Abstract 1531: SCN5A Promoter and Enhancer Variants associated with Atrial Fibrillation

Abstract

We have recently reported that 5.9% of patients with atrial fibrillation (AF) have rare variants in the coding region of the predominant cardiac sodium channel gene SCN5A . In this study, we tested the hypothesis that AF susceptibility is also influenced by variants in the SCN5A core promoter and short non-coding nucleotide sequences highly conserved across species (CNS) that we previously identified. We resequenced the SCN5A core promoter region (~3 kb) and CNS regions in intron 1 (<1 kb for each) in 376 patients with AF (111 patients with lone AF and 234 patients with AF and cardiac disease) and 47 ethnically-defined controls. The promoter activity of variants showing different frequencies in patients with AF compared to controls was studied using promoter-reporter assays in CHO cells and in neonatal mouse ventricular myocytes. Identification of variants Four common variants were identified in the core promoter in controls, and one of the variants (c.−225– 834 T>C) was significantly more common in patients with AF than in controls (minor allele frequency: lone AF, 17%; AF and heart disease, 17%; control, 7%; P<0.05 vs. control for each). In addition, 10 novel rare promoter variants were identified in patients with AF and were absent in controls. In CNS28, a 406 bp region in intron 1 that includes three TEF-1 binding sites, one variant (c.−53±15307 C>T) which is predicted to disrupt one of the TEF-1 binding sites was identified in 7 out of 376 patients with AF (1 with lone AF, 6 with AF and heart disease), but not in controls. Functional study There was no difference in promoter activity between wild-type and c.−225– 834 T>C SCN5A core promoters expressed in CHO cells. Wild-type CNS28 coexpressed with the SCN5A core promoter increased reporter activity by 77 ± 14% (P=0.03) in CHO cells and 261 ± 8% (P=0.001) in cardiomyocytes, compared to SCN5A promoter alone. However, c.−53+15307 C>T CNS28 showed smaller effects on promoter activity in both CHO cells (52 ± 2 % of wild-type, P<0.05) and cardiomyocytes (62 ± 8%, P<0.05) compared to wild-type CNS28. Variants in the SCN5A promoter and an enhancer region in intron 1 were associated with AF. Variability in SCN5A transcription may affect AF susceptibility.