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Walsh SM, Worrell JC, Fabre A, Hinz B, Kane R, Keane MP. Novel differences in gene expression and functional capabilities of myofibroblast populations in idiopathic pulmonary fibrosis. Am J Physiol Lung Cell Mol Physiol 2018; 315:L697-L710. [PMID: 30091381 DOI: 10.1152/ajplung.00543.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), a chronic progressive interstitial pneumonia, is characterized by excessive fibroproliferation. Key effector cells in IPF are myofibroblasts that are recruited from three potential sources: resident fibroblasts, fibrocytes, and epithelial cells. We hypothesized that IPF myofibroblasts from different sources display unique gene expression differences and distinct functional characteristics. Primary human pulmonary fibroblasts (normal and IPF), fibrocytes, and epithelial cells were activated using the profibrotic factors TGF-β and TNF-α. The resulting myofibroblasts were characterized using cell proliferation, soluble collagen, and contractility assays, ELISA, and human fibrosis PCR arrays. Genes of significance in human whole lung were validated by immunohistochemistry on human lung sections. Fibroblast-derived myofibroblasts exhibited the greatest increase in expression of profibrotic genes and genes involved in extracellular matrix remodeling and signal transduction. Functional studies demonstrated that myofibroblasts derived from fibrocytes expressed mostly soluble collagen and chemokine (C-C) motif ligand (CCL) 18 but were the least proliferative of the myofibroblast progeny. Activated IPF fibroblasts displayed the highest levels of contractility and CCL2 production. This study identified novel differences in gene expression and functional characteristics of different myofibroblast populations. Further investigation into the myofibroblast phenotype may lead to potential therapeutic targets in future IPF research.
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Affiliation(s)
- Sinead M Walsh
- School of Medicine and Conway Institute of Biomedical and Biomolecular Science, University College Dublin , Dublin , Ireland.,Department of Respiratory Medicine, Saint Vincent's University Hospital, Elm Park, Dublin , Ireland
| | - Julie C Worrell
- School of Medicine and Conway Institute of Biomedical and Biomolecular Science, University College Dublin , Dublin , Ireland
| | - Aurelie Fabre
- Department of Pathology, Saint Vincent's University Hospital , Dublin , Ireland
| | - Boris Hinz
- Laboratory of Tissue Repair and Regeneration, Matrix Dynamics Group, Faculty of Dentistry, University of Toronto , Toronto, Ontario , Canada
| | - Rosemary Kane
- School of Medicine and Conway Institute of Biomedical and Biomolecular Science, University College Dublin , Dublin , Ireland
| | - Michael P Keane
- School of Medicine and Conway Institute of Biomedical and Biomolecular Science, University College Dublin , Dublin , Ireland.,Department of Respiratory Medicine, Saint Vincent's University Hospital, Elm Park, Dublin , Ireland
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Guenther A, Krauss E, Tello S, Wagner J, Paul B, Kuhn S, Maurer O, Heinemann S, Costabel U, Barbero MAN, Müller V, Bonniaud P, Vancheri C, Wells A, Vasakova M, Pesci A, Sofia M, Klepetko W, Seeger W, Drakopanagiotakis F, Crestani B. The European IPF registry (eurIPFreg): baseline characteristics and survival of patients with idiopathic pulmonary fibrosis. Respir Res 2018; 19:141. [PMID: 30055613 PMCID: PMC6064050 DOI: 10.1186/s12931-018-0845-5] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/13/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Since 2009, IPF patients across Europe are recruited into the eurIPFreg, providing epidemiological data and biomaterials for translational research. METHODS The registry data are based on patient and physician baseline and follow-up questionnaires, comprising 1700 parameters. The mid- to long-term objectives of the registry are to provide clues for a better understanding of IPF phenotype sub-clusters, triggering factors and aggravating conditions, regional and environmental characteristics, and of disease behavior and management. RESULTS This paper describes baseline data of 525 IPF subjects recruited from 11/2009 until 10/2016. IPF patients had a mean age of 68.1 years, and seeked medical advice due to insidious dyspnea (90.1%), fatigue (69.2%), and dry coughing (53.2%). A surgical lung biopsy was performed in 32% in 2009, but in only 8% of the cases in 2016, possibly due to increased numbers of cryobiopsy. At the time of inclusion in the eurIPFreg, FVC was 68.4% ± 22.6% of predicted value, DLco ranged at 42.1% ± 17.8% of predicted value (mean value ± SD). Signs of pulmonary hypertension were found in 16.8%. Steroids, immunosuppressants and N-Acetylcysteine declined since 2009, and were replaced by antifibrotics, under which patients showed improved survival (p = 0.001). CONCLUSIONS Our data provide important insights into baseline characteristics, diagnostic and management changes as well as outcome data in European IPF patients over time. TRIAL REGISTRATION The eurIPFreg and eurIPFbank are listed in ClinicalTrials.gov( NCT02951416 ).
