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Mohammed SM, Al-Saedi HFS, Mohammed AQ, Amir AA, Radi UK, Sattar R, Ahmad I, Ramadan MF, Alshahrani MY, Balasim HM, Alawadi A. Mechanisms of Bleomycin-induced Lung Fibrosis: A Review of Therapeutic Targets and Approaches. Cell Biochem Biophys 2024:10.1007/s12013-024-01384-9. [PMID: 38955925 DOI: 10.1007/s12013-024-01384-9] [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] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Pulmonary toxicity is a serious side effect of some specific anticancer drugs. Bleomycin is a well-known anticancer drug that triggers severe reactions in the lungs. It is an approved drug that may be prescribed for the treatment of testicular cancers, Hodgkin's and non-Hodgkin's lymphomas, ovarian cancer, head and neck cancers, and cervical cancer. A large number of experimental studies and clinical findings show that bleomycin can concentrate in lung tissue, leading to massive oxidative stress, alveolar epithelial cell death, the proliferation of fibroblasts, and finally the infiltration of immune cells. Chronic release of pro-inflammatory and pro-fibrotic molecules by immune cells and fibroblasts leads to pneumonitis and fibrosis. Both fibrosis and pneumonitis are serious concerns for patients who receive bleomycin and may lead to death. Therefore, the management of lung toxicity following cancer therapy with bleomycin is a critical issue. This review explains the cellular and molecular mechanisms of pulmonary injury following treatment with bleomycin. Furthermore, we review therapeutic targets and possible promising strategies for ameliorating bleomycin-induced lung injury.
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Affiliation(s)
- Shaimaa M Mohammed
- Department of Pharmacy, Al- Mustaqbal University College, 51001, Hilla, Babylon, Iraq
| | | | | | - Ahmed Ali Amir
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq
| | - Usama Kadem Radi
- College of Pharmacy, National University of Science and Technology, Nasiriyah, Dhi Qar, Iraq
| | - Ruaa Sattar
- Al-Hadi University College, Baghdad, 10011, Iraq
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia.
| | - Halah Majeed Balasim
- Department of Medical Laboratory Technologies, Al Rafidain University College, Bagdad, Iraq
| | - Ahmed Alawadi
- College of technical engineering, the Islamic University, Najaf, Iraq
- College of technical engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of technical engineering, the Islamic University of Babylon, Hilla, Iraq
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2
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Huang G, Geng Y, Kulur V, Liu N, Liu X, Taghavifar F, Liang J, Noble PW, Jiang D. Arrestin beta 1 Regulates Alveolar Progenitor Renewal and Lung Fibrosis. JOURNAL OF RESPIRATORY BIOLOGY AND TRANSLATIONAL MEDICINE 2024; 1:10006. [PMID: 38736470 PMCID: PMC11087074 DOI: 10.35534/jrbtm.2024.10006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
The molecular mechanisms that regulate progressive pulmonary fibrosis remain poorly understood. Type 2 alveolar epithelial cells (AEC2s) function as adult stem cells in the lung. We previously showed that there is a loss of AEC2s and a failure of AEC2 renewal in the lungs of idiopathic pulmonary fibrosis (IPF) patients. We also reported that beta-arrestins are the key regulators of fibroblast invasion, and beta-arrestin 1 and 2 deficient mice exhibit decreased mortality, decreased matrix deposition, and increased lung function in bleomycin-induced lung fibrosis. However, the role of beta-arrestins in AEC2 regeneration is unclear. In this study, we investigated the role and mechanism of Arrestin beta 1 (ARRB1) in AEC2 renewal and in lung fibrosis. We used conventional deletion as well as cell type-specific deletion of ARRB1 in mice and found that Arrb1 deficiency in fibroblasts protects mice from lung fibrosis, and the knockout mice exhibit enhanced AEC2 regeneration in vivo, suggesting a role of fibroblast-derived ARRB1 in AEC2 renewal. We further found that Arrb1-deficient fibroblasts promotes AEC2 renewal in 3D organoid assays. Mechanistically, we found that CCL7 is among the top downregulated cytokines in Arrb1 deficient fibroblasts and CCL7 inhibits AEC2 regeneration in 3D organoid experiments. Therefore, fibroblast ARRB1 mediates AEC2 renewal, possibly by releasing chemokine CCL7, leading to fibrosis in the lung.
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Affiliation(s)
- Guanling Huang
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Current Address: GH, Sanofi, 500 Kendall Street, Cambridge, MA 02142, USA
| | - Yan Geng
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Current Address: YG, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, China
| | - Vrishika Kulur
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ningshan Liu
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xue Liu
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Forough Taghavifar
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jiurong Liang
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W. Noble
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dianhua Jiang
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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3
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Mukhatayev Z, Adilbayeva A, Kunz J. CTHRC1: An Emerging Hallmark of Pathogenic Fibroblasts in Lung Fibrosis. Cells 2024; 13:946. [PMID: 38891078 PMCID: PMC11171484 DOI: 10.3390/cells13110946] [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: 02/29/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Pulmonary fibrosis is a chronic, progressive, irreversible lung disease characterized by fibrotic scarring in the lung parenchyma. This condition involves the excessive accumulation of extracellular matrix (ECM) due to the aberrant activation of myofibroblasts in the alveolar environment. Transforming growth factor beta (TGF-β) signaling is a crucial driver of fibrogenesis because it promotes excessive ECM deposition, thereby leading to scar formation and lung damage. A primary target of TGF-β signaling in fibrosis is Collagen Triple Helix Repeat Containing 1 (CTHRC1), a secreted glycoprotein that plays a pivotal role in ECM deposition and wound repair. TGF-β transcriptionally regulates CTHRC1 in response to tissue injury and controls the wound healing response through functional activity. CTHRC1 may also play an essential role in re-establishing and maintaining tissue homeostasis after wound closure by modulating both the TGF-β and canonical Wnt signaling pathways. This dual function suggests that CTHRC1 regulates tissue remodeling and homeostasis. However, deregulated CTHRC1 expression in pathogenic fibroblasts has recently emerged as a hallmark of fibrosis in multiple organs and tissues. This review highlights recent studies suggesting that CTHRC1 can serve as a diagnostic and prognostic biomarker for fibrosis in idiopathic pulmonary fibrosis, systemic sclerosis, and post-COVID-19 lung fibrosis. Notably, CTHRC1 expression is responsive to antifibrotic drugs that target the TGF-β pathway, such as pirfenidone and bexotegrast, indicating its potential as a biomarker of treatment success. These findings suggest that CTHRC1 may present new opportunities for diagnosing and treating patients with lung fibrosis.
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Affiliation(s)
| | | | - Jeannette Kunz
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, 5/1 Kerey and Zhanibek Khans St., 020000 Astana, Kazakhstan; (Z.M.); (A.A.)
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4
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Liu X, Yang M, Li J, Liu H, Dong Y, Zheng J, Huang Y. Identification of CFH and FHL2 as biomarkers for idiopathic pulmonary fibrosis. Front Med (Lausanne) 2024; 11:1363643. [PMID: 38784225 PMCID: PMC11111937 DOI: 10.3389/fmed.2024.1363643] [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: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a fatal disease of unknown etiology with a poor prognosis, characterized by a lack of effective diagnostic and therapeutic interventions. The role of immunity in the pathogenesis of IPF is significant, yet remains inadequately understood. This study aimed to identify potential key genes in IPF and their relationship with immune cells by integrated bioinformatics analysis and verify by in vivo and in vitro experiments. Methods Gene microarray data were obtained from the Gene Expression Omnibus (GEO) for differential expression analysis. The differentially expressed genes (DEGs) were identified and subjected to functional enrichment analysis. By utilizing a combination of three machine learning algorithms, specific genes associated with idiopathic pulmonary fibrosis (IPF) were pinpointed. Then their diagnostic significance and potential co-regulators were elucidated. We further analyzed the correlation between key genes and immune infiltrating cells via single-sample gene set enrichment analysis (ssGSEA). Subsequently, a single-cell RNA sequencing data (scRNA-seq) was used to explore which cell types expressed key genes in IPF samples. Finally, a series of in vivo and in vitro experiments were conducted to validate the expression of candidate genes by western blot (WB), quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) analysis. Results A total of 647 DEGs of IPF were identified based on two datasets, including 225 downregulated genes and 422 upregulated genes. They are closely related to biological functions such as cell migration, structural organization, immune cell chemotaxis, and extracellular matrix. CFH and FHL2 were identified as key genes with diagnostic accuracy for IPF by three machine learning algorithms. Analysis using ssGSEA revealed a significant association of both CFH and FHL2 with diverse immune cells, such as B cells and NK cells. Further scRNA-seq analysis indicated CFH and FHL2 were specifically upregulated in human IPF tissues, which was confirmed by in vitro and in vivo experiments. Conclusion In this study, CFH and FHL2 have been identified as novel potential biomarkers for IPF, with potential diagnostic utility in future clinical applications. Subsequent investigations into the functions of these genes in IPF and their interactions with immune cells may enhance comprehension of the disease's pathogenesis and facilitate the identification of therapeutic targets.
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Affiliation(s)
- Xingchen Liu
- Department of Pathology, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Meng Yang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Jiayu Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Hangxu Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Jianming Zheng
- Department of Pathology, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Yi Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
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5
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Ji K, Zhang M, Du L, Wang J, Liu Y, Xu C, He N, Wang Q, Gu Y, Song H, Wang Y, Liu Q. Exploring the Role of Inulin in Targeting the Gut Microbiota: An Innovative Strategy for Alleviating Colonic Fibrosis Induced By Irradiation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5710-5724. [PMID: 38457473 PMCID: PMC10958509 DOI: 10.1021/acs.jafc.3c03432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 02/13/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
The use of radiation therapy to treat pelvic and abdominal cancers can lead to the development of either acute or chronic radiation enteropathy. Radiation-induced chronic colonic fibrosis is a common gastrointestinal disorder resulting from the above radiation therapy. In this study, we establish the efficacy of inulin supplements in safeguarding against colonic fibrosis caused by irradiation therapy. Studies have demonstrated that inulin supplements enhance the proliferation of bacteria responsible to produce short-chain fatty acids (SCFAs) and elevate the levels of SCFAs in feces. In a mouse model of chronic radiation enteropathy, the transplantation of gut microbiota and its metabolites from feces of inulin-treated mice were found to reduce colonic fibrosis in validation experiments. Administering inulin-derived metabolites from gut microbiota led to a notable decrease in the expression of genes linked to fibrosis and collagen production in mouse embryonic fibroblast cell line NIH/3T3. In the cell line, inulin-derived metabolites also suppressed the expression of genes linked to the extracellular matrix synthesis pathway. The results indicate a novel and practical approach to safeguarding against chronic radiation-induced colonic fibrosis.
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Affiliation(s)
| | | | - Liqing Du
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Jinhan Wang
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Yang Liu
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Chang Xu
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Ningning He
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Qin Wang
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Yeqing Gu
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Huijuan Song
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Yan Wang
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
| | - Qiang Liu
- Tianjin Key Laboratory of
Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy
of Medical Science & Peking Union Medical College, State Key Laboratory
of Advanced Medical Materials and Devices, Tianjin 300192, PR China
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6
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Zhang S, Wang Y, Luo D, Cheng Z, Zeng Q, Wang G, Chen M, Zhang S, Luo P. Pirfenidone inhibits TGF-β1-induced metabolic reprogramming during epithelial-mesenchymal transition in non-small cell lung cancer. J Cell Mol Med 2024; 28:e18059. [PMID: 38140828 PMCID: PMC10844763 DOI: 10.1111/jcmm.18059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Metastasis is an important contributor to increased mortality rates in non-small cell lung cancer (NSCLC). The TGF-β signalling pathway plays a crucial role in facilitating tumour metastasis through epithelial-mesenchymal transition (EMT). Glycolysis, a key metabolic process, is strongly correlated with NSCLC metastasis. Pirfenidone (PFD) has been shown to safely and effectively inhibit TGF-β1 in patients with lung diseases. Furthermore, TGF-β1 and glycolysis demonstrate an interdependent relationship within the tumour microenvironment. Our previous study demonstrated that PFD effectively inhibited glycolysis in NSCLC cells, prompting further investigation into its potential antitumour effects in this context. Therefore, the present study aims to investigate the potential antitumour effect of PFD in NSCLC and explore the relationship among TGF-β1, glycolysis and EMT through further experimentation. The antitumour effects of PFD were evaluated using five different NSCLC cell lines and a xenograft tumour model. Notably, PFD demonstrated a significant antitumour effect specifically in highly glycolytic H1299 cells. To elucidate the underlying mechanism, we compared the efficacy of PFD after pretreatment with either TGF-β1 or a TGF-β receptor inhibitor (LY2109761). The energy metabolomics analysis of tumour tissue demonstrated that PFD, a chemosensitizing agent, reduced lactate and ATP production, thereby inhibiting glycolysis and exerting synergistic antineoplastic effects. Additionally, PFD combined with cisplatin targeted TGF-β1 to inhibit glycolysis during EMT and enhanced the chemosensitization of A549 and H1299 cells. The magnitude of the anticancer effect exhibited by PFD was intricately linked to its metabolic properties.
