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Liu X, Zhang D, Zhao F, Li S, Zhu H, Zhang X. Deciphering the role of oxidative stress genes in idiopathic pulmonary fibrosis: a multi-omics mendelian randomization approach. Genes Immun 2024:10.1038/s41435-024-00292-5. [PMID: 39174688 DOI: 10.1038/s41435-024-00292-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/01/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024]
Abstract
Oxidative stress (OS) is crucial in idiopathic pulmonary fibrosis (IPF) pathogenesis, with its genes potentially acting as both causes and consequences of the disease. We identified OS-related genes from GeneCards and performed a meta-analysis on pulmonary transcriptome datasets to discover differentially expressed genes (DEGs) related to OS in IPF. We integrated this data with the largest available IPF GWAS summaries, expression quantitative trait loci (eQTLs), and DNA methylation QTLs (mQTLs) from blood. This approach aimed to identify blood OS genes and regulatory elements linked to IPF risk, incorporating the latest pulmonary eQTLs and bronchoalveolar lavage fluid microbial QTLs (bmQTLs) for a comprehensive view of gene-lung microbiota interactions through SMR and colocalization analyses. Sensitivity analyses were conducted using two additional mendelian randomization (MR) methods. Meta-analysis revealed 1090 differentially expressed OS genes between IPF patients and controls. Integration with IPF GWAS, eQTL, and mQTL data identified key genes and regulatory elements involved in IPF pathogenesis, highlighting the role of specific genes such as KCNMA1 and SLC22A5 in modulating IPF risk through epigenetic mechanisms. Colocalization analysis further identified potential interactions between gene expression and lung microbiota. Our findings elucidate the complex interplay between OS genes and IPF, suggesting potential therapeutic targets and highlighting the importance of considering epigenetic and microbial interactions in the disease's etiology and progression.
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Affiliation(s)
- Xin Liu
- Second Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Dengfeng Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Haiyong Zhu
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Xu Zhang
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
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2
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Adegunsoye A, Kropski JA, Behr J, Blackwell TS, Corte TJ, Cottin V, Glanville AR, Glassberg MK, Griese M, Hunninghake GM, Johannson KA, Keane MP, Kim JS, Kolb M, Maher TM, Oldham JM, Podolanczuk AJ, Rosas IO, Martinez FJ, Noth I, Schwartz DA. Genetics and Genomics of Pulmonary Fibrosis: Charting the Molecular Landscape and Shaping Precision Medicine. Am J Respir Crit Care Med 2024; 210:401-423. [PMID: 38573068 PMCID: PMC11351799 DOI: 10.1164/rccm.202401-0238so] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024] Open
Abstract
Recent genetic and genomic advancements have elucidated the complex etiology of idiopathic pulmonary fibrosis (IPF) and other progressive fibrotic interstitial lung diseases (ILDs), emphasizing the contribution of heritable factors. This state-of-the-art review synthesizes evidence on significant genetic contributors to pulmonary fibrosis (PF), including rare genetic variants and common SNPs. The MUC5B promoter variant is unusual, a common SNP that markedly elevates the risk of early and established PF. We address the utility of genetic variation in enhancing understanding of disease pathogenesis and clinical phenotypes, improving disease definitions, and informing prognosis and treatment response. Critical research gaps are highlighted, particularly the underrepresentation of non-European ancestries in PF genetic studies and the exploration of PF phenotypes beyond usual interstitial pneumonia/IPF. We discuss the role of telomere length, often critically short in PF, and its link to progression and mortality, underscoring the genetic complexity involving telomere biology genes (TERT, TERC) and others like SFTPC and MUC5B. In addition, we address the potential of gene-by-environment interactions to modulate disease manifestation, advocating for precision medicine in PF. Insights from gene expression profiling studies and multiomic analyses highlight the promise for understanding disease pathogenesis and offer new approaches to clinical care, therapeutic drug development, and biomarker discovery. Finally, we discuss the ethical, legal, and social implications of genomic research and therapies in PF, stressing the need for sound practices and informed clinical genetic discussions. Looking forward, we advocate for comprehensive genetic testing panels and polygenic risk scores to improve the management of PF and related ILDs across diverse populations.
