Mutations in the SCN5A promoter associated with Brugada syndrome

Abstract

Purpose: Loss-of-function-mutations in the coding sequence of SCN5A, which encodes the α-subunit of predominant cardiac Na+ channels, have been associated with Brugada syndrome and decreased expression of Na+ channels by mutations in SCN5A is one of the mechanisms. However, the majority of patients are genotype-negative in Brugada syndrome. Here, we tested the hypothesis that variants in the promoter region of SCN5A also contribute to susceptibility to Brugada syndrome. Methods: We resequenced the core-promoter region of SCN5A (∼2.8 kb) in 503 patients with Brugada syndrome. We studied the effects of identified variants on promoter activity using luciferase reporter assay in heterologous expression system. We mapped the promoter variants to the mouse genome and studied the association with key factors of the transcriptional machinery using ChIP-Seq analyses. Results: We identified 18 novel rare variants in the SCN5A promoter in 19 unrelated patients with Brugada syndrome. All variants were absent in >2,500 controls. Using luciferase reporter assay, 5 promoter variants were functionally characterized, and each displayed significant decrease of promoter activity (57±17% of wild-type) compared to wild-type sequences. ChIP-Seq analyses revealed that majority of these promoter variants, for which the wild-type nucleotide is conserved, are located at the regions directly bound by the transcription factors that are important for the development and function of heart including TBX3, TBX5, and NKX2-5, and by the chromatin and insulator associated factor CTCF, important for insulator establishment and chromatin looping regulation. Conclusions: Variants in the core-promoter region of SCN5A were identified in patients with Brugada syndrome and were associated with the decreased promoter activity. Altered SCN5A transcription levels, possibly by negative consequences for the binding of transcription factors to the promoter region, may modulate susceptibility to Brugada syndrome.