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Affiliation(s)
- Shuling Zhang
- Guizhou Medical UniversityGuiyangChina
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of EducationSchool of Public HealthGuiyangChina
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical UniversityGuiyangChina
- Guizhou Provincial Engineering Research Center of Food Nutrition and HealthGuizhou Medical UniversityGuiyangChina
| | - Yuanmei Wang
- Guizhou Medical UniversityGuiyangChina
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of EducationSchool of Public HealthGuiyangChina
| | | | | | - Qibing Zeng
- Guizhou Medical UniversityGuiyangChina
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of EducationSchool of Public HealthGuiyangChina
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical UniversityGuiyangChina
- Guizhou Provincial Engineering Research Center of Food Nutrition and HealthGuizhou Medical UniversityGuiyangChina
| | - Guoze Wang
- Guizhou Medical UniversityGuiyangChina
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of EducationSchool of Public HealthGuiyangChina
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical UniversityGuiyangChina
- Guizhou Provincial Engineering Research Center of Food Nutrition and HealthGuizhou Medical UniversityGuiyangChina
| | | | - Shuai Zhang
- Guizhou Medical UniversityGuiyangChina
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of EducationSchool of Public HealthGuiyangChina
| | - Peng Luo
- Guizhou Medical UniversityGuiyangChina
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of EducationSchool of Public HealthGuiyangChina
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical UniversityGuiyangChina
- Guizhou Provincial Engineering Research Center of Food Nutrition and HealthGuizhou Medical UniversityGuiyangChina
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7
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Bahudhanapati H, Tan J, Apel RM, Seeliger B, Schupp J, Li X, Sullivan DI, Sembrat J, Rojas M, Tabib T, Valenzi E, Lafyatis R, Mitash N, Hernandez Pineda R, Jawale C, Peroumal D, Biswas P, Tedrow J, Adams T, Kaminski N, Wuyts WA, McDyer JF, Gibson KF, Alder JK, Königshoff M, Zhang Y, Nouraie M, Prasse A, Kass DJ. Increased expression of CXCL6 in secretory cells drives fibroblast collagen synthesis and is associated with increased mortality in idiopathic pulmonary fibrosis. Eur Respir J 2024; 63:2300088. [PMID: 37918852 DOI: 10.1183/13993003.00088-2023] [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: 01/14/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
Abstract
RATIONALE Recent data suggest that the localisation of airway epithelial cells in the distal lung in idiopathic pulmonary fibrosis (IPF) may drive pathology. We set out to discover whether chemokines expressed in these ectopic airway epithelial cells may contribute to the pathogenesis of IPF. METHODS We analysed whole lung and single-cell transcriptomic data obtained from patients with IPF. In addition, we measured chemokine levels in blood, bronchoalveolar lavage (BAL) of IPF patients and air-liquid interface cultures. We employed ex vivo donor and IPF lung fibroblasts and an animal model of pulmonary fibrosis to test the effects of chemokine signalling on fibroblast function. RESULTS By analysis of whole-lung transcriptomics, protein and BAL, we discovered that CXCL6 (a member of the interleukin-8 family) was increased in patients with IPF. Elevated CXCL6 levels in the BAL of two cohorts of patients with IPF were associated with poor survival (hazard ratio of death or progression 1.89, 95% CI 1.16-3.08; n=179, p=0.01). By immunostaining and single-cell RNA sequencing, CXCL6 was detected in secretory cells. Administration of mCXCL5 (LIX, murine CXCL6 homologue) to mice increased collagen synthesis with and without bleomycin. CXCL6 increased collagen I levels in donor and IPF fibroblasts 4.4-fold and 1.7-fold, respectively. Both silencing of and chemical inhibition of CXCR1/2 blocked the effects of CXCL6 on collagen, while overexpression of CXCR2 increased collagen I levels 4.5-fold in IPF fibroblasts. CONCLUSIONS CXCL6 is expressed in ectopic airway epithelial cells. Elevated levels of CXCL6 are associated with IPF mortality. CXCL6-driven collagen synthesis represents a functional consequence of ectopic localisation of airway epithelial cells in IPF.
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Affiliation(s)
- Harinath Bahudhanapati
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Denotes equal contribution
| | - Jiangning Tan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Denotes equal contribution
| | - Rosa Marie Apel
- Fraunhofer ITEM, Hannover, Germany
- DZL BREATH, Hannover, Germany
| | - Benjamin Seeliger
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Centre for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover, Hannover, Germany
| | - Jonas Schupp
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Centre for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover, Hannover, Germany
| | - Xiaoyun Li
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel I Sullivan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Sembrat
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Pulmonary, Critical Care and Sleep Medicine, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eleanor Valenzi
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nilay Mitash
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ricardo Hernandez Pineda
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chetan Jawale
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Partha Biswas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Tedrow
- Norman Regional Health System, Norman, OK, USA
| | - Taylor Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wim A Wuyts
- Unit for Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - John F McDyer
- Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kevin F Gibson
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Melanie Königshoff
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yingze Zhang
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mehdi Nouraie
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Antje Prasse
- Fraunhofer ITEM, Hannover, Germany
- DZL BREATH, Hannover, Germany
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Centre for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover, Hannover, Germany
- Denotes equal contribution
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Denotes equal contribution
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8
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Casanova NG, Camp SM, Gonzalez-Garay ML, Batai K, Garman L, Montgomery CG, Ellis N, Kittles R, Bime C, Hsu AP, Holland S, Lussier YA, Karnes J, Sweiss N, Maier LA, Koth L, Moller DR, Kaminski N, Garcia JGN. Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects. EUROPEAN JOURNAL OF RESPIRATORY MEDICINE 2023; 5:359-371. [PMID: 38390497 PMCID: PMC10883688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Background A limited pool of SNPs are linked to the development and severity of sarcoidosis, a systemic granulomatous inflammatory disease. By integrating genome-wide association studies (GWAS) data and expression quantitative trait loci (eQTL) single nuclear polymorphisms (SNPs), we aimed to identify novel sarcoidosis SNPs potentially influencing the development of complicated sarcoidosis. Methods A GWAS (Affymetrix 6.0) involving 209 African-American (AA) and 193 European-American (EA, 75 and 51 complicated cases respectively) and publicly-available GWAS controls (GAIN) was utilized. Annotation of multi-tissue eQTL SNPs present on the GWAS created a pool of ~46,000 eQTL SNPs examined for association with sarcoidosis risk and severity (Logistic Model, Plink). The most significant EA/AA eQTL SNPs were genotyped in a sarcoidosis validation cohort (n=1034) and cross-validated in two independent GWAS cohorts. Results No single GWAS SNP achieved significance (p<1x10-8), however, analysis of the eQTL/GWAS SNP pool yielded 621 eQTL SNPs (p<10-4) associated with 730 genes that highlighted innate immunity, MHC Class II, and allograft rejection pathways with multiple SNPs validated in an independent sarcoidosis cohort (105 SNPs analyzed) (NOTCH4, IL27RA, BTNL2, ANXA11, HLA-DRB1). These studies confirm significant association of eQTL/GWAS SNPs in EAs and AAs with sarcoidosis risk and severity (complicated sarcoidosis) involving HLA region and innate immunity. Conclusion Despite the challenge of deciphering the genetic basis for sarcoidosis risk/severity, these results suggest that integrated eQTL/GWAS approaches may identify novel variants/genes and support the contribution of dysregulated innate immune responses to sarcoidosis severity.
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Affiliation(s)
- Nancy G Casanova
- Department of Molecular Medicine, Univeristy of Florida, Scripps, Jupiter FL, USA
| | - Sara M Camp
- Center for Inflammation Science and Systems Medicine, University of Florida, Wertheim Scripps Research Institute, Jupiter FL, USA
| | - Manuel L Gonzalez-Garay
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Ken Batai
- Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lori Garman
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | - Nathan Ellis
- University of Arizona Cancer Center, Tucson, AZ, USA
| | - Rick Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Christian Bime
- Department of Medicine University of Arizona, Tucson, AZ, USA
| | - Amy P Hsu
- National Institute of Allergy and Infectious Diseases. National Institutes of Health, USA
| | - Steven Holland
- National Institute of Allergy and Infectious Diseases. National Institutes of Health, USA
| | - Yves A Lussier
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Jason Karnes
- Department of Pharmacology, University of Arizona, College of Pharmacy, Tucson, AZ, USA
| | - Nadera Sweiss
- Department of Medicine University of Illinois, Chicago, IL, USA
| | - Lisa A Maier
- Department of Medicine National Jewish Health, University of Colorado, Denver, CO, USA
| | - Laura Koth
- Department of Medicine University of California San Francisco, San Francisco, CA, US, USA
| | - David R Moller
- Department of Medicine Johns Hopkins University School of Medicine, Baltimore Maryland, USA
| | - Naftali Kaminski
- Department of Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Joe G N Garcia
- Center for Inflammation Science and Systems Medicine, University of Florida, Wertheim Scripps Research Institute, Jupiter FL, USA
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9
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Trempus CS, Papas BN, Sifre MI, Bortner CD, Scappini E, Tucker CJ, Xu X, Johnson KL, Deterding LJ, Williams JG, Johnson DJ, Li JL, Sutton D, Ganta C, Mahapatra D, Arif M, Basu A, Pommerolle L, Cinar R, Perl AK, Garantziotis S. Functional Pdgfra fibroblast heterogeneity in normal and fibrotic mouse lung. JCI Insight 2023; 8:e164380. [PMID: 37824216 PMCID: PMC10721331 DOI: 10.1172/jci.insight.164380] [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: 08/09/2022] [Accepted: 10/06/2023] [Indexed: 10/14/2023] Open
Abstract
Aberrant fibroblast function plays a key role in the pathogenesis of idiopathic pulmonary fibrosis, a devastating disease of unrelenting extracellular matrix deposition in response to lung injury. Platelet-derived growth factor α-positive (Pdgfra+) lipofibroblasts (LipoFBs) are essential for lung injury response and maintenance of a functional alveolar stem cell niche. Little is known about the effects of lung injury on LipoFB function. Here, we used single-cell RNA-Seq (scRNA-Seq) technology and PdgfraGFP lineage tracing to generate a transcriptomic profile of Pdgfra+ fibroblasts in normal and injured mouse lungs 14 days after bleomycin exposure, generating 11 unique transcriptomic clusters that segregated according to treatment. While normal and injured LipoFBs shared a common gene signature, injured LipoFBs acquired fibrogenic pathway activity with an attenuation of lipogenic pathways. In a 3D organoid model, injured Pdgfra+ fibroblast-supported organoids were morphologically distinct from those cultured with normal fibroblasts, and scRNA-Seq analysis suggested distinct transcriptomic changes in alveolar epithelia supported by injured Pdgfra+ fibroblasts. In summary, while LipoFBs in injured lung have not migrated from their niche and retain their lipogenic identity, they acquire a potentially reversible fibrogenic profile, which may alter the kinetics of epithelial regeneration and potentially contribute to dysregulated repair, leading to fibrosis.
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Affiliation(s)
| | | | | | | | | | | | - Xin Xu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Katina L. Johnson
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Leesa J. Deterding
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Jason G. Williams
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | | | | | - Deloris Sutton
- Comparative & Molecular Pathogenesis Branch, National Institute of Environmental Health Sciences, Division of Translational Toxicology, Research Triangle Park, North Carolina, USA
| | - Charan Ganta
- Comparative & Molecular Pathogenesis Branch, National Institute of Environmental Health Sciences, Division of Translational Toxicology, Research Triangle Park, North Carolina, USA
- Inotiv, Research Triangle Park, North Carolina, USA
| | | | - Muhammad Arif
- Section on Fibrotic Disorders, and
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland, USA
| | | | | | | | - Anne K. Perl
- Division of Pulmonary Biology, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
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10
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Lee SH, Lee CJ, Kang Y, Park JM, Lee JH. A randomized trial of genotype-guided perindopril use. J Hypertens 2023; 41:1768-1774. [PMID: 37602458 DOI: 10.1097/hjh.0000000000003536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
OBJECTIVE Cough caused by angiotensin-converting enzyme inhibitors (ACEIs) limits their clinical application and cardiovascular benefits. This randomized trial investigated whether genotype-guided perindopril use could reduce drug-related cough in 20 to 79-year-old individuals with hypertension. METHODS After screening 120 patients and randomization, 68 were assigned to genotyping ( n = 41) and control ( n = 27) groups. NELL1 p.Arg382Trp (rs8176786) and intron (rs10766756) genotype information was used to subdivide the genotyping group into high-risk and low-risk subgroups with at least one or no risk alleles for ACEI-related cough, respectively. The high-risk subgroup received candesartan (8 mg/day) for 6 weeks, whereas the low-risk subgroup received perindopril (4 mg/day). The control group, which was not genotyped, received perindopril (4 mg/day). The primary outcome variables were cough and moderate/severe cough; the secondary outcome variable was any adverse event. RESULTS During the 6-week period, the risk of cough was lower in the genotyping group than in the control group [five (12.2%) and nine (33.3%) participants, respectively; hazard ratio: 0.25; log-rank P = 0.017]. The moderate/severe cough risk was also lower in the genotyping group [one (2.4%) and five (18.5%) participants, respectively; hazard ratio: 0.12; log-rank P = 0.025]. Differences in cough (hazard ratio: 0.56; log-rank P = 0.32) and moderate/severe cough risk (hazard ratio: 0.26; log-rank P = 0.19) between the low-risk and control groups were not significant. The risk of total adverse events was similar between any two groups. CONCLUSION Cough risk was lower during genotype-guided treatment than during conventional treatment. These results support the utility of NELL1 variant data in clinical decision making to personalize renin-angiotensin system blocker therapy use. TRIAL REGISTRATION ClinicalTrials.gov number: NCT05535595 (retrospectively registered at September 7, 2022).