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Affiliation(s)
- Ayodeji Adegunsoye
- Pulmonary/Critical Care, and
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Juergen Behr
- Department of Medicine V, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Comprehensive Pneumology Center Munich, member of the German Center for Lung Research (DZL), Munich, Germany
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Tamera J. Corte
- Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, New South Wales, Australia
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Vincent Cottin
- National Reference Center for Rare Pulmonary Diseases (OrphaLung), Louis Pradel Hospital, Hospices Civils de Lyon, ERN-LUNG (European Reference Network on Rare Respiratory Diseases), Lyon, France
- Claude Bernard University Lyon, Lyon, France
| | - Allan R. Glanville
- Lung Transplant Unit, St. Vincent’s Hospital Sydney, Sydney, New South Wales, Australia
| | - Marilyn K. Glassberg
- Department of Medicine, Loyola Chicago Stritch School of Medicine, Chicago, Illinois
| | - Matthias Griese
- Department of Pediatric Pneumology, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, German Center for Lung Research, Munich, Germany
| | - Gary M. Hunninghake
- Harvard Medical School, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - Michael P. Keane
- Department of Respiratory Medicine, St. Vincent’s University Hospital and School of Medicine, University College Dublin, Dublin, Ireland
| | - John S. Kim
- Department of Medicine, School of Medicine, and
| | - Martin Kolb
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Toby M. Maher
- Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | | | | | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - David A. Schwartz
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
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3
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Hussein ZA, Abu-Raghif AR, Tahseen NJ, Rashed KA, Shaker NS, Fawzi HA. Vinpocetine alleviated alveolar epithelial cells injury in experimental pulmonary fibrosis by targeting PPAR-γ/NLRP3/NF-κB and TGF-β1/Smad2/3 pathways. Sci Rep 2024; 14:11131. [PMID: 38750140 PMCID: PMC11096407 DOI: 10.1038/s41598-024-61269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
This study aimed to investigate the potential anti-fibrotic activity of vinpocetine in an experimental model of pulmonary fibrosis by bleomycin and in the MRC-5 cell line. Pulmonary fibrosis was induced in BALB/c mice by oropharyngeal aspiration of a single dose of bleomycin (5 mg/kg). The remaining induced animals received a daily dose of pirfenidone (as a standard anti-fibrotic drug) (300 mg/kg/PO) and vinpocetine (20 mg/kg/PO) on day 7 of the induction till the end of the experiment (day 21). The results of the experiment revealed that vinpocetine managed to alleviate the fibrotic endpoints by statistically improving (P ≤ 0.05) the weight index, histopathological score, reduced expression of fibrotic-related proteins in immune-stained lung sections, as well as fibrotic markers measured in serum samples. It also alleviated tissue levels of oxidative stress and inflammatory and pro-fibrotic mediators significantly elevated in bleomycin-only induced animals (P ≤ 0.05). Vinpocetine managed to express a remarkable attenuating effect in pulmonary fibrosis both in vivo and in vitro either directly by interfering with the classical TGF-β1/Smad2/3 signaling pathway or indirectly by upregulating the expression of Nrf2 enhancing the antioxidant system, activating PPAR-γ and downregulating the NLRP3/NF-κB pathway making it a candidate for further clinical investigation in cases of pulmonary fibrosis.
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Affiliation(s)
- Zeena A Hussein
- Department of Pharmacology, College of Medicine, Al-Nahrain University, Baghdad, Iraq
- Department of Pharmacology and Toxicology, College of Pharmacy, Al-Nahrain University, Baghdad, Iraq
| | - Ahmed R Abu-Raghif
- Department of Pharmacology, College of Medicine, Al-Nahrain University, Baghdad, Iraq
| | - Nibras J Tahseen
- Department of Pharmacology and Toxicology, College of Pharmacy, Al-Bayan University, Baghdad, Iraq
| | | | - Nada S Shaker
- Department of Pharmacology and Toxicology, College of Pharmacy, Mustansiriyah University, Baghdad, Iraq
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4
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Shi X, Chen Y, Shi M, Gao F, Huang L, Wang W, Wei D, Shi C, Yu Y, Xia X, Song N, Chen X, Distler JHW, Lu C, Chen J, Wang J. The novel molecular mechanism of pulmonary fibrosis: insight into lipid metabolism from reanalysis of single-cell RNA-seq databases. Lipids Health Dis 2024; 23:98. [PMID: 38570797 PMCID: PMC10988923 DOI: 10.1186/s12944-024-02062-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Pulmonary fibrosis (PF) is a severe pulmonary disease with limited available therapeutic choices. Recent evidence increasingly points to abnormal lipid metabolism as a critical factor in PF pathogenesis. Our latest research identifies the dysregulation of low-density lipoprotein (LDL) is a new risk factor for PF, contributing to alveolar epithelial and endothelial cell damage, and fibroblast activation. In this study, we first integrative summarize the published literature about lipid metabolite changes found in PF, including phospholipids, glycolipids, steroids, fatty acids, triglycerides, and lipoproteins. We then reanalyze two single-cell RNA-sequencing (scRNA-seq) datasets of PF, and the corresponding lipid metabolomic genes responsible for these lipids' biosynthesis, catabolism, transport, and modification processes are uncovered. Intriguingly, we found that macrophage is the most active cell type in lipid metabolism, with almost all lipid metabolic genes being altered in macrophages of PF. In type 2 alveolar epithelial cells, lipid metabolic differentially expressed genes (DEGs) are primarily associated with the cytidine diphosphate diacylglycerol pathway, cholesterol metabolism, and triglyceride synthesis. Endothelial cells are partly responsible for sphingomyelin, phosphatidylcholine, and phosphatidylethanolamines reprogramming as their metabolic genes are dysregulated in PF. Fibroblasts may contribute to abnormal cholesterol, phosphatidylcholine, and phosphatidylethanolamine metabolism in PF. Therefore, the reprogrammed lipid profiles in PF may be attributed to the aberrant expression of lipid metabolic genes in different cell types. Taken together, these insights underscore the potential of targeting lipid metabolism in developing innovative therapeutic strategies, potentially leading to extended overall survival in individuals affected by PF.
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Affiliation(s)
- Xiangguang Shi
- Department of Dermatology, Huashan Hospital, and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yahui Chen
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Fei Gao
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Lihao Huang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Wei Wang
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Dong Wei
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Chenyi Shi
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuexin Yu
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Xueyi Xia
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Nana Song
- Department of Nephrology, Zhongshan Hospital, Fudan University, Fudan Zhangjiang Institute, Shanghai, People's Republic of China
| | - Xiaofeng Chen
- Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jörg H W Distler
- Department of Internal Medicine 3 and Institute for Clinical Immunology, University of Erlangen, Nuremberg, Germany
| | - Chenqi Lu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Jingyu Chen
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China.