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Affiliation(s)
- Andreas Guenther
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany. .,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany. .,Excellence Cluster Cardiopulmonary System (ECCPS), Justus-Liebig University Giessen and Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany. .,AGAPLESION Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany. .,Clinical Research Unit "Pulmonary Fibrosis", University of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.
| | - Ekaterina Krauss
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Silke Tello
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Jasmin Wagner
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Bettina Paul
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Stefan Kuhn
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Olga Maurer
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,AGAPLESION Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany
| | - Sabine Heinemann
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Ulrich Costabel
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Ruhrlandklinik, University Hospital, Essen, Germany
| | | | - Veronika Müller
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Philippe Bonniaud
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Reference Center for Rare Pulmonary Diseases, Centre Hospitalier Universitaire Dijon-Bourgogne, INSERMU1231, Université Bourgogne/Franche-Comté, Dijon, France
| | - Carlo Vancheri
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Department of Clinical and Molecular Biomedicine, Università degli Studi di Catania, Catania, Italy
| | - Athol Wells
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Interstitial Lung Disease Unit, Royal Brompton Hospital, London, UK
| | - Martina Vasakova
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,First Faculty of Medicine and Thomayer Hospital, Prague, Czech Republic
| | - Alberto Pesci
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Ospedale San Gerardo, Monza, Italy
| | - Matteo Sofia
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Università degli Studi di Napoli Federico II, Naples, Italy
| | - Walter Klepetko
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Department of Thoracic Surgery, Vienna University Hospital, Vienna, Austria
| | - Werner Seeger
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany.,Excellence Cluster Cardiopulmonary System (ECCPS), Justus-Liebig University Giessen and Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Fotios Drakopanagiotakis
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Bruno Crestani
- European IPF Registry & Biobank (eurIPFreg/bank), Giessen, Germany.,Competence Center for Rare Pulmonary Diseases, Hopital Bichat, Paris, France
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Spagnolo P, Tzouvelekis A, Bonella F. The Management of Patients With Idiopathic Pulmonary Fibrosis. Front Med (Lausanne) 2018; 5:148. [PMID: 30013972 PMCID: PMC6036121 DOI: 10.3389/fmed.2018.00148] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), the most common form of fibrosing idiopathic interstitial pneumonia, is an inexorably progressive disease with a 5-year survival of ~20%. In the last decade, our understanding of disease pathobiology has increased significantly and this has inevitably impacted on the approach to treatment. Indeed, the paradigm shift from a chronic inflammatory disorder to a primarily fibrotic one coupled with a more precise disease definition and redefined diagnostic criteria have resulted in a massive increase in the number of clinical trials evaluating novel candidate drugs. Most of these trials, however, have been negative, probably because of the multitude and redundancy of cell types, growth factors and profibrotic pathways involved in disease pathogenesis. As a consequence, until recently IPF has lacked effective therapies. Finally, in 2014, two large phase 3 clinical trials have provided robust evidence that pirfenidone, a compound with anti-fibrotic, anti-oxidant and anti-inflammatory properties, and nintedanib, a tyrosine kinase inhibitor with selectivity for vascular endothelial growth factor, platelet-derived growth factor and fibroblast growth factor receptors are able to slow down functional decline and disease progression with an acceptable safety profile. While this is a major achievement, neither pirfenidone nor nintedanib cures IPF and most patients continue to experience disease progression and/or exacerbation despite treatment. Therefore, in recent years increasingly more attention has been paid to preservation of quality of life and, in the advanced phase of the disease, palliation of symptoms. Lung transplantation, the only curative treatment, remains a viable option for only a minority of highly selected patients. The unmet medical need in IPF remains high, and more efficacious and better tolerated drugs are urgently needed. However, a truly effective therapeutic approach should also address quality of life and highly prevalent concomitant conditions and complications of IPF.