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Affiliation(s)
- Sang-Hak Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine
| | - Chan Joo Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine
| | - Yura Kang
- Department of Biostatistics and Computing, Graduate School, Yonsei University, Seoul
| | - Jung Mi Park
- Health Insurance Review & Assessment Service, Wonju
| | - Ji Hyun Lee
- Department of Pharmacology and Therapeutics, Kyung Hee University College of Medicine
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul, Korea
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11
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Lv W, Mao H, Ruan Y, Li S, Shimizu K, Zhang L, Zhang C. Identification and immunological characterization of PLA2G2A and cell death-associated molecular clusters in idiopathic pulmonary fibrosis. Life Sci 2023; 331:122071. [PMID: 37673297 DOI: 10.1016/j.lfs.2023.122071] [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: 05/25/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
AIMS Idiopathic pulmonary fibrosis (IPF) is a severe pulmonary interstitial pneumonia. Our study focuses on the role of PLA2 enzyme in the IPF to explore a more effective diagnosis and treatment mechanism of IPF. MAIN METHODS Transcriptome data of IPF from GEO database and bleomycin-induced pulmonary fibrosis mice were analyzed to identify PLA2 enzyme and their metabolite, lysophosphatidylcholines 18:0, in IPF. Based on PLA2G2A and PLA2G2D / PLA2G2A-associated cell death genes (PCDs), the consensus clustering analysis was used to identify the subtypes of IPF and the correlation between PLA2G2A and prognosis was analyzed. The machine learning (ML) models and artificial neural network (ANN) model was used to validate the diagnostic accuracy of PLA2s and PCDs in diagnosing IPF. The gene and protein expression of NLRP3, GSDMD, and CASP-1 was estimated in recombinant PLA2G2A protein induced MLE-12 cells. KEY FINDINGS The expression of PLA2G2D, PLA2G2A, and LPC18 significantly changed in IPF. Furtherly, PLA2G2A has a significant correlation with poor patient prognosis, which could predict the 2 or 3-years mortality rates of IPF. Two subtypes of IPF patients, identified based on PCDs, showed significant different immunoinfiltration. Recombinant PLA2G2A protein could induce the pyrotosis in the MLE-12 cell. The generalized linear model and ANN model of PLA2s or PCDs accurate diagnosis IPF. SIGNIFICANCE PLA2G2A is the most robustly associated gene with IPF among the PLA2s, which demonstrates a potential in diagnosing and prognostic value in IPF, and provides a foundation for further understanding and breakthroughs in IPF diagnosis and treatment.
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Affiliation(s)
- Weichao Lv
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hongcai Mao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yang Ruan
- Laboratory of Systematic Forest and Forest Products Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Shuaiyu Li
- Saigo Laboratory, School of Information Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Kuniyoshi Shimizu
- Laboratory of Systematic Forest and Forest Products Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Louqian Zhang
- Department of Thoratic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China.
| | - Chaofeng Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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12
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Weckerle J, Mayr CH, Fundel-Clemens K, Lämmle B, Boryn L, Thomas MJ, Bretschneider T, Luippold AH, Huber HJ, Viollet C, Rist W, Veyel D, Ramirez F, Klee S, Kästle M. Transcriptomic and Proteomic Changes Driving Pulmonary Fibrosis Resolution in Young and Old Mice. Am J Respir Cell Mol Biol 2023; 69:422-440. [PMID: 37411041 DOI: 10.1165/rcmb.2023-0012oc] [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: 01/09/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023] Open
Abstract
Bleomycin-induced pulmonary fibrosis in mice mimics major hallmarks of idiopathic pulmonary fibrosis. Yet in this model, it spontaneously resolves over time. We studied molecular mechanisms of fibrosis resolution and lung repair, focusing on transcriptional and proteomic signatures and the effect of aging. Old mice showed incomplete and delayed lung function recovery 8 weeks after bleomycin instillation. This shift in structural and functional repair in old bleomycin-treated mice was reflected in a temporal shift in gene and protein expression. We reveal gene signatures and signaling pathways that underpin the lung repair process. Importantly, the downregulation of WNT, BMP, and TGFβ antagonists Frzb, Sfrp1, Dkk2, Grem1, Fst, Fstl1, and Inhba correlated with lung function improvement. Those genes constitute a network with functions in stem cell pathways, wound, and pulmonary healing. We suggest that insufficient and delayed downregulation of those antagonists during fibrosis resolution in old mice explains the impaired regenerative outcome. Together, we identified signaling pathway molecules with relevance to lung regeneration that should be tested in-depth experimentally as potential therapeutic targets for pulmonary fibrosis.
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Affiliation(s)
| | | | | | - Bärbel Lämmle
- Global Computational Biology and Digital Sciences, and
| | | | | | - Tom Bretschneider
- Department of Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany; and
| | - Andreas H Luippold
- Department of Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany; and
| | | | | | - Wolfgang Rist
- Department of Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany; and
| | - Daniel Veyel
- Department of Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany; and
| | - Fidel Ramirez
- Global Computational Biology and Digital Sciences, and
| | - Stephan Klee
- Department of Immunology and Respiratory Disease Research
| | - Marc Kästle
- Department of Immunology and Respiratory Disease Research
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13
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Bonatti M, Pitozzi V, Caruso P, Pontis S, Pittelli MG, Frati C, Mangiaracina C, Lagrasta CAM, Quaini F, Cantarella S, Ottonello S, Villetti G, Civelli M, Montanini B, Trevisani M. Time-course transcriptome analysis of a double challenge bleomycin-induced lung fibrosis rat model uncovers ECM homoeostasis-related translationally relevant genes. BMJ Open Respir Res 2023; 10:e001476. [PMID: 37730279 PMCID: PMC10510891 DOI: 10.1136/bmjresp-2022-001476] [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: 09/28/2022] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is an irreversible disorder with a poor prognosis. The incomplete understanding of IPF pathogenesis and the lack of accurate animal models is limiting the development of effective treatments. Thus, the selection of clinically relevant animal models endowed with similarities with the human disease in terms of lung anatomy, cell biology, pathways involved and genetics is essential. The bleomycin (BLM) intratracheal murine model is the most commonly used preclinical assay to evaluate new potential therapies for IPF. Here, we present the findings derived from an integrated histomorphometric and transcriptomic analysis to investigate the development of lung fibrosis in a time-course study in a BLM rat model and to evaluate its translational value in relation to IPF. METHODS Rats were intratracheally injected with a double dose of BLM (days 0-4) and sacrificed at days 7, 14, 21, 28 and 56. Histomorphometric analysis of lung fibrosis was performed on left lung sections. Transcriptome profiling by RNAseq was performed on the right lung lobes and results were compared with nine independent human gene-expression IPF studies. RESULTS The histomorphometric and transcriptomic analyses provided a detailed overview in terms of temporal gene-expression regulation during the establishment and repair of the fibrotic lesions. Moreover, the transcriptomic analysis identified three clusters of differentially coregulated genes whose expression was modulated in a time-dependent manner in response to BLM. One of these clusters, centred on extracellular matrix (ECM)-related process, was significantly correlated with histological parameters and gene sets derived from human IPF studies. CONCLUSIONS The model of lung fibrosis presented in this study lends itself as a valuable tool for preclinical efficacy evaluation of new potential drug candidates. The main finding was the identification of a group of persistently dysregulated genes, mostly related to ECM homoeostasis, which are shared with human IPF.
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Affiliation(s)
- Martina Bonatti
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Department of Medicine Solna (MedS) and Center for Molecular Medicine (CMM), Karolinska Institutet, Solna, Sweden
| | - Vanessa Pitozzi
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Paola Caruso
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Silvia Pontis
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | | | - Caterina Frati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | - Federico Quaini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simona Cantarella
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- DKFZ - German Cancer Research Center, Heidelberg, Germany
| | - Simone Ottonello
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gino Villetti
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Maurizio Civelli
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Barbara Montanini
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, Parma, Italy
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14
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Lu W, Sun C, Hou J. Predicting key gene related to immune infiltration and myofibroblast-like valve interstitial cells in patients with calcified aortic valve disease based on bioinformatics analysis. J Thorac Dis 2023; 15:3726-3740. [PMID: 37559614 PMCID: PMC10407485 DOI: 10.21037/jtd-23-72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/09/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Calcified aortic valve disease (CAVD) is the most prevalent valvular disease that can be treated only through valve replacement. We aimed to explore potential biomarkers and the role of immune cell infiltration in CAVD progression through bioinformatics analysis. METHODS Differentially ex-pressed genes (DEGs) were screened out based on three microarray datasets: GSE12644, GSE51472 and GSE83453. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to evaluate gene expression differences. Machine learning algorithms and DEGs were used to screen key gene. We used CIBERSORT to evaluate the immune cell infiltration of CAVD and evaluated the correlation between the biomarkers and infiltrating immune cells. We also compared bioinformatics analysis results with the valve interstitial cells (VICs) gene expression in single-cell RNA sequencing. RESULTS Collagen triple helix repeat containing 1 (CTHRC1) was identified as the key gene of CAVD. We identified a cell subtype valve interstitial cells-fibroblast, which was closely associated with fibro-calcific progress of aortic valve. CTHRC1 highly expressed in the VIC subpopulation. Immune infiltration analysis demonstrated that mast cells, B cells, dendritic cells and eosinophils were involved in pathogenesis of CAVD. Correlation analysis demonstrated that CTHRC1 was correlated with mast cells mostly. CONCLUSIONS In summary, the study suggested that CTHRC1 was a key gene of CAVD and CTHRC1 might participate in the potential molecular pathways involved in the connection between infiltrating immune cells and myofibroblast phenotype VICs.
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Affiliation(s)
- Wenyuan Lu
- Cardiac Surgery Centre, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Sun
- Cardiac Surgery Centre, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianfeng Hou
- Cardiac Surgery Centre, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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15
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Jaiswal A, Rehman R, Dutta J, Singh S, Ray A, Shridhar M, Jaisankar J, Bhatt M, Khandelwal D, Sahoo B, Ram A, Mabalirajan U. Cellular Distribution of Secreted Phospholipase A2 in Lungs of IPF Patients and Its Inhibition in Bleomycin-Induced Pulmonary Fibrosis in Mice. Cells 2023; 12:cells12071044. [PMID: 37048117 PMCID: PMC10092981 DOI: 10.3390/cells12071044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/29/2023] [Indexed: 04/03/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease with a very poor prognosis as it has a 2.5 to 5 years mean survival after proper diagnosis. Even nintedanib and pirfenidone cannot halt the progression, though they slow the progression of IPF. Hence, there is a need to understand the novel pathophysiology. Phospholipase A2 (PLA2) could be the ideal candidate to study in IPF, as they have a role in both inflammation and fibrosis. In the present study, we have shown the expression profile of various secretory Phospholipase A2 (PLA2) isoforms by analyzing publicly available transcriptome data of single cells from the lungs of healthy individuals and IPF patients. Among 11 members of sPLA2, PLA2G2A is found to be increased in the fibroblasts and mesothelial cells while PLA2G5 is found to be increased in the fibroblasts of IPF patients. We identified a subset of fibroblasts expressing high PLA2G2A with moderate expression of PLA2G5 and which are specific to IPF only; we named it as PLA2G2A+ IPF fibroblast. Pathway analysis revealed that these PLA2G2A+ IPF fibroblast have upregulation of both inflammatory and fibrosis-related pathways like the TGF-β signaling pathway, IL-17 signaling, the arachidonic acid metabolism pathway and ECM-receptor interaction. In addition to this, we found elevated levels of sPLA2-IIA in plasma samples of IPF patients in our cohort. PLA2G3, PLA2G10 and PLA2G12B are found in to be increased in certain epithelial cells of IPF patients. Thus, these findings indicate that these five isoforms have a disease-dominant role along with innate immune roles as these isoforms are found predominantly in structural cells of IPF patients. Further, we have targeted sPLA2 in mice model of bleomycin-induced lung fibrosis by pBPB, a known sPLA2 inhibitor. pBPB treatment attenuated lung fibrosis induced by bleomycin along with a reduction in TGF-β and deposition of extracellular matrix in lung. Thus, these findings indicate that these sPLA2 isoforms especially PLA2G2A may serve as a therapeutic target in lung fibrosis.
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16
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Age-associated microenvironmental changes highlight the role of PDGF-C in ER + breast cancer metastatic relapse. NATURE CANCER 2023; 4:468-484. [PMID: 36914817 PMCID: PMC10132974 DOI: 10.1038/s43018-023-00525-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 02/07/2023] [Indexed: 03/16/2023]
Abstract
Patients with estrogen receptor (ER)-positive breast cancer are at risk of metastatic relapse for decades after primary tumor resection and treatment, a consequence of dormant disseminated tumor cells (DTCs) reawakening at secondary sites. Here we use syngeneic ER+ mouse models in which DTCs display a dormant phenotype in young mice but accelerated metastatic outgrowth in an aged or fibrotic microenvironment. In young mice, low-level Pdgfc expression by ER+ DTCs is required for their maintenance in secondary sites but is insufficient to support development of macrometastases. By contrast, the platelet-derived growth factor (PDGF)-Chi environment of aging or fibrotic lungs promotes DTC proliferation and upregulates tumor cell Pdgfc expression stimulating further stromal activation, events that can be blocked by pharmacological inhibition of PDGFRα or with a PDGF-C-blocking antibody. These results highlight the role of the changing microenvironment in regulating DTC outgrowth and the opportunity to target PDGF-C signaling to limit metastatic relapse in ER+ breast cancer.
