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Hamvas A, Chaudhari BP, Nogee LM. Genetic testing for diffuse lung diseases in children. Pediatr Pulmonol 2024; 59:2286-2297. [PMID: 37191361 DOI: 10.1002/ppul.26447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
Newly developing genomic technologies are an increasingly important part of clinical care and thus, it is not only important to understand the technologies and their limitations, but to also interpret the findings in an actionable fashion. Clinical geneticists and genetic counselors are now an integral part of the clinical team and are able to bridge the complexities of this rapidly changing science between the bedside clinicians and patients. This manuscript reviews the terminology, the current technology, some of the known genetic disorders that result in lung disease, and indications for genetic testing with associated caveats. Because this field is evolving quickly, we also provide links to websites that provide continuously updated information important for integrating genomic technology results into clinical decision-making.
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Affiliation(s)
- Aaron Hamvas
- Department of Pediatrics, Division of Neonatology, Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bimal P Chaudhari
- Divisions of Genetics and Genomic Medicine, Neonatology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lawrence M Nogee
- Department of Pediatrics, Eudowood Neonatal Pulmonary Division, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Casey A, Fiorino EK, Wambach J. Innovations in Childhood Interstitial and Diffuse Lung Disease. Clin Chest Med 2024; 45:695-715. [PMID: 39069332 PMCID: PMC11366208 DOI: 10.1016/j.ccm.2024.04.002] [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] [Indexed: 07/30/2024]
Abstract
Children's interstitial and diffuse lung diseases (chILDs) are a heterogenous and diverse group of lung disorders presenting during childhood. Infants and children with chILD disorders present with respiratory signs and symptoms as well as diffuse lung imaging abnormalities. ChILD disorders are associated with significant health care resource utilization and high morbidity and mortality. The care of patients with chILD has been improved through multidisciplinary care, multicenter collaboration, and the establishment of patient research networks in the United Stated and abroad. This review details past and current innovations in the diagnosis and clinical care of children with chILD.
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Affiliation(s)
- Alicia Casey
- Department of Pediatrics, Division of Pulmonary Medicine, Harvard Medical School, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Elizabeth K Fiorino
- Department of Science Education and Pediatrics, Donald and Barabara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Jennifer Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
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3
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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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4
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Singh P, Guin D, Pattnaik B, Kukreti R. Mapping the genetic architecture of idiopathic pulmonary fibrosis: Meta-analysis and epidemiological evidence of case-control studies. Gene 2024; 895:147993. [PMID: 37977320 DOI: 10.1016/j.gene.2023.147993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a rare and devastating fibrotic lung disorder with unknown etiology. Although it is believed that genetic component is an important risk factor for IPF, a comprehensive understanding of its genetic landscape is lacking. Hence, we aimed to highlight the susceptibility genes and pathways implicated in IPF pathogenesis through a two-staged systematic literature search of genetic association studies on IPF, followed by meta-analysis and pathway enrichment analysis. METHODS This study was performed based on PRISMA guidelines (PROSPERO, registration number: CRD42022297970). The first search was performed (using PubMed and Web of Science) retrieving a total of 5642 articles, of which 52 were eligible for inclusion in the first stage. The second search was performed (using PubMed, Web of Science and Scopus) for ten polymorphisms, identified from the first search, with 2 or more studies. Finally, seven polymorphisms, [rs35705950/MUC5B, rs2736100/TERT, rs2609255/FAM13A, rs2076295/DSP, rs12610495/DPP9, rs111521887/TOLLIP and rs1800470/TGF-β1] qualified for meta-analyses. The epidemiological credibility was evaluated using Venice criteria. RESULTS From the systematic review, 222 polymorphisms in 118 genes showed a significant association with IPF susceptibility. Meta-analyses findings revealed significant association of rs35705950/T [OR = 3.92(3.26-4.57)], rs2609255/G [OR = 1.50(1.18-1.82)], rs2076295/G [OR = 1.19(0.82-1.756)], rs12610495/G [OR = 1.28(1.12-1.44)], rs2736100/C [OR = 0.68(0.54-0.82), rs111521887/G [OR = 1.34(1.06-1.61)] and suggestive evidence for rs1800470/T [OR = 1.08(0.82-1.34)] with IPF susceptibility. Four polymorphisms- rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk. Gene ontology and pathway enrichment analysis performed on IPF risk-associated genes identified a critical role of genes in mucin production, immune response and inflammation, host defence, cell-cell adhesion and telomere maintenance. CONCLUSIONS Our findings present the most prominent IPF-associated genetic risk variants involved in alveolar epithelial injuries (MUC5B, TERT, FAM13A, DSP, DPP9) and epithelial-mesenchymal transition (TOLLIP, TGF-β1), providing genetic and biological insights into IPF pathogenesis. However, further experimental research and human studies with larger sample sizes, diverse ethnic representation, and rigorous design are warranted.
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Affiliation(s)
- Pooja Singh
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Debleena Guin
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Bijay Pattnaik
- Centre of Excellence for Translational Research in Asthma and Lung Diseases, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ritushree Kukreti
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India.
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5
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Koudstaal T, Funke-Chambour M, Kreuter M, Molyneaux PL, Wijsenbeek MS. Pulmonary fibrosis: from pathogenesis to clinical decision-making. Trends Mol Med 2023; 29:1076-1087. [PMID: 37716906 DOI: 10.1016/j.molmed.2023.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/21/2023] [Accepted: 08/28/2023] [Indexed: 09/18/2023]
Abstract
Pulmonary fibrosis (PF) encompasses a spectrum of chronic lung diseases that progressively impact the interstitium, resulting in compromised gas exchange, breathlessness, diminished quality of life (QoL), and ultimately respiratory failure and mortality. Various diseases can cause PF, with their underlying causes primarily affecting the lung interstitium, leading to their referral as interstitial lung diseases (ILDs). The current understanding is that PF arises from abnormal wound healing processes triggered by various factors specific to each disease, leading to excessive inflammation and fibrosis. While significant progress has been made in understanding the molecular mechanisms of PF, its pathogenesis remains elusive. This review provides an in-depth exploration of the latest insights into PF pathophysiology, diagnosis, treatment, and future perspectives.
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Affiliation(s)
- Thomas Koudstaal
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Manuela Funke-Chambour
- Department of Pulmonary Medicine, Inselspital, University Hospital Bern, Bern, Switzerland
| | - Michael Kreuter
- Mainz Center for Pulmonary Medicine, Departments of Pneumology, Mainz University Medical Center and of Pulmonary, Critical Care & Sleep Medicine, Marienhaus Clinic Mainz, Mainz, Germany
| | - Philip L Molyneaux
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Marlies S Wijsenbeek
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
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Fan Y, Zheng C, Ma R, Wang J, Yang S, Ye Q. MMP19 Variants in Familial and Sporadic Idiopathic Pulmonary Fibrosis. Lung 2023; 201:571-580. [PMID: 37971547 DOI: 10.1007/s00408-023-00652-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Gene variants have been identified in patients with familial or sporadic idiopathic pulmonary fibrosis (IPF). These variants may partially account for the genetic risk of IPF. The aim of this study was to identify potential genes involved in both familial and sporadic IPF. METHODS A Han family in northern China with four members diagnosed with IPF was investigated in this observational study. Whole-exome sequencing (WES) was used to identify germline variants underlying disease phenotypes in five members of this family. Candidate rare variants were validated by Sanger sequencing in samples from 16 family members and 119 patients with sporadic IPF. The plasma levels of proteins encoded by the above candidate genes were also examined in 16 family members, 119 other patients with sporadic IPF and 120 age- and sex-matched healthy controls. RESULTS In a Chinese Han family, MMP19 c.1222 C > T was identified in all familial IPF patients and six offspring from generations III and IV. This variant introduces a premature stop codon, which may damage protein function. Sanger sequencing revealed that 7.6% (9/119) of sporadic IPF patients harbored three MMP19 variants. The genetic risk analysis for pulmonary fibrosis showed that MMP19 c.1499 C > T and c.1316G > A were significantly associated with an increased risk of IPF (OR 3.66, p = 0.028 and OR 8.64, p < 0.001, respectively). The plasma levels of MMP19 were significantly higher in patients with sporadic or familial IPF than in healthy controls (all p < 0.001). CONCLUSIONS MMP19 variants were identified in familial or sporadic IPF, thus providing a potential new clue into IPF pathogenesis.
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Affiliation(s)
- Yali Fan
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Department of Respiratory Medicine and Critical Care, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Chunming Zheng
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Department of Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Ruimin Ma
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
| | - Jingwei Wang
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
| | - Shuqiao Yang
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Department of Respiratory and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Qiao Ye
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China.
- Department of Occupational Medicine and Toxicology, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China.
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7
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Koudstaal T, Wijsenbeek MS. Idiopathic pulmonary fibrosis. Presse Med 2023; 52:104166. [PMID: 37156412 DOI: 10.1016/j.lpm.2023.104166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive devastating lung disease with substantial morbidity. It is associated with cough, dyspnea and impaired quality of life. If left untreated, IPF has a median survival of 3 years. IPF affects ∼3 million people worldwide, with increasing incidence in older patients. The current concept of pathogenesis is that pulmonary fibrosis results from repetitive injury to the lung epithelium, with fibroblast accumulation, myofibroblast activation, and deposition of matrix. These injuries, in combination with innate and adaptive immune responses, dysregulated wound repair and fibroblast dysfunction, lead to recurring tissue remodeling and self-perpetuating fibrosis as seen in IPF. The diagnostic approach includes the exclusion of other interstitial lung diseases or underlying conditions and depends on a multidisciplinary team-based discussion combining radiological and clinical features and well as in some cases histology. In the last decade, considerable progress has been made in the understanding of IPF clinical management, with the availability of two drugs, pirfenidone and nintedanib, that decrease pulmonary lung function decline. However, current IPF therapies only slow disease progression and prognosis remains poor. Fortunately, there are multiple clinical trials ongoing with potential new therapies targeting different disease pathways. This review provides an overview of IPF epidemiology, current insights in pathophysiology, diagnostic and therapeutic management approaches. Finally, a detailed description of current and evolving therapeutic approaches is also provided.
