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Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis
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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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“More recently, a genetic locus associated with DEPTOR , a gene involved in several cellular functions including negative regulation of mTOR (mechanistic target of rapamycin), has also been associated with increased risk of developing IPF (Allen et al., 2020).”
From Pulmonary fibrosis: Emerging diagnostic and therapeutic strategies (2023) · cites this paper as Allen et al., 2020
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Self-citation
Metadata
- Authors
- Allen, R. J., Guillen-Guio, B., Oldham, J. M., Ma, S.-F., Dressen, A., Paynton, M. L., Kraven, L. M., Obeidat, M., Li, X., Ng, M., Braybrooke, R., Molina-Molina, M., Hobbs, B. D., Putman, R. K., Sakornsakolpat, P., Booth, H. L., Fahy, W. A., Hart, S. P., Hill, M. R., Hirani, N., Hubbard, R. B., McAnulty, R. J., Millar, A. B., Navaratnam, V., Oballa, E., Parfrey, H., Saini, G., Whyte, M. K. B., Zhang, Y., Kaminski, N., Adegunsoye, A., Strek, M. E., Neighbors, M., Sheng, X. R., Gudmundsson, G., Gudnason, V., Hatabu, H., Lederer, D. J., Manichaikul, A., Newell, J. D., O’Connor, G. T., Ortega, V. E., Xu, H., Fingerlin, T. E., Bossé, Y., Hao, K., Joubert, P., Nickle, D. C., Sin, D. D., Timens, W., Furniss, D., Morris, A. P., Zondervan, K. T., Hall, I. P., Sayers, I., Tobin, M. D., Maher, T. M., Cho, M. H., Hunninghake, G. M., Schwartz, D. A., Yaspan, B. L., Molyneaux, P. L., Flores, C., Noth, I., Jenkins, R. G., & Wain, L. V.
- Affiliations
- University of Leicester (GB)
- Unidad de Investigacion, Hospital Universitario Ntra. Sra. de Candelaria and
- University of California, Davis (US)
- Division of Pulmonary and Critical Care Medicine
- Genentech (US)
- University of British Columbia (CA)
- Nuffield Orthopaedic Centre (GB)
- National Institute for Health and Care Research (GB)
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Channing Division of Network Medicine
- Siriraj Hospital (TH)
- University College London Hospitals NHS Foundation Trust (GB)
- GlaxoSmithKline (United Kingdom) (GB)
- Castle Hill Hospital (GB)
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health
- Centre for Inflammation Research (GB)
- University College London (GB)
- University of Bristol (GB)
- Division of Epidemiology and Public Health and
- Royal Papworth Hospital (GB)
- Nottingham University Hospitals NHS Trust (GB)
- University of Pittsburgh (US)
- Yale University (US)
- University of Chicago (US)
- Department of Respiratory Medicine, Landspital University Hospital, Reykjavik, Iceland
- University of Iceland (IS)
- Brigham and Women's Hospital (US)
- Columbia University (US)
- University of Virginia (US)
- University of Iowa (US)
- Boston University (US)
- Wake Forest University Health Sciences (US)
- National Jewish Health (US)
- Institut universitaire de cardiologie et de pneumologie de Québec (CA)
- Icahn School of Medicine at Mount Sinai (US)
- Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
- University Medical Center Groningen (NL)
- Centre for Human Genetics (GB)
- University of Nottingham (GB)
- Universidad de La Laguna (ES)
- National Institute for Health Research, Nottingham Biomedical Research Centre and
- Corresponding author
- Wain, Louise V.
- ORCID
- Allen, Richard J.
- Oldham, Justin M.
- Ma, Shwu-Fan
- Dressen, Amy
- Paynton, Megan L.
- Kraven, Luke M.
- Obeidat, Ma'en
- Li, Xuan
- Ng, Michael
- Braybrooke, Rebecca
- Hobbs, Brian D.
- Putman, Rachel K.
- Sakornsakolpat, Phuwanat
- Fahy, William A.
- Hart, Simon P.
- Hirani, Nik
- Hubbard, Richard B.
- McAnulty, Robin J.
- Navaratnam, Vidyia
- Parfrey, Helen
- Saini, Gauri
- Whyte, Moira K. B.
- Zhang, Yingze
- Kaminski, Naftali
- Adegunsoye, Ayodeji
- Strek, Mary E.
- Neighbors, Margaret
- Gudnason, Vilmundur
- Hatabu, Hiroto
- Lederer, David J.
- Manichaikul, Ani
- Newell, John D.
- O’Connor, George T.
- Ortega, Victor E.
- Xu, Hanfei
- Fingerlin, Tasha E.
- Bossé, Yohan
- Hao, Ke
- Joubert, Philippe
- Nickle, David C.
- Sin, Don D.
- Timens, Wim
- Furniss, Dominic
- Morris, Andrew P.
- Zondervan, Krina T.
- Hall, Ian P.
- Sayers, Ian
- Tobin, Martin D.
- Maher, Toby M.
- Cho, Michael H.
- Hunninghake, Gary M.
- Schwartz, David A.
- Yaspan, Brian L.
- Molyneaux, Philip L.
- Flores, Carlos
- Noth, Imre
- Wain, Louise V.