- Center for Lung Transplantation, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jiucun Wang
- Department of Dermatology, Huashan Hospital, and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China.
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China.
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China.
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5
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Ding Y, Liu A, Wang Y, Zhao S, Huang S, Zhu H, Ma L, Han L, Shu S, Zheng L, Chen X. Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine. Front Genet 2023; 14:1187415. [PMID: 37693312 PMCID: PMC10483403 DOI: 10.3389/fgene.2023.1187415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction: Dexmedetomidine (DXM) is widely used as an adjuvant to anesthesia or a sedative medicine, and differences in individual sensitivity to the drug exist. This study aimed to investigate the effect of genetic polymorphisms on these differences. Methods: A total of 112 patients undergoing hand surgery were recruited. DXM 0.5 μg/kg was administered within 10 min and then continuously injected (0.4 μg/kg/h). Narcotrend index, effective dose and onset time of sedation, MAP, and HR were measured. Forty-five single nucleotide polymorphisms (SNPs) were selected for genotype. Results: We observed individual differences in the sedation and hemodynamics induced by DXM. ABCG2 rs2231142, CYP2D6 rs16947, WBP2NL rs5758550, KATP rs141294036, KCNMB1 rs11739136, KCNMA1 rs16934182, ABCC9 rs11046209, ADRA2A rs1800544, and ADRB2 rs1042713 were shown to cause statistically significant (p < 0.05) influence on the individual variation of DXM on sedation and hemodynamics. Moreover, the multiple linear regression analysis indicated sex, BMI, and ADRA2A rs1800544 are statistically related to the effective dose of DXM sedation. Discussion: The evidence suggests that the nine SNPs involved in transport proteins, metabolic enzymes, and target proteins of DXM could explain the individual variability in the sedative and hemodynamic effects of DXM. Therefore, with SNP genotyping, these results could guide personalized medication and promote clinical and surgical management.
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Affiliation(s)
- Yuanyuan Ding
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aiqing Liu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yafeng Wang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Zhao
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiqian Huang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongyu Zhu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lulin Ma
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linlin Han
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaofang Shu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lidong Zheng
- Department of Anesthesiology, Lu’an Hospital Affiliated to Anhui Medical University, Lu’an, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Liu Y, Wen D, Ho C, Yu L, Zheng D, O'Reilly S, Gao Y, Li Q, Zhang Y. Epigenetics as a versatile regulator of fibrosis. J Transl Med 2023; 21:164. [PMID: 36864460 PMCID: PMC9983257 DOI: 10.1186/s12967-023-04018-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Fibrosis, a process caused by excessive deposition of extracellular matrix (ECM), is a common cause and outcome of organ failure and even death. Researchers have made many efforts to understand the mechanism of fibrogenesis and to develop therapeutic strategies; yet, the outcome remains unsatisfactory. In recent years, advances in epigenetics, including chromatin remodeling, histone modification, DNA methylation, and noncoding RNA (ncRNA), have provided more insights into the fibrotic process and have suggested the possibility of novel therapy for organ fibrosis. In this review, we summarize the current research on the epigenetic mechanisms involved in organ fibrosis and their possible clinical applications.
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Affiliation(s)
- Yangdan Liu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Dongsheng Wen
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Chiakang Ho
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Li Yu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Danning Zheng
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | | | - Ya Gao
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Yifan Zhang
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
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Scheraga RG, Olman MA. TRP Channels in Pulmonary Fibrosis: Variety Is a Spice of Life. Am J Respir Cell Mol Biol 2023; 68:241-242. [PMID: 36413749 PMCID: PMC9989481 DOI: 10.1165/rcmb.2022-0446ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Simonson B, Chaffin M, Hill MC, Atwa O, Guedira Y, Bhasin H, Hall AW, Hayat S, Baumgart S, Bedi KC, Margulies KB, Klattenhoff CA, Ellinor PT. Single-nucleus RNA sequencing in ischemic cardiomyopathy reveals common transcriptional profile underlying end-stage heart failure. Cell Rep 2023; 42:112086. [PMID: 36790929 PMCID: PMC10423750 DOI: 10.1016/j.celrep.2023.112086] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ischemic cardiomyopathy (ICM) is the leading cause of heart failure worldwide, yet the cellular and molecular signature of this disease is largely unclear. Using single-nucleus RNA sequencing (snRNA-seq) and integrated computational analyses, we profile the transcriptomes of over 99,000 human cardiac nuclei from the non-infarct region of the left ventricle of 7 ICM transplant recipients and 8 non-failing (NF) controls. We find the cellular composition of the ischemic heart is significantly altered, with decreased cardiomyocytes and increased proportions of lymphatic, angiogenic, and arterial endothelial cells in patients with ICM. We show that there is increased LAMININ signaling from endothelial cells to other cell types in ICM compared with NF. Finally, we find that the transcriptional changes that occur in ICM are similar to those in hypertrophic and dilated cardiomyopathies and that the mining of these combined datasets can identify druggable genes that could be used to target end-stage heart failure.