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Affiliation(s)
- Thomas Koudstaal
- Center for Interstitial Lung Diseases and Sarcoidosis, Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Marlies S Wijsenbeek
- Center for Interstitial Lung Diseases and Sarcoidosis, Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
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Peljto AL, Blumhagen RZ, Walts AD, Cardwell J, Powers J, Corte TJ, Dickinson JL, Glaspole I, Moodley YP, Vasakova MK, Bendstrup E, Davidsen JR, Borie R, Crestani B, Dieude P, Bonella F, Costabel U, Gudmundsson G, Donnelly SC, Egan J, Henry MT, Keane MP, Kennedy MP, McCarthy C, McElroy AN, Olaniyi JA, O’Reilly KMA, Richeldi L, Leone PM, Poletti V, Puppo F, Tomassetti S, Luzzi V, Kokturk N, Mogulkoc N, Fiddler CA, Hirani N, Jenkins RG, Maher TM, Molyneaux PL, Parfrey H, Braybrooke R, Blackwell TS, Jackson PD, Nathan SD, Porteous MK, Brown KK, Christie JD, Collard HR, Eickelberg O, Foster EE, Gibson KF, Glassberg M, Kass DJ, Kropski JA, Lederer D, Linderholm AL, Loyd J, Mathai SK, Montesi SB, Noth I, Oldham JM, Palmisciano AJ, Reichner CA, Rojas M, Roman J, Schluger N, Shea BS, Swigris JJ, Wolters PJ, Zhang Y, Prele CMA, Enghelmayer JI, Otaola M, Ryerson CJ, Salinas M, Sterclova M, Gebremariam TH, Myllärniemi M, Carbone RG, Furusawa H, Hirose M, Inoue Y, Miyazaki Y, Ohta K, Ohta S, Okamoto T, Kim DS, Pardo A, Selman M, Aranda AU, Park MS, Park JS, Song JW, Molina-Molina M, Planas-Cerezales L, Westergren-Thorsson G, Smith AV, Manichaikul AW, Kim JS, Rich SS, Oelsner EC, Barr RG, Rotter JI, Dupuis J, O’Connor G, Vasan RS, Cho MH, Silverman EK, Schwarz MI, Steele MP, Lee JS, Yang IV, Fingerlin TE, Schwartz DA. Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants. Am J Respir Crit Care Med 2023; 207:1194-1202. [PMID: 36602845 PMCID: PMC10161752 DOI: 10.1164/rccm.202207-1331oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to nongenetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants, genome-wide, may contribute to the risk of IPF remains unknown. Objectives: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk. Methods: As part of the Trans-Omics for Precision Medicine Program, we sequenced 2,180 cases of IPF. Association testing focused on the aggregated effect of rare variants (minor allele frequency ⩽0.01) within genes or regions. We also identified individual rare variants that are influential within genes and estimated the heritability of IPF on the basis of rare and common variants. Measurements and Main Results: Rare variants in both TERT and RTEL1 were significantly associated with IPF. A single rare variant in each of the TERT and RTEL1 genes was found to consistently influence the aggregated test statistics. There was no significant evidence of association with other previously reported rare variants. The SNP heritability of IPF was estimated to be 32% (SE = 3%). Conclusions: Rare variants within the TERT and RTEL1 genes and well-established common variants have the largest contribution to IPF risk overall. Efforts in risk profiling or the development of therapies for IPF that focus on TERT, RTEL1, common variants, and environmental risk factors are likely to have the largest impact on this complex disease.
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Affiliation(s)
- Anna L. Peljto
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Rachel Z. Blumhagen
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
- National Jewish Health, Denver, Colorado
| | | | - Jonathan Cardwell
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Julia Powers
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Tamera J. Corte
- Royal Prince Alfred Hospital, University of Sydney, Sydney, Australia
| | - Joanne L. Dickinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Ian Glaspole
- Allergy, Asthma and Clinical Immunology Clinic, Alfred Health, Sydney, Australia
| | - Yuben P. Moodley
- Department of Respiratory Medicine, University of Western Australia, Perth, Australia
| | | | - Elisabeth Bendstrup
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jesper R. Davidsen
- South Danish Center for Interstitial Lung Diseases, Department of Respiratory Medicine, Odense University Hospital, Odense, Denmark
| | | | - Bruno Crestani
- Service de Pneumologie A and
- Université Paris Cité, INSERM, Physiopathologie et Épidémiologie des Maladies Respiratoires, Paris, France
| | | | - Francesco Bonella
- Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Costabel
- Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Gunnar Gudmundsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Respiratory Medicine and Sleep, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Jim Egan
- National Lung Transplantation Centre, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Michael T. Henry
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Michael P. Keane
- St. Vincent’s University Hospital, University College Dublin, Dublin, Ireland
| | - Marcus P. Kennedy
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Cormac McCarthy
- St. Vincent’s University Hospital, University College Dublin, Dublin, Ireland
| | | | | | | | - Luca Richeldi
- Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paolo M. Leone
- Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, G. B. Morgagni Hospital, Forlì, Italy
- Department of Medical and Surgical Sciences, DIMES University of Bologna, Bologna, Italy
| | - Francesco Puppo
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Valentina Luzzi
- Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | | | - Nesrin Mogulkoc
- Department of Pulmonology, Ege University Hospital, Izmir, Turkey
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Keck Medicine of USC, University of Southern California, Los Angeles, California
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Rebecca Braybrooke
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Peter D. Jackson
- Department of Pulmonary and Critical Care Medicine, Virginia Commonwealth University, Richmond, Virginia
| | | | - Mary K. Porteous
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Jason D. Christie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold R. Collard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elena E. Foster
- Division of Pulmonary, Critical Care, and Sleep Medicine, School of Medicine, University of California, Davis, Sacramento, California
| | - Kevin F. Gibson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marilyn Glassberg
- Division of Pulmonary, Critical Care and Sleep Medicine, College of Medicine, University of Arizona, Phoenix, Arizona
| | - Daniel J. Kass
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - David Lederer
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Angela L. Linderholm
- Department of Internal Medicine, University of California, Davis, Davis, California
| | - Jim Loyd
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Amy J. Palmisciano
- Division of Pulmonary, Critical Care and Sleep Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | - Cristina A. Reichner
- Division of Pulmonary, Critical Care and Sleep Medicine, MedStar Georgetown University Hospital, Washington, DC
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Ohio State University, Columbus, Ohio
| | - Jesse Roman
- Division of Pulmonary, Allergy, and Critical Care, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Neil Schluger
- Columbia University Medical Center, New York, New York
| | - Barry S. Shea
- Division of Pulmonary, Critical Care and Sleep Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | | | - Paul J. Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Yingze Zhang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Cecilia M. A. Prele
- Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - Juan I. Enghelmayer
- Brown University, Providence, Rhode Island
- Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria Otaola
- Instituto de Rehabilitación Psicofísica de Buenos Aires, Buenos Aires, Argentina
| | - Christopher J. Ryerson
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Martina Sterclova
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marjukka Myllärniemi
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | | | - Haruhiko Furusawa
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Hirose
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yoshikazu Inoue
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Ohta
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Shin Ohta
- Department of Medicine, Showa University, Tokyo, Japan
| | - Tsukasa Okamoto
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Dong Soon Kim
- Asan Medical Center, University of Ulsan, Seoul, Republic of Korea
| | - Annie Pardo
- Faculty of Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alvaro U. Aranda
- Cardiopulmonary Research Center, Alliance Pulmonary Group, Guaynabo, Puerto Rico
| | - Moo Suk Park
- Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Sun Park
- Seoul National University Bundang Hospital, Seoul National University, Seongnam, Republic of Korea
| | - Jin Woo Song
- Asan Medical Center, University of Ulsan, Seoul, Republic of Korea
| | | | - Lurdes Planas-Cerezales
- Interstitial Lung Disease Multidisciplinary Unit, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | | | - Albert V. Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | | | | | - Stephen S. Rich
- Center for Public Health Genomics, and
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Elizabeth C. Oelsner
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - R. Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Josee Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - George O’Connor
- Pulmonary Center, School of Medicine, Boston University, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Boston University and National Heart, Lung, and Blood Institute Framingham Heart Study, Boston, Massachusetts; and
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marvin I. Schwarz
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Mark P. Steele
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Joyce S. Lee
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | | | - David A. Schwartz
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
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9
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Groen K, van der Vis JJ, van Batenburg AA, Kazemier KM, Grutters JC, van Moorsel CHM. Genetic Variant Overlap Analysis Identifies Established and Putative Genes Involved in Pulmonary Fibrosis. Int J Mol Sci 2023; 24:ijms24032790. [PMID: 36769106 PMCID: PMC9917193 DOI: 10.3390/ijms24032790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
In only around 40% of families with pulmonary fibrosis (PF) a suspected genetic cause can be found. Genetic overlap analysis of Whole Exome Sequencing (WES) data may be a powerful tool to discover new shared variants in novel genes for PF. As a proof of principle, we first selected unrelated PF patients for whom a genetic variant was detected (n = 125) in established PF genes and searched for overlapping variants. Second, we performed WES (n = 149) and identified novel potentially deleterious variants shared by at least two unrelated PF patients. These variants were genotyped in validation cohorts (n = 2748). In 125 unrelated patients, a potentially deleterious variant was detected in known PF genes of which 15 variants in six genes overlapped, involving 51 patients. Overlap analysis of WES data identified two novel variants of interest: TOM1L2 c.421T > C p.(Y141H) and TDP1c.1373dupG p.(S459fs*5), neither gene had been related to pulmonary fibrosis before. Both proteins were present in the alveolar epithelium. No apparent characteristics of telomere disease were observed. This study underlines the potential of searching for overlapping rare potentially deleterious variants to identify disease-associated variants and genes. A previously unreported variant was found in two putative new PF genes, but further research is needed to determine causality.
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Affiliation(s)
- Karlijn Groen
- Department of Pulmonology, St. Antonius ILD Center of Excellence, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
| | - Joanne J. van der Vis
- Department of Pulmonology, St. Antonius ILD Center of Excellence, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
- Department of Clinical Chemistry, St. Antonius ILD Center of Excellence, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
| | - Aernoud A. van Batenburg
- Department of Pulmonology, St. Antonius ILD Center of Excellence, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
| | - Karin M. Kazemier
- Center of Translational Immunology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
- Division of Hearts and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jan C. Grutters
- Department of Pulmonology, St. Antonius ILD Center of Excellence, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
- Division of Hearts and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Coline H. M. van Moorsel
- Department of Pulmonology, St. Antonius ILD Center of Excellence, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
- Correspondence:
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10
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[Interstitial lung diseases in children of genetic origin]. Rev Mal Respir 2023; 40:38-46. [PMID: 36564324 DOI: 10.1016/j.rmr.2022.11.003] [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: 03/14/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
Abstract
Interstitial lung diseases in children of genetic origin. Interstitial lung disease (ILD) in children (chILD) encompasses a heterogeneous group of rare respiratory disorders, most of which are chronic and severe. In more and more of these cases, a genetic cause has been identified. As of now, the main mutations have been localized in the genes encoding the surfactant proteins (SP)-C (SFTPC), SP-B (SFTPB), their transporter ATP-binding cassette, family 1, member 3 (ABCA3), transcription factor NK2 homeobox 1 (NKX2-1) and, more rarely, SP-A1 (SFTPA1) or SP-A2 (SFTPA2). Pediatric pulmonary alveolar proteinosis (PAP) is associated with mutations in CSF2RA, CSF2RB, and MARS; more recently, mutations in STING1 and COPA have been associated with specific auto-inflammatory disorders including ILD manifestations. The relationships between the molecular abnormalities and the phenotypic expressions generally remain poorly understood. In the coming years, it is expected that newly identified molecular defects will help to more accurately predict disease courses and to produce individualized targeted therapies.
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11
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Alonso-Gonzalez A, Tosco-Herrera E, Molina-Molina M, Flores C. Idiopathic pulmonary fibrosis and the role of genetics in the era of precision medicine. Front Med (Lausanne) 2023; 10:1152211. [PMID: 37181377 PMCID: PMC10172674 DOI: 10.3389/fmed.2023.1152211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, rare progressive lung disease, characterized by lung scarring and the irreversible loss of lung function. Two anti-fibrotic drugs, nintedanib and pirfenidone, have been demonstrated to slow down disease progression, although IPF mortality remains a challenge and the patients die after a few years from diagnosis. Rare pathogenic variants in genes that are involved in the surfactant metabolism and telomere maintenance, among others, have a high penetrance and tend to co-segregate with the disease in families. Common recurrent variants in the population with modest effect sizes have been also associated with the disease risk and progression. Genome-wide association studies (GWAS) support at least 23 genetic risk loci, linking the disease pathogenesis with unexpected molecular pathways including cellular adhesion and signaling, wound healing, barrier function, airway clearance, and innate immunity and host defense, besides the surfactant metabolism and telomere biology. As the cost of high-throughput genomic technologies continuously decreases and new technologies and approaches arise, their widespread use by clinicians and researchers is efficiently contributing to a better understanding of the pathogenesis of progressive pulmonary fibrosis. Here we provide an overview of the genetic factors known to be involved in IPF pathogenesis and discuss how they will continue to further advance in this field. We also discuss how genomic technologies could help to further improve IPF diagnosis and prognosis as well as for assessing genetic risk in unaffected relatives. The development and validation of evidence-based guidelines for genetic-based screening of IPF will allow redefining and classifying this disease relying on molecular characteristics and contribute to the implementation of precision medicine approaches.
