Identification of rare sequence variation underlying heritable pulmonary arterial hypertension
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Abstract
Pulmonary arterial hypertension (PAH) is a rare disorder with a poor prognosis. Deleterious variation within components of the transforming growth factor-β pathway, particularly the bone morphogenetic protein type 2 receptor ( BMPR2 ), underlies most heritable forms of PAH. To identify the missing heritability we perform whole-genome sequencing in 1038 PAH index cases and 6385 PAH-negative control subjects. Case-control analyses reveal significant overrepresentation of rare variants in ATP13A3, AQP1 and SOX17 , and provide independent validation of a critical role for GDF2 in PAH. We demonstrate familial segregation of mutations in SOX17 and AQP1 with PAH. Mutations in GDF2 , encoding a BMPR2 ligand, lead to reduced secretion from transfected cells. In addition, we identify pathogenic mutations in the majority of previously reported PAH genes, and provide evidence for further putative genes. Taken together these findings contribute new insights into the molecular basis of PAH and indicate unexplored pathways for therapeutic intervention.
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Protein-truncating variants in ATP13A3 have been associated with pulmonary artery hypertension, and loss of ATP13A3 inhibits proliferation and stimulates apoptosis in endothelial cells.
“Protein-truncating variants in this gene have previously been associated with pulmonary artery hypertension. Functional studies have linked the loss of ATP13A3 to inhibition of proliferation and stimulation of apoptosis in endothelial cells25.”
From Integrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation (2024) · cites this paper as [25]
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GermlineBMP9mutation causes idiopathic pulmonary arterial hypertension
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Selective BMP-9 Inhibition Partially Protects Against Experimental Pulmonary Hypertension
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Self-citationThe hallmarks of severe pulmonary arterial hypertension: the cancer hypothesis—ten years later
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Self-citationUnited States Pulmonary Hypertension Scientific Registry
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Self-citationTargeting RUNX1 as a novel treatment modality for pulmonary arterial hypertension
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Self-citationGenetic Delivery and Gene Therapy in Pulmonary Hypertension
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Gene panel diagnostics reveals new pathogenic variants in pulmonary arterial hypertension
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Self-citationSOX17 Deficiency Mediates Pulmonary Hypertension: At the Crossroads of Sex, Metabolism, and Genetics
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Self-citationRole of biomarkers in evaluation, treatment and clinical studies of pulmonary arterial hypertension
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DNA Damage and Repair in Pulmonary Arterial Hypertension
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Self-citationPulmonary Hypertension and ATP-Sensitive Potassium Channels
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Genetic analyses in a cohort of 191 pulmonary arterial hypertension patients
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Self-citationSpiekerkoetter, E. F., Goncharova, E. A., Guignabert, C., Stenmark, K. R., Kwapiszewska, G., Rabinovitch, M., Voelkel, N. F., Bogaard, H. J., Graham, B. B., Pullamsetti, S. S., et al. (2019) · Pulmonary Circulation · doi:10.1177/2045894019889775 · Cited by 34 · see citing works
Self-citationGenes that drive the pathobiology of pediatric pulmonary arterial hypertension
Welch, C. L., Austin, E. D., & Chung, W. K. (2020) · Pediatric Pulmonology · doi:10.1002/ppul.24637 · Cited by 34 · see citing works
Genetics and Other Omics in Pediatric Pulmonary Arterial Hypertension
Welch, C. L., & Chung, W. K. (2020) · CHEST Journal · doi:10.1016/j.chest.2020.01.013 · Cited by 34 · see citing works
- Authors
- Gräf, S., Haimel, M., Bleda, M., Hadinnapola, C., Southgate, L., Li, W., Hodgson, J., Liu, B., Salmon, R. M., Southwood, M., Machado, R. D., Martin, J. M., Treacy, C. M., Yates, K., Daugherty, L. C., Shamardina, O., Whitehorn, D., Holden, S., Aldred, M., Bogaard, H. J., Church, C., Coghlan, G., Condliffe, R., Corris, P. A., Danesino, C., Eyries, M., Gall, H., Ghio, S., Ghofrani, H.-A., Gibbs, J. S. R., Girerd, B., Houweling, A. C., Howard, L., Humbert, M., Kiely, D. G., Kovacs, G., MacKenzie Ross, R. V., Moledina, S., Montani, D., Newnham, M., Olschewski, A., Olschewski, H., Peacock, A. J., Pepke-Zaba, J., Prokopenko, I., Rhodes, C. J., Scelsi, L., Seeger, W., Soubrier, F., Stein, D. F., Suntharalingam, J., Swietlik, E. M., Toshner, M. R., van Heel, D. A., Vonk Noordegraaf, A., Waisfisz, Q., Wharton, J., Wort, S. J., Ouwehand, W. H., Soranzo, N., Lawrie, A., Upton, P. D., Wilkins, M. R., Trembath, R. C., & Morrell, N. W.