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Affiliation(s)
- Bridget Simonson
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark Chaffin
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew C Hill
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ondine Atwa
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yasmine Guedira
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Harshit Bhasin
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amelia W Hall
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sikander Hayat
- Precision Cardiology Laboratory, Bayer US, LLC, Cambridge, MA 02142, USA
| | - Simon Baumgart
- Precision Cardiology Laboratory, Bayer US, LLC, Cambridge, MA 02142, USA
| | - Kenneth C Bedi
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth B Margulies
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Patrick T Ellinor
- Precision Cardiology Laboratory, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.
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9
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Septembre-Malaterre A, Boina C, Douanier A, Gasque P. Deciphering the Antifibrotic Property of Metformin. Cells 2022; 11:cells11244090. [PMID: 36552855 PMCID: PMC9777391 DOI: 10.3390/cells11244090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Fibrosis is a chronic progressive and incurable disease leading to organ dysfunction. It is characterized by the accumulation of extracellular matrix proteins produced by mesenchymal stem cells (MSCs) differentiating into myofibroblasts. Given the complexity of its pathophysiology, the search for effective treatments for fibrosis is of paramount importance. Metformin, a structural dimethyl analog of the galegine guanide extracted from the "French Lilac" (Fabaceae Galega officinalis), is the most widely used antidiabetic drug, recently recognized for its antifibrotic effects through ill-characterized mechanisms. The in vitro model of TGF-β1-induced fibrosis in human primary pulmonary mesenchymal stem cells (HPMSCs), identified as CD248+ and CD90+ cells, was used to study the effects of metformin extracts. These effects were tested on the expression of canonical MSC differentiation markers, immune/inflammatory factors and antioxidative stress molecules using qRT-PCR (mRNA, miRNA), immunofluorescence and ELISA experiments. Interestingly, metformin is able to reduce/modulate the expression of different actors involved in fibrosis. Indeed, TGF-β1 effects were markedly attenuated by metformin, as evidenced by reduced expression of three collagen types and Acta2 mRNAs. Furthermore, metformin attenuated the effects of TGF-β1 on the expression of PDGF, VEGF, erythropoietin, calcitonin and profibrotic miRs, possibly by controlling the expression of several key TGF/Smad factors. The expression of four major fibrogenic MMPs was also reduced by metformin treatment. In addition, metformin controlled MSC differentiation into lipofibroblasts and osteoblasts and had the ability to restore redox balance via the Nox4/Nrf2, AMP and Pi3K pathways. Overall, these results show that metformin is a candidate molecule for antifibrotic effect and/or aiming to combat the development of chronic inflammatory diseases worldwide.
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Affiliation(s)
- Axelle Septembre-Malaterre
- Unité de Recherche, EPI ‘Etudes en Pharmaco-Immunologie’, Université de la Réunion, Allée des Topazes, CS11021, 97400 Saint Denis, France
- Laboratoire D’immunologie Clinique et Expérimentale de la Zone de L’océan Indien (LICE-OI), CHU La Réunion Site Félix Guyon Allée des Topazes, CS11021, 97400 Saint Denis, France
- Correspondence:
| | - Chailas Boina
- Unité de Recherche, EPI ‘Etudes en Pharmaco-Immunologie’, Université de la Réunion, Allée des Topazes, CS11021, 97400 Saint Denis, France
- Laboratoire D’immunologie Clinique et Expérimentale de la Zone de L’océan Indien (LICE-OI), CHU La Réunion Site Félix Guyon Allée des Topazes, CS11021, 97400 Saint Denis, France
| | - Audrey Douanier
- Unité de Recherche, EPI ‘Etudes en Pharmaco-Immunologie’, Université de la Réunion, Allée des Topazes, CS11021, 97400 Saint Denis, France
- Laboratoire D’immunologie Clinique et Expérimentale de la Zone de L’océan Indien (LICE-OI), CHU La Réunion Site Félix Guyon Allée des Topazes, CS11021, 97400 Saint Denis, France
| | - Philippe Gasque
- Unité de Recherche, EPI ‘Etudes en Pharmaco-Immunologie’, Université de la Réunion, Allée des Topazes, CS11021, 97400 Saint Denis, France
- Laboratoire D’immunologie Clinique et Expérimentale de la Zone de L’océan Indien (LICE-OI), CHU La Réunion Site Félix Guyon Allée des Topazes, CS11021, 97400 Saint Denis, France
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10
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Li J, Wang R, Shi W, Chen X, Yi J, Yang X, Jin S. Epigenetic regulation in radiation-induced pulmonary fibrosis. Int J Radiat Biol 2022; 99:384-395. [PMID: 35895014 DOI: 10.1080/09553002.2022.2089365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
PURPOSE Radiation-induced pulmonary fibrosis (RIPF) is a common and serious adverse effect of radiotherapy for thoracic tumors, which occurs in the irreversible stage of radiation-induced lung injury (RILI) >6 months after irradiation. It is characterized by progressive and irreversible destruction of lung tissue and deterioration of lung function, which may impair quality of life and lead to respiratory failure and death. We hope this will draw attention to the involvement of epigenetics in the regulation of RIPF. CONCLUSIONS This review summarizes research progress on the role and mechanism of DNA methylation, noncoding RNA and RNA methylation in RIPF or RILI, and the possible role and mechanism of histone modification in RIPF. We have noticed that in tissue fibrosis, the epigenetic regulation mechanisms inside and outside the nucleus can influence each other. We speculate that RIPF may be regulated by an epigenetic regulatory network during its development, and believe that TGF-β, SNAIL, PTEN and EZH2 are four targets worthy of in-depth study.
