A non-coding SCN5A variant that reduces sodium channel function in hiPSC-derived cardiomyocytes is significantly enriched in Brugada syndrome patients from Thailand

Abstract

Abstract Background/Introduction Brugada syndrome (BrS) is an inherited arrhythmia condition that can cause sudden cardiac death. Rare coding and common non-coding genetic variation in the Nav1.5 cardiac sodium channel-encoding SCN5A gene is robustly associated with BrS, but the role of rare and low frequency non-coding variants remains unexplored. BrS is several times more prevalent in Southeast Asia compared to other populations, indicating ancestry-specific genetic risk factors remain to be discovered. Purpose To identify and characterise novel genetic risk factors in BrS patients from Southeast Asia. Methods We performed genome sequencing in 231 BrS probands from Thailand and 500 population-matched controls to identify novel disease associated variants across the entire SCN5A locus. The candidate variant was engineered into human induced pluripotent stem cells (hiPSCs) by CRISPR-Cas9 and its effect was evaluated by single cell electrophysiology analysis on hiPSC-derived cardiomyocytes. Results We identified a rare (absent in gnomAD), non-coding variant in a regulatory element of the SCN5A gene (GRCh38:3-38580380-A-C) that was significantly enriched in cases (3.9%) vs controls (0.2%) (OR=20.2[2.5-160.6], p=2e-04). Transcription factor motif scanning analysis suggested the variant is likely to disrupt a Mef2 site that is conserved across species (Figure 1) – the MEF2 family of transcription factors play a critical role in cardiac transcriptional regulation. In hiPSC-derived cardiomyocytes, a significant reduction of peak Nav1.5-mediated sodium-current (INa) density (30% decrease at -20mV, p=8e-03), without changes in gating properties, was observed in cardiomyocytes carrying the variant in heterozygosity compared to isogenic controls (Figure 2). The variant also significantly reduced luciferase activity of the candidate regulatory element in HEK cells in the presence of cardiac transcription factors (Tbx5, Gata4, Mef2A, Mef2D). Conclusion A novel, non-coding variant in an SCN5A enhancer region is associated with BrS and was functionally validated using single cell electrophysiology in hiPSC-derived cardiomyocytes. This variant is found in ∼1 in every 25 BrS patients from Thailand and therefore may at least partially explain the increased prevalence of BrS in this region. Our study highlights the importance of research in understudied populations to understand the genetic aetiology of disease in diverse ancestries and to identify novel disease risk factors.