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Affiliation(s)
- Aitana Alonso-Gonzalez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Eva Tosco-Herrera
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, IDIBELL, Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- *Correspondence: Carlos Flores,
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12
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Sutton RM, Bittar HT, Sullivan DI, Silva AG, Bahudhanapati H, Parikh AH, Zhang Y, Gibson K, McDyer JF, Kass DJ, Alder JK. Rare surfactant-related variants in familial and sporadic pulmonary fibrosis. Hum Mutat 2022; 43:2091-2101. [PMID: 36135709 PMCID: PMC9771972 DOI: 10.1002/humu.24476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/01/2022] [Accepted: 09/14/2022] [Indexed: 01/25/2023]
Abstract
The role of constitutional genetic defects in idiopathic pulmonary fibrosis (IPF) is increasingly appreciated. Monogenic disorders associated with IPF affect two pathways: telomere maintenance, accounting for approximately 10% of all patients with IPF, and surfactant biology, responsible for 1%-3% of cases and often co-occurring with lung cancer. We examined the prevalence of rare variants in five surfactant-related genes, SFTPA1, SFPTA2, SFTPC, ABCA3, and NKX2-1, that were previously linked to lung disease in whole genome sequencing data from 431 patients with IPF. We identified functionally deleterious rare variants in SFTPA2 with a prevalence of 1.3% in individuals with and without a family history of IPF. All individuals had no personal history of lung cancer, but substantial bronchiolar metaplasia was noted on lung explants and biopsies. Five patients had novel missense variants in NKX2-1, but the contribution to disease is unclear. In general, patients were younger and had longer telomeres compared with the majority of patients with IPF suggesting that these features may be useful for identifying this subset of patients in the clinic. These data suggest that SFTPA2 variants may be more common in unselected IPF cohorts and may manifest in the absence of personal/family history of lung cancer or IPF.
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Affiliation(s)
- Rachel M Sutton
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Humberto Trejo Bittar
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel I Sullivan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Agustin Gil Silva
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Harinath Bahudhanapati
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Anishka H Parikh
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Yingze Zhang
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kevin Gibson
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - John F McDyer
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
| | - Jonathan K Alder
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Pittsburgh, Pennsylvania, USA
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13
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Mota PC, Soares ML, Vasconcelos CD, Ferreira AC, Lima BA, Manduchi E, Moore JH, Melo N, Novais-Bastos H, Pereira JM, Guimarães S, Moura CS, Marques JA, Morais A. Predictive value of common genetic variants in idiopathic pulmonary fibrosis survival. J Mol Med (Berl) 2022; 100:1341-1353. [DOI: 10.1007/s00109-022-02242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/13/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
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14
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Falfán-Valencia R. ABCA3 mutations in adults with interstitial lung disease: is there a link? SARCOIDOSIS, VASCULITIS, AND DIFFUSE LUNG DISEASES : OFFICIAL JOURNAL OF WASOG 2022; 39:e2022022. [PMID: 36118543 PMCID: PMC9437763 DOI: 10.36141/svdld.v39i2.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico
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15
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Chen F, Xie Z, Zhang VW, Chen C, Fan H, Zhang D, Jiang W, Wang C, Wu P. Case Report: Report of Two Cases of Interstitial Lung Disease Caused by Novel Compound Heterozygous Variants in the ABCA3 Gene. Front Genet 2022; 13:875015. [PMID: 35464853 PMCID: PMC9019779 DOI: 10.3389/fgene.2022.875015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Interstitial lung disease (ILD) is a heterogeneous group of pulmonary disorders involving the lung interstitium and distal airways, also known as diffuse lung disease. The genetic defects resulting in alveolar surfactant protein dysfunction are a rare cause of ILD in pediatric patients. We report two unrelated pediatric patients with shortness of breath, dyspnea and hypoxemia, and the chest CT findings including patchy ground-glass opacity in both lung fields, suggestive of diffuse ILD. One patient was a full-term male infant who had shortness of breath a few hours after the birth, and then developed into severe respiratory distress syndrome (RDS). Whole exome sequencing revealed novel compound heterozygous variants in the ABCA3 gene (NM_001,089.3): paternally inherited c.4035+5G > A and c.668T > C (p.M223T), and maternally inherited c.1285+4A > C. The second patient was a 34-month-old boy with onset of chronic repeated cough and hypoxemia at 9 months of age. We unveiled novel compound heterozygous ABCA3 variants (c.704T > C, p.F235S; c.4037_4040del, p.T1346Nfs*15) in this patient. Surfactant protein dysfunction due to bi-allelic mutations in the ABCA3 gene was the cause of ILD in two patients. The novel mutations found in this study expanded the spectrum of known mutations in the ABCA3 gene.
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Affiliation(s)
- Fang Chen
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zhiwei Xie
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Victor Wei Zhang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.,AmCare Genomics Lab, Guangzhou, China
| | - Chen Chen
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Huifeng Fan
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Dongwei Zhang
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Wenhui Jiang
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
| | | | - Peiqiong Wu
- Respiratory Department of Guangzhou Women and Children's Medical Center, Guangzhou, China
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16
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Molecular pathways and role of epigenetics in the idiopathic pulmonary fibrosis. Life Sci 2022; 291:120283. [PMID: 34998839 DOI: 10.1016/j.lfs.2021.120283] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/19/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease with unknown etiological factors that can progress to other dangerous diseases like lung cancer. Environmental and genetic predisposition are the two major etiological or risk factors involved in the pathology of the IPF. Among the environmental risk factors, smoking is one of the major causes for the development of IPF. Epigenetic pathways like nucleosomes remodeling, DNA methylation, histone modifications and miRNA mediated genes play a crucial role in development of IPF. Mutations in the genes make the epigenetic factors as important drug targets in IPF. Transcriptional changes due to environmental factors are also involved in the progression of IPF. The mutations in human telomerase reverse transcriptase (hTERT) have shown decreased life expectancy in IPF patients. The TERT-gene is highly expressed in chronic smokers and makes the role of epigenetics evident. Drug like nintedanib acts through vascular endothelial growth factor receptors (VEGFR), while drug pirfenidone acts through transforming growth factor (TGF), which is useful in IPF. Gefitinib, a tyrosine kinase inhibitor of EGFR, is useful as an anti-fibrosis agent in preclinical models. Newer drugs such as Celgene-CC90001 and FibroGen-FG-3019 are currently under investigations acts through the modulating epigenetic mechanisms. Thus, the study on epigenetics opens a wide window for the discovery of newer drugs. This study provides an elementary analysis of multiple regulators of epigenetics and their roles associated with the pathology of IPF. Further, this review also includes epigenetic drugs under development in preclinical and clinical stages.
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17
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Onnée M, Fanen P, Callebaut I, de Becdelièvre A. Structure-Based Understanding of ABCA3 Variants. Int J Mol Sci 2021; 22:ijms221910282. [PMID: 34638622 PMCID: PMC8508924 DOI: 10.3390/ijms221910282] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
ABCA3 is a crucial protein of pulmonary surfactant biosynthesis, associated with recessive pulmonary disorders such as neonatal respiratory distress and interstitial lung disease. Mutations are mostly private, and accurate interpretation of variants is mandatory for genetic counseling and patient care. We used 3D structure information to complete the set of available bioinformatics tools dedicated to medical decision. Using the experimental structure of human ABCA4, we modeled at atomic resolution the human ABCA3 3D structure including transmembrane domains (TMDs), nucleotide-binding domains (NBDs), and regulatory domains (RDs) in an ATP-bound conformation. We focused and mapped known pathogenic missense variants on this model. We pinpointed amino-acids within the NBDs, the RDs and within the interfaces between the NBDs and TMDs intracellular helices (IHs), which are predicted to play key roles in the structure and/or the function of the ABCA3 transporter. This theoretical study also highlighted the possible impact of ABCA3 variants in the cytosolic part of the protein, such as the well-known p.Glu292Val and p.Arg288Lys variants.
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Affiliation(s)
- Marion Onnée
- Institut Mondor de Recherche Biomédicale, Université Paris Est Creteil, F-94010 Créteil, France; (M.O.); (P.F.)
| | - Pascale Fanen
- Institut Mondor de Recherche Biomédicale, Université Paris Est Creteil, F-94010 Créteil, France; (M.O.); (P.F.)
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, F-94010 Créteil, France
| | - Isabelle Callebaut
- Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Muséum National d’Histoire Naturelle, UMR CNRS 7590, Sorbonne Université, F-75005 Paris, France
- Correspondence: (I.C.); (A.d.B.)
| | - Alix de Becdelièvre
- Institut Mondor de Recherche Biomédicale, Université Paris Est Creteil, F-94010 Créteil, France; (M.O.); (P.F.)
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, F-94010 Créteil, France
- Correspondence: (I.C.); (A.d.B.)
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18
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Liu L, Liu YJ, Guo T, Luo H. A novel variant of SFTPA2 in a Han Chinese family with interstitial lung disease and lung cancer. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1977722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Lv Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Yi-Jie Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Ting Guo
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Hong Luo
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
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19
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Spagnolo P, Kropski JA, Jones MG, Lee JS, Rossi G, Karampitsakos T, Maher TM, Tzouvelekis A, Ryerson CJ. Idiopathic pulmonary fibrosis: Disease mechanisms and drug development. Pharmacol Ther 2021; 222:107798. [PMID: 33359599 PMCID: PMC8142468 DOI: 10.1016/j.pharmthera.2020.107798] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disease of unknown cause characterized by relentless scarring of the lung parenchyma leading to reduced quality of life and earlier mortality. IPF is an age-related disorder, and with the population aging worldwide, the economic burden of IPF is expected to steadily increase in the future. The mechanisms of fibrosis in IPF remain elusive, with favored concepts of disease pathogenesis involving recurrent microinjuries to a genetically predisposed alveolar epithelium, followed by an aberrant reparative response characterized by excessive collagen deposition. Pirfenidone and nintedanib are approved for treatment of IPF based on their ability to slow functional decline and disease progression; however, they do not offer a cure and are associated with tolerability issues. In this review, we critically discuss how cutting-edge research in disease pathogenesis may translate into identification of new therapeutic targets, thus facilitate drug discovery. There is a growing portfolio of treatment options for IPF. However, targeting the multitude of profibrotic cytokines and growth factors involved in disease pathogenesis may require a combination of therapeutic strategies with different mechanisms of action.
