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Moore C, Blumhagen RZ, Yang IV, Walts A, Powers J, Walker T, Bishop M, Russell P, Vestal B, Cardwell J, Markin CR, Mathai SK, Schwarz MI, Steele MP, Lee J, Brown KK, Loyd JE, Crapo JD, Silverman EK, Cho MH, James JA, Guthridge JM, Cogan JD, Kropski JA, Swigris JJ, Bair C, Kim DS, Ji W, Kim H, Song JW, Maier LA, Pacheco KA, Hirani N, Poon AS, Li F, Jenkins RG, Braybrooke R, Saini G, Maher TM, Molyneaux PL, Saunders P, Zhang Y, Gibson KF, Kass DJ, Rojas M, Sembrat J, Wolters PJ, Collard HR, Sundy JS, O’Riordan T, Strek ME, Noth I, Ma SF, Porteous MK, Kreider ME, Patel NB, Inoue Y, Hirose M, Arai T, Akagawa S, Eickelberg O, Fernandez IE, Behr J, Mogulkoc N, Corte TJ, Glaspole I, Tomassetti S, Ravaglia C, Poletti V, Crestani B, Borie R, Kannengiesser C, Parfrey H, Fiddler C, Rassl D, Molina-Molina M, Machahua C, Worboys AM, Gudmundsson G, Isaksson HJ, Lederer DJ, Podolanczuk AJ, Montesi SB, Bendstrup E, Danchel V, Selman M, Pardo A, Henry MT, Keane MP, Doran P, Vašáková M, Sterclova M, Ryerson CJ, Wilcox PG, Okamoto T, Furusawa H, Miyazaki Y, Laurent G, Baltic S, Prele C, Moodley Y, Shea BS, Ohta K, Suzukawa M, Narumoto O, Nathan SD, Venuto DC, Woldehanna ML, Kokturk N, de Andrade JA, Luckhardt T, Kulkarni T, Bonella F, Donnelly SC, McElroy A, Armstong ME, Aranda A, Carbone RG, Puppo F, Beckman KB, Nickerson DA, Fingerlin TE, Schwartz DA. Resequencing Study Confirms That Host Defense and Cell Senescence Gene Variants Contribute to the Risk of Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2019; 200:199-208. [PMID: 31034279 PMCID: PMC6635791 DOI: 10.1164/rccm.201810-1891oc] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/22/2019] [Indexed: 12/20/2022] Open
Abstract
Rationale: Several common and rare genetic variants have been associated with idiopathic pulmonary fibrosis, a progressive fibrotic condition that is localized to the lung. Objectives: To develop an integrated understanding of the rare and common variants located in multiple loci that have been reported to contribute to the risk of disease. Methods: We performed deep targeted resequencing (3.69 Mb of DNA) in cases (n = 3,624) and control subjects (n = 4,442) across genes and regions previously associated with disease. We tested for associations between disease and 1) individual common variants via logistic regression and 2) groups of rare variants via sequence kernel association tests. Measurements and Main Results: Statistically significant common variant association signals occurred in all 10 of the regions chosen based on genome-wide association studies. The strongest risk variant is the MUC5B promoter variant rs35705950, with an odds ratio of 5.45 (95% confidence interval, 4.91-6.06) for one copy of the risk allele and 18.68 (95% confidence interval, 13.34-26.17) for two copies of the risk allele (P = 9.60 × 10-295). In addition to identifying for the first time that rare variation in FAM13A is associated with disease, we confirmed the role of rare variation in the TERT and RTEL1 gene regions in the risk of IPF, and found that the FAM13A and TERT regions have independent common and rare variant signals. Conclusions: A limited number of common and rare variants contribute to the risk of idiopathic pulmonary fibrosis in each of the resequencing regions, and these genetic variants focus on biological mechanisms of host defense and cell senescence.