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Affiliation(s)
- Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Argyris Tzouvelekis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Francesco Bonella
- Interstitial and Rare Lung Disease Unit, Ruhrlandklinik, University of Duisburg-Essen, Essen, Germany
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Prazeres PHDM, Turquetti AOM, Azevedo PO, Barreto RSN, Miglino MA, Mintz A, Delbono O, Birbrair A. Perivascular cell αv integrins as a target to treat skeletal muscle fibrosis. Int J Biochem Cell Biol 2018; 99:109-113. [PMID: 29627438 PMCID: PMC6159891 DOI: 10.1016/j.biocel.2018.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 02/06/2023]
Abstract
Fibrosis following injury leads to aberrant regeneration and incomplete functional recovery of skeletal muscle, but the lack of detailed knowledge about the cellular and molecular mechanisms involved hampers the design of effective treatments. Using state-of-the-art technologies, Murray et al. (2017) found that perivascular PDGFRβ-expressing cells generate fibrotic cells in the skeletal muscle. Strikingly, genetic deletion of αv integrins from perivascular PDGFRβ-expressing cells significantly inhibited skeletal muscle fibrosis without affecting muscle vascularization or regeneration. In addition, the authors showed that a small molecule inhibitor of αv integrins, CWHM 12, attenuates skeletal muscle fibrosis. From a drug-development perspective, this study identifies a new cellular and molecular target to treat skeletal muscle fibrosis.
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Affiliation(s)
- Pedro H D M Prazeres
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anaelise O M Turquetti
- Anatomy of Domestic and Wild Animals Program, Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | - Patrick O Azevedo
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo S N Barreto
- Anatomy of Domestic and Wild Animals Program, Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | - Maria A Miglino
- Anatomy of Domestic and Wild Animals Program, Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Osvaldo Delbono
- Department of Internal Medicine-Gerontology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Anatomy of Domestic and Wild Animals Program, Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil; Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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Molina-Molina M, Aburto M, Acosta O, Ancochea J, Rodríguez-Portal JA, Sauleda J, Lines C, Xaubet A. Importance of early diagnosis and treatment in idiopathic pulmonary fibrosis. Expert Rev Respir Med 2018; 12:537-539. [PMID: 29718749 DOI: 10.1080/17476348.2018.1472580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- María Molina-Molina
- a ILD Unit, Pulmonology Department , University Hospital of Bellvitge, IDIBELL. CIBERES. PII EPID SEPAR , Barcelona , Spain
| | - Myriam Aburto
- b ILD Unit, Pulmonology Department , Galdakao Hospital. Galdakao- Vizcay. PII EID SEPAR , Galdakao , Spain
| | - Orlando Acosta
- c Pneumology Department , University Hospital of Canarias Tenerife. PII EPID SEPAR , Santa Cruz de Tenerife , Spain
| | - Julio Ancochea
- d Pneumology Department , Hospital La Princesa, PII EPID SEPAR , Madrid , Spain
| | | | - Jaume Sauleda
- f Pneumology Department , Hospital Son Espases, CIBERES. IdISBa. PII EPID SEPAR , Mallorca , Spain
| | - Carlos Lines
- g President of the European Federation of Idiopathic Pulmonary Fibrosis and related Disorders (EU-IPFF) and the Spanish Association of Patients and Relatives with IPF (AFEFPI) , Alcorcón , Spain
| | - Antoni Xaubet
- h Senior consultant PII EPID SEPAR , Barcelona , Spain
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57
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Kaner RJ. Seeing Deeply into the Lung in Interstitial Lung Disease. Am J Respir Crit Care Med 2018; 197:857-858. [DOI: 10.1164/rccm.201709-1798ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Robert J. Kaner
- Department of Medicineand
- Department of Genetic MedicineWeill Cornell MedicineNew York, New York