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Affiliation(s)
- Jiale Li
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Rui Wang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Wen Shi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiaoyi Chen
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Junxuan Yi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiangshan Yang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Shunzi Jin
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
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11
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Artlett CM. The Mechanism and Regulation of the NLRP3 Inflammasome during Fibrosis. Biomolecules 2022; 12:biom12050634. [PMID: 35625564 PMCID: PMC9138796 DOI: 10.3390/biom12050634] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
Fibrosis is often the end result of chronic inflammation. It is characterized by the excessive deposition of extracellular matrix. This leads to structural alterations in the tissue, causing permanent damage and organ dysfunction. Depending on the organ it effects, fibrosis can be a serious threat to human life. The molecular mechanism of fibrosis is still not fully understood, but the NLRP3 (NOD-, LRR- and pyrin–domain–containing protein 3) inflammasome appears to play a significant role in the pathogenesis of fibrotic disease. The NLRP3 inflammasome has been the most extensively studied inflammatory pathway to date. It is a crucial component of the innate immune system, and its activation mediates the secretion of interleukin (IL)-1β and IL-18. NLRP3 activation has been strongly linked with fibrosis and drives the differentiation of fibroblasts into myofibroblasts by the chronic upregulation of IL-1β and IL-18 and subsequent autocrine signaling that maintains an activated inflammasome. Both IL-1β and IL-18 are profibrotic, however IL-1β can have antifibrotic capabilities. NLRP3 responds to a plethora of different signals that have a common but unidentified unifying trigger. Even after 20 years of extensive investigation, regulation of the NLRP3 inflammasome is still not completely understood. However, what is known about NLRP3 is that its regulation and activation is complex and not only driven by various activators but controlled by numerous post-translational modifications. More recently, there has been an intensive attempt to discover NLRP3 inhibitors to treat chronic diseases. This review addresses the role of the NLRP3 inflammasome in fibrotic disorders across many different tissues. It discusses the relationships of various NLRP3 activators to fibrosis and covers different therapeutics that have been developed, or are currently in development, that directly target NLRP3 or its downstream products as treatments for fibrotic disorders.
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Affiliation(s)
- Carol M Artlett
- Department of Microbiology & Immunology, College of Medicine, Drexel University, Philadelphia, PA 19129, USA
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12
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Orzechowska B, Awsiuk K, Wnuk D, Pabijan J, Stachura T, Soja J, Sładek K, Raczkowska J. Discrimination between NSIP- and IPF-Derived Fibroblasts Based on Multi-Parameter Characterization of Their Growth, Morphology and Physic-Chemical Properties. Int J Mol Sci 2022; 23:ijms23042162. [PMID: 35216278 PMCID: PMC8880018 DOI: 10.3390/ijms23042162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Background: The aim of the research presented here was to find a set of parameters enabling discrimination between three types of fibroblasts, i.e., healthy ones and those derived from two disorders mimicking each other: idiopathic pulmonary fibrosis (IPF), and nonspecific interstitial pneumonia (NSIP). Methods: The morphology and growth of cells were traced using fluorescence microscopy and analyzed quantitatively using cell proliferation and substrate cytotoxicity indices. The viability of cells was recorded using MTS assays, and their stiffness was examined using atomic force microscopy (AFM) working in force spectroscopy (FS) mode. To enhance any possible difference in the examined parameters, experiments were performed with cells cultured on substrates of different elasticities. Moreover, the chemical composition of cells was determined using time-of-flight secondary ion mass spectrometry (ToF-SIMS), combined with sophisticated analytical tools, i.e., Multivariate Curve Resolution (MCR) and Principal Component Analysis (PCA). Results: The obtained results demonstrate that discrimination between cell lines derived from healthy and diseased patients is possible based on the analysis of the growth of cells, as well as their physical and chemical properties. In turn, the comparative analysis of the cellular response to altered stiffness of the substrates enables the identification of each cell line, including distinguishing between IPF- and NSIP-derived fibroblasts.
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Affiliation(s)
- Barbara Orzechowska
- Institute of Nuclear Physics Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland; (B.O.); (J.P.)
| | - Kamil Awsiuk
- The Marian Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-428 Krakow, Poland;
- Jagiellonian Center of Biomedical Imaging, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Dawid Wnuk
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Joanna Pabijan
- Institute of Nuclear Physics Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland; (B.O.); (J.P.)
| | - Tomasz Stachura
- 2nd Department of Internal Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688 Krakow, Poland; (T.S.); (J.S.); (K.S.)
| | - Jerzy Soja
- 2nd Department of Internal Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688 Krakow, Poland; (T.S.); (J.S.); (K.S.)
| | - Krzysztof Sładek
- 2nd Department of Internal Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688 Krakow, Poland; (T.S.); (J.S.); (K.S.)