- Affiliations
- University of Cambridge (GB)
- St George's, University of London (GB)
- Royal Papworth Hospital (GB)
- Addenbrooke's Hospital (GB)
- Cleveland Clinic (US)
- Amsterdam UMC Location Vrije Universiteit Amsterdam (NL)
- Golden Jubilee National Hospital (GB)
- The Royal Free Hospital (GB)
- Royal Hallamshire Hospital (GB)
- Newcastle University (GB)
- University of Pavia (IT)
- Inserm (FR)
- Justus-Liebig-Universität Gießen (DE)
- Policlinico San Matteo Fondazione (IT)
- Imperial College London (GB)
- Université Paris-Sud (FR)
- Great Ormond Street Hospital (GB)
- Ludwig Boltzmann Institute for Lung Vascular Research (AT)
- Medical University of Graz (AT)
- Royal United Hospital (GB)
- Royal Brompton Hospital (GB)
- University of Sheffield (GB)
- King's College London (GB)
- Corresponding author
- Gräf, Stefan
- Morrell, Nicholas W.
- ORCID
- Gräf, Stefan
- Haimel, Matthias
- Bleda, Marta
- Hadinnapola, Charaka
- Southgate, Laura
- Li, Wei
- Hodgson, Joshua
- Liu, Bin
- Salmon, Richard M.
- Southwood, Mark
- Machado, Rajiv D.
- Martin, Jennifer M.
- Daugherty, Louise C.
- Shamardina, Olga
- Holden, Simon
- Aldred, Micheala
- Bogaard, Harm J.
- Church, Colin
- Coghlan, Gerry
- Condliffe, Robin
- Danesino, Cesare
- Eyries, Mélanie
- Gall, Henning
- Ghio, Stefano
- Ghofrani, Hossein-Ardeschir
- Gibbs, J. Simon R.
- Houweling, Arjan C.
- Howard, Luke
- Humbert, Marc
- Kiely, David G.
- Moledina, Shahin
- Montani, David
- Newnham, Michael
- Olschewski, Andrea
- Olschewski, Horst
- Peacock, Andrew J.
- Prokopenko, Inga
- Rhodes, Christopher J.
- Scelsi, Laura
- Seeger, Werner
- Soubrier, Florent
- Stein, Dan F.
- Suntharalingam, Jay
- Swietlik, Emilia M.
- Toshner, Mark R.
- van Heel, David A.
- Waisfisz, Quinten
- Wharton, John
- Wort, Stephen J.
- Ouwehand, Willem H.
- Soranzo, Nicole
- Lawrie, Allan
- Upton, Paul D.
- Wilkins, Martin R.
- Trembath, Richard C.
- Morrell, Nicholas W.
- Venue
- Nature Communications
- Published
- 2018-04-12
- Volume
- 9
- Issue
- 1
- Pages
- 1416-1416
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5897357
- OpenAlex
- W2797926700
- Cited by
- 380
- References
- 66
- Citations by year
- 2026: 22 · 2025: 36 · 2024: 36 · 2023: 50 · 2022: 55 · 2021: 56 · 2020: 60 · 2019: 36 · 2018: 28
- FWCI
- 33.91
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, cc-by)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion, other-oa)
- University of Birmingham Research Portal (University of Birmingham) (publishedVersion, cc-by)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- St George's Online Research Archive (St George's University of London) (acceptedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Research Portal (King's College London) (submittedVersion, cc-by)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Apollo (cc-by)
- Funders
- Pulmonary Hypertension Association
- Wellcome Trust (204809/Z/16/Z, 204809, 204809/Z/16)
- National Institute for Health and Care Research (NF-SI-0514-10086, 204809/Z/16/Z)
- British Heart Foundation (PG/17/58/33134, RG/13/4/30107, PG/12/54/29734, FS/13/48/30453, RG/08/006/25302, PG/15/39/31519, SP/12/12/29836, PG/17/1/32532, FS/18/52/33808, FS/15/59/31839)
- University of Cambridge
- ZonMw
- Cambridge University Hospitals (BRC 2012-2017, 146281)
- Nederlandse Federatie van Universitair Medische Centra
- Dinosaur Trust
- NIHR BioResource
- Medical Research Council (MR/K020919/1, 204809/Z/16/Z)
- St. George's, University of London
- NIHR Cambridge Biomedical Research Centre
- National Heart, Lung, and Blood Institute (R01HL098199)
- Topics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Pulmonary Hypertension Research and Treatments
- Health Sciences › Medicine › Genetics › Vascular Anomalies and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- heritable pulmonary arterial hypertension, missing heritability, TGF-beta signaling, BMPR2, BMP9, SOX17, aquaporin-1, ATP13A3, family segregation, pathogenic variants, whole genome sequencing
- MeSH terms
- Whole Genome Sequencing, Adenosine Triphosphatases, Adult, Base Sequence, Female, Gene Expression Regulation, Humans, Male, Models, Molecular, Mutation, Prognosis, Signal Transduction, Case-Control Studies, Transforming Growth Factor beta, Genetic Predisposition to Disease, Membrane Transport Proteins, Aquaporin 1, Bone Morphogenetic Protein Receptors, Type II, Growth Differentiation Factors, Growth Differentiation Factor 2, SOXF Transcription Factors, HEK293 Cells, Familial Primary Pulmonary Hypertension
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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