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Affiliation(s)
- Camille Moore
- National Jewish Health, Denver, Colorado
- School of Public Health
| | | | | | | | | | | | | | | | | | | | - Cheryl R. Markin
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | | | | | - James E. Loyd
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - James D. Crapo
- National Jewish Health, Denver, Colorado
- Department of Medicine, and
| | - Edwin K. Silverman
- Brigham and Women’s Hospital, Harvard School of Medicine, Boston, Massachusetts
| | - Michael H. Cho
- Brigham and Women’s Hospital, Harvard School of Medicine, Boston, Massachusetts
| | - Judith A. James
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | | | - Joy D. Cogan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jonathan A. Kropski
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Carol Bair
- National Jewish Health, Denver, Colorado
| | - Dong Soon Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Wonjun Ji
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hocheol Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Woo Song
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Lisa A. Maier
- National Jewish Health, Denver, Colorado
- School of Public Health
- Department of Medicine, and
| | | | - Nikhil Hirani
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- Respiratory Medicine Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Azin S. Poon
- Respiratory Medicine Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Feng Li
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - R. Gisli Jenkins
- Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Braybrooke
- Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Gauri Saini
- Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Toby M. Maher
- Royal Brompton Hospital and Imperial College, London, United Kingdom
| | | | - Peter Saunders
- Royal Brompton Hospital and Imperial College, London, United Kingdom
| | - Yingze Zhang
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kevin F. Gibson
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daniel J. Kass
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mauricio Rojas
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John Sembrat
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Paul J. Wolters
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Harold R. Collard
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | | | - Mary E. Strek
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Mary K. Porteous
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maryl E. Kreider
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Namrata B. Patel
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yoshikazu Inoue
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Masaki Hirose
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Toru Arai
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Shinobu Akagawa
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Oliver Eickelberg
- Department of Medicine, and
- Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Nesrin Mogulkoc
- Department of Pulmonology, Ege University Hospital, Bornova, Izmir, Turkey
| | - Tamera J. Corte
- Royal Prince Alfred Hospital and University of Sydney, Sydney, Australia
| | - Ian Glaspole
- Alfred Hospital and Monash University, Melbourne, Australia
| | | | - Claudia Ravaglia
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Bruno Crestani
- Université Paris Diderot and Hôpital Bichat, Paris, France
| | - Raphael Borie
- Université Paris Diderot and Hôpital Bichat, Paris, France
| | | | - Helen Parfrey
- Royal Papworth Hospital and Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Christine Fiddler
- Royal Papworth Hospital and Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Doris Rassl
- Royal Papworth Hospital and Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Maria Molina-Molina
- Respiratory Department, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | - Carlos Machahua
- Respiratory Department, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | - Ana Montes Worboys
- Respiratory Department, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | - Gunnar Gudmundsson
- National University Hospital of Iceland, University of Iceland, Reykjavik, Iceland
| | - Helgi J. Isaksson
- National University Hospital of Iceland, University of Iceland, Reykjavik, Iceland
| | - David J. Lederer
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Anna J. Podolanczuk
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Elisabeth Bendstrup
- Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | - Vivi Danchel
- Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas,” México City, México
| | - Annie Pardo
- Universidad Nacional Autónoma de México, México City, México
| | - Michael T. Henry
- Cork University Hospital and University College Cork, Cork, Ireland
| | - Michael P. Keane
- St. Vincent’s University Hospital, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Peter Doran
- St. Vincent’s University Hospital, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Martina Vašáková
- Department of Respiratory Medicine, First Faculty of Medicine Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Martina Sterclova
- Department of Respiratory Medicine, First Faculty of Medicine Charles University and Thomayer Hospital, Prague, Czech Republic
| | | | | | - Tsukasa Okamoto
- Department of Medicine, and
- Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruhiko Furusawa
- Department of Medicine, and
- Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Geoffrey Laurent
- Institute for Respiratory Health and
- Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | | | - Cecilia Prele
- Institute for Respiratory Health and
- Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | | | - Barry S. Shea
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Ken Ohta
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Maho Suzukawa
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Osamu Narumoto
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Steven D. Nathan
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia
| | - Drew C. Venuto
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia
| | - Merte L. Woldehanna
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia
| | - Nurdan Kokturk
- Department of Pulmonary Medicine, Gazi University School of Medicine, Ankara, Turkey
| | - Joao A. de Andrade
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tracy Luckhardt
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tejaswini Kulkarni
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Francesco Bonella
- Ruhrlandklinik, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Seamus C. Donnelly
- Department of Medicine, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Aoife McElroy
- Department of Medicine, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Michelle E. Armstong
- Department of Medicine, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Alvaro Aranda
- CardioPulmonary Reserach Center, Alliance Pulmonary Group, Guaynabo, Puerto Rico
| | | | - Francesco Puppo
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Kenneth B. Beckman
- Biomedical Genomics Center, University of Minnesota; Minneapolis, Minnesota; and
| | | | - Tasha E. Fingerlin
- National Jewish Health, Denver, Colorado
- School of Public Health
- Department of Medicine, and
| | - David A. Schwartz
- National Jewish Health, Denver, Colorado
- Department of Medicine, and
- Department of Immunology, University of Colorado Denver, Denver, Colorado
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Karo-Atar D, Bordowitz A, Wand O, Pasmanik-Chor M, Fernandez IE, Itan M, Frenkel R, Herbert DR, Finkelman FD, Eickelberg O, Munitz A. A protective role for IL-13 receptor α 1 in bleomycin-induced pulmonary injury and repair. Mucosal Immunol 2016; 9:240-53. [PMID: 26153764 PMCID: PMC4703942 DOI: 10.1038/mi.2015.56] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/14/2015] [Indexed: 02/04/2023]
Abstract
Molecular mechanisms that regulate lung repair vs. progressive scarring in pulmonary fibrosis remain elusive. Interleukin (IL)-4 and IL-13 are pro-fibrotic cytokines that share common receptor chains including IL-13 receptor (R) α1 and are key pharmacological targets in fibrotic diseases. However, the roles of IL-13Rα1 in mediating lung injury/repair are unclear. We report dysregulated levels of IL-13 receptors in the lungs of bleomycin-treated mice and to some extent in idiopathic pulmonary fibrosis patients. Transcriptional profiling demonstrated an epithelial cell-associated gene signature that was homeostatically dependent on IL-13Rα1 expression. IL-13Rα1 regulated a striking array of genes in the lung following bleomycin administration and Il13ra1 deficiency resulted in exacerbated bleomycin-induced disease. Increased pathology in bleomycin-treated Il13ra1(-/-) mice was due to IL-13Rα1 expression in structural and hematopoietic cells but not due to increased responsiveness to IL-17, IL-4, IL-13, increased IL-13Rα2 or type 1 IL-4R signaling. These data highlight underappreciated protective roles for IL-13Rα1 in lung injury and homeostasis.