| | - Joanna Raczkowska
- The Marian Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-428 Krakow, Poland;
- Jagiellonian Center of Biomedical Imaging, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
- Correspondence:
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13
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Spix B, Jeridi A, Ansari M, Yildirim AÖ, Schiller HB, Grimm C. Endolysosomal Cation Channels and Lung Disease. Cells 2022; 11:304. [PMID: 35053420 PMCID: PMC8773812 DOI: 10.3390/cells11020304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/25/2021] [Indexed: 12/28/2022] Open
Abstract
Endolysosomal cation channels are emerging as key players of endolysosomal function such as endolysosomal trafficking, fusion/fission, lysosomal pH regulation, autophagy, lysosomal exocytosis, and endocytosis. Diseases comprise lysosomal storage disorders (LSDs) and neurodegenerative diseases, metabolic diseases, pigmentation defects, cancer, immune disorders, autophagy related diseases, infectious diseases and many more. Involvement in lung diseases has not been a focus of attention so far but recent developments in the field suggest critical functions in lung physiology and pathophysiology. Thus, loss of TRPML3 was discovered to exacerbate emphysema formation and cigarette smoke induced COPD due to dysregulated matrix metalloproteinase 12 (MMP-12) levels in the extracellular matrix of the lung, a known risk factor for emphysema/COPD. While direct lung function measurements with the exception of TRPML3 are missing for other endolysosomal cation channels or channels expressed in lysosome related organelles (LRO) in the lung, links between those channels and important roles in lung physiology have been established such as the role of P2X4 in surfactant release from alveolar epithelial Type II cells. Other channels with demonstrated functions and disease relevance in the lung such as TRPM2, TRPV2, or TRPA1 may mediate their effects due to plasma membrane expression but evidence accumulates that these channels might also be expressed in endolysosomes, suggesting additional and/or dual roles of these channels in cell and intracellular membranes. We will discuss here the current knowledge on cation channels residing in endolysosomes or LROs with respect to their emerging roles in lung disease.
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Affiliation(s)
- Barbara Spix
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-University, 80336 Munich, Germany;
| | - Aicha Jeridi
- Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, 85764 Munich, Germany; (A.J.); (M.A.); (A.Ö.Y.); (H.B.S.)
| | - Meshal Ansari
- Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, 85764 Munich, Germany; (A.J.); (M.A.); (A.Ö.Y.); (H.B.S.)
| | - Ali Önder Yildirim
- Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, 85764 Munich, Germany; (A.J.); (M.A.); (A.Ö.Y.); (H.B.S.)
| | - Herbert B. Schiller
- Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, 85764 Munich, Germany; (A.J.); (M.A.); (A.Ö.Y.); (H.B.S.)
| | - Christian Grimm
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-University, 80336 Munich, Germany;
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14
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Guntur D, Olschewski H, Enyedi P, Csáki R, Olschewski A, Nagaraj C. Revisiting the Large-Conductance Calcium-Activated Potassium (BKCa) Channels in the Pulmonary Circulation. Biomolecules 2021; 11:1629. [PMID: 34827626 PMCID: PMC8615660 DOI: 10.3390/biom11111629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 01/13/2023] Open
Abstract
Potassium ion concentrations, controlled by ion pumps and potassium channels, predominantly govern a cell's membrane potential and the tone in the vessels. Calcium-activated potassium channels respond to two different stimuli-changes in voltage and/or changes in intracellular free calcium. Large conductance calcium-activated potassium (BKCa) channels assemble from pore forming and various modulatory and auxiliary subunits. They are of vital significance due to their very high unitary conductance and hence their ability to rapidly cause extreme changes in the membrane potential. The pathophysiology of lung diseases in general and pulmonary hypertension, in particular, show the implication of either decreased expression and partial inactivation of BKCa channel and its subunits or mutations in the genes encoding different subunits of the channel. Signaling molecules, circulating humoral molecules, vasorelaxant agents, etc., have an influence on the open probability of the channel in pulmonary arterial vascular cells. BKCa channel is a possible therapeutic target, aimed to cause vasodilation in constricted or chronically stiffened vessels, as shown in various animal models. This review is a comprehensive collation of studies on BKCa channels in the pulmonary circulation under hypoxia (hypoxic pulmonary vasoconstriction; HPV), lung pathology, and fetal to neonatal transition, emphasising pharmacological interventions as viable therapeutic options.
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Affiliation(s)
- Divya Guntur
- Experimental Anaesthesiology, Department of Anaesthesiology and Intensive Care Medicine, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria;
| | - Horst Olschewski
- Department of Internal Medicine, Division of Pulmonology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
- Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstraße 6, 8010 Graz, Austria;
| | - Péter Enyedi
- Department of Physiology, Semmelweis University, Tűzoltó utca 37-47, 1094 Budapest, Hungary; (P.E.); (R.C.)
| | - Réka Csáki
- Department of Physiology, Semmelweis University, Tűzoltó utca 37-47, 1094 Budapest, Hungary; (P.E.); (R.C.)
| | - Andrea Olschewski
- Experimental Anaesthesiology, Department of Anaesthesiology and Intensive Care Medicine, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria;
- Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstraße 6, 8010 Graz, Austria;
| | - Chandran Nagaraj
- Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstraße 6, 8010 Graz, Austria;
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15
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Xue T, Qiu X, Liu H, Gan C, Tan Z, Xie Y, Wang Y, Ye T. Epigenetic regulation in fibrosis progress. Pharmacol Res 2021; 173:105910. [PMID: 34562602 DOI: 10.1016/j.phrs.2021.105910] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/23/2021] [Accepted: 09/15/2021] [Indexed: 02/08/2023]
Abstract
Fibrosis, a common process of chronic inflammatory diseases, is defined as a repair response disorder when organs undergo continuous damage, ultimately leading to scar formation and functional failure. Around the world, fibrotic diseases cause high mortality, unfortunately, with limited treatment means in clinical practice. With the development and application of deep sequencing technology, comprehensively exploring the epigenetic mechanism in fibrosis has been allowed. Extensive remodeling of epigenetics controlling various cells phenotype and molecular mechanisms involved in fibrogenesis was subsequently verified. In this review, we summarize the regulatory mechanisms of DNA methylation, histone modification, noncoding RNAs (ncRNAs) and N6-methyladenosine (m6A) modification in organ fibrosis, focusing on heart, liver, lung and kidney. Additionally, we emphasize the diversity of epigenetics in the cellular and molecular mechanisms related to fibrosis. Finally, the potential and prospect of targeted therapy for fibrosis based on epigenetic is discussed.
