Whole-Exome Sequencing Identifies Rare Variants in Multiple Genes Associated with Total Anomalous Pulmonary Venous Connection

Abstract

Background: Total anomalous pulmonary venous connection (TAPVC) is recognized as a rare congenital heart defect (CHD). With a high mortality rate of approximately 80%, the outcomes of TAPVC patients are not satisfactory. However, its genetic etiology and mechanism remains elusive. This study was an effort to investigate the underlying genomic risks of TAPVC through whole exome sequencing (WES). Methods: Rare variants were identified through WES in 78 sporadic TAPVC cases and 100 controls using Fisher's exact test and gene-based burden test. Then we detected expression patterns of candidate genes in cells, pulmonary vein tissues (mouse and human), and embryos (zebrafish and human). At last, we validated these genes using target sequencing (TS) in another 100 cases. Findings: We found 42 rare variants in 7 genes (CLTCL1, CST3, GXYLT1, HMGA2, SNAI1, VAV2, ZDHHC8) in TAPVC cases compared with controls. These genes were highly expressed in HUVECs, mouse pulmonary veins and human embryonic hearts. Their mRNA expressions in human pulmonary vein samples were significantly different between cases and controls. Through network analysis and expression patterns of zebrafish embryos we revealed that SNAI1, HMGA2 and VAV2 are the most important genes for TAPVC. Interpretation: Our study provides novel candidate genes potentially related to this rare congenital birth defect and discloses the possible molecular pathogenesis of TAPVC. Furthermore, SNAI1, HMGA2 and VAV2 are novel TAPVC candidate genes which have not previously been reported in either humans or animals. Funding: National Natural Science Foundation of China. Declaration of Interest: We declare that no interest conflict is present. Ethical Approval: The animals used in this research were treated humanely according to the Institutional Animal Care and Use Committee of the Institute for Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University. The study was conducted in accordance with the Declaration of Helsinki and the protocol that was used to collect the human samples from blood, pulmonary veins, and embryonic hearts was approved by Ethics Committee of Xinhua Hospital.