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Sgalla G, Iovene B, Calvello M, Ori M, Varone F, Richeldi L. Idiopathic pulmonary fibrosis: pathogenesis and management. Respir Res 2018; 19:32. [PMID: 29471816 PMCID: PMC5824456 DOI: 10.1186/s12931-018-0730-2] [Citation(s) in RCA: 318] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive disease characterized by the aberrant accumulation of fibrotic tissue in the lungs parenchyma, associated with significant morbidity and poor prognosis. This review will present the substantial advances achieved in the understanding of IPF pathogenesis and in the therapeutic options that can be offered to patients, and will address the issues regarding diagnosis and management that are still open. Main body Over the last two decades much has been clarified about the pathogenic pathways underlying the development and progression of the lung scarring in IPF. Sustained alveolar epithelial micro-injury and activation has been recognised as the trigger of several biological events of disordered repair occurring in genetically susceptible ageing individuals. Despite multidisciplinary team discussion has demonstrated to increase diagnostic accuracy, patients can still remain unclassified when the current diagnostic criteria are strictly applied, requiring the identification of a Usual Interstitial Pattern either on high-resolution computed tomography scan or lung biopsy. Outstanding achievements have been made in the management of these patients, as nintedanib and pirfenidone consistently proved to reduce the rate of progression of the fibrotic process. However, many uncertainties still lie in the correct use of these drugs, ranging from the initial choice of the drug, the appropriate timing for treatment and the benefit-risk ratio of a combined treatment regimen. Several novel compounds are being developed in the perspective of a more targeted therapeutic approach; in the meantime, the supportive care of these patients and their carers should be appropriately prioritized, and greater efforts should be made toward the prompt identification and management of relevant comorbidities. Conclusions Building on the advances in the understanding of IPF pathobiology, the further investigation of the role of gene variants, epigenetic alterations and other molecular biomarkers reflecting disease activity and behaviour will hopefully enable earlier and more confident diagnosis, improve disease phenotyping and support the development of novel agents for personalized treatment of IPF.
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Affiliation(s)
- Giacomo Sgalla
- Fondazione Policlinico Universitario Agostino Gemelli, Università Cattolica del Sacro Cuore, Unità Operativa Complessa di Pneumologia, Largo A. Gemelli, 8 -00168, Rome, Italy.
| | - Bruno Iovene
- Fondazione Policlinico Universitario Agostino Gemelli, Università Cattolica del Sacro Cuore, Unità Operativa Complessa di Pneumologia, Largo A. Gemelli, 8 -00168, Rome, Italy
| | - Mariarosaria Calvello
- Fondazione Policlinico Universitario Agostino Gemelli, Università Cattolica del Sacro Cuore, Unità Operativa Complessa di Pneumologia, Largo A. Gemelli, 8 -00168, Rome, Italy
| | - Margherita Ori
- Dipartimento di Scienze Mediche e Chirurgiche, Azienda Ospedaliero-Universitaria di Modena, Università di Modena e Reggio Emilia, Struttura Complessa di Malattie dell'Apparato respiratorio , Via Del Pozzo, 71-41124, Modena, Italy
| | - Francesco Varone
- Fondazione Policlinico Universitario Agostino Gemelli, Università Cattolica del Sacro Cuore, Unità Operativa Complessa di Pneumologia, Largo A. Gemelli, 8 -00168, Rome, Italy
| | - Luca Richeldi
- Fondazione Policlinico Universitario Agostino Gemelli, Università Cattolica del Sacro Cuore, Unità Operativa Complessa di Pneumologia, Largo A. Gemelli, 8 -00168, Rome, Italy
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FOXO1/3: Potential suppressors of fibrosis. Ageing Res Rev 2018; 41:42-52. [PMID: 29138094 DOI: 10.1016/j.arr.2017.11.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/07/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023]
Abstract
Fibrosis is a universally age-related disease that involves nearly all organs. It is typically initiated by organic injury and eventually results in organ failure. There are still few effective therapeutic strategy targets for fibrogenesis. Forkhead box proteins O1 and O3 (FOXO1/3) have been shown to have favorable inhibitory effects on fibroblast activation and subsequent extracellular matrix production and can ameliorate fibrosis levels in numerous organs, including the heart, liver, lung, and kidney; they are therefore promising targets for anti-fibrosis therapy. Moreover, we can develop appropriate strategies to make the best use of FOXO1/3's anti-fibrosis properties. The information reviewed here should be significant for understanding the roles of FOXO1/3 in fibrosis and should contribute to the design of further studies related to FOXO1/3 and the fibrotic response and shed light on a potential treatment for fibrosis.