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17
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Bueno M, Calyeca J, Khaliullin T, Miller MP, Alvarez D, Rosas L, Brands J, Baker C, Nasser A, Shulkowski S, Mathien A, Uzoukwu N, Sembrat J, Mays BG, Fiedler K, Hahn SA, Salvatore SR, Schopfer FJ, Rojas M, Sandner P, Straub AC, Mora AL. CYB5R3 in type II alveolar epithelial cells protects against lung fibrosis by suppressing TGF-β1 signaling. JCI Insight 2023; 8:e161487. [PMID: 36749633 PMCID: PMC10077481 DOI: 10.1172/jci.insight.161487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023] Open
Abstract
Type II alveolar epithelial cell (AECII) redox imbalance contributes to the pathogenesis of idiopathic pulmonary fibrosis (IPF), a deadly disease with limited treatment options. Here, we show that expression of membrane-bound cytochrome B5 reductase 3 (CYB5R3), an enzyme critical for maintaining cellular redox homeostasis and soluble guanylate cyclase (sGC) heme iron redox state, is diminished in IPF AECIIs. Deficiency of CYB5R3 in AECIIs led to sustained activation of the pro-fibrotic factor TGF-β1 and increased susceptibility to lung fibrosis. We further show that CYB5R3 is a critical regulator of ERK1/2 phosphorylation and the sGC/cGMP/protein kinase G axis that modulates activation of the TGF-β1 signaling pathway. We demonstrate that sGC agonists (BAY 41-8543 and BAY 54-6544) are effective in reducing the pulmonary fibrotic outcomes of in vivo deficiency of CYB5R3 in AECIIs. Taken together, these results show that CYB5R3 in AECIIs is required to maintain resilience after lung injury and fibrosis and that therapeutic manipulation of the sGC redox state could provide a basis for treating fibrotic conditions in the lung and beyond.
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Affiliation(s)
- Marta Bueno
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jazmin Calyeca
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Timur Khaliullin
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Megan P. Miller
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Diana Alvarez
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lorena Rosas
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Judith Brands
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christian Baker
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amro Nasser
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephanie Shulkowski
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - August Mathien
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nneoma Uzoukwu
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Sembrat
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brenton G. Mays
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kaitlin Fiedler
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott A. Hahn
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Francisco J. Schopfer
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Pharmacology and Chemical Biology
- Pittsburgh Liver Research Center (PLRC), and
- Center for Metabolism and Mitochondrial Medicine (C3M), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mauricio Rojas
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Peter Sandner
- Bayer Pharmaceuticals Wuppertal, Germany
- Hannover Medical School, Hannover, Germany
| | | | - Ana L. Mora
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
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18
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Klee S, Picart-Armada S, Wenger K, Birk G, Quast K, Veyel D, Rist W, Violet C, Luippold A, Haslinger C, Thomas M, Fernandez-Albert F, Kästle M. Transcriptomic and proteomic profiling of young and old mice in the bleomycin model reveals high similarity. Am J Physiol Lung Cell Mol Physiol 2023; 324:L245-L258. [PMID: 36625483 DOI: 10.1152/ajplung.00253.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The most common preclinical, in vivo model to study lung fibrosis is the bleomycin-induced lung fibrosis model in 2- to 3-mo-old mice. Although this model resembles key aspects of idiopathic pulmonary fibrosis (IPF), there are limitations in its predictability for the human disease. One of the main differences is the juvenile age of animals that are commonly used in experiments, resembling humans of around 20 yr. Because IPF patients are usually older than 60 yr, aging appears to play an important role in the pathogenesis of lung fibrosis. Therefore, we compared young (3 months) and old mice (21 months) 21 days after intratracheal bleomycin instillation. Analyzing lung transcriptomics (mRNAs and miRNAs) and proteomics, we found most pathways to be similarly regulated in young and old mice. However, old mice show imbalanced protein homeostasis as well as an increased inflammatory state in the fibrotic phase compared to young mice. Comparisons with published human transcriptomic data sets (GSE47460, GSE32537, and GSE24206) revealed that the gene signature of old animals correlates significantly better with IPF patients, and it also turned human healthy individuals better into "IPF patients" using an approach based on predictive disease modeling. Both young and old animals show similar molecular hallmarks of IPF in the bleomycin-induced lung fibrosis model, although old mice more closely resemble several features associated with IPF in comparison to young animals.
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Affiliation(s)
- Stephan Klee
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sergio Picart-Armada
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kathrin Wenger
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gerald Birk
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Karsten Quast
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Daniel Veyel
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Wolfgang Rist
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Coralie Violet
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Andreas Luippold
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christian Haslinger
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthew Thomas
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Francesc Fernandez-Albert
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Marc Kästle
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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19
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Sieber P, Schäfer A, Lieberherr R, Caimi SL, Lüthi U, Ryge J, Bergmann JH, Le Goff F, Stritt M, Blattmann P, Renault B, Rammelt P, Sempere B, Freti D, Studer R, White ES, Birker-Robaczewska M, Boucher M, Nayler O. NF-κB drives epithelial-mesenchymal mechanisms of lung fibrosis in a translational lung cell model. JCI Insight 2023; 8:154719. [PMID: 36520540 PMCID: PMC9977429 DOI: 10.1172/jci.insight.154719] [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: 09/03/2021] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
In the progression phase of idiopathic pulmonary fibrosis (IPF), the normal alveolar structure of the lung is lost and replaced by remodeled fibrotic tissue and by bronchiolized cystic airspaces. Although these are characteristic features of IPF, knowledge of specific interactions between these pathological processes is limited. Here, the interaction of lung epithelial and lung mesenchymal cells was investigated in a coculture model of human primary airway epithelial cells (EC) and lung fibroblasts (FB). Single-cell RNA sequencing revealed that the starting EC population was heterogenous and enriched for cells with a basal cell signature. Furthermore, fractions of the initial EC and FB populations adopted distinct pro-fibrotic cell differentiation states upon cocultivation, resembling specific cell populations that were previously identified in lungs of patients with IPF. Transcriptomic analysis revealed active NF-κB signaling early in the cocultured EC and FB, and the identified NF-κB expression signatures were found in "HAS1 High FB" and "PLIN2+ FB" populations from IPF patient lungs. Pharmacological blockade of NF-κB signaling attenuated specific phenotypic changes of EC and prevented FB-mediated interleukin-6, interleukin-8, and CXC chemokine ligand 6 cytokine secretion, as well as collagen α-1(I) chain and α-smooth muscle actin accumulation. Thus, we identified NF-κB as a potential mediator, linking epithelial pathobiology with fibrogenesis.
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Affiliation(s)
| | - Anny Schäfer
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | | | | | - Urs Lüthi
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | - Jesper Ryge
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | | | | | - Manuel Stritt
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | | | | | | | - Bruno Sempere
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | - Diego Freti
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | - Rolf Studer
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
| | - Eric S. White
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | | | - Oliver Nayler
- Idorsia Pharmaceuticals Ltd., Allschwil, Switzerland
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20
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Hoffman ET, Uhl FE, Asarian L, Deng B, Becker C, Uriarte JJ, Downs I, Young B, Weiss DJ. Regional and disease specific human lung extracellular matrix composition. Biomaterials 2023; 293:121960. [PMID: 36580718 PMCID: PMC9868084 DOI: 10.1016/j.biomaterials.2022.121960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Chronic lung diseases, such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), are characterized by regional extracellular matrix (ECM) remodeling which contributes to disease progression. Previous proteomic studies on whole decellularized lungs have provided detailed characterization on the impact of COPD and IPF on total lung ECM composition. However, such studies are unable to determine the differences in ECM composition between individual anatomical regions of the lung. Here, we employ a post-decellularization dissection method to compare the ECM composition of whole decellularized lungs (wECM) and specific anatomical lung regions, including alveolar-enriched ECM (aECM), airway ECM (airECM), and vasculature ECM (vECM), between non-diseased (ND), COPD, and IPF human lungs. We demonstrate, using mass spectrometry, that individual regions possess a unique ECM signature characterized primarily by differences in collagen composition and basement-membrane associated proteins, including ECM glycoproteins. We further demonstrate that both COPD and IPF lead to alterations in lung ECM composition in a region-specific manner, including enrichment of type-III collagen and fibulin in IPF aECM. Taken together, this study provides methodology for future studies, including isolation of region-specific lung biomaterials, as well as a dataset that may be applied for the identification of novel ECM targets for therapeutics.
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Affiliation(s)
- Evan T. Hoffman
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Franziska E. Uhl
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
| | - Loredana Asarian
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Bin Deng
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Chloe Becker
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Juan J. Uriarte
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Isaac Downs
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Brad Young
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Daniel J. Weiss
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
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21
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Usual interstitial pneumonia as a stand-alone diagnostic entity: the case for a paradigm shift? THE LANCET. RESPIRATORY MEDICINE 2023; 11:188-196. [PMID: 36640788 DOI: 10.1016/s2213-2600(22)00475-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
Usual interstitial pneumonia (UIP) is characterised by a distinctive morphological and radiological appearance that was considered the pathognomonic hallmark of idiopathic pulmonary fibrosis (IPF). However, this peculiar lung remodelling pattern is also seen in other fibrotic interstitial lung diseases, including hypersensitivity pneumonitis, and connective tissue diseases. In this Personal View, we advocate the designation of a UIP pattern as a single, discrete diagnostic entity, amalgamating its primary form and secondary processes in disorders such as hypersensitivity pneumonitis (hypersensitivity pneumonitis with UIP), rheumatoid arthritis (rheumatoid arthritis with UIP), and others. The current separation between primary and secondary UIP is in keeping with the view that every individual interstitial lung disease must be viewed as a separate entity but does not reflect striking similarities between primary and secondary UIP in the morphological or radiological appearance, clinical behaviour, pathogenic pathways, and the efficacy of anti-fibrotic therapy. We believe that the unification of UIP as a single diagnostic entity has undeniable advantages.
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22
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Wu Y, Zhong L, Qiu L, Dong L, Yang L, Chen L. A potential three-gene-based diagnostic signature for idiopathic pulmonary fibrosis. Front Genet 2023; 13:985217. [PMID: 36685820 PMCID: PMC9857386 DOI: 10.3389/fgene.2022.985217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 11/30/2022] [Indexed: 01/09/2023] Open
Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a life-threatening disease whose etiology remains unknown. This study aims to explore diagnostic biomarkers and pathways involved in IPF using bioinformatics analysis. Methods: IPF-related gene expression datasets were retrieved and downloaded from the NCBI Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened, and weighted correlation network analysis (WGCNA) was performed to identify key module and genes. Functional enrichment analysis was performed on genes in the clinically significant module. Then least absolute shrinkage and selection operator (LASSO) logistic regression and support vector machine-recursive feature elimination (SVM-RFE) algorithms were run to screen candidate biomarkers. The expression and diagnostic value of the biomarkers in IPF were further validated in external test datasets (GSE110147). Results: 292 samples and 1,163 DEGs were screened to construct WGCNA. In WGCNA, the blue module was identified as the key module, and 59 genes in this module correlated highly with IPF. Functional enrichment analysis of blue module genes revealed the importance of extracellular matrix-associated pathways in IPF. IL13RA2, CDH3, and COMP were identified as diagnostic markers of IPF via LASSO and SVM-RFE. These genes showed good diagnostic value for IPF and were significantly upregulated in IPF. Conclusion: This study indicates that IL13RA2, CDH3, and COMP could serve as diagnostic signature for IPF and might offer new insights in the underlying diagnosis of IPF.
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Affiliation(s)
- Yi Wu
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
| | - Lin Zhong
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
| | - Li Qiu
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
| | - Liqun Dong
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
| | - Lin Yang
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China,*Correspondence: Lin Yang, ; Lina Chen,
| | - Lina Chen
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China,*Correspondence: Lin Yang, ; Lina Chen,
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23
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Wan X, Xiao Y, Tian X, Lu Y, Chu H. Selective depletion of CD11b-positive monocytes/macrophages potently suppresses bleomycin-induced pulmonary fibrosis. Int Immunopharmacol 2023; 114:109570. [PMID: 36700767 DOI: 10.1016/j.intimp.2022.109570] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/09/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
The understanding of pathogenesis underlying idiopathic pulmonary fibrosis (IPF) is still limited presently. Monocytes or macrophages are involved in progression of the pulmonary injury and repair. The aim of this study is to investigate the roles of CD11b+ monocytes/macrophages in the progression of pulmonary fibrosis. In this study, the expression levels of CD11B gene and inflammatory genes in the IPF patients are evaluated using the available datasets. CD11b cells are conditionally depleted in a CD11b-diptheria toxin receptor (CD11b-DTR) mouse by administration of diptheria toxin (DT). Pulmonary fibrosis in mice is induced using intranasalbleomycin. The mRNAs and proteins expression in lung tissues are determined by quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence (IF) staining and Western-blot assays. It shows that the expression of CD11B mRNA is up-regulated in fibrotic lungs and alveolar macrophages of IPF patients and bleomycin-treated rodents. Selective depletion of CD11b+ monocytes/macrophages in CD11b-DTR mice potently halts bleomycin-induced pulmonary fibrosis progression. CD11b depletion inhibits the polarization of macrophages in the fibrotic lungs. Mechanically, CD11b deficiency represses the activation of sphingosine 1-phosphate receptor 2 (S1PR2)/sphingosine kinase 2 (SphK2) signaling during pulmonary fibrosis. In conclusion, our data suggest that CD11b+ monocytes/macrophages contribute to pulmonary fibrosis and represent a potential therapeutic target for IPF.
