Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH
Authors: Zhu Na , Swietlik Emilia M. , Welch Carrie L. , Pauciulo Michael W. , Hagen Jacob J. , Zhou Xueya , Guo Yicheng , Karten Johannes , Pandya Divya , Tilly Tobias , Lutz Katie A. , Martin Jennifer M. , Treacy Carmen M. , Rosenzweig Erika B. , Krishnan Usha , Coleman Anna W. , Gonzaga-Jauregui Claudia , Lawrie Allan , Trembath Richard C. , Wilkins Martin R. ,   Regeneron Genetics Center,   PAH Biobank Enrolling Centers’ Investigators, Hirsch Russel , White R. James , Simon Marc , Badesch David , Rosenzweig Erika , Burger Charles , Chakinala Murali , Thenappan Thenappan , Elliott Greg , Simms Robert , Farber Harrison , Frantz Robert , Elwing Jean , Hill Nicholas , Ivy Dunbar , Klinger James , Nathan Steven , Oudiz Ronald , Robbins Ivan , Schilz Robert , Fortin Terry , Wilt Jeffrey , Yung Delphine , Austin Eric , Ahmad Ferhaan , Bhatt Nitin , Lahm Tim , Frost Adaani , Safdar Zeenat , Rehman Zia , Walter Robert , Torres Fernando , Bakshi Sahil , Archer Stephen , Argula Rahul , Barnett Christopher , Benza Raymond , Desai Ankit , Maddipati Veeranna ,   NIHR BioResource for Translational Research - Rare Diseases, Bogaard Harm J. , Church Colin , Coghlin Gerry , Condliffe Robin , Eyries Mélanie , Gall Henning , Ghio Stefano , Girerd Barbara , Holden Simon , Howard Luke , Humbert Marc , Kiely David G. , Kovacs Gabor , Lordan Jim , Machado Rajiv D. , MacKenzie Ross Robert V. , McCabe Colm , Martin Jennifer M. , Moledina Shahin , Montani David , Olschewski Horst , Penkett Christopher J. , Pepke-Zaba Joanna , Price Laura , Rhodes Christopher J. , Seeger Werner , Soubrier Florent , Southgate Laura , Suntharalingam Jay , Swift Andrew J. , Toshner Mark R. , Treacy Carmen M. , Vonk Noordegraaf Anton , Wharton John , Wild Jim , Wort Stephen John ,   National Cohort Study of Idiopathic and Heritable PAH, Bogaard Harm J. , Church Colin , Coghlin Gerry , Condliffe Robin , Eyries Mélanie , Gall Henning , Ghio Stefano , Girerd Barbara , Holden Simon , Howard Luke , Humbert Marc , Kiely David G. , Kovacs Gabor , Lordan Jim , Machado Rajiv D. , MacKenzie Ross Robert V. , McCabe Colm , Martin Jennifer M. , Moledina Shahin , Montani David , Olschewski Horst , Penkett Christopher J. , Pepke-Zaba Joanna , Price Laura , Rhodes Christopher J. , Seeger Werner , Soubrier Florent , Southgate Laura , Suntharalingam Jay , Swift Andrew J. , Toshner Mark R. , Treacy Carmen M. , Vonk Noordegraaf Anton , Wharton John , Wild Jim , Wort Stephen John , Morrell Nicholas W. , Shen Yufeng , Gräf Stefan , Nichols William C. , Chung Wendy K. 
Published: May 2021

Background

Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 (BMPR2) are the cause of most heritable cases but the vast majority of other cases are genetically undefined.

Methods

To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource – Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD.

Results

Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes (BMPR2, GDF2, and TBX4), two recently identified candidate genes (SOX17, KDR), and two new candidate genes (fibulin 2, FBLN2; platelet-derived growth factor D, PDGFD). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e−5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development.

Conclusions

Rare variant analysis of a large international consortium identified two new candidate genes—FBLN2 and PDGFD. The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.