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Affiliation(s)
- Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy.
| | | | - Mark G Jones
- NIHR Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Joyce S Lee
- University of Colorado, School of Medicine, Department of Medicine, Aurora, CO, United States
| | - Giulio Rossi
- Pathology Unit, AUSL della Romagna, St. Maria delle Croci Hospital, Ravenna, Italy
| | | | - Toby M Maher
- National Heart and Lung Institute, Imperial College London and National Institute for Health Research Clinical Research Facility, Royal Brompton Hospital, London, UK; Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Argyrios Tzouvelekis
- Department of Respiratory Medicine, University Hospital of Patras, Patras, Greece
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia and Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, Canada
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20
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Baratella E, Ruaro B, Giudici F, Wade B, Santagiuliana M, Salton F, Confalonieri P, Simbolo M, Scarpa A, Tollot S, Marrocchio C, Cova MA, Confalonieri M. Evaluation of Correlations between Genetic Variants and High-Resolution Computed Tomography Patterns in Idiopathic Pulmonary Fibrosis. Diagnostics (Basel) 2021; 11:diagnostics11050762. [PMID: 33922858 PMCID: PMC8146750 DOI: 10.3390/diagnostics11050762] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background. Idiopathic pulmonary fibrosis (IPF) is a progressive fibrosing interstitial lung disease (ILD). This prospective observational study aimed at the evaluation of any correlation between genetic variants associated with IPF susceptibility and high-resolution computed tomography (HRCT) patterns. It also aimed at evidencing any differences in the HRTC pattern between the familial and sporadic form at diagnosis and after two years. Methods. A total of 65 IPF patients (mean age at diagnosis 65 ± 10) were enrolled after having given written informed consent. HRCT and genetic evaluations were performed. Results. A total of 19 familial (mean age 62 ± 15) and 46 sporadic (mean age 70 ± 9) IPF patients were enrolled. A statistically significant difference was evidenced in the HRTC pattern at diagnosis between the two groups. Sporadic IPF patients had a predominantly usual interstitial pneumonia (UIP) pattern compared with those patients with familial IPF (60.0% vs. 21.1%, respectively). Moreover, familial IPF patients had more alternative diagnoses than those with sporadic IPF (31.6% vs. 2.2%, respectively). Furthermore, there was a slight increase in the typical UIP pattern in the familial IPF group at two years from diagnosis. Conclusions. Genetic factors play a pivotal role in the risk of developing IPF. However, further studies are required to clarify how these genetic factors may guide clinical treatment decisions.
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Affiliation(s)
- Elisa Baratella
- Department of Radiology, Cattinara Hospital, University of Trieste, 34127 Trieste, Italy; (S.T.); (C.M.); (M.A.C.)
- Correspondence: ; Tel.: +39-040-399-4372
| | - Barbara Ruaro
- Department of Pulmonology, University Hospital of Cattinara, 34127 Trieste, Italy; (B.R.); (M.S.); (F.S.); (P.C.); (M.C.)
| | - Fabiola Giudici
- Biostatistics Unit, Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, 34127 Trieste, Italy;
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, 35131 Padua, Italy
| | - Barbara Wade
- AOU City of Health and Science of Turin, Department of Science of Public Health and Pediatrics, University of Torino, 10126 Torino, Italy;
| | - Mario Santagiuliana
- Department of Pulmonology, University Hospital of Cattinara, 34127 Trieste, Italy; (B.R.); (M.S.); (F.S.); (P.C.); (M.C.)
| | - Francesco Salton
- Department of Pulmonology, University Hospital of Cattinara, 34127 Trieste, Italy; (B.R.); (M.S.); (F.S.); (P.C.); (M.C.)
| | - Paola Confalonieri
- Department of Pulmonology, University Hospital of Cattinara, 34127 Trieste, Italy; (B.R.); (M.S.); (F.S.); (P.C.); (M.C.)
| | - Michele Simbolo
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, 37219 Verona, Italy; (M.S.); (A.S.)
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, 37219 Verona, Italy; (M.S.); (A.S.)
| | - Saverio Tollot
- Department of Radiology, Cattinara Hospital, University of Trieste, 34127 Trieste, Italy; (S.T.); (C.M.); (M.A.C.)
| | - Cristina Marrocchio
- Department of Radiology, Cattinara Hospital, University of Trieste, 34127 Trieste, Italy; (S.T.); (C.M.); (M.A.C.)
| | - Maria Assunta Cova
- Department of Radiology, Cattinara Hospital, University of Trieste, 34127 Trieste, Italy; (S.T.); (C.M.); (M.A.C.)
| | - Marco Confalonieri
- Department of Pulmonology, University Hospital of Cattinara, 34127 Trieste, Italy; (B.R.); (M.S.); (F.S.); (P.C.); (M.C.)
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21
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Si X, Steffes LC, Schymick JC, Hazard FK, Tracy MC, Cornfield DN. Three Infants with Pathogenic Variants in the ABCA3 Gene: Presentation, Treatment, and Clinical Course. J Pediatr 2021; 231:278-283.e2. [PMID: 33359301 PMCID: PMC8031471 DOI: 10.1016/j.jpeds.2020.12.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/17/2020] [Indexed: 11/29/2022]
Abstract
ABCA3 deficiency is a rare cause of neonatal respiratory failure. Biallelic complete loss of function variants lead to neonatal demise without lung transplantation, but children with partial function variants have variable outcomes. The favorable clinical course of 3 such infants presenting with respiratory distress at birth is described.
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Affiliation(s)
- Xin Si
- Division of Pediatric Pulmonary, Center for Excellence in Pulmonary Biology, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Lucile Packard Children's Hospital at Stanford University, Stanford, CA.
| | - Lea C Steffes
- Division of Pediatric Pulmonary, Center for Excellence in Pulmonary Biology, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Lucile Packard Children's Hospital at Stanford University, Stanford, CA
| | - Jennifer C Schymick
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Lucile Packard Children's Hospital at Stanford University, Stanford, CA
| | - Florette K Hazard
- Division of Pathology, Department of Pediatrics, Stanford University School of Medicine, Lucile Packard Children's Hospital at Stanford University, Stanford, CA
| | - Michael C Tracy
- Division of Pediatric Pulmonary, Center for Excellence in Pulmonary Biology, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Lucile Packard Children's Hospital at Stanford University, Stanford, CA
| | - David N Cornfield
- Division of Pediatric Pulmonary, Center for Excellence in Pulmonary Biology, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Lucile Packard Children's Hospital at Stanford University, Stanford, CA
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22
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van Moorsel CHM, van der Vis JJ, Grutters JC. Genetic disorders of the surfactant system: focus on adult disease. Eur Respir Rev 2021; 30:30/159/200085. [PMID: 33597124 DOI: 10.1183/16000617.0085-2020] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Genes involved in the production of pulmonary surfactant are crucial for the development and maintenance of healthy lungs. Germline mutations in surfactant-related genes cause a spectrum of severe monogenic pulmonary diseases in patients of all ages. The majority of affected patients present at a very young age, however, a considerable portion of patients have adult-onset disease. Mutations in surfactant-related genes are present in up to 8% of adult patients with familial interstitial lung disease (ILD) and associate with the development of pulmonary fibrosis and lung cancer.High disease penetrance and variable expressivity underscore the potential value of genetic analysis for diagnostic purposes. However, scarce genotype-phenotype correlations and insufficient knowledge of mutation-specific pathogenic processes hamper the development of mutation-specific treatment options.This article describes the genetic origin of surfactant-related lung disease and presents spectra for gene, age, sex and pulmonary phenotype of adult carriers of germline mutations in surfactant-related genes.
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Affiliation(s)
- Coline H M van Moorsel
- Dept of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, The Netherlands.,Division of Hearts and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joanne J van der Vis
- Dept of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, The Netherlands.,Dept of Clinical Chemistry, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, The Netherlands
| | - Jan C Grutters
- Dept of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, The Netherlands.,Division of Hearts and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
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23
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Dhindsa RS, Mattsson J, Nag A, Wang Q, Wain LV, Allen R, Wigmore EM, Ibanez K, Vitsios D, Deevi SVV, Wasilewski S, Karlsson M, Lassi G, Olsson H, Muthas D, Monkley S, Mackay A, Murray L, Young S, Haefliger C, Maher TM, Belvisi MG, Jenkins G, Molyneaux PL, Platt A, Petrovski S. Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis. Commun Biol 2021; 4:392. [PMID: 33758299 PMCID: PMC7988141 DOI: 10.1038/s42003-021-01910-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disorder characterised by progressive, destructive lung scarring. Despite substantial progress, the genetic determinants of this disease remain incompletely defined. Using whole genome and whole exome sequencing data from 752 individuals with sporadic IPF and 119,055 UK Biobank controls, we performed a variant-level exome-wide association study (ExWAS) and gene-level collapsing analyses. Our variant-level analysis revealed a novel association between a rare missense variant in SPDL1 and IPF (NM_017785.5:g.169588475 G > A p.Arg20Gln; p = 2.4 × 10-7, odds ratio = 2.87, 95% confidence interval: 2.03-4.07). This signal was independently replicated in the FinnGen cohort, which contains 1028 cases and 196,986 controls (combined p = 2.2 × 10-20), firmly associating this variant as an IPF risk allele. SPDL1 encodes Spindly, a protein involved in mitotic checkpoint signalling during cell division that has not been previously described in fibrosis. To the best of our knowledge, these results highlight a novel mechanism underlying IPF, providing the potential for new therapeutic discoveries in a disease of great unmet need.
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Affiliation(s)
- Ryan S Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Johan Mattsson
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences George Davies Centre, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Richard Allen
- Genetic Epidemiology Group, Department of Health Sciences George Davies Centre, University of Leicester, Leicester, UK
| | - Eleanor M Wigmore
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kristina Ibanez
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sri V V Deevi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sebastian Wasilewski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Maria Karlsson
- Lung Regeneration, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Glenda Lassi
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Henric Olsson
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Daniel Muthas
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Susan Monkley
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alex Mackay
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lynne Murray
- Lung Regeneration, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Simon Young
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Carolina Haefliger
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Toby M Maher
- Royal Brompton Hospital, London, UK
- Hastings Centre for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maria G Belvisi
- National Heart and Lung Institute, Imperial College, London, UK
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Respiratory Pharmacology Group, London, UK
| | - Gisli Jenkins
- Respiratory Research Unit, Division of Respiratory Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Philip L Molyneaux
- Royal Brompton Hospital, London, UK.
- National Heart and Lung Institute, Imperial College, London, UK.
| | - Adam Platt
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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24
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Pardo A, Selman M. The Interplay of the Genetic Architecture, Aging, and Environmental Factors in the Pathogenesis of Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 64:163-172. [PMID: 32946290 DOI: 10.1165/rcmb.2020-0373ps] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic fibrosing lung disease of indeterminate etiology and limited therapeutic options. The initiation, development, and progression of IPF are influenced by genetic predisposition, aging, and host and environmental factors, but the magnitude of the contribution of each of them and the sequence of the pathogenic events are uncertain. Current evidence indicates that accumulated environmental exposures in a genetically predisposed individual, usually over 60 years of age, leads to phenotypic and functional alterations of the lung epithelium. Aberrant activation of epithelial cells results, through a complex release of numerous mediators, in the local expansion of peculiar subsets of aggressive fibroblasts and myofibroblasts, which are crucial effector cells of fibrotic remodeling and loss of the normal lung architecture and function. Progressive increase of the mechanical stiffness activates cell-autonomous and matrix-dependent processes contributing to the perpetuation of the fibrotic response. This Perspective provides an integral overview of the major risk factors underpinning the pathogenesis of IPF, including gene variants, aging alterations, environmental factors, host risk factors, and epigenetic reprogramming.