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Affiliation(s)
- Xiaoyu Wan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yongtao Xiao
- Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinbei Tian
- Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Lu
- Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
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24
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Papazoglou A, Huang M, Bulik M, Lafyatis A, Tabib T, Morse C, Sembrat J, Rojas M, Valenzi E, Lafyatis R. Epigenetic Regulation of Profibrotic Macrophages in Systemic Sclerosis-Associated Interstitial Lung Disease. Arthritis Rheumatol 2022; 74:2003-2014. [PMID: 35849803 PMCID: PMC9771864 DOI: 10.1002/art.42286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Systemic sclerosis-associated interstitial lung disease (SSc-ILD) is the leading cause of death in patients with SSc with unclear pathogenesis and limited treatment options. Evidence strongly supports an important role for profibrotic secreted phosphoprotein 1 (SPP1)-expressing macrophages in SSc-ILD. This study was undertaken to define the transcriptome and chromatin structural changes of SPP1 SSc-ILD macrophages in order to better understand their role in promoting fibrosis and to identify transcription factors associated with open chromatin driving their altered phenotype. METHODS We performed single-cell RNA sequencing (scRNA-Seq) on 11 explanted SSc-ILD and healthy control lung samples, as well as single-cell assay for transposase-accessible chromatin sequencing on 5 lung samples to define altered chromatin accessibility of SPP1 macrophages. We predicted transcription factors regulating SPP1 macrophages using single-cell regulatory network inference and clustering (SCENIC) and determined transcription factor binding sites associated with global alterations in SPP1 chromatin accessibility using Signac/Seurat. RESULTS We identified distinct macrophage subpopulations using scRNA-Seq analysis in healthy and SSc-ILD lungs and assessed gene expression changes during the change of healthy control macrophages into SPP1 macrophages. Analysis of open chromatin validated SCENIC predictions, indicating that microphthalmia-associated transcription factor, transcription factor EB, activating transcription factor 6, sterol regulatory element binding transcription factor 1, basic helix-loop-helix family member E40, Kruppel-like factor 6, ETS variant transcription factor 5, and/or members of the activator protein 1 family of transcription factors regulate SPP1 macrophage differentiation. CONCLUSION Our findings shed light on the underlying changes in chromatin structure and transcription factor regulation of profibrotic SPP1 macrophages in SSc-ILD. Similar alterations in SPP1 macrophages may underpin fibrosis in other organs involved in SSc and point to novel targets for the treatment of SSc-ILD, specifically targeting profibrotic macrophages.
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Affiliation(s)
- Anna Papazoglou
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melissa Bulik
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Annika Lafyatis
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University, Columbus, OH, USA
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
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25
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Moita MR, Silva MM, Diniz C, Serra M, Hoet RM, Barbas A, Simão D. Transcriptome and proteome profiling of activated cardiac fibroblasts supports target prioritization in cardiac fibrosis. Front Cardiovasc Med 2022; 9:1015473. [PMID: 36531712 PMCID: PMC9751336 DOI: 10.3389/fcvm.2022.1015473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/15/2022] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Activated cardiac fibroblasts (CF) play a central role in cardiac fibrosis, a condition associated with most cardiovascular diseases. Conversion of quiescent into activated CF sustains heart integrity upon injury. However, permanence of CF in active state inflicts deleterious heart function effects. Mechanisms underlying this cell state conversion are still not fully disclosed, contributing to a limited target space and lack of effective anti-fibrotic therapies. MATERIALS AND METHODS To prioritize targets for drug development, we studied CF remodeling upon activation at transcriptomic and proteomic levels, using three different cell sources: primary adult CF (aHCF), primary fetal CF (fHCF), and induced pluripotent stem cells derived CF (hiPSC-CF). RESULTS All cell sources showed a convergent response upon activation, with clear morphological and molecular remodeling associated with cell-cell and cell-matrix interactions. Quantitative proteomic analysis identified known cardiac fibrosis markers, such as FN1, CCN2, and Serpine1, but also revealed targets not previously associated with this condition, including MRC2, IGFBP7, and NT5DC2. CONCLUSION Exploring such targets to modulate CF phenotype represents a valuable opportunity for development of anti-fibrotic therapies. Also, we demonstrate that hiPSC-CF is a suitable cell source for preclinical research, displaying significantly lower basal activation level relative to primary cells, while being able to elicit a convergent response upon stimuli.
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Affiliation(s)
- Maria Raquel Moita
- iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Marta M. Silva
- iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Cláudia Diniz
- iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Margarida Serra
- iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - René M. Hoet
- Department of Pathology, CARIM - School of Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | | | - Daniel Simão
- iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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26
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Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging. Am J Respir Crit Care Med 2022; 206:459-475. [PMID: 35687485 DOI: 10.1164/rccm.202109-2151oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/06/2022] [Indexed: 01/10/2023] Open
Abstract
Rationale: A prevailing paradigm recognizes idiopathic pulmonary fibrosis (IPF) originating from various alveolar epithelial cell (AEC) injuries, and there is a growing appreciation of AEC aging as a key driver of the pathogenesis. Despite this progress, it is incompletely understood what main factor(s) contribute to the worsened alveolar epithelial aging in lung fibrosis. It remains a challenge how to dampen AEC aging and thereby mitigate the disease progression. Objectives: To determine the role of AEC CD38 (cluster of differentiation 38) in promoting cellular aging and lung fibrosis. Methods: We used single-cell RNA sequencing, real-time PCR, flow cytometry, and Western blotting. Measurements and Main Results: We discovered a pivotal role of CD38, a cardinal nicotinamide adenine dinucleotide (NAD) hydrolase, in AEC aging and its promotion of lung fibrosis. We found increased CD38 expression in IPF lungs that inversely correlated with the lung functions of patients. CD38 was primarily located in the AECs of human lung parenchyma and was markedly induced in IPF AECs. Similarly, CD38 expression was elevated in the AECs of fibrotic lungs of young mice and further augmented in those of old mice, which was in accordance with a worsened AEC aging phenotype and an aggravated lung fibrosis in the old animals. Mechanistically, we found that CD38 elevation downregulated intracellular NAD, which likely led to the aging promoting impairment of the NAD-dependent cellular and molecular activities. Furthermore, we demonstrated that genetic and pharmacological inactivation of CD38 improved these NAD dependent events and ameliorated bleomycin-induced lung fibrosis. Conclusions: Our study suggests targeting alveolar CD38 as a novel and effective therapeutic strategy to treat this pathology.
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Affiliation(s)
- Huachun Cui
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Na Xie
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sami Banerjee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tapan Dey
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rui-Ming Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Veena B Antony
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Victor J Thannickal
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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Towards Treatable Traits for Pulmonary Fibrosis. J Pers Med 2022; 12:jpm12081275. [PMID: 36013224 PMCID: PMC9410230 DOI: 10.3390/jpm12081275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/24/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
Interstitial lung diseases (ILD) are a heterogeneous group of disorders, of which many have the potential to lead to progressive pulmonary fibrosis. A distinction is usually made between primarily inflammatory ILD and primarily fibrotic ILD. As recent studies show that anti-fibrotic drugs can be beneficial in patients with primarily inflammatory ILD that is characterized by progressive pulmonary fibrosis, treatment decisions have become more complicated. In this perspective, we propose that the ‘treatable trait’ concept, which is based on the recognition of relevant exposures, various treatable phenotypes (disease manifestations) or endotypes (shared molecular mechanisms) within a group of diseases, can be applied to progressive pulmonary fibrosis. These targets for medical intervention can be identified through validated biomarkers and are not necessarily related to specific diagnostic labels. Proposed treatable traits are: cigarette smoking, occupational, allergen or drug exposures, excessive (profibrotic) auto- or alloimmunity, progressive pulmonary fibrosis, pulmonary hypertension, obstructive sleep apnea, tuberculosis, exercise intolerance, exertional hypoxia, and anxiety and depression. There are also several potential traits that have not been associated with relevant outcomes or for which no effective treatment is available at present: air pollution, mechanical stress, viral infections, bacterial burden in the lungs, surfactant-related pulmonary fibrosis, telomere-related pulmonary fibrosis, the rs35705950 MUC5B promoter polymorphism, acute exacerbations, gastro-esophageal reflux, dyspnea, and nocturnal hypoxia. The ‘treatable traits’ concept can be applied in new clinical trials for patients with progressive pulmonary fibrosis and could be used for developing new treatment strategies.
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Sinha S, Castillo V, Espinoza CR, Tindle C, Fonseca AG, Dan JM, Katkar GD, Das S, Sahoo D, Ghosh P. COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis. EBioMedicine 2022; 82:104185. [PMID: 35870428 PMCID: PMC9297827 DOI: 10.1016/j.ebiom.2022.104185] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In the aftermath of Covid-19, some patients develop a fibrotic lung disease, i.e., post-COVID-19 lung disease (PCLD), for which we currently lack insights into pathogenesis, disease models, or treatment options. METHODS Using an AI-guided approach, we analyzed > 1000 human lung transcriptomic datasets associated with various lung conditions using two viral pandemic signatures (ViP and sViP) and one covid lung-derived signature. Upon identifying similarities between COVID-19 and idiopathic pulmonary fibrosis (IPF), we subsequently dissected the basis for such similarity from molecular, cytopathic, and immunologic perspectives using a panel of IPF-specific gene signatures, alongside signatures of alveolar type II (AT2) cytopathies and of prognostic monocyte-driven processes that are known drivers of IPF. Transcriptome-derived findings were used to construct protein-protein interaction (PPI) network to identify the major triggers of AT2 dysfunction. Key findings were validated in hamster and human adult lung organoid (ALO) pre-clinical models of COVID-19 using immunohistochemistry and qPCR. FINDINGS COVID-19 resembles IPF at a fundamental level; it recapitulates the gene expression patterns (ViP and IPF signatures), cytokine storm (IL15-centric), and the AT2 cytopathic changes, e.g., injury, DNA damage, arrest in a transient, damage-induced progenitor state, and senescence-associated secretory phenotype (SASP). These immunocytopathic features were induced in pre-clinical COVID models (ALO and hamster) and reversed with effective anti-CoV-2 therapeutics in hamsters. PPI-network analyses pinpointed ER stress as one of the shared early triggers of both diseases, and IHC studies validated the same in the lungs of deceased subjects with COVID-19 and SARS-CoV-2-challenged hamster lungs. Lungs from tg-mice, in which ER stress is induced specifically in the AT2 cells, faithfully recapitulate the host immune response and alveolar cytopathic changes that are induced by SARS-CoV-2. INTERPRETATION Like IPF, COVID-19 may be driven by injury-induced ER stress that culminates into progenitor state arrest and SASP in AT2 cells. The ViP signatures in monocytes may be key determinants of prognosis. The insights, signatures, disease models identified here are likely to spur the development of therapies for patients with IPF and other fibrotic interstitial lung diseases. FUNDING This work was supported by the National Institutes for Health grants R01- GM138385 and AI155696 and funding from the Tobacco-Related disease Research Program (R01RG3780).
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Affiliation(s)
- Saptarshi Sinha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Vanessa Castillo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Celia R Espinoza
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ayden G Fonseca
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Gajanan D Katkar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Debashis Sahoo
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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Sinha S, Castillo V, Espinoza CR, Tindle C, Fonseca AG, Dan JM, Katkar GD, Das S, Sahoo D, Ghosh P. COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.11.28.470269. [PMID: 34873597 PMCID: PMC8647648 DOI: 10.1101/2021.11.28.470269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Background In the aftermath of Covid-19, some patients develop a fibrotic lung disease, i.e., p ost- C OVID-19 l ung d isease (PCLD), for which we currently lack insights into pathogenesis, disease models, or treatment options. Method Using an AI-guided approach, we analyzed > 1000 human lung transcriptomic datasets associated with various lung conditions using two viral pandemic signatures (ViP and sViP) and one covid lung-derived signature. Upon identifying similarities between COVID-19 and idiopathic pulmonary fibrosis (IPF), we subsequently dissected the basis for such similarity from molecular, cytopathic, and immunologic perspectives using a panel of IPF-specific gene signatures, alongside signatures of alveolar type II (AT2) cytopathies and of prognostic monocyte-driven processes that are known drivers of IPF. Transcriptome-derived findings were used to construct protein-protein interaction (PPI) network to identify the major triggers of AT2 dysfunction. Key findings were validated in hamster and human adult lung organoid (ALO) pre-clinical models of COVID-19 using immunohistochemistry and qPCR. Findings COVID-19 resembles IPF at a fundamental level; it recapitulates the gene expression patterns (ViP and IPF signatures), cytokine storm (IL15-centric), and the AT2 cytopathic changes, e.g., injury, DNA damage, arrest in a transient, damage-induced progenitor state, and senescence-associated secretory phenotype (SASP). These immunocytopathic features were induced in pre-clinical COVID models (ALO and hamster) and reversed with effective anti-CoV-2 therapeutics in hamsters. PPI-network analyses pinpointed ER stress as one of the shared early triggers of both diseases, and IHC studies validated the same in the lungs of deceased subjects with COVID-19 and SARS-CoV-2-challenged hamster lungs. Lungs from tg - mice, in which ER stress is induced specifically in the AT2 cells, faithfully recapitulate the host immune response and alveolar cytopathic changes that are induced by SARS-CoV-2. Interpretation Like IPF, COVID-19 may be driven by injury-induced ER stress that culminates into progenitor state arrest and SASP in AT2 cells. The ViP signatures in monocytes may be key determinants of prognosis. The insights, signatures, disease models identified here are likely to spur the development of therapies for patients with IPF and other fibrotic interstitial lung diseases. Funding This work was supported by the National Institutes for Health grants R01-GM138385 and AI155696 and funding from the Tobacco-Related disease Research Program (R01RG3780). One Sentence Summary Severe COVID-19 triggers cellular processes seen in fibrosing Interstitial Lung Disease. RESEARCH IN CONTEXT Evidence before this study: In its aftermath, the COVID-19 pandemic has left many survivors, almost a third of those who recovered, with a mysterious long-haul form of the disease which culminates in a fibrotic form of interstitial lung disease (post-COVID-19 ILD). Post-COVID-19 ILD remains a largely unknown entity. Currently, we lack insights into the core cytopathic features that drive this condition.Added value of this study: Using an AI-guided approach, which involves the use of sets of gene signatures, protein-protein network analysis, and a hamster model of COVID-19, we have revealed here that COVID-19 -lung fibrosis resembles IPF, the most common form of ILD, at a fundamental levelâ€"showing similar gene expression patterns in the lungs and blood, and dysfunctional AT2 processes (ER stress, telomere instability, progenitor cell arrest, and senescence). These findings are insightful because AT2 cells are known to contain an elegant quality control network to respond to intrinsic or extrinsic stress; a failure of such quality control results in diverse cellular phenotypes, of which ER stress appears to be a point of convergence, which appears to be sufficient to drive downstream fibrotic remodeling in the lung.Implications of all the available evidence: Because unbiased computational methods identified the shared fundamental aspects of gene expression and cellular processes between COVID-19 and IPF, the impact of our findings is likely to go beyond COVID-19 or any viral pandemic. The insights, tools (disease models, gene signatures, and biomarkers), and mechanisms identified here are likely to spur the development of therapies for patients with IPF and, other fibrotic interstitial lung diseases, all of whom have limited or no treatment options. To dissect the validated prognostic biomarkers to assess and track the risk of pulmonary fibrosis and develop therapeutics to halt fibrogenic progression.