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Batra K, Butt Y, Gokaslan T, Burguete D, Glazer C, Torrealba JR. Pathology and radiology correlation of idiopathic interstitial pneumonias. Hum Pathol 2017; 72:1-17. [PMID: 29180253 DOI: 10.1016/j.humpath.2017.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022]
Abstract
By nature, idiopathic interstitial pneumonias have been diagnosed in a multidisciplinary manner. As classifications have been subject to significant refinement over the last decade, the importance of correlating clinical, radiologic, and pathologic information to arrive at a diagnosis, which will predict prognosis in any given patient, has become increasingly recognized. In 2013, the American Thoracic Society and European Respiratory Society updated the idiopathic interstitial pneumonias classification scheme, addressing the most recent updates in the field. The purpose of this review is to highlight the correlations between radiologic and pathologic findings in idiopathic interstitial pneumonias while using updated classification schemes and naming conventions.
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Affiliation(s)
- Kiran Batra
- University of Texas Southwestern, Department of Radiology, Dallas, Texas, 75235
| | - Yasmeen Butt
- University of Texas Southwestern, Department of Pathology, Dallas, Texas, 75235
| | - Tunc Gokaslan
- University of Texas Southwestern, Department of Pathology, Dallas, Texas, 75235
| | - Daniel Burguete
- University of Texas Southwestern, School of Medicine, Dallas, Texas, 75390
| | - Craig Glazer
- University of Texas Southwestern, Department of Medicine, Pulmonology, Dallas, Texas, 75390
| | - Jose R Torrealba
- University of Texas Southwestern, Department of Pathology, Dallas, Texas, 75235.
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Wang Y, Yella J, Chen J, McCormack FX, Madala SK, Jegga AG. Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. BMC Pulm Med 2017; 17:133. [PMID: 29058630 PMCID: PMC5649521 DOI: 10.1186/s12890-017-0472-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/01/2017] [Indexed: 12/30/2022] Open
Abstract
Background Idiopathic Pulmonary Fibrosis (IPF) is a fatal fibrotic lung disease occurring predominantly in middle-aged and older adults. The traditional diagnostic classification of IPF is based on clinical, radiological, and histopathological features. However, the considerable heterogeneity in IPF presentation suggests that differences in gene expression profiles can help to characterize and distinguish disease severity. Methods We used data-driven unsupervised clustering analysis, combined with a knowledge-based approach to identify and characterize IPF subgroups. Results Using transcriptional profiles on lung tissue from 131 patients with IPF/UIP and 12 non-diseased controls, we identified six subgroups of IPF that generally correlated with the disease severity and lung function decline. Network-informed clustering identified the most severe subgroup of IPF that was enriched with genes regulating inflammatory processes, blood pressure and branching morphogenesis of the lung. The differentially expressed genes in six subgroups of IPF compared to healthy control include transcripts of extracellular matrix, epithelial-mesenchymal cell cross-talk, calcium ion homeostasis, and oxygen transport. Further, we compiled differentially expressed gene signatures to identify unique gene clusters that can segregate IPF from normal, and severe from mild IPF. Additional validations of these signatures were carried out in three independent cohorts of IPF/UIP. Finally, using knowledge-based approaches, we identified several novel candidate genes which may also serve as potential biomarkers of IPF. Conclusions Discovery of unique and redundant gene signatures for subgroups in IPF can be greatly facilitated through unsupervised clustering. Findings derived from such gene signatures may provide insights into pathogenesis of IPF and facilitate the development of clinically useful biomarkers. Electronic supplementary material The online version of this article (10.1186/s12890-017-0472-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunguan Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jaswanth Yella
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francis X McCormack
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Satish K Madala
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH, USA.