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Affiliation(s)
- Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, Mexico; and
| | - Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," México City, Mexico
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25
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Role of various imbalances centered on alveolar epithelial cell/fibroblast apoptosis imbalance in the pathogenesis of idiopathic pulmonary fibrosis. Chin Med J (Engl) 2021; 134:261-274. [PMID: 33522725 PMCID: PMC7846426 DOI: 10.1097/cm9.0000000000001288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There have been recent extensive studies and rapid advancement on the pathogenesis underlying idiopathic pulmonary fibrosis (IPF), and intricate pathogenesis of IPF has been suggested. The purpose of this study was to clarify the logical relationship between these mechanisms. An extensive search was undertaken of the PubMed using the following keywords: “etiology,” “pathogenesis,” “alveolar epithelial cell (AEC),” “fibroblast,” “lymphocyte,” “macrophage,” “epigenomics,” “histone,” acetylation,” “methylation,” “endoplasmic reticulum stress,” “mitochondrial dysfunction,” “telomerase,” “proteases,” “plasminogen,” “epithelial-mesenchymal transition,” “oxidative stress,” “inflammation,” “apoptosis,” and “idiopathic pulmonary fibrosis.” This search covered relevant research articles published up to April 30, 2020. Original articles, reviews, and other articles were searched and reviewed for content; 240 highly relevant studies were obtained after screening. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors: environmental exposures affect epigenetic marks; epigenetic processes translate environmental exposures into the regulation of chromatin; epigenetic processes shape gene expression profiles; in turn, an individual's genetic background determines epigenetic marks; finally, these genetic and epigenetic factors act in concert to dysregulate gene expression in IPF lung tissue. The pathogenesis of IPF involves various imbalances including endoplasmic reticulum, telomere length homeostasis, mitochondrial dysfunction, oxidant/antioxidant imbalance, Th1/Th2 imbalance, M1–M2 polarization of macrophages, protease/antiprotease imbalance, and plasminogen activation/inhibition imbalance. These affect each other, promote each other, and ultimately promote AEC/fibroblast apoptosis imbalance directly or indirectly. Excessive AEC apoptosis and impaired apoptosis of fibroblasts contribute to fibrosis. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors. The pathogenesis of IPF involves various imbalances centered on AEC/fibroblast apoptosis imbalance.
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26
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Legendre M, Butt A, Borie R, Debray MP, Bouvry D, Filhol-Blin E, Desroziers T, Nau V, Copin B, Dastot-Le Moal F, Héry M, Duquesnoy P, Allou N, Bergeron A, Bermudez J, Cazes A, Chene AL, Cottin V, Crestani B, Dalphin JC, Dombret C, Doray B, Dupin C, Giraud V, Gondouin A, Gouya L, Israël-Biet D, Kannengiesser C, Le Borgne A, Leroy S, Longchampt E, Lorillon G, Nunes H, Picard C, Reynaud-Gaubert M, Traclet J, de Vuyst P, Coulomb L'Hermine A, Clement A, Amselem S, Nathan N. Functional assessment and phenotypic heterogeneity of SFTPA1 and SFTPA2 mutations in interstitial lung diseases and lung cancer. Eur Respir J 2020; 56:13993003.02806-2020. [PMID: 32855221 DOI: 10.1183/13993003.02806-2020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Interstitial lung diseases (ILDs) can be caused by mutations in the SFTPA1 and SFTPA2 genes, which encode the surfactant protein (SP) complex SP-A. Only 11 SFTPA1 or SFTPA2 mutations have so far been reported worldwide, of which five have been functionally assessed. In the framework of ILD molecular diagnosis, we identified 14 independent patients with pathogenic SFTPA1 or SFTPA2 mutations. The present study aimed to functionally assess the 11 different mutations identified and to accurately describe the disease phenotype of the patients and their affected relatives. METHODS The consequences of the 11 SFTPA1 or SFTPA2 mutations were analysed both in vitro, by studying the production and secretion of the corresponding mutated proteins and ex vivo, by analysing SP-A expression in lung tissue samples. The associated disease phenotypes were documented. RESULTS For the 11 identified mutations, protein production was preserved but secretion was abolished. The expression pattern of lung SP-A available in six patients was altered and the family history reported ILD and/or lung adenocarcinoma in 13 out of 14 families (93%). Among the 28 SFTPA1 or SFTPA2 mutation carriers, the mean age at ILD onset was 45 years (range 0.6-65 years) and 48% underwent lung transplantation (mean age 51 years). Seven carriers were asymptomatic. DISCUSSION This study, which expands the molecular and clinical spectrum of SP-A disorders, shows that pathogenic SFTPA1 or SFTPA2 mutations share similar consequences for SP-A secretion in cell models and in lung tissue immunostaining, whereas they are associated with a highly variable phenotypic expression of disease, ranging from severe forms requiring lung transplantation to incomplete penetrance.
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Affiliation(s)
- Marie Legendre
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France.,Dept of Genetics, Armand Trousseau Hospital, Sorbonne University, Assistance Publique Hôpitaux de Paris (APHP), Paris, France.,Both authors contributed equally
| | - Afifaa Butt
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France.,Both authors contributed equally
| | - Raphaël Borie
- Pulmonology Dept A, Bichat Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Marie-Pierre Debray
- Radiology Dept, Bichat Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Diane Bouvry
- Pulmonology Dept, EA 2363, Avicenne Hospital, Assistance Publique Hôpitaux de Paris (APHP), Paris 13 University, COMUE Sorbonne Paris Cité, Bobigny, France
| | - Emilie Filhol-Blin
- Dept of Genetics, Armand Trousseau Hospital, Sorbonne University, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Tifenn Desroziers
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France
| | - Valérie Nau
- Dept of Genetics, Armand Trousseau Hospital, Sorbonne University, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Bruno Copin
- Dept of Genetics, Armand Trousseau Hospital, Sorbonne University, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Florence Dastot-Le Moal
- Dept of Genetics, Armand Trousseau Hospital, Sorbonne University, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Mélanie Héry
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France
| | - Philippe Duquesnoy
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France
| | - Nathalie Allou
- Pulmonology Dept, Felix Guyon Hospital, Saint Denis de La Reunion, France
| | - Anne Bergeron
- Pulmonology Dept, Saint Louis Hospital, Université de Paris, Paris, France
| | - Julien Bermudez
- Pulmonology Dept and Lung Transplant Team, North Hospital - Assistance Publique Hôpitaux de Marseille (APHM), Marseille - MEPHI, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Aurélie Cazes
- Pathology Dept, Bichat Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | | | - Vincent Cottin
- Pulmonology Dept and Coordinating Reference Center for Rare Pulmonary Diseases OrphaLung, Hospices Civils de Lyon, Claude Bernard University Lyon 1, Lyon, France
| | - Bruno Crestani
- Radiology Dept, Bichat Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Jean-Charles Dalphin
- Pulmonology Dept, UMR-CNRS Chrono-Environnement 6249, CNRS and CHU, Besançon, France
| | - Christine Dombret
- Radiology Dept, Bichat Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Bérénice Doray
- Genetic Dept, Felix Guyon Hospital, Saint Denis de La Reunion, France
| | - Clairelyne Dupin
- Pulmonology Dept, Saint Louis Hospital, Université de Paris, Paris, France
| | - Violaine Giraud
- Pulmonology Dept, Ambroise Paré Hospital, Assistance Publique Hôpitaux de Paris (APHP), Boulogne Billancourt, France
| | - Anne Gondouin
- Pulmonology Dept, UMR-CNRS Chrono-Environnement 6249, CNRS and CHU, Besançon, France
| | - Laurent Gouya
- Pulmonology Dept, Saint Louis Hospital, Université de Paris, Paris, France
| | - Dominique Israël-Biet
- Pulmonology Dept, Georges Pompidou European Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Caroline Kannengiesser
- Genetic Dept, Bichat Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | | | - Sylvie Leroy
- Pulmonology Dept, Pasteur Hospital, Nice, France
| | | | - Gwenaël Lorillon
- Pulmonology Dept, Saint Louis Hospital, Université de Paris, Paris, France
| | - Hilario Nunes
- Pulmonology Dept, EA 2363, Avicenne Hospital, Assistance Publique Hôpitaux de Paris (APHP), Paris 13 University, COMUE Sorbonne Paris Cité, Bobigny, France
| | | | - Martine Reynaud-Gaubert
- Pulmonology Dept and Lung Transplant Team, North Hospital - Assistance Publique Hôpitaux de Marseille (APHM), Marseille - MEPHI, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Julie Traclet
- Pulmonology Dept and Coordinating Reference Center for Rare Pulmonary Diseases OrphaLung, Hospices Civils de Lyon, Claude Bernard University Lyon 1, Lyon, France
| | - Paul de Vuyst
- Pulmonology Dept, Erasme Hospital, Brussels, Belgium
| | | | - Annick Clement
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France.,Pediatric Pulmonology Dept and Reference Center for Rare Lung Diseases RespiRare, Armand Trousseau Hospital, Paris, France
| | - Serge Amselem
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France.,Dept of Genetics, Armand Trousseau Hospital, Sorbonne University, Assistance Publique Hôpitaux de Paris (APHP), Paris, France.,Both authors contributed equally
| | - Nadia Nathan
- Sorbonne Université, Inserm Childhood Genetic Disorders, Armand Trousseau Hospital, Paris, France.,Pediatric Pulmonology Dept and Reference Center for Rare Lung Diseases RespiRare, Armand Trousseau Hospital, Paris, France.,Both authors contributed equally
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27
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Lou HQ, Huang CX, Li GY, Li P, Zhang SM, Li HG, Han L, Bao MH. The Association between MUC5B Rs35705950 and Risks of Idiopathic Interstitial Pneumonia, Systemic Sclerosis Interstitial Lung Disease, and Familial Interstitial Pneumonia: A Meta-Analysis. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:2240-2250. [PMID: 34178730 PMCID: PMC8215073 DOI: 10.18502/ijph.v49i12.4801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background: Interstitial lung disease (ILD) is a category of chronic lung diseases with more than 200 subtypes. Idiopathic interstitial pneumonia (IIP), systemic sclerosis (SSc) ILD, and familial interstitial pneumonia (FIP) are three major groups of lung diseases with different causes or with unknown causes. Mucin5B (MUC5B) belongs to the mucin family, which contribute to the lubricating and viscoelastic properties of the whole saliva, normal lung mucus, and cervical mucus. The association between MUC5B rs35705950 and ILDs risks has been widely studied. However, the results were inconclusive and inconsistent. Methods: In the present meta-analysis, the database PubMed, Embase, Cochrane Central Register of Controlled Trials, CNKI and Chinese Biomedical Literature Database were searched till Aug 20th, 2018. Overall 16 publications with 28 studies, 76345 cases and 18402 controls were included. Results: The results indicated a significant increase of overall IIP risk for TT genotype and T allele of the rs35705950 in all genetic models (TT vs GG, OR=9.11; TT vs GT+TT, OR=5.80; GT+TT vs GG, OR=4.34; T vs G, OR=4.03. P<0.0001). Subgroup analysis by subtypes of IIP revealed higher risks of TT genotype and T allele for IPF and iNSIP (P<0.05). A significant increase of FIP risk was also found for the TT genotype and T allele of the rs35705950 (TT vs GG, OR=17.08; GT+TT vs GG, OR=6.02; T vs G, OR=1.64.P<0.05). Conclusion: No significant relations existed between the rs35705950 and SSc-ILD risks. MUC5B rs35705950 might be a predictor for the susceptibility of IIP and FIP.