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Time and phenotype-dependent transcriptome analysis in AAV-TGFβ1 and Bleomycin-induced lung fibrosis models. Sci Rep 2022; 12:12190. [PMID: 35842487 PMCID: PMC9288451 DOI: 10.1038/s41598-022-16344-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/08/2022] [Indexed: 11/19/2022] Open
Abstract
We have previously established a novel mouse model of lung fibrosis based on Adeno-associated virus (AAV)-mediated pulmonary overexpression of TGFβ1. Here, we provide an in-depth characterization of phenotypic and transcriptomic changes (mRNA and miRNA) in a head-to-head comparison with Bleomycin-induced lung injury over a 4-week disease course. The analyses delineate the temporal state of model-specific and commonly altered pathways, thereby providing detailed insights into the processes underlying disease development. They further guide appropriate model selection as well as interventional study design. Overall, Bleomycin-induced fibrosis resembles a biphasic process of acute inflammation and subsequent transition into fibrosis (with partial resolution), whereas the TGFβ1-driven model is characterized by pronounced and persistent fibrosis with concomitant inflammation and an equally complex disease phenotype as observed upon Bleomycin instillation. Finally, based on an integrative approach combining lung function data, mRNA/miRNA profiles, their correlation and miRNA target predictions, we identify putative drug targets and miRNAs to be explored as therapeutic candidates for fibrotic diseases. Taken together, we provide a comprehensive analysis and rich data resource based on RNA-sequencing, along with a strategy for transcriptome-phenotype coupling. The results will be of value for TGFβ research, drug discovery and biomarker identification in progressive fibrosing interstitial lung diseases.
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Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H. Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. JCI Insight 2022; 7:e142984. [PMID: 35420997 PMCID: PMC9220956 DOI: 10.1172/jci.insight.142984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease with limited treatment options. The role of the developmental transcription factor Sine oculis homeobox homolog 1 (SIX1) in the pathophysiology of lung fibrosis is not known. IPF lung tissue samples and IPF-derived alveolar type II cells (AT2) showed a significant increase in SIX1 mRNA and protein levels, and the SIX1 transcriptional coactivators EYA1 and EYA2 were elevated. Six1 was also upregulated in bleomycin-treated (BLM-treated) mice and in a model of spontaneous lung fibrosis driven by deletion of Telomeric Repeat Binding Factor 1 (Trf1) in AT2 cells. Conditional deletion of Six1 in AT2 cells prevented or halted BLM-induced lung fibrosis, as measured by a significant reduction in histological burden of fibrosis, reduced fibrotic mediator expression, and improved lung function. These effects were associated with increased macrophage migration inhibitory factor (MIF) in lung epithelial cells in vivo following SIX1 overexpression in BLM-induced fibrosis. A MIF promoter-driven luciferase assay demonstrated direct binding of Six1 to the 5'-TCAGG-3' consensus sequence of the MIF promoter, identifying a likely mechanism of SIX1-driven MIF expression in the pathogenesis of lung fibrosis and providing a potentially novel pathway for targeting in IPF therapy.
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Affiliation(s)
- Cory Wilson
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Tinne C.J. Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Pooja Shivshankar
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Weizen Bi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Scott D. Collum
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Nancy Wareing
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Junsuk Ko
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Tingting Weng
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Ram P. Naikawadi
- Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF, San Francisco, California, USA
| | - Paul J. Wolters
- Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF, San Francisco, California, USA
| | - Pascal Maire
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Soma S.K. Jyothula
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, UTHealth, Houston, Texas, USA
| | | | - Dewei Ren
- Methodist J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Institute, University of Rochester School of Medicine and Dentistry, KMRB G.9629, Rochester, New York, USA
| | - Howard J. Huang
- Methodist J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Burton F. Dickey
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Heide L. Ford
- Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, UTHealth, Houston, Texas, USA
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Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. Int J Mol Sci 2022; 23:ijms23105447. [PMID: 35628257 PMCID: PMC9141193 DOI: 10.3390/ijms23105447] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe fibrotic lung disease characterized by irreversible scarring of the lung parenchyma leading to dyspnea, progressive decline in lung function, and respiratory failure. We analyzed lung transcriptomic data from independent IPF cohorts using weighted gene co-expression network analysis (WGCNA) to identify gene modules based on their preservation status in these cohorts. The consensus gene modules were characterized by leveraging existing clinical and molecular data such as lung function, biological processes, pathways, and lung cell types. From a total of 32 consensus gene modules identified, two modules were found to be significantly correlated with the disease, lung function, and preserved in other IPF datasets. The upregulated gene module was enriched for extracellular matrix, collagen metabolic process, and BMP signaling while the downregulated module consisted of genes associated with tube morphogenesis, blood vessel development, and cell migration. Using a combination of connectivity-based and trait-based significance measures, we identified and prioritized 103 "hub" genes (including 25 secretory candidate biomarkers) by their similarity to known IPF genetic markers. Our validation studies demonstrate the dysregulated expression of CRABP2, a retinol-binding protein, in multiple lung cells of IPF, and its correlation with the decline in lung function.
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Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:1341. [PMID: 35456020 PMCID: PMC9027113 DOI: 10.3390/cells11081341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Antibodies are central effectors of the adaptive immune response, widespread used therapeutics, but also potentially disease-causing biomolecules. Antibody folding catalysts in the plasma cell are incompletely defined. Idiopathic pulmonary fibrosis (IPF) is a fatal chronic lung disease with increasingly recognized autoimmune features. We found elevated expression of FK506-binding protein 11 (FKBP11) in IPF lungs where FKBP11 specifically localized to antibody-producing plasma cells. Suggesting a general role in plasma cells, plasma cell-specific FKBP11 expression was equally observed in lymphatic tissues, and in vitro B cell to plasma cell differentiation was accompanied by induction of FKBP11 expression. Recombinant human FKBP11 was able to refold IgG antibody in vitro and inhibited by FK506, strongly supporting a function as antibody peptidyl-prolyl cis-trans isomerase. Induction of ER stress in cell lines demonstrated induction of FKBP11 in the context of the unfolded protein response in an X-box-binding protein 1 (XBP1)-dependent manner. While deficiency of FKBP11 increased susceptibility to ER stress-mediated cell death in an alveolar epithelial cell line, FKBP11 knockdown in an antibody-producing hybridoma cell line neither induced cell death nor decreased expression or secretion of IgG antibody. Similarly, antibody secretion by the same hybridoma cell line was not affected by knockdown of the established antibody peptidyl-prolyl isomerase cyclophilin B. The results are consistent with FKBP11 as a novel XBP1-regulated antibody peptidyl-prolyl cis-trans isomerase and indicate significant redundancy in the ER-resident folding machinery of antibody-producing hybridoma cells.
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Affiliation(s)
- Stefan Preisendörfer
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Yoshihiro Ishikawa
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; (Y.I.); (H.P.B.)
| | - Elisabeth Hennen
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Stephan Winklmeier
- Institute of Clinical Neuroimmunology, Biomedical Center and LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; (S.W.); (E.M.)
| | - Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
- Department of Respiratory Medicine, Hannover Medical School, Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Larissa Knüppel
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Isis E. Fernandez
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Leonhard Binzenhöfer
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Brenda M. Juan-Guardela
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
| | - Clemens Ruppert
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), 35392 Giessen, Germany; (C.R.); (A.G.)
| | - Andreas Guenther
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), 35392 Giessen, Germany; (C.R.); (A.G.)
| | - Marion Frankenberger
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Rudolf A. Hatz
- Thoraxchirurgisches Zentrum, Klinik für Allgemeine-, Viszeral-, Transplantations-, Gefäß- und Thoraxchirurgie, LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany;
- Asklepios Fachkliniken München-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Jürgen Behr
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
| | - Edgar Meinl
- Institute of Clinical Neuroimmunology, Biomedical Center and LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; (S.W.); (E.M.)
| | - Hans Peter Bächinger
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; (Y.I.); (H.P.B.)
| | - Oliver Eickelberg
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Claudia A. Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
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Lee CJ, Choi B, Pak H, Park JM, Lee JH, Lee SH. Genetic Variants Associated with Adverse Events after Angiotensin-Converting Enzyme Inhibitor Use: Replication after GWAS-Based Discovery. Yonsei Med J 2022; 63:342-348. [PMID: 35352885 PMCID: PMC8965428 DOI: 10.3349/ymj.2022.63.4.342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Angiotensin-converting enzyme inhibitors (ACEIs) are medications generally prescribed for patients with high cardiovascular risk; however, they are suboptimally used due to frequent adverse events (AEs). The present study aimed to identify and replicate the genetic variants associated with ACEI-related AEs in the Korean population. MATERIALS AND METHODS A two-stage approach employing genome-wide association study (GWAS)-based discovery and replication through target sequencing was used. In total, 1300 individuals received ACEIs from 2001 to 2007; among these, 228 were selected for GWAS. An additional 336 patients were selected for replication after screening 1186 subjects treated from 2008 to 2018. Candidate genes for target sequencing were selected based on the present GWAS, previous GWASs, and data from the PharmGKB database. Furthermore, association analyses were performed between no AE and AE or cough groups after target sequencing. RESULTS Five genes, namely CRIM1, NELL1, CACNA1D, VOPP1, and MYBPC1, were identified near variants associated with ACEI-related AEs. During target sequencing of 34 candidate genes, six single-nucleotide polymorphisms (SNPs; rs5224, rs8176786, rs10766756, rs561868018, rs4974539, and rs10946364) were replicated for association with all ACEI-related AEs. Four of these SNPs and rs147912715 exhibited associations with ACEI-related cough, whereas four SNPs (rs5224, rs81767786, rs10766756, and rs4974539 near BDKRB2, NELL1, NELL1 intron, and CPN2, respectively) were significantly associated with both categories of AEs. CONCLUSION Several variants, including novel and known variants, were successfully replicated and found to have associations with ACEI-related AEs. These results provide rare and clinically relevant information for safer use of ACEIs.
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Affiliation(s)
- Chan Joo Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Bogeum Choi
- Kyung Hee University College of Medicine, Seoul, Korea
| | - Hayeon Pak
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Korea
| | - Jung Mi Park
- Department of Biostatistics and Computing, Graduate School, Yonsei University, Seoul, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, Kyung Hee University College of Medicine, Seoul, Korea
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul, Korea.
| | - Sang-Hak Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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Zheng P, Sun S, Wang J, Cheng ZJ, Lei KC, Xue M, Zhang T, Huang H, Zhang XD, Sun B. Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis. Cell Mol Life Sci 2022; 79:66. [PMID: 35015148 PMCID: PMC11075137 DOI: 10.1007/s00018-021-04094-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.
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Affiliation(s)
- Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Shixue Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Jingxian Wang
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Province Key Laboratory of Regenerative Medicine, Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guizhou, 550025, China
| | - Zhangkai Jason Cheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Mingshan Xue
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Teng Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Huimin Huang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | | | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
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Shi B, Wu Y, Chen H, Ding J, Qi J. Understanding of mouse and human bladder at single-cell resolution: integrated analysis of trajectory and cell-cell interactive networks based on multiple scRNA-seq datasets. Cell Prolif 2021; 55:e13170. [PMID: 34951074 PMCID: PMC8780900 DOI: 10.1111/cpr.13170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/11/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives To elaborately decipher the mouse and human bladders at single‐cell levels. Materials and Methods We collected more than 50,000 cells from multiple datasets and created, up to date, the largest integrated bladder datasets. Pseudotime trajectory of urothelium and interstitial cells, as well as dynamic cell‐cell interactions, was investigated. Biological activity scores and different roles of signaling pathways between certain cell clusters were also identified. Results The glucose score was significantly high in most urothelial cells, while the score of H3 acetylation was roughly equally distributed across all cell types. Several genes via a pseudotime pattern in mouse (Car3, Dkk2, Tnc, etc.) and human (FBLN1, S100A10, etc.) were discovered. S100A6, TMSB4X, and typical uroplakin genes seemed as shared pseudotime genes for urothelial cells in both human and mouse datasets. In combinational mouse (n = 16,688) and human (n = 22,080) bladders, we verified 1,330 and 1,449 interactive ligand‐receptor pairs, respectively. The distinct incoming and outgoing signaling was significantly associated with specific cell types. Collagen was the strongest signal from fibroblasts to urothelial basal cells in mouse, while laminin pathway for urothelial basal cells to smooth muscle cells (SMCs) in human. Fibronectin 1 pathway was intensely sent by myofibroblasts, received by urothelial cells, and almost exclusively mediated by SMCs in mouse bladder. Interestingly, the cell cluster of SMCs 2 was the dominant sender and mediator for Notch signaling in the human bladder, while SMCs 1 was not. The expression of integrin superfamily (the most common communicative pairs) was depicted, and their co‐expression patterns were located in certain cell types (eg, Itgb1 and Itgb4 in mouse and human basal cells). Conclusions This study provides a complete interpretation of the normal bladder at single‐cell levels, offering an in‐depth resource and foundation for future research.