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Affiliation(s)
- Taixiong Xue
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Qiu
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongyao Liu
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cailing Gan
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zui Tan
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuting Xie
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuxi Wang
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.
| | - Tinghong Ye
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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16
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Podolanczuk AJ, Wong AW, Saito S, Lasky JA, Ryerson CJ, Eickelberg O. Update in Interstitial Lung Disease 2020. Am J Respir Crit Care Med 2021; 203:1343-1352. [PMID: 33835899 DOI: 10.1164/rccm.202103-0559up] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Anna J Podolanczuk
- Division of Pulmonary and Critical Care, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Alyson W Wong
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Shigeki Saito
- Section of Pulmonary Disease, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, Louisiana; and
| | - Joseph A Lasky
- Section of Pulmonary Disease, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, Louisiana; and
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Oliver Eickelberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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17
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Li S, Xu A, Li Y, Tan C, La Regina G, Silvestri R, Wang H, Qi W. RS4651 suppresses lung fibroblast activation via the TGF-β1/SMAD signalling pathway. Eur J Pharmacol 2021; 903:174135. [PMID: 33940030 DOI: 10.1016/j.ejphar.2021.174135] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a progressive disease resulting in respiratory failure with no efficient treatment options. We investigated the protective effect of RS4651 on pulmonary fibrosis in mice and the mechanism. METHODS Intratracheal injection of bleomycin (BLM) was used to induce pulmonary fibrosis in mice. RS4561 was administered intraperitoneally at different doses. Histopathological changes were observed. The level of alpha-smooth muscle actin (α-SMA) were also tested. In vitro, the proliferation and migratory effects of RS4651 treatment on MRC-5 cells pre-treated with transforming growth factor (TGF-β1) were examined. RNA-sequencing was used to detect differentially expressed target genes. Then, the expression of α-SMA, pSMAD2 and SMAD7 were analysed during RS4651 treatment of MRC-5 cells with or without silencing by SMAD7 siRNA. RESULTS Histopathological staining results showed decreased collagen deposition in RS4651 administered mice. Additionally, a lower level of α-SMA was also observed compared to the BLM group. The results of in vitro studies confirmed that RS4651 can inhibit the proliferation and migration, as well as α-SMA and pSMAD2 expression in MRC-5 cells treated with TGF-β1. RNA-sequencing data identified the target gene SMAD7. We found that RS4651 could upregulate SMAD7 expression and inhibit the proliferation and migration of MRC-5 cells via SMAD7, and RS4651 inhibition of α-SMA and pSMAD2 expression was blocked in SMAD7-siRNA MRC-5 cells. In vivo studies further confirmed that RS4651 could upregulate SMAD7 expression in BLM-induced lung fibrosis in mice. CONCLUSIONS Our data suggest that RS4651 alleviates BLM-induced pulmonary fibrosis in mice by inhibiting the TGF-β1/SMAD signalling pathway.
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Affiliation(s)
- Shirong Li
- Department of Infectious Disease, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Anjian Xu
- Experimental Center, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing 100050, PR China
| | - Yanmeng Li
- Experimental Center, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing 100050, PR China
| | - Chunting Tan
- Department of Respiratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Giuseppe La Regina
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185, Roma, Italy
| | - Romano Silvestri
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185, Roma, Italy.
| | - Haoyan Wang
- Department of Respiratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
| | - Wenjie Qi
- Department of Infectious Disease, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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18
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Zhang JX, Huang PJ, Wang DP, Yang WY, Lu J, Zhu Y, Meng XX, Wu X, Lin QH, Lv H, Xie H, Wang RL. m 6A modification regulates lung fibroblast-to-myofibroblast transition through modulating KCNH6 mRNA translation. Mol Ther 2021; 29:3436-3448. [PMID: 34111558 DOI: 10.1016/j.ymthe.2021.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/02/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, fatal lung disease characterized by progressive and non-reversible abnormal matrix deposition in lung parenchyma. Myofibroblasts origin mainly from resident fibroblasts via fibroblast-to-myofibroblast transition (FMT) are the dominant collagen-producing cells in pulmonary fibrosis. N6-methyladenosine (m6A) modification has been implicated in various biological process. However, the role of m6A modification in pulmonary fibrosis remains elusive. In this study, we reveal that m6A modification is up-regulated in bleomycin induced pulmonary fibrosis mice model, FMT-derived myofibroblasts and idiopathic pulmonary fibrosis patient lung samples. Lowering m6A level through silencing METTL3 inhibits FMT process in vitro and vivo. Mechanistically, KCNH6 is involved in m6A-regulated FMT process. m6A modification regulates the expression of KCNH6 by modulating its translation in a YTHDF1 dependent manner. Together, our study highlights the critical role of m6A modification in pulmonary fibrosis. Manipulation of m6A modification through targeting METTL3 may become a promising strategy for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Jia-Xiang Zhang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Pei-Jie Huang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Da-Peng Wang
- Department of Intensive Medicine,Wuxi People's Hospital Affiliated to Nanjing Medical University,Wuxi,Jiangsu, 214021,China
| | - Wen-Yu Yang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Jian Lu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Yong Zhu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Xiao-Xiao Meng
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Xin Wu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Qiu-Hai Lin
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Hui Lv
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Hui Xie
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China.
| | - Rui-Lan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China.