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Affiliation(s)
- Huai-Qing Lou
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China.,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410007, China
| | - Chun-Xia Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, 410007, China
| | - Guang-Yi Li
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Ping Li
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Shou-Ming Zhang
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Hai-Gang Li
- Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China
| | - Li Han
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410007, China
| | - Mei-Hua Bao
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China
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Nathan N, Berdah L, Delestrain C, Sileo C, Clement A. Interstitial lung diseases in children. Presse Med 2020; 49:103909. [PMID: 32563946 DOI: 10.1016/j.lpm.2019.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023] Open
Abstract
Interstitial lung disease (ILD) in children (chILD) is a heterogeneous group of rare respiratory disorders that are mostly chronic and associated with high morbidity and mortality. The pathogenesis of the various chILD is complex and the diseases share common features of inflammatory and fibrotic changes of the lung parenchyma that impair gas exchanges. The etiologies of chILD are numerous. In this review, we chose to classify them as ILD related to exposure/environment insults, ILD related to systemic and immunological diseases, ILD related to primary lung parenchyma dysfunctions and ILD specific to infancy. A growing part of the etiologic spectrum of chILD is being attributed to molecular defects. Currently, the main genetic mutations associated with chILD are identified in the surfactant genes SFTPA1, SFTPA2, SFTPB, SFTPC, ABCA3 and NKX2-1. Other genetic contributors include mutations in MARS, CSF2RA and CSF2RB in pulmonary alveolar proteinosis, and mutations in TMEM173 and COPA in specific auto-inflammatory forms of chILD. However, only few genotype-phenotype correlations could be identified so far. Herein, information is provided about the clinical presentation and the diagnosis approach of chILD. Despite improvements in patient management, the therapeutic strategies are still relying mostly on corticosteroids although specific therapies are emerging. Larger longitudinal cohorts of patients are being gathered through ongoing international collaborations to improve disease knowledge and targeted therapies. Thus, it is expected that children with ILD will be able to reach the adulthood transition in a better condition.
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Affiliation(s)
- Nadia Nathan
- Pediatric pulmonology department, Trousseau hospital, reference center for rare lung diseases RespiRare, Assistance publique-Hôpitaux de Paris (AP-HP), , 75012 Paris, France; Sorbonne université and Inserm UMRS933, 75012 Paris, France
| | - Laura Berdah
- Pediatric pulmonology department, Trousseau hospital, reference center for rare lung diseases RespiRare, Assistance publique-Hôpitaux de Paris (AP-HP), , 75012 Paris, France; Sorbonne université and Inserm UMRS933, 75012 Paris, France
| | - Céline Delestrain
- Pediatric pulmonology department, Trousseau hospital, reference center for rare lung diseases RespiRare, Assistance publique-Hôpitaux de Paris (AP-HP), , 75012 Paris, France
| | - Chiara Sileo
- Radiology department, AP-HP, Trousseau hospital, 75012 Paris, France
| | - Annick Clement
- Pediatric pulmonology department, Trousseau hospital, reference center for rare lung diseases RespiRare, Assistance publique-Hôpitaux de Paris (AP-HP), , 75012 Paris, France; Sorbonne université and Inserm UMRS933, 75012 Paris, France.
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29
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Allen RJ, Guillen-Guio B, Oldham JM, Ma SF, Dressen A, Paynton ML, Kraven LM, Obeidat M, Li X, Ng M, Braybrooke R, Molina-Molina M, Hobbs BD, Putman RK, Sakornsakolpat P, Booth HL, Fahy WA, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Whyte MKB, Zhang Y, Kaminski N, Adegunsoye A, Strek ME, Neighbors M, Sheng XR, Gudmundsson G, Gudnason V, Hatabu H, Lederer DJ, Manichaikul A, Newell JD, O’Connor GT, Ortega VE, Xu H, Fingerlin TE, Bossé Y, Hao K, Joubert P, Nickle DC, Sin DD, Timens W, Furniss D, Morris AP, Zondervan KT, Hall IP, Sayers I, Tobin MD, Maher TM, Cho MH, Hunninghake GM, Schwartz DA, Yaspan BL, Molyneaux PL, Flores C, Noth I, Jenkins RG, Wain LV. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2020; 201:564-574. [PMID: 31710517 PMCID: PMC7047454 DOI: 10.1164/rccm.201905-1017oc] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/07/2019] [Indexed: 01/10/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a complex lung disease characterized by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. Genome-wide association studies have reported signals of association implicating multiple pathways including host defense, telomere maintenance, signaling, and cell-cell adhesion.Objectives: To improve our understanding of factors that increase IPF susceptibility by identifying previously unreported genetic associations.Methods: We conducted genome-wide analyses across three independent studies and meta-analyzed these results to generate the largest genome-wide association study of IPF to date (2,668 IPF cases and 8,591 controls). We performed replication in two independent studies (1,456 IPF cases and 11,874 controls) and functional analyses (including statistical fine-mapping, investigations into gene expression, and testing for enrichment of IPF susceptibility signals in regulatory regions) to determine putatively causal genes. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF.Measurements and Main Results: We identified and replicated three new genome-wide significant (P < 5 × 10-8) signals of association with IPF susceptibility (associated with altered gene expression of KIF15, MAD1L1, and DEPTOR) and confirmed associations at 11 previously reported loci. Polygenic risk score analyses showed that the combined effect of many thousands of as yet unreported IPF susceptibility variants contribute to IPF susceptibility.Conclusions: The observation that decreased DEPTOR expression associates with increased susceptibility to IPF supports recent studies demonstrating the importance of mTOR signaling in lung fibrosis. New signals of association implicating KIF15 and MAD1L1 suggest a possible role of mitotic spindle-assembly genes in IPF susceptibility.
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Affiliation(s)
- Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Justin M. Oldham
- Department of Internal Medicine, University of California Davis, Davis, California
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine
| | | | - Megan L. Paynton
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Luke M. Kraven
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences
| | - Rebecca Braybrooke
- Division of Epidemiology and Public Health and
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Brian D. Hobbs
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Helen L. Booth
- Department of Thoracic Medicine, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - William A. Fahy
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | - Simon P. Hart
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, United Kingdom
| | - Mike R. Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health
| | - Nik Hirani
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Richard B. Hubbard
- Division of Epidemiology and Public Health and
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Robin J. McAnulty
- UCL Respiratory Centre for Inflammation and Tissue Repair, University College London, London, United Kingdom
| | - Ann B. Millar
- Academic Respiratory Unit, School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
| | - Vidyia Navaratnam
- Division of Epidemiology and Public Health and
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Eunice Oballa
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | - Helen Parfrey
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Gauri Saini
- Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Moira K. B. Whyte
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine and
- Simmons Center for Interstitial Lung Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Mary E. Strek
- Section of Pulmonary and Critical Care, Department of Medicine, The University of Chicago, Chicago, Illinois
| | | | | | - Gunnar Gudmundsson
- Department of Respiratory Medicine, Landspital University Hospital, Reykjavik, Iceland
- Faculty of Medicine University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Faculty of Medicine University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Hiroto Hatabu
- Department of Radiology, and
- Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Boston, Massachusetts
| | - David J. Lederer
- Department of Medicine, College of Physicians and Surgeons and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Ani Manichaikul
- Center for Public Health Genomics, and
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - John D. Newell
- Division of Cardiovascular and Pulmonary Imaging, Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
- Department of Radiology, University of Washington, Seattle, Washington
| | - George T. O’Connor
- Department of Medicine, Pulmonary Center, Boston University, Boston, Massachusetts
- NHLBI’s Framingham Heart Study, Framingham, Massachusetts
| | - Victor E. Ortega
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colarado
- Department of Biostatistics and Informatics
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, Québec, Canada
| | - Ke Hao
- Department of Genetics and Genomic Sciences and
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, Québec, Canada
| | - David C. Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, Massachusetts
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology and
- Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences
| | - Andrew P. Morris
- Wellcome Centre for Human Genetics, and
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
- Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, United Kingdom
| | - Krina T. Zondervan
- Wellcome Centre for Human Genetics, and
- Oxford Endometriosis Care and Research Centre, Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Toby M. Maher
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom; and
| | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | - Gary M. Hunninghake
- Division of Pulmonary and Critical Care Medicine
- Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Boston, Massachusetts
| | - David A. Schwartz
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colarado
- Department of Medicine, and
- Department of Immunology, University of Colorado Denver, Denver, Colorado
| | | | - Philip L. Molyneaux
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom; and
| | - Carlos Flores
- Unidad de Investigacion, Hospital Universitario Ntra. Sra. de Candelaria and
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Tecnológico y de Energías Renovables, S.A., Santa Cruz de Tenerife, Spain
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine
| | - R. Gisli Jenkins
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
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Idiopathic Pulmonary Fibrosis: Pathogenesis and the Emerging Role of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21020524. [PMID: 31947693 PMCID: PMC7013390 DOI: 10.3390/ijms21020524] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive chronic disease characterized by excessing scarring of the lungs leading to irreversible decline in lung function. The aetiology and pathogenesis of the disease are still unclear, although lung fibroblast and epithelial cell activation, as well as the secretion of fibrotic and inflammatory mediators, have been strongly associated with the development and progression of IPF. Significantly, long non-coding RNAs (lncRNAs) are emerging as modulators of multiple biological processes, although their function and mechanism of action in IPF is poorly understood. LncRNAs have been shown to be important regulators of several diseases and their aberrant expression has been linked to the pathophysiology of fibrosis including IPF. This review will provide an overview of this emerging role of lncRNAs in the development of IPF.
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31
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Ley B, Torgerson DG, Oldham JM, Adegunsoye A, Liu S, Li J, Elicker BM, Henry TS, Golden JA, Jones KD, Dressen A, Yaspan BL, Arron JR, Noth I, Hoffmann TJ, Wolters PJ. Rare Protein-Altering Telomere-related Gene Variants in Patients with Chronic Hypersensitivity Pneumonitis. Am J Respir Crit Care Med 2019; 200:1154-1163. [PMID: 31268371 PMCID: PMC6888660 DOI: 10.1164/rccm.201902-0360oc] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/02/2019] [Indexed: 12/30/2022] Open
Abstract
Rationale: Rare genetic variants in telomere-related genes have been identified in familial, idiopathic, and rheumatoid arthritis-associated pulmonary fibrosis. Short peripheral blood leukocyte (PBL) telomere length predicts poor outcomes in chronic hypersensitivity pneumonitis (CHP).Objectives: Determine the prevalence and clinical relevance of rare protein-altering variants in telomere-related genes in patients with CHP.Methods: Next-generation sequences from two CHP cohorts were analyzed to identify variants in TERT (telomerase reverse transcriptase), TERC (telomerase RNA component), DKC1 (dyskerin pseudouridine synthase 1), RTEL1 (regulator of telomere elongation helicase 1), PARN (poly[A]-specific RNase), and TINF2 (TERF1-interacting nuclear factor 2). To qualify, variants were required to have a minor allele frequency less than 0.005 and be predicted to be damaging to protein function. Variant status (binary variable) was used in statistical association tests, including Cox proportional hazard models for transplant-free survival. PBL telomere length was measured using quantitative PCR.Measurements and Main Results: Qualifying variants were identified in 16 of 144 patients (11.1%; 95% confidence interval [CI], 6.5-17.4) in the discovery cohort and 17 of 209 patients (8.1%; 95% CI, 4.8-12.7) in the replication cohort. Age- and ancestry-adjusted PBL telomere length was significantly shorter in the presence of a variant in both cohorts (discovery: -561 bp; 95% CI, -933 to -190; P = 0.003; replication: -612 bp; 95% CI, -870 to -354; P = 5.30 × 10-6). Variant status was significantly associated with transplant-free survival in both cohorts (discovery: age-, sex-, and ancestry-adjusted hazard ratio, 3.73; 95% CI, 1.92-7.28; P = 0.0001; replication: hazard ratio, 2.72; 95% CI, 1.26-5.88; P = 0.011).Conclusions: A substantial proportion of patients diagnosed with CHP have rare, protein-altering variants in telomere-related genes, which are associated with short peripheral blood telomere length and significantly reduced transplant-free survival.