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Affiliation(s)
- Bowen Shi
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Yanyuan Wu
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Haojie Chen
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Jie Ding
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Jun Qi
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J 2021; 58:2002950. [PMID: 34083402 PMCID: PMC9759791 DOI: 10.1183/13993003.02950-2020] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/20/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits. METHODS RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50). RESULTS Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg. CONCLUSION Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada
- Equally contributing authors
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Equally contributing authors
| | - Kevin F Gibson
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Mridu Gulati
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Buqu Hu
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Antun Mihaljinec
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Tony N Woolard
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Heather Lynn
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- University of Arizona Health Sciences, Tucson, AZ, USA
| | - Nkiruka Emeagwali
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Erica L Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Alison Morris
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Joseph K Leader
- Dept of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yingze Zhang
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | | | | | | | | | - Michael J Becich
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Harry Hochheiser
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven R Wisniewski
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Panayiotis V Benos
- Dept of Computational and Systems Biology and Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Antje Prasse
- Hannover Medical School (MHH), Hannover, Germany
- Fraunhofer ITEM, Hannover, Germany
| | - Laura L Koth
- University of California San Francisco, San Francisco, CA, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
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Xia Y, Cheng M, Hu Y, Li M, Shen L, Ji X, Cui X, Liu X, Wang W, Gao H. Combined transcriptomic and lipidomic analysis of D-4F ameliorating bleomycin-induced pulmonary fibrosis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1424. [PMID: 34733976 PMCID: PMC8506780 DOI: 10.21037/atm-21-3777] [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: 06/29/2021] [Accepted: 08/26/2021] [Indexed: 11/06/2022]
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease that leads to respiratory failure, and for which there is no effective treatment. Apolipoprotein A-1 (ApoA-1) has been reported to ameliorate the bleomycin (BLM)-induced IPF model. Methods To examine the function of D-4F, an ApoA-1 mimetic polypeptide, in IPF, we used an in-vivo BLM-induced model. We assigned mice into the following 3 groups: the Blank Group (BLK Group), the Bleomycin Treatment Group (Model Group), and the D-4F Interference Group (Inter Group). The BLM-induced fibrosis was examined by hematoxylin and eosin, Masson’s trichrome (M-T) staining and immunohistochemical staining. An untargeted lipidomic and transcriptomic analysis were used to examine the function of D-4F. Results There were 35 differentially altered lipids (DALs) in the BLK, Model and Inter Groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that glycerophospholipid metabolism was the most highly enriched of the 35 DALs. There were 99 differentially expressed genes (DEGs) in the BLK, Model and Inter Groups. The enriched KEGG pathway analysis showed that the mitogen-activated protein kinase (MAPK) pathway was 1 of the top 10 pathways. The results of the untargeted lipidomic and transcriptomic analysis showed that phospholipase A2 group 4c (Pla2g4c) was a crucial gene in both the MAPK pathway and glycerophospholipid metabolism. Pla2g4c was increased in the Model Group but decreased in the Inter Group. Conclusions It may be that D-4F prevented the BLM-induced pulmonary fibrosis model by inhibiting the expression of pla2g4c. Our findings suggest that D-4F may be a potential treatment of IPF.
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Affiliation(s)
- Yong Xia
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Mei Cheng
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Yanyan Hu
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Man Li
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Lin Shen
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Xiang Ji
- Department of Respiratory, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Respiratory Diseases, Jinan, China
| | - Xiaopei Cui
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Xiangju Liu
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Weiling Wang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
| | - Haiqing Gao
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Shandong provincial Key Laboratory of Cardiovascular Proteomics, Shandong University, Jinan, China
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Mekhael O, Naiel S, Vierhout M, Hayat AI, Revill SD, Abed S, Inman MD, Kolb MRJ, Ask K. Mouse Models of Lung Fibrosis. Methods Mol Biol 2021; 2299:291-321. [PMID: 34028751 DOI: 10.1007/978-1-0716-1382-5_21] [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] [Indexed: 04/07/2023]
Abstract
The drug discovery pipeline, from discovery of therapeutic targets through preclinical and clinical development phases, to an approved product by health authorities, is a time-consuming and costly process, where a lead candidates' success at reaching the final stage is rare. Although the time from discovery to final approval has been reduced over the last decade, there is still potential to further optimize and streamline the evaluation process of each candidate as it moves through the different development phases. In this book chapter, we describe our preclinical strategies and overall decision-making process designed to evaluate the tolerability and efficacy of therapeutic candidates suitable for patients diagnosed with fibrotic lung disease. We also describe the benefits of conducting preliminary discovery trials, to aid in the selection of suitable primary and secondary outcomes to be further evaluated and assessed in subsequent internal and external validation studies. We outline all relevant research methodologies and protocols routinely performed by our research group and hope that these strategies and protocols will be a useful guide for biomedical and translational researchers aiming to develop safe and beneficial therapies for patients with fibrotic lung disease.
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Affiliation(s)
- Olivia Mekhael
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Safaa Naiel
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Megan Vierhout
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Aaron I Hayat
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Spencer D Revill
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Soumeya Abed
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Mark D Inman
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Martin R J Kolb
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Kjetil Ask
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada.
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Hanmandlu A, Zhu L, Mertens TC, Collum S, Bi W, Xiong F, Wang R, Amirthalingam RT, Ren D, Han L, Jyothula SS, Li W, Zheng WJ, Karmouty-Quintana H. Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis (IPF). Am J Respir Cell Mol Biol 2021; 66:53-63. [PMID: 34370624 DOI: 10.1165/rcmb.2020-0437oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), a devastating, fibro-proliferative chronic lung disorder, is associated with expansion of fibroblasts/myofibroblasts, which leads to excessive production and deposition of extracellular matrix (ECM). IPF is typically clinically identified as end-stage lung disease, after fibrotic processes are well-established and advanced. Fibroblasts have been shown to be critically important in the development and progression of IPF. We hypothesize that differential chromatin access can drive genetic differences in IPF fibroblasts relative to healthy fibroblasts. To this end, we performed Assay of Transposase-Accessible Chromatin (ATAC)-sequencing to identify differentially accessible regions within the genomes of fibroblasts from healthy and IPF lungs. Multiple motifs were identified to be enriched in IPF fibroblasts compared to healthy fibroblasts, including binding motifs for TWIST1 and FOXA1. RNA-sequencing identified 93 genes that could be annotated to differentially accessible regions. Pathway analysis of the annotated genes identified cellular adhesion, cytoskeletal anchoring, and cell differentiation as important biological processes. In addition, single nucleotide polymorphisms (SNPs) analysis showed that linkage disequilibrium (LD) blocks of IPF risk SNPs with IPF accessible regions that have been identified to be located in genes which are important in IPF, including MUC5B, TERT and TOLLIP. Validation studies in isolated lung tissue confirmed increased expression for TWIST1 and FOXA1 in addition to revealing SHANK2 and CSPR2 as novel targets. Thus, modulation of differential chromatin access may be an important mechanism in the pathogenesis of lung fibrosis.
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Affiliation(s)
- Ankit Hanmandlu
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Lisha Zhu
- University of Texas Health Science Center at Houston, 12340, School of Biomedical Informatics, Houston, Texas, United States
| | - Tinne Cj Mertens
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Scott Collum
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Weizhen Bi
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Feng Xiong
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Ruoyu Wang
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | | | - Dewei Ren
- Houston Methodist Hospital, 23534, J.C. Walter Jr. Transplant Center, Houston, Texas, United States
| | - Leng Han
- The University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Soma Sk Jyothula
- University of Texas Health Science Center at Houston, 12340, Internal Medicine, Houston, Texas, United States
| | - Wenbo Li
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - W Jim Zheng
- The University of Texas Health Science Center at Houston, 12340, School of Biomedical Informatics, Houston, Texas, United States
| | - Harry Karmouty-Quintana
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States;
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George NS, Bell R, Paredes JJ, Taub PJ, Andarawis-Puri N. Superior mechanical recovery in male and female MRL/MpJ tendons is associated with a unique genetic profile. J Orthop Res 2021; 39:1344-1354. [PMID: 32352601 PMCID: PMC7606617 DOI: 10.1002/jor.24705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 02/04/2023]
Abstract
Tendon ruptures heal by forming a mechanically inferior scar. We have shown that male Murphy Roths large (MRL/MpJ) mice exhibit improved tendon healing, suggesting that they can inform biological mechanisms that lead to effective tendon healing. As sex impacts healing, we assessed the effect of sex on tendon healing in MRL/MpJ and normal healer C57BL/6 (B6) mice and compared the associated biological environment with identify genes that may be integral to the improved healing outcome. We hypothesized that (a) male MRL/MpJ mice will heal with improved mechanical properties compared to females; and (b) that regenerative tendon healing will be associated with decreased fibrotic pathways, decreased inflammation, and increased activity of matrix metalloproteinases (MMPs). A midsubstance punch was introduced, and tendons were harvested after (a) 1 or 7 days for profiling of 84 genes; (b) 7 or 14 days for the assessment of MMP-2 and MMP-9 activity; and (c) 6 weeks for mechanical assessment. MRL/MpJ tendons healed with the better restoration of mechanical properties than B6 tendons. Sex did not affect the mechanical properties of healing B6 or MRL/MpJ tendons. Comparison of the gene expression profiles in the context of the mechanical outcome revealed several differences between MRL/MpJ and B6 tendon healing, including, lower inflammation, an earlier higher expression of TGF-β-related genes that diminish by 7 days, and genes associated with enhanced cell migration in MRL/MpJ in comparison to B6 tendons. We expect that the timecourse and expression levels of these genes in scarless MRL/MpJ tendon healing represent the balanced environment that leads to improved tendon healing.
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Affiliation(s)
- Nisha S. George
- Leni and Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rebecca Bell
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York
| | - J. J. Paredes
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Peter J. Taub
- Leni and Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nelly Andarawis-Puri
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
- Hospital for Special Surgery Research Division, New York, New York
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Xie T, Kulur V, Liu N, Deng N, Wang Y, Rowan SC, Yao C, Huang G, Liu X, Taghavifar F, Liang J, Hogaboam C, Stripp B, Chen P, Jiang D, Noble PW. Mesenchymal growth hormone receptor deficiency leads to failure of alveolar progenitor cell function and severe pulmonary fibrosis. SCIENCE ADVANCES 2021; 7:7/24/eabg6005. [PMID: 34108218 PMCID: PMC8189579 DOI: 10.1126/sciadv.abg6005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Recent studies have identified impaired type 2 alveolar epithelial cell (ATII) renewal in idiopathic pulmonary fibrosis (IPF) human organoids and severe fibrosis when ATII is defective in mice. ATIIs function as progenitor cells and require supportive signals from the surrounding mesenchymal cells. The mechanisms by which mesenchymal cells promote ATII progenitor functions in lung fibrosis are incompletely understood. We identified growth hormone receptor (GHR) is mainly expressed in mesenchymal cells, and its expression is substantially decreased in IPF lungs. Higher levels of GHR expression correlated with better lung function in patients with IPF. Profibrotic mesenchymal cells retarded ATII growth and were associated with suppressed vesicular GHR expression. Vesicles enriched with Ghr promote ATII proliferation and diminished pulmonary fibrosis in mesenchymal Ghr-deficient mice. Our findings demonstrate a previously unidentified mesenchymal paracrine signaling coordinated by GHR that is capable of supporting ATII progenitor cell renewal and limiting the severity of lung fibrosis.
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Affiliation(s)
- Ting Xie
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Vrishika Kulur
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ningshan Liu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nan Deng
- Biostatistics and Bioinformatics Research Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yizhou Wang
- Genomics Core, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Simon Coyle Rowan
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Changfu Yao
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Guanling Huang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xue Liu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Taghavifar
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jiurong Liang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cory Hogaboam
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Barry Stripp
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Peter Chen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dianhua Jiang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul W Noble
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Shah H, Hacker A, Langburt D, Dewar M, McFadden MJ, Zhang H, Kuzmanov U, Zhou YQ, Hussain B, Ehsan F, Hinz B, Gramolini AO, Heximer SP. Myocardial Infarction Induces Cardiac Fibroblast Transformation within Injured and Noninjured Regions of the Mouse Heart. J Proteome Res 2021; 20:2867-2881. [PMID: 33789425 DOI: 10.1021/acs.jproteome.1c00098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heart failure (HF) is associated with pathological remodeling of the myocardium, including the initiation of fibrosis and scar formation by activated cardiac fibroblasts (CFs). Although early CF-dependent scar formation helps prevent cardiac rupture by maintaining the heart's structural integrity, ongoing deposition of the extracellular matrix in the remote and infarct regions can reduce tissue compliance, impair cardiac function, and accelerate progression to HF. In our study, we conducted mass spectrometry (MS) analysis to identify differentially altered proteins and signaling pathways between CFs isolated from 7 day sham and infarcted murine hearts. Surprisingly, CFs from both the remote and infarct regions of injured hearts had a wide number of similarly altered proteins and signaling pathways that were consistent with fibrosis and activation into pathological myofibroblasts. Specifically, proteins enriched in CFs isolated from MI hearts were involved in pathways pertaining to cell-cell and cell-matrix adhesion, chaperone-mediated protein folding, and collagen fibril organization. These results, together with principal component analyses, provided evidence of global CF activation postinjury. Interestingly, however, direct comparisons between CFs from the remote and infarct regions of injured hearts identified 15 differentially expressed proteins between MI remote and MI infarct CFs. Eleven of these proteins (Gpc1, Cthrc1, Vmac, Nexn, Znf185, Sprr1a, Specc1, Emb, Limd2, Pawr, and Mcam) were higher in MI infarct CFs, whereas four proteins (Gstt1, Gstm1, Tceal3, and Inmt) were higher in MI remote CFs. Collectively, our study shows that MI injury induced global changes to the CF proteome, with the magnitude of change reflecting their relative proximity to the site of injury.