- Venue
- American Journal of Respiratory and Critical Care Medicine
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-03-01
- Volume
- 201
- Issue
- 5
- Pages
- 564-574
- ISSN
- 1073-449X (ISSN-L)
- 1535-4970
- PMC
- PMC7047454
- OpenAlex
- W2983449145
- Cited by
- 329
- References
- 62
- Citations by year
- 2026: 37 · 2025: 49 · 2024: 37 · 2023: 67 · 2022: 53 · 2021: 54 · 2020: 28
- FWCI
- 26.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- American Journal of Respiratory and Critical Care Medicine (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- Edinburgh Research Explorer (University of Edinburgh) (acceptedVersion, other-oa)
- Repository@Hull (Worktribe) (University of Hull) (submittedVersion, cc-by)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Opin vísindi (Opin vísindi) (submittedVersion, cc-by)
- Research Explorer (The University of Manchester) (submittedVersion, cc-by-nc-nd)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Hirsla (Landspítali University Hospital) (submittedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- U.S. Department of Veterans Affairs (CDA13-017)
- Wellcome Trust (WT202849/Z/16/Z, 95161, /Z/11/Z, WT202849, 097152, 097152/Z/11/Z)
- Broad Institute
- Ministerio de Ciencia, Innovación y Universidades (RTC-2017-6471-1, OA17/008, RTC-2017, PT17/0019)
- Instituto Tecnológico y de Energías Renovables (OA17/008, RTC-2017-6471-1)
- Michael Smith Health Research BC
- National Institute for Health and Care Research (RP-2017-08-ST2-014, NF-SI-0617-10096, CS-2013-13-017)
- British Lung Foundation (C17-3, WT202849/Z/16/Z)
- Asthma and Lung UK (RP-2017-08-ST2-014, AUK-PG-2013-188)
- University of Leicester
- European Commission (2013-2016, PT17/0019)
- Agencia Canaria de Investigación, Innovación y Sociedad de la Información (OA17/008, TESIS2015010057)
- National Institutes of Health (n01hc95164-17-0-1, UL1TR001420, n01hc95165-34-0-1, n01hc95161-24-0-1, n01hc095169-003, N01-HC- 95166, 2013-2016, n01hc95166-21-0-1, N01-HC9-5168, R01130974, n01hc95162-31-0-1, n01hc95168-27-0-1, n01hc95160-18-0-1, n01hc095167-000, N01-HC- 95159, UL1TR001079, n01hc95163-22-0-1, PT17/0019, HHSN263201500003I, n02hl64278-6-0-0, HHSN268201500003I, n01hc95159-40-0-1, UL1TR000040, UL1-TR-, N01‐HC‐95161, N01- HC-95163, N01- HC-95165, N01‐HC‐95160, N01 HC95164, N01-HC-95167, N02-HL-64278, N01-HC95162, N01‐HC‐95169, HL136928, DK-063491, UL1TR001863, UL1TR001881)
- Medical Research Council (MC_PC_12010, G1000861, MR/N005953/1)
- Instituto de Salud Carlos III (2013-2016, PT17/0019)
- European Regional Development Fund (RTC-2017-6471-1, PT17/0019, of the PE I+D+i 2013-2016, RTC-2017, PE I+D+i 2013-2016, OA17/008, PT17/0019, 000040, 2013-2016)
- Agencia Estatal de Investigación (RTC-2017-6471-1)
- NIHR Leicester Biomedical Research Centre
- NIHR Nottingham Biomedical Research Centre
- National Heart, Lung, and Blood Institute (DK-063491, R01HL130796, N01 HC-95159, N01-HC-95160, R01HL097163, N01-HC095169, RTC-2017-6471-1, WT202849/Z/16/Z, N01 HC-95168, N01-HC-095165, R01HL113264, HL131565, N01 HC95167, K23HL138190, (N01-HC-95163, N01 HC095163, N01 HC-95161, N01 HC95165, N01HC95164, HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, N01-HC-95167, N01-HC-95168, N01-HC-95169, N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166, R01HL137927, R01HL103676, N02 HL064278, CS-2013-13-017, UG3HL151865, N01-HC-95167, N01-HC-95168, UL1-TR-, N01-HC-095159, N01-HC, N01 HC095168, N02- HL-64278, N01-HC-095162, N01-HC-95164, N01-HC-95165, N01-HC-95166, N01-HC-95161, N01-HC-95162, N01-HC-95163, HC-95168, N01-HC-095161, HL136928, R01HL111024, HHSN268201500003C, HHSN26820150 0003I, R01HL149836, HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01, N01 HC095167, C17-3, K08HL136928, K08HL140087, N01-HC-095160, R01HL137234, N01 HC095166, HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01 HC095164, UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, N01‐HC‐95166, R33HL120770, P01HL092870, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, N01-HC-95169, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, RP-2017-08-ST2-014, N01-HC-95159, N01-HC-95160, N01 HC-95162, R01HL131565, HC95159, UH3HL151865, R01HL130974, T32HL007085, R01HL135142, HL64278, N01 HC95169)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK063491)
- National Center for Advancing Translational Sciences
- Topics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Occupational and environmental lung diseases
- Keywords
- idiopathic pulmonary fibrosis, genetic susceptibility, genome-wide association study, KIF15, MAD1L1, DEPTOR, mTOR signaling, mitotic spindle assembly, polygenic risk score, gene expression, regulatory elements, pulmonary fibrosis
- MeSH terms
- Aged, Female, Humans, Male, Middle Aged, Spindle Apparatus, Signal Transduction, Gene Expression, Case-Control Studies, Kinesins, Risk Assessment, Cell Cycle Proteins, Genetic Predisposition to Disease, Intracellular Signaling Peptides and Proteins, Idiopathic Pulmonary Fibrosis, Genome-Wide Association Study, TOR Serine-Threonine Kinases
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