STX18-AS1 is a Long Noncoding RNA predisposing to Atrial Septal Defect via downregulation of NKX2-5 in differentiating cardiomyocytes

Abstract: Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 associated with the risk of Atrial Septal Defect (ASD), which is among the commonest Congenital Heart Disease (CHD) phenotypes. Here, we identify the responsible gene in the region and elucidate disease mechanisms. Linkage disequilibrium in the region, eQTL analyses in human atrial tissues, and spatio-temporal gene expression studies in human embryonic hearts concordantly suggested the long noncoding RNA (lncRNA) STX18-AS1 as the causative gene in the region. Using CRISPR/Cas9 knockdown in HepG2 cells, STX18-AS1 was shown to regulate the expression of the key cardiac transcription factor NKX2-5 via a trans-acting effect on promoter histone methylation. Furthermore, STX18-AS1 knockdown depleted the potential of human embryonic stem cells (H9) to differentiate into cardiomyocytes, without affecting their viability and pluripotency, providing a mechanistic explanation for the clinical association.