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Affiliation(s)
- Haisam Shah
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Alison Hacker
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Dylan Langburt
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Michael Dewar
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Meghan J McFadden
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Hangjun Zhang
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Uros Kuzmanov
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Yu-Qing Zhou
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Bilal Hussain
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Fahad Ehsan
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Boris Hinz
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada M5G 1G6
| | - Anthony O Gramolini
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Scott P Heximer
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1.,Department of Physiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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44
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Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms. PLoS One 2021; 16:e0248889. [PMID: 33755690 PMCID: PMC7987152 DOI: 10.1371/journal.pone.0248889] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/07/2021] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a progressive and debilitating lung disease with large unmet medical need and few treatment options. We describe an analysis connecting single cell gene expression with bulk gene expression-based subsetting of patient cohorts to identify IPF patient subsets with different underlying pathogenesis and cellular changes. We reproduced earlier findings indicating the existence of two major subsets in IPF and showed that these subsets display different alterations in cellular composition of the lung. We developed classifiers based on the cellular changes in disease to distinguish subsets. Specifically, we showed that one subset of IPF patients had significant increases in gene signature scores for myeloid cells versus a second subset that had significantly increased gene signature scores for ciliated epithelial cells, suggesting a differential pathogenesis among IPF subsets. Ligand-receptor analyses suggested there was a monocyte-macrophage chemoattractant axis (including potentially CCL2-CCR2 and CCL17-CCR4) among the myeloid-enriched IPF subset and a ciliated epithelium-derived chemokine axis (e.g. CCL15) among the ciliated epithelium-enriched IPF subset. We also found that these IPF subsets had differential expression of pirfenidone-responsive genes suggesting that our findings may provide an approach to identify patients with differential responses to pirfenidone and other drugs. We believe this work is an important step towards targeted therapies and biomarkers of response.
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Dhindsa RS, Mattsson J, Nag A, Wang Q, Wain LV, Allen R, Wigmore EM, Ibanez K, Vitsios D, Deevi SVV, Wasilewski S, Karlsson M, Lassi G, Olsson H, Muthas D, Monkley S, Mackay A, Murray L, Young S, Haefliger C, Maher TM, Belvisi MG, Jenkins G, Molyneaux PL, Platt A, Petrovski S. Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis. Commun Biol 2021; 4:392. [PMID: 33758299 PMCID: PMC7988141 DOI: 10.1038/s42003-021-01910-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disorder characterised by progressive, destructive lung scarring. Despite substantial progress, the genetic determinants of this disease remain incompletely defined. Using whole genome and whole exome sequencing data from 752 individuals with sporadic IPF and 119,055 UK Biobank controls, we performed a variant-level exome-wide association study (ExWAS) and gene-level collapsing analyses. Our variant-level analysis revealed a novel association between a rare missense variant in SPDL1 and IPF (NM_017785.5:g.169588475 G > A p.Arg20Gln; p = 2.4 × 10-7, odds ratio = 2.87, 95% confidence interval: 2.03-4.07). This signal was independently replicated in the FinnGen cohort, which contains 1028 cases and 196,986 controls (combined p = 2.2 × 10-20), firmly associating this variant as an IPF risk allele. SPDL1 encodes Spindly, a protein involved in mitotic checkpoint signalling during cell division that has not been previously described in fibrosis. To the best of our knowledge, these results highlight a novel mechanism underlying IPF, providing the potential for new therapeutic discoveries in a disease of great unmet need.
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Affiliation(s)
- Ryan S Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Johan Mattsson
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences George Davies Centre, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Richard Allen
- Genetic Epidemiology Group, Department of Health Sciences George Davies Centre, University of Leicester, Leicester, UK
| | - Eleanor M Wigmore
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kristina Ibanez
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sri V V Deevi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sebastian Wasilewski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Maria Karlsson
- Lung Regeneration, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Glenda Lassi
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Henric Olsson
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Daniel Muthas
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Susan Monkley
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alex Mackay
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lynne Murray
- Lung Regeneration, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Simon Young
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Carolina Haefliger
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Toby M Maher
- Royal Brompton Hospital, London, UK
- Hastings Centre for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maria G Belvisi
- National Heart and Lung Institute, Imperial College, London, UK
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Respiratory Pharmacology Group, London, UK
| | - Gisli Jenkins
- Respiratory Research Unit, Division of Respiratory Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Philip L Molyneaux
- Royal Brompton Hospital, London, UK.
- National Heart and Lung Institute, Imperial College, London, UK.
| | - Adam Platt
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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46
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The Role of Collagen Triple Helix Repeat-Containing 1 Protein (CTHRC1) in Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms22052426. [PMID: 33670905 PMCID: PMC7957534 DOI: 10.3390/ijms22052426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 01/15/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease causing inflammation of joints, cartilage destruction and bone erosion. Biomarkers and new drug targets are actively sought and progressed to improve available options for patient treatment. The Collagen Triple Helix Repeat Containing 1 protein (CTHRC1) may have an important role as a biomarker for rheumatoid arthritis, as CTHRC1 protein concentration is significantly elevated in the peripheral blood of rheumatoid arthritis patients compared to osteoarthritis (OA) patients and healthy individuals. CTHRC1 is a secreted glycoprotein that promotes cell migration and has been implicated in arterial tissue-repair processes. Furthermore, high CTHRC1 expression is observed in many types of cancer and is associated with cancer metastasis to the bone and poor patient prognosis. However, the function of CTHRC1 in RA is still largely undefined. The aim of this review is to summarize recent findings on the role of CTHRC1 as a potential biomarker and pathogenic driver of RA progression. We will discuss emerging evidence linking CTHRC1 to the pathogenic behavior of fibroblast-like synoviocytes and to cartilage and bone erosion through modulation of the balance between bone resorption and repair.
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47
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Zhang Y, Lu S, Fan S, Xu L, Jiang X, Wang K, Cai B. Macrophage migration inhibitory factor activates the inflammatory response in joint capsule fibroblasts following post-traumatic joint contracture. Aging (Albany NY) 2021; 13:5804-5823. [PMID: 33601337 PMCID: PMC7950233 DOI: 10.18632/aging.202505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022]
Abstract
Objectives: Joint capsule fibrosis caused by excessive inflammation leading to post-traumatic joint contracture (PTJC). Fibroblasts trigger inflammation under the challenge of various proinflammatory cytokines. Macrophage migration inhibitory factor (MIF) is a prominent proinflammatory cytokine involved in inflammation- and fibrosis-associated pathophysiology, we investigated the role of MIF in PTJC. Methods: Using rat PTJC model and fibroblast inflammation model, we detected MIF expression in posterior joint capsule. Primary joint capsule fibroblasts (JFs) were used to investigate the effects of MIF on cell proliferation, migration and proinflammatory cytokines production. The mechanism of JF-mediated events was evaluated by qRT-PCR, western blot and immunoprecipitation. We screened the mRNA expression profile to identify gene candidates that mediate the effect of MIF on JFs. Results: MIF increased in posterior joint capsule following PTJC and co-localized with fibroblasts. Injection of MIF inhibitor significantly suppressed joint capsule inflammation and fibrosis. In vitro, MIF promoted JF proliferation, migration, and inflammation by regulating mitogen-activated protein kinase/nuclear factor-κB pathway through coupling with CD74. Transcriptome analysis revealed that lipid metabolism-related factors Pla2g2a, Angptl4, and Sgpp2, downstream of MIF/CD74, were potentially implicated in JF inflammation. Conclusion: MIF/CD74 axis elicited JF inflammation and may provide new therapeutic targets for joint capsule fibrosis in PTJC.
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Affiliation(s)
- Yuxin Zhang
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Shenji Lu
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Shuai Fan
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Lili Xu
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xin Jiang
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Kexin Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Bin Cai
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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48
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Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease. JCI Insight 2021; 6:134218. [PMID: 33290275 PMCID: PMC7934877 DOI: 10.1172/jci.insight.134218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
The pathogenesis of chronic obstructive pulmonary disease (COPD) involves aberrant responses to cellular stress caused by chronic cigarette smoke (CS) exposure. However, not all smokers develop COPD and the critical mechanisms that regulate cellular stress responses to increase COPD susceptibility are not understood. Because microRNAs are well-known regulators of cellular stress responses, we evaluated microRNA expression arrays performed on distal parenchymal lung tissue samples from 172 subjects with and without COPD. We identified miR-24-3p as the microRNA that best correlated with radiographic emphysema and validated this finding in multiple cohorts. In a CS exposure mouse model, inhibition of miR-24-3p increased susceptibility to apoptosis, including alveolar type II epithelial cell apoptosis, and emphysema severity. In lung epithelial cells, miR-24-3p suppressed apoptosis through the BH3-only protein BIM and suppressed homology-directed DNA repair and the DNA repair protein BRCA1. Finally, we found BIM and BRCA1 were increased in COPD lung tissue, and BIM and BRCA1 expression inversely correlated with miR-24-3p. We concluded that miR-24-3p, a regulator of the cellular response to DNA damage, is decreased in COPD, and decreased miR-24-3p increases susceptibility to emphysema through increased BIM and apoptosis.
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Affiliation(s)
- Jessica Nouws
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Feng Wan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Anatomy, Beijing University of Chinese Medicine, Beijing, China
| | - Eric Finnemore
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Willy Roque
- Department of Internal Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - So-Jin Kim
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Isabel Bazan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chuan-Xing Li
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - C Magnus Skold
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Qile Dai
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Maurizio Chioccioli
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Veronique Neumeister
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Clemente J Britto
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann Sweasy
- Department of Radiation Oncology, University of Arizona College of Medicine, Tucson, Arizona, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Åsa M Wheelock
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jose L Gomez
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Patty J Lee
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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Guillotin D, Taylor AR, Platé M, Mercer PF, Edwards LM, Haggart R, Miele G, McAnulty RJ, Maher TM, Hynds RE, Jamal-Hanjani M, Marshall RP, Fisher AJ, Blanchard AD, Chambers RC. Transcriptome analysis of IPF fibroblastic foci identifies key pathways involved in fibrogenesis. Thorax 2021; 76:73-82. [PMID: 33214245 DOI: 10.1136/thoraxjnl-2020-214902] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Fibroblastic foci represent the cardinal pathogenic lesion in idiopathic pulmonary fibrosis (IPF) and comprise activated fibroblasts and myofibroblasts, the key effector cells responsible for dysregulated extracellular matrix deposition in multiple fibrotic conditions. The aim of this study was to define the major transcriptional programmes involved in fibrogenesis in IPF by profiling unmanipulated myofibroblasts within fibrotic foci in situ by laser capture microdissection. METHODS The challenges associated with deriving gene calls from low amounts of RNA and the absence of a meaningful comparator cell type were overcome by adopting novel data mining strategies and by using weighted gene co-expression network analysis (WGCNA), as well as an eigengene-based approach to identify transcriptional signatures, which correlate with fibrillar collagen gene expression. RESULTS WGCNA identified prominent clusters of genes associated with cell cycle, inflammation/differentiation, translation and cytoskeleton/cell adhesion. Collagen eigengene analysis revealed that transforming growth factor β1 (TGF-β1), RhoA kinase and the TSC2/RHEB axis formed major signalling clusters associated with collagen gene expression. Functional studies using CRISPR-Cas9 gene-edited cells demonstrated a key role for the TSC2/RHEB axis in regulating TGF-β1-induced mechanistic target of rapamycin complex 1 activation and collagen I deposition in mesenchymal cells reflecting IPF and other disease settings, including cancer-associated fibroblasts. CONCLUSION These data provide strong support for the human tissue-based and bioinformatics approaches adopted to identify critical transcriptional nodes associated with the key pathogenic cell responsible for fibrogenesis in situ and further identify the TSC2/RHEB axis as a potential novel target for interfering with excessive matrix deposition in IPF and other fibrotic conditions.
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Affiliation(s)
- Delphine Guillotin
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK
| | - Adam R Taylor
- Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Manuela Platé
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK
| | - Paul F Mercer
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK
| | - Lindsay M Edwards
- Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | | | | | - Robin J McAnulty
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Robert E Hynds
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Richard P Marshall
- Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Andrew J Fisher
- Newcastle Fibrosis Research Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals, Newcastle Upon Tyne, UK
| | - Andy D Blanchard
- Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Rachel C Chambers
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK
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50
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Ng B, Cook SA, Schafer S. Interleukin-11 signaling underlies fibrosis, parenchymal dysfunction, and chronic inflammation of the airway. Exp Mol Med 2020; 52:1871-1878. [PMID: 33262481 PMCID: PMC7705429 DOI: 10.1038/s12276-020-00531-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/16/2023] Open
Abstract
Interleukin (IL)-11 evolved as part of the innate immune response. In the human lung, IL-11 upregulation has been associated with viral infections and a range of fibroinflammatory diseases, including idiopathic pulmonary fibrosis. Transforming growth factor-beta (TGFβ) and other disease factors can initiate an autocrine loop of IL-11 signaling in pulmonary fibroblasts, which, in a largely ERK-dependent manner, triggers the translation of profibrotic proteins. Lung epithelial cells also express the IL-11 receptor and transition into a mesenchymal-like state in response to IL-11 exposure. In mice, therapeutic targeting of IL-11 with antibodies can arrest and reverse bleomycin-induced pulmonary fibrosis and inflammation. Intriguingly, fibroblast-specific blockade of IL-11 signaling has anti-inflammatory effects, which suggests that lung inflammation is sustained, in part, through IL-11 activity in the stroma. Proinflammatory fibroblasts and their interaction with the damaged epithelium may represent an important but overlooked driver of lung disease. Initially thought of as a protective cytokine, IL-11 is now increasingly recognized as an important determinant of lung fibrosis, inflammation, and epithelial dysfunction.
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Affiliation(s)
- Benjamin Ng
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Stuart A Cook
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore.,MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, United Kingdom.,National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Sebastian Schafer
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore. .,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore.
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