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Affiliation(s)
- D Karo-Atar
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, The Tel-Aviv University, Ramat Aviv, Israel
| | - A Bordowitz
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, The Tel-Aviv University, Ramat Aviv, Israel
| | - O Wand
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, The Tel-Aviv University, Ramat Aviv, Israel
| | - M Pasmanik-Chor
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - I E Fernandez
- Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Grosshadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany
| | - M Itan
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, The Tel-Aviv University, Ramat Aviv, Israel
| | - R Frenkel
- Department of Math, Physics and Computer Science, University of Cincinnati, Cincinnati, Ohio, USA
| | - D R Herbert
- Division of Experimental Medicine, University of California, San Francisco, California, USA
| | - F D Finkelman
- Division of Allergy, Immunology and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA,Department of Medicine, Cincinnati Veterans Affairs Medical Center, Cincinnati, Ohio, USA,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - O Eickelberg
- Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Grosshadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany
| | - A Munitz
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, The Tel-Aviv University, Ramat Aviv, Israel,()
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4
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Yaroshenko A, Hellbach K, Yildirim AÖ, Conlon TM, Fernandez IE, Bech M, Velroyen A, Meinel FG, Auweter S, Reiser M, Eickelberg O, Pfeiffer F. Improved In vivo Assessment of Pulmonary Fibrosis in Mice using X-Ray Dark-Field Radiography. Sci Rep 2015; 5:17492. [PMID: 26619958 PMCID: PMC4664921 DOI: 10.1038/srep17492] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease with a median life expectancy of 4–5 years after initial diagnosis. Early diagnosis and accurate monitoring of IPF are limited by a lack of sensitive imaging techniques that are able to visualize early fibrotic changes at the epithelial-mesenchymal interface. Here, we report a new x-ray imaging approach that directly visualizes the air-tissue interfaces in mice in vivo. This imaging method is based on the detection of small-angle x-ray scattering that occurs at the air-tissue interfaces in the lung. Small-angle scattering is detected with a Talbot-Lau interferometer, which provides the so-called x-ray dark-field signal. Using this imaging modality, we demonstrate-for the first time-the quantification of early pathogenic changes and their correlation with histological changes, as assessed by stereological morphometry. The presented radiography method is significantly more sensitive in detecting morphological changes compared with conventional x-ray imaging, and exhibits a significantly lower radiation dose than conventional x-ray CT. As a result of the improved imaging sensitivity, this new imaging modality could be used in future to reduce the number of animals required for pulmonary research studies.
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Affiliation(s)
- Andre Yaroshenko
- Lehrstuhl für Biomedizinische Physik, Physik-Department &Institut für Medizintechnik, Technische Universität München, Garching, Germany
| | - Katharina Hellbach
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas M Conlon
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, Neuherberg, Germany
| | - Isis Enlil Fernandez
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Bech
- Department of Medical Radiation Physics, Lund University, Lund, Sweden
| | - Astrid Velroyen
- Lehrstuhl für Biomedizinische Physik, Physik-Department &Institut für Medizintechnik, Technische Universität München, Garching, Germany
| | - Felix G Meinel
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich
| | - Sigrid Auweter
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich
| | - Maximilian Reiser
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, Neuherberg, Germany.,Institute for Experimental Pneumology, Ludwig-Maximilians-University Hospital Munich, Munich
| | - Franz Pfeiffer
- Lehrstuhl für Biomedizinische Physik, Physik-Department &Institut für Medizintechnik, Technische Universität München, Garching, Germany
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