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Affiliation(s)
| | - Dara G. Torgerson
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Justin M. Oldham
- Department of Medicine, University of California Davis, Davis, California
| | | | - Shuo Liu
- Department of Respiratory Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| | - Jie Li
- University of California Davis Bioinformatics Core, Davis, California
| | | | | | | | | | - Amy Dressen
- Genentech, South San Francisco, California; and
| | | | | | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California San Francisco, San Francisco, California
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32
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Nathan N, Sileo C, Thouvenin G, Berdah L, Delestrain C, Manali E, Papiris S, Léger PL, Pointe HDL, l'Hermine AC, Clement A. Pulmonary Fibrosis in Children. J Clin Med 2019; 8:E1312. [PMID: 31455000 PMCID: PMC6780823 DOI: 10.3390/jcm8091312] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
: Pulmonary fibrosis (PF) is a very rare condition in children, which may be observed in specific forms of interstitial lung disease. None of the clinical, radiological, or histological descriptions used for PF diagnosis in adult patients, especially in situations of idiopathic PF, can apply to pediatric situations. This observation supports the view that PF expression may differ with age and, most likely, may cover distinct entities. The present review aims at summarizing the current understanding of PF pathophysiology in children and identifying suitable diagnostic criteria.
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Affiliation(s)
- Nadia Nathan
- Pediatric Pulmonology Department, Reference Center for Rare Lung Diseases (RespiRare), Armand Trousseau Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), 75012 Paris, France.
- Inserm UMR_S933, Sorbonne Université, 75012 Paris, France.
| | - Chiara Sileo
- Pediatric Radiology Department, Armand Trousseau Hospital, AP-HP, 75012 Paris, France
| | - Guillaume Thouvenin
- Pediatric Pulmonology Department, Reference Center for Rare Lung Diseases (RespiRare), Armand Trousseau Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), 75012 Paris, France
| | - Laura Berdah
- Pediatric Pulmonology Department, Reference Center for Rare Lung Diseases (RespiRare), Armand Trousseau Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), 75012 Paris, France
| | - Céline Delestrain
- Pediatric Pulmonology Department, Reference Center for Rare Lung Diseases (RespiRare), Armand Trousseau Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), 75012 Paris, France
| | - Effrosyne Manali
- nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Spyros Papiris
- nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Pierre-Louis Léger
- Intensive Care Unit, Armand Trousseau Hospital, AP-HP, 75012 Paris, France
| | | | | | - Annick Clement
- Pediatric Pulmonology Department, Reference Center for Rare Lung Diseases (RespiRare), Armand Trousseau Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), 75012 Paris, France
- Inserm UMR_S933, Sorbonne Université, 75012 Paris, France
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33
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Manali ED, Legendre M, Nathan N, Kannengiesser C, Coulomb-L'Hermine A, Tsiligiannis T, Tomos P, Griese M, Borie R, Clement A, Amselem S, Crestani B, Papiris SA. Bi-allelic missense ABCA3 mutations in a patient with childhood ILD who reached adulthood. ERJ Open Res 2019; 5:00066-2019. [PMID: 31360696 PMCID: PMC6646961 DOI: 10.1183/23120541.00066-2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022] Open
Abstract
The adenosine triphosphate (ATP)-binding cassette subfamily A member 3 (ABCA3) is a transmembrane glycoprotein that uses energy of ATP hydrolysis to transport phospholipids into the lamellar bodies of type 2 alveolar epithelial cells (AEC) and regulates lung surfactant homeostasis. More than 200 mutations have already been described in ABCA3, located on chromosome 16 [1, 2]. Patients present with a great heterogeneity of phenotypes, from lethal neonatal respiratory distress syndrome (RDS) to childhood and rarely adult interstitial lung disease (ILD) [3, 4]. ABCA3 mutations-related lung disease inheritance is autosomal recessive, as it requires two disease-causing (bi-allelic) mutations, one from each parent. Children with ABCA3 mutations may survive beyond infancy and reach adulthood. Genetic mechanisms should always be examined in adult patients with childhood onset ILD and molecular analysis should be performed accordingly in specialised referral centres.http://bit.ly/2LzMNOE
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Affiliation(s)
- Effrosyni D Manali
- 2nd Pulmonary Medicine Dept, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Athens, Greece.,These authors contributed equally
| | - Marie Legendre
- Sorbonne Université, INSERM UMR_S933, and Assistance Publique Hôpitaux de Paris, Service de Génétique et d'Embryologie Médicales, Hôpital Armand Trousseau, Paris, France.,These authors contributed equally
| | - Nadia Nathan
- Sorbonne Université, INSERM UMR_S933, France, Assistance Publique Hôpitaux de Paris, Service de Pneumologie Pédiatrique, Hôpital Armand Trousseau, Centre National de Référence des Maladies Respiratoires Rares RespiRare, Paris, France
| | - Caroline Kannengiesser
- Service de Génétique, Hôpital Bichat, Assistance Publique Hôpitaux de Paris, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Aurore Coulomb-L'Hermine
- Service d'Anatomie et de Cytologie Pathologiques, Sorbonne Université, Hôpital d'Enfants Armand Trousseau, Paris, France
| | | | - Pericles Tomos
- Dept of Thoracic Surgery, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Matthias Griese
- Dept of Pediatric Pneumology, Dr von Hauner Children's Hospital, Ludwig-Maximilians-University, German Center for Lung Research, Munich, Germany
| | - Raphael Borie
- Service de Pneumologie A, Hôpital Bichat, Assistance Publique Hôpitaux de Paris, Centre de Référence des Maladies Pulmonaires Rares, Université Paris Diderot, Sorbonne Paris Cité, DHU FIRE, Paris, France
| | - Annick Clement
- Sorbonne Université, INSERM UMR_S933, France, Assistance Publique Hôpitaux de Paris, Service de Pneumologie Pédiatrique, Hôpital Armand Trousseau, Centre National de Référence des Maladies Respiratoires Rares RespiRare, Paris, France
| | - Serge Amselem
- Sorbonne Université, INSERM UMR_S933, and Assistance Publique Hôpitaux de Paris, Service de Génétique et d'Embryologie Médicales, Hôpital Armand Trousseau, Paris, France
| | - Bruno Crestani
- Service de Génétique, Hôpital Bichat, Assistance Publique Hôpitaux de Paris, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Service de Pneumologie A, Hôpital Bichat, Assistance Publique Hôpitaux de Paris, Centre de Référence des Maladies Pulmonaires Rares, Université Paris Diderot, Sorbonne Paris Cité, DHU FIRE, Paris, France.,These authors contributed equally
| | - Spyros A Papiris
- 2nd Pulmonary Medicine Dept, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Athens, Greece.,These authors contributed equally
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Allen R, Ortega VE. Resequencing to Fine Map Known Idiopathic Pulmonary Fibrosis Risk Genes. Homing in on Causal Variants. Am J Respir Crit Care Med 2019; 200:125-127. [PMID: 31113211 PMCID: PMC6635787 DOI: 10.1164/rccm.201905-0925ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Richard Allen
- 1 Department of Health Sciences University of Leicester Leicester, United Kingdom and
| | - Victor E Ortega
- 2 Department of Internal Medicine Center for Precision Medicine Winston-Salem, North Carolina
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Barros A, Oldham J, Noth I. Genetics of Idiopathic Pulmonary Fibrosis. Am J Med Sci 2019; 357:379-383. [PMID: 31010464 PMCID: PMC10538522 DOI: 10.1016/j.amjms.2019.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/28/2019] [Accepted: 02/10/2019] [Indexed: 01/02/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common form of interstitial lung disease. IPF is a complex disease, with environmental and genetic factors variably contributing to disease susceptibility and outcomes. A host of common gene variants with modest effect size impart disease risk in patients with sporadic IPF, while rare variants with large effect size influence disease risk in those with familial interstitial pneumonia. In this review, we highlight several common and rare variants underpinning IPF risk and call attention to recently published studies informing our understanding of this risk.
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Affiliation(s)
- Andrew Barros
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia.
| | - Justin Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The University of California at Davis, Sacramento, California.
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia.
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36
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Bowdish DM. The Aging Lung. Chest 2019; 155:391-400. [DOI: 10.1016/j.chest.2018.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/13/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
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Nathan N, Berdah L, Borensztajn K, Clement A. Chronic interstitial lung diseases in children: diagnosis approaches. Expert Rev Respir Med 2018; 12:1051-1060. [PMID: 30345849 DOI: 10.1080/17476348.2018.1538795] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Introduction: Children interstitial lung disease (chILD) is a heterogeneous group of rare respiratory disorders characterized by inflammatory and fibrotic changes of the lung parenchyma. They include ILD related to exposure/environment insults, ILD related to systemic diseases processes, ILD related to primary lung parenchyma dysfunctions and ILD specific to infancy. Areas covered: This review provides an update on chILD pathophysiology and diagnosis approaches in immunocompetent children. It includes current information on genetic causes. Expert commentary: ChILD covers a large spectrum of entities with heterogeneous disease expression. Various classifications have been reported, but none of them seems completely satisfactory. Recently, progress in molecular genetics has allowed identifying some genetic contributors, with, so far, a lack of correlations between gene disorders and disease expression. Despite improvements in patient management, chILD prognosis is still burdened by significant morbidity and mortality. Ongoing international collaborations will allow gathering larger longitudinal cohorts of patients to improve disease knowledge and personalized care. The overall goal is to help the children with ILD to reach the adulthood transition in a better condition, and to structure genetic counseling for their family.
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Affiliation(s)
- Nadia Nathan
- a Service de pneumologie pédiatrique, Centre national de référence des maladies respiratoires rares RespiRare , Hôpital Armand Trousseau, Assistance Publique Hôpitaux de Paris (AP-HP) , Paris , France.,b Sorbonne Université and Inserm UMRS933 , Paris , France
| | - Laura Berdah
- a Service de pneumologie pédiatrique, Centre national de référence des maladies respiratoires rares RespiRare , Hôpital Armand Trousseau, Assistance Publique Hôpitaux de Paris (AP-HP) , Paris , France
| | | | - Annick Clement
- a Service de pneumologie pédiatrique, Centre national de référence des maladies respiratoires rares RespiRare , Hôpital Armand Trousseau, Assistance Publique Hôpitaux de Paris (AP-HP) , Paris , France.,b Sorbonne Université and Inserm UMRS933 , Paris , France
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39
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Wain L. Towards genetic reclassification of idiopathic pulmonary fibrosis. THE LANCET. RESPIRATORY MEDICINE 2018; 6:569-570. [PMID: 29891357 DOI: 10.1016/s2213-2600(18)30173-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Louise Wain
- Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
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41
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Schindlbeck U, Wittmann T, Höppner S, Kinting S, Liebisch G, Hegermann J, Griese M. ABCA3 missense mutations causing surfactant dysfunction disorders have distinct cellular phenotypes. Hum Mutat 2018; 39:841-850. [PMID: 29505158 DOI: 10.1002/humu.23416] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/25/2018] [Accepted: 02/27/2018] [Indexed: 11/11/2022]
Abstract
Mutations in the ATP-binding cassette subfamily A member 3 (ABCA3) gene are the most common monogenetic cause of surfactant dysfunction disorders in newborns and interstitial lung diseases in children and young adults. Although the effect of mutations resulting in truncated or incomplete proteins can be predicted, the consequences of missense variants cannot be as easily. Our aim was to investigate the intracellular handling and disturbance of the cellular surfactant system in a stable cell model with several different clinically relevant ABCA3 missense mutations. We found that the investigated missense mutations within the ABCA3 gene affect surfactant homeostasis in different ways: first by disrupting intracellular ABCA3 protein localization (c.643C > A, p.Q215K; c.2279T > G, p.M760R), second by impairing the lipid transport of ABCA3 protein (c.875A > T, p.E292V; c.4164G > C, p.K1388N), and third by yet undetermined mechanisms predisposing for the development of interstitial lung diseases despite correct localization and normal lipid transport of the variant ABCA3 protein (c.622C > T, p.R208W; c.863G > A, p.R288K; c.2891G > A, p.G964D). In conclusion, we classified cellular consequences of missense ABCA3 sequence variations leading to pulmonary disease of variable severity. The corresponding molecular pathomechanisms of such ABCA3 variants may specifically be addressed by targeted treatments.
