,
| | - Lauren K. Troy
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
| | - Tamera J. Corte
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
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50
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Zhou S, Zhu J, Zhou PK, Gu Y. Alveolar type 2 epithelial cell senescence and radiation-induced pulmonary fibrosis. Front Cell Dev Biol 2022; 10:999600. [PMID: 36407111 PMCID: PMC9666897 DOI: 10.3389/fcell.2022.999600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
Radiation-induced pulmonary fibrosis (RIPF) is a chronic and progressive respiratory tract disease characterized by collagen deposition. The pathogenesis of RIPF is still unclear. Type 2 alveolar epithelial cells (AT2), the essential cells that maintain the structure and function of lung tissue, are crucial for developing pulmonary fibrosis. Recent studies indicate the critical role of AT2 cell senescence during the onset and progression of RIPF. In addition, clearance of senescent AT2 cells and treatment with senolytic drugs efficiently improve lung function and radiation-induced pulmonary fibrosis symptoms. These findings indicate that AT2 cell senescence has the potential to contribute significantly to the innovative treatment of fibrotic lung disorders. This review summarizes the current knowledge from basic and clinical research about the mechanism and functions of AT2 cell senescence in RIPF and points to the prospects for clinical treatment by targeting senescent AT2 cells.
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Affiliation(s)
- Shenghui Zhou
- Hengyang Medical College, University of South China, Hengyang, China,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - Jiaojiao Zhu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - Ping-Kun Zhou
- Hengyang Medical College, University of South China, Hengyang, China,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China,*Correspondence: Yongqing Gu, ; Ping-Kun Zhou,
| | - Yongqing Gu
- Hengyang Medical College, University of South China, Hengyang, China,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China,*Correspondence: Yongqing Gu, ; Ping-Kun Zhou,
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