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Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease characterized by progressive lung scarring and the histological picture of usual interstitial pneumonia (UIP). It is associated with increasing cough and dyspnoea and impaired quality of life. IPF affects ∼3 million people worldwide, with incidence increasing dramatically with age. The diagnostic approach includes the exclusion of other interstitial lung diseases or overlapping conditions and depends on the identification of the UIP pattern, usually with high-resolution CT; lung biopsy might be required in some patients. The UIP pattern is predominantly bilateral, peripheral and with a basal distribution of reticular changes associated with traction bronchiectasis and clusters of subpleural cystic airspaces. The biological processes underlying IPF are thought to reflect an aberrant reparative response to repetitive alveolar epithelial injury in a genetically susceptible ageing individual, although many questions remain on how to define susceptibility. Substantial progress has been made in the understanding of the clinical management of IPF, with the availability of two pharmacotherapeutic agents, pirfenidone and nintedanib, that decrease physiological progression and likely improve progression-free survival. Current efforts are directed at identifying IPF early, potentially relying on combinations of biomarkers that include circulating factors, demographics and imaging data.
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63
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Abstract
INTRODUCTION Idiopathic Pulmonary Fibrosis (IPF) is a relentlessly progressive, fibrosing interstitial pneumonia characterized by a radiologic and/or histologic pattern of usual interstitial pneumonia (UIP). The availability of two effective anti-fibrotic drugs in IPF has encouraged the identification and treatment of patients in early stages in order to maximize clinical benefit. The ability of high-resolution computed tomography (HRCT) to identify a 'definite' UIP pattern is suboptimal, particularly in the absence of honeycombing. Therefore, radiologic criteria for UIP are currently being redefined. Histology represents the major source of information to define a UIP pattern. Novel and less invasive approaches (particularly cryobiopsy) to sample interstitial lung diseases have demonstrated high sensitivity and specificity. In parallel, researchers are focusing on molecular mechanisms underlying IPF with the aim to identify more specific druggable targets. Lung tissue is therefore essential for diagnostic, pathogenetic and therapeutic purposes. Areas covered: We identified and critically reviewed the most relevant recent literature related to the limitations of current radiologic criteria, new lung sampling procedures, and molecular pathways in support of the need of lung tissue to better understand IPF. Expert commentary: The development of truly effective treatments for IPF requires the identification of key pathogenetic molecules and pathways. To this end, the availability of lung tissue is vital.
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Affiliation(s)
- Giulio Rossi
- a Operative Unit of Pathologic Anatomy , Azienda USL , Aosta , Italy
| | - Paolo Spagnolo
- b Section of Respiratory Diseases, Department of Cardiac , Thoracic, and Vascular Sciences, University of Padua , Padova , Italy
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Abstract
INTRODUCTION Many forms of interstitial lung disease (ILD) can progress to extensive fibrosis and respiratory failure. Idiopathic pulmonary fibrosis (IPF), which generally has a poor prognosis, has been thoroughly studied over the past two decades, and many important discoveries have been made that pertain to genetic predisposition, epidemiology, disease pathogenesis, diagnosis, and management. Additionally, non-IPF forms of ILD can have radiologic and histopathologic manifestations that mimic IPF, and making an accurate diagnosis is key to providing personalized medicine to patients with pulmonary fibrosis. Areas covered: This manuscript discusses current knowledge pertaining to the genetics, epidemiology, pathogenesis, and diagnosis of pulmonary fibrosis with an emphasis on IPF. The material upon which this discussion is based was obtained from various published texts and manuscripts identified via literature searching (e.g. PubMed). Expert commentary: Many genetic variants have been identified that are associated with risk of developing pulmonary fibrosis, and an improved understanding of the influence of both genomic and epigenomic factors in the development of pulmonary fibrosis is rapidly evolving. Because many forms of fibrosing ILD can have similar radiologic and histopathologic patterns yet have different responses to therapeutic interventions, making an accurate diagnosis of specific forms of pulmonary fibrosis is increasingly important.
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Affiliation(s)
- Keith C Meyer
- a Department of Medicine , University of Wisconsin School of Medicine and Public Health - Medicine , Madison , WI , United States
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Homer R, Lederer DJ. Diagnosing idiopathic pulmonary fibrosis without a lung biopsy: honeycombing not required. Thorax 2017; 72:391-392. [DOI: 10.1136/thoraxjnl-2016-209831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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