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Affiliation(s)
- Ulrike Schindlbeck
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, German Centre for Lung Research (DZL), Munich, Germany
| | - Thomas Wittmann
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, German Centre for Lung Research (DZL), Munich, Germany
| | - Stefanie Höppner
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, German Centre for Lung Research (DZL), Munich, Germany
| | - Susanna Kinting
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, German Centre for Lung Research (DZL), Munich, Germany
| | - Gerhard Liebisch
- Institute for Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, German Center for Lung Research (DZL), Hannover, Germany
| | - Matthias Griese
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, German Centre for Lung Research (DZL), Munich, Germany
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42
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Kropski JA, Young LR, Cogan JD, Mitchell DB, Lancaster LH, Worrell JA, Markin C, Liu N, Mason WR, Fingerlin TE, Schwartz DA, Lawson WE, Blackwell TS, Phillips JA, Loyd JE. Genetic Evaluation and Testing of Patients and Families with Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2017; 195:1423-1428. [PMID: 27786550 DOI: 10.1164/rccm.201609-1820pp] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Jonathan A Kropski
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Lisa R Young
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine.,2 Division of Pulmonary Medicine and
| | - Joy D Cogan
- 3 Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, and
| | - Daphne B Mitchell
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Lisa H Lancaster
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - John A Worrell
- 4 Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cheryl Markin
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Na Liu
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Wendi R Mason
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Tasha E Fingerlin
- 5 Department of Biomedical Research, National Jewish Health, Denver, Colorado
| | - David A Schwartz
- 6 Department of Medicine, University of Colorado, Denver, Colorado
| | - William E Lawson
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine.,7 Department of Veterans Affairs Medical Center, Nashville, Tennessee; and
| | - Timothy S Blackwell
- 7 Department of Veterans Affairs Medical Center, Nashville, Tennessee; and.,8 Department of Cancer Biology.,9 Department of Cell and Developmental Biology, and
| | - John A Phillips
- 3 Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, and.,10 Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - James E Loyd
- 1 Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
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43
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Mora AL, Rojas M, Pardo A, Selman M. Emerging therapies for idiopathic pulmonary fibrosis, a progressive age-related disease. Nat Rev Drug Discov 2017; 16:810. [PMID: 29081515 DOI: 10.1038/nrd.2017.225] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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44
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Mora AL, Rojas M, Pardo A, Selman M. Emerging therapies for idiopathic pulmonary fibrosis, a progressive age-related disease. Nat Rev Drug Discov 2017; 16:755-772. [DOI: 10.1038/nrd.2017.170] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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45
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Helling BA, Gerber AN, Kadiyala V, Sasse SK, Pedersen BS, Sparks L, Nakano Y, Okamoto T, Evans CM, Yang IV, Schwartz DA. Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2017; 57:91-99. [PMID: 28272906 DOI: 10.1165/rcmb.2017-0046oc] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The gain-of-function mucin 5B (MUC5B) promoter variant, rs35705950, confers the largest risk, genetic or otherwise, for the development of idiopathic pulmonary fibrosis; however, the mechanisms underlying the regulation of MUC5B expression have yet to be elucidated. Here, we identify a critical regulatory domain that contains the MUC5B promoter variant and has a highly conserved forkhead box protein A2 (FOXA2) binding motif. This region is differentially methylated in association with idiopathic pulmonary fibrosis, MUC5B expression, and rs35705950. In addition, we show that this locus binds FOXA2 dynamically, and that binding of FOXA2 is necessary for enhanced expression of MUC5B. In aggregate, our findings identify novel targets to regulate the expression of MUC5B.
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Affiliation(s)
- Britney A Helling
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Anthony N Gerber
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Vineela Kadiyala
- 2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Sarah K Sasse
- 2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Brent S Pedersen
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Lenore Sparks
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Yasushi Nakano
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Tsukasa Okamoto
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Christopher M Evans
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Ivana V Yang
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,3 University of Colorado-Denver, School of Public Health, Denver, Colorado
| | - David A Schwartz
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,2 Department of Medicine, National Jewish Health, Denver, Colorado; and
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46
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Petrovski S, Todd JL, Durheim MT, Wang Q, Chien JW, Kelly FL, Frankel C, Mebane CM, Ren Z, Bridgers J, Urban TJ, Malone CD, Finlen Copeland A, Brinkley C, Allen AS, O'Riordan T, McHutchison JG, Palmer SM, Goldstein DB. An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis. Am J Respir Crit Care Med 2017; 196:82-93. [PMID: 28099038 DOI: 10.1164/rccm.201610-2088oc] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RATIONALE Idiopathic pulmonary fibrosis (IPF) is an increasingly recognized, often fatal lung disease of unknown etiology. OBJECTIVES The aim of this study was to use whole-exome sequencing to improve understanding of the genetic architecture of pulmonary fibrosis. METHODS We performed a case-control exome-wide collapsing analysis including 262 unrelated individuals with pulmonary fibrosis clinically classified as IPF according to American Thoracic Society/European Respiratory Society/Japanese Respiratory Society/Latin American Thoracic Association guidelines (81.3%), usual interstitial pneumonia secondary to autoimmune conditions (11.5%), or fibrosing nonspecific interstitial pneumonia (7.2%). The majority (87%) of case subjects reported no family history of pulmonary fibrosis. MEASUREMENTS AND MAIN RESULTS We searched 18,668 protein-coding genes for an excess of rare deleterious genetic variation using whole-exome sequence data from 262 case subjects with pulmonary fibrosis and 4,141 control subjects drawn from among a set of individuals of European ancestry. Comparing genetic variation across 18,668 protein-coding genes, we found a study-wide significant (P < 4.5 × 10-7) case enrichment of qualifying variants in TERT, RTEL1, and PARN. A model qualifying ultrarare, deleterious, nonsynonymous variants implicated TERT and RTEL1, and a model specifically qualifying loss-of-function variants implicated RTEL1 and PARN. A subanalysis of 186 case subjects with sporadic IPF confirmed TERT, RTEL1, and PARN as study-wide significant contributors to sporadic IPF. Collectively, 11.3% of case subjects with sporadic IPF carried a qualifying variant in one of these three genes compared with the 0.3% carrier rate observed among control subjects (odds ratio, 47.7; 95% confidence interval, 21.5-111.6; P = 5.5 × 10-22). CONCLUSIONS We identified TERT, RTEL1, and PARN-three telomere-related genes previously implicated in familial pulmonary fibrosis-as significant contributors to sporadic IPF. These results support the idea that telomere dysfunction is involved in IPF pathogenesis.
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Affiliation(s)
- Slavé Petrovski
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,2 Department of Medicine, Austin Health and Royal Melbourne Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jamie L Todd
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina.,4 Duke Clinical Research Institute, Durham, North Carolina
| | - Michael T Durheim
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina.,4 Duke Clinical Research Institute, Durham, North Carolina
| | - Quanli Wang
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | | | - Fran L Kelly
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Courtney Frankel
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Caroline M Mebane
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Zhong Ren
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joshua Bridgers
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Thomas J Urban
- 6 Division of Pharmacotherapy and Experimental Therapeutics, Center for Pharmacogenomics and Individualized Therapy, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina; and
| | - Colin D Malone
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Ashley Finlen Copeland
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Christie Brinkley
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Andrew S Allen
- 7 Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | | | | | - Scott M Palmer
- 3 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina.,4 Duke Clinical Research Institute, Durham, North Carolina
| | - David B Goldstein
- 1 Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
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47
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Zhou W, Zhuang Y, Sun J, Wang X, Zhao Q, Xu L, Wang Y. Variants of the ABCA3 gene might contribute to susceptibility to interstitial lung diseases in the Chinese population. Sci Rep 2017; 7:4097. [PMID: 28642621 PMCID: PMC5481373 DOI: 10.1038/s41598-017-04486-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/16/2017] [Indexed: 01/06/2023] Open
Abstract
ATP-binding cassette A3 (ABCA3) is a phospholipid carrier that is mainly expressed in the alveolar epithelium. Biallelic mutations of ABCA3 has been associated with fatal respiratory distress syndrome and interstitial lung disease (ILD) in children. However, whether variations in ABCA3 have a role in the development of adult ILD, including idiopathic pulmonary fibrosis (IPF), remains to be addressed. In this study, we screened for germline variants of ABCA3 by exons-sequencing in 30 patients with sporadic IPF and in 30 matched healthy controls. Eleven missense variants, predominantly in heterozygous, were found in 13 of these patients, but only two missenses in 2 healthy controls. We then selected four of the detected missense variants (p.L39V, p.S828F, p.V968M and p.G1205R) to performed cohort analysis in 1,024 ILD patients, containing 250 IPF and 774 connective tissue disease-ILD (CTD-ILD) patients, and 1,054 healthy individuals. Our results showed that the allele frequency of p.G1205R, but not p.L39V, was significantly higher in ILD patients than in healthy controls. However, no additional subject carrying the variant p.S828F or p.V968M was detected in the cohort analysis. These results indicate that the heterozygous ABCA3 gene variants may contribute to susceptibility to diseases in the Chinese population.
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Affiliation(s)
- Wei Zhou
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Yi Zhuang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Department of Respirology, Medical School Affiliated Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Jiapeng Sun
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Xiaofen Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Qingya Zhao
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Lizhi Xu
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Yaping Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China.
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu, China.
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48
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Kropski JA, Young LR, Blackwell TS, Loyd JE. Reply: The Genetic Diagnosis of Interstitial Lung Disease: A Need for an International Consensus. Am J Respir Crit Care Med 2017; 195:1539-1540. [PMID: 28569574 DOI: 10.1164/rccm.201612-2520le] [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)
| | - Lisa R Young
- 1 Vanderbilt University Medical Center Nashville, Tennessee
| | | | - James E Loyd
- 1 Vanderbilt University Medical Center Nashville, Tennessee
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49
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Wolters PJ. A recurring theme in pulmonary fibrosis genetics. Eur Respir J 2017; 49:49/5/1700545. [DOI: 10.1183/13993003.00545-2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/16/2022]
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50
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Borie R, Kannengiesser C, Sicre de Fontbrune F, Gouya L, Nathan N, Crestani B. Management of suspected monogenic lung fibrosis in a specialised centre. Eur Respir Rev 2017; 26:26/144/160122. [DOI: 10.1183/16000617.0122-2016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/21/2017] [Indexed: 12/20/2022] Open
Abstract
At least 10% of patients with interstitial lung disease present monogenic lung fibrosis suspected on familial aggregation of pulmonary fibrosis, specific syndromes or early age of diagnosis. Approximately 25% of families have an identified mutation in genes mostly involved in telomere homeostasis, and more rarely in surfactant homeostasis.Beyond pathophysiological knowledge, detection of these mutations has practical consequence for patients. For instance, mutations involved in telomere homeostasis are associated with haematological complications after lung transplantation and may require adapted immunosuppression. Moreover, relatives may benefit from a clinical and genetic evaluation that should be specifically managed.The field of genetics of pulmonary fibrosis has made great progress in the last 10 years, raising specific problems that should be addressed by a specialised team.
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