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Marwick JA, Elliott RJR, Longden J, Makda A, Hirani N, Dhaliwal K, Dawson JC, Carragher NO. Application of a High-Content Screening Assay Utilizing Primary Human Lung Fibroblasts to Identify Antifibrotic Drugs for Rapid Repurposing in COVID-19 Patients. SLAS DISCOVERY 2021; 26:1091-1106. [PMID: 34078171 PMCID: PMC8458684 DOI: 10.1177/24725552211019405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lung imaging and autopsy reports among COVID-19 patients show elevated lung scarring (fibrosis). Early data from COVID-19 patients as well as previous studies from severe acute respiratory syndrome, Middle East respiratory syndrome, and other respiratory disorders show that the extent of lung fibrosis is associated with a higher mortality, prolonged ventilator dependence, and poorer long-term health prognosis. Current treatments to halt or reverse lung fibrosis are limited; thus, the rapid development of effective antifibrotic therapies is a major global medical need that will continue far beyond the current COVID-19 pandemic. Reproducible fibrosis screening assays with high signal-to-noise ratios and disease-relevant readouts such as extracellular matrix (ECM) deposition (the hallmark of fibrosis) are integral to any antifibrotic therapeutic development. Therefore, we have established an automated high-throughput and high-content primary screening assay measuring transforming growth factor-β (TGFβ)-induced ECM deposition from primary human lung fibroblasts in a 384-well format. This assay combines longitudinal live cell imaging with multiparametric high-content analysis of ECM deposition. Using this assay, we have screened a library of 2743 small molecules representing approved drugs and late-stage clinical candidates. Confirmed hits were subsequently profiled through a suite of secondary lung fibroblast phenotypic screening assays quantifying cell differentiation, proliferation, migration, and apoptosis. In silico target prediction and pathway network analysis were applied to the confirmed hits. We anticipate this suite of assays and data analysis tools will aid the identification of new treatments to mitigate against lung fibrosis associated with COVID-19 and other fibrotic diseases.
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Affiliation(s)
- John A Marwick
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Richard J R Elliott
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Longden
- Center for Clinical Brain Sciences, Chancellors Building, University of Edinburgh, Edinburgh, UK
| | - Ashraff Makda
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nik Hirani
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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20
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Affiliation(s)
- Steven K Huang
- Division of Pulmonary and Critical Care Medicine University of Michigan Ann Arbor, Michigan
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21
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Agarwal M, Goheen M, Jia S, Ling S, White ES, Kim KK. Type I Collagen Signaling Regulates Opposing Fibrotic Pathways through α 2β 1 Integrin. Am J Respir Cell Mol Biol 2020; 63:613-622. [PMID: 32692932 DOI: 10.1165/rcmb.2020-0150oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Fibrosis is characterized by fibroblast activation, leading to matrix remodeling culminating in a stiff, type I collagen-rich fibrotic matrix. Alveolar epithelial cell (AEC) apoptosis is also a major feature of fibrogenesis, and AEC apoptosis is sufficient to initiate a robust lung fibrotic response. TGF-β (transforming growth factor-β) is a major driver of fibrosis and can induce both AEC apoptosis and fibroblast activation. We and others have previously shown that changes in extracellular matrix stiffness and composition can regulate the cellular response to TGF-β. In the present study, we find that type I collagen signaling promotes TGF-β-mediated fibroblast activation and inhibits TGF-β-induced AEC death. Fibroblasts cultured on type I collagen or fibrotic decellularized lung matrix had augmented activation in response to TGF-β, whereas AECs on cultured on type I collagen or fibrotic lung matrix were more resistant to TGF-β-induced apoptosis. Both of these responses were mediated by integrin α2β1, a major collagen receptor. AECs treated with an α2 integrin inhibitor or with deletion of α2 integrin had loss of collagen-mediated protection from apoptosis. We found that mice with fibroblast-specific deletion of α2 integrin were protected from fibrosis whereas mice with AEC-specific deletion of α2 integrin had more lung injury and a greater fibrotic response to bleomycin. Intrapulmonary delivery of an α2 integrin-activating collagen peptide inhibited AEC apoptosis in vitro and in vivo and attenuated the fibrotic response. These studies underscore the need for a thorough understanding of the divergent response to matrix signaling.
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Affiliation(s)
- Manisha Agarwal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Mitchell Goheen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Shijing Jia
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Song Ling
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Eric S White
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kevin K Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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22
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Affiliation(s)
- Rachel G Scheraga
- Respiratory Instituteand.,Lerner Research InstituteCleveland Clinic FoundationCleveland, Ohio
| | - Mitchell A Olman
- Respiratory Instituteand.,Lerner Research InstituteCleveland Clinic FoundationCleveland, Ohio
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