Influence of common SCN1A promoter variants on the severity of SCN1A-related phenotypes

Abstract

Background: Pathogenic variants in SCN1A cause variable epilepsy disorders with different disease severities. We here investigate whether common variation in the promoter region of the unaffected SCN1A allele could reduce normal expression, leading to a decreased residual function of Nav1.1, and therefore to more severe clinical outcomes in patients affected by pathogenic SCN1A variants.

Methods: Five different SCN1A promoter-haplotypes were functionally assessed in SH-SY5Y cells using Firefly and Renilla luciferase assays. The SCN1A promoter region was analyzed in a cohort of 143 participants with SCN1A pathogenic variants. Differences in clinical features and outcomes between participants with and without common variants in the SCN1A promoter-region of their unaffected allele were investigated.

Results: All non-wildtype haplotypes showed a significant reduction in luciferase expression, compared to the wildtype promoter-region (65%-80%, p = 0.039-0.0023). No statistically significant differences in clinical outcomes were observed between patients with and without common promoter variants. However, patients with a wildtype promoter-haplotype on their unaffected SCN1A allele showed a nonsignificant trend for milder phenotypes.

Conclusion: The nonsignificant observed trends in our study warrant replication studies in larger cohorts to explore the potential modifying role of these common SCN1A promoter-haplotypes.

Keywords: SCN1A; Dravet; GEFS+; promoter; variable expression.

Figure 1

Overview SCN1A 5' UTR. SCN1A has a complex 5’ UTR. Three major promoter regions (blue) and five 5’ UE (pink) are currently known. The half‐tick up lines indicate a promoter region with a subsequent 5’ UE which together carry consensus regions for multiple transcription factor binding sites and initiator elements. Transcription start sites are indicated with an arrow. Dashed lines indicate the distance to next element. Underlined elements indicate the remaining two 5’ UEs and the first coding exon of SCN1A (green). Figure established based on previous work (Dong et al., 2014; Long et al., 2008; Nakayama et al., 2010)

Figure 2

Functional effect of common promoter variants in SCN1A. Top: Simplified SCN1A 5’ UTR, adapted from Figure 1. Middle: Promoter haplotypes tested in this study. Haplotype 1 depicts a promoter + h1u region without common variants. Haplotype 2, 3, 4 and 5 carry multiple common variants spread over the promoter region: −1964 (rs2212657, MAF 0.43), −1663 (rs151217464, MAF 0.01), −1449 (rs7606233, MAF 0.50), −1036 (rs4319946, MAF 0.49), −688 (rs16851669, MAF 0.50), −244 (rs80169419, MAF 0.07), −52 (rs16851666, MAF 0.50) and 34 (rs757291646, MAF < 0.01). Bottom: Luciferase expression analysis of SCN1A promoter haplotypes as depicted above. Empty vector (SV40) expression was set to 100%. Haplotype 1, without common variants was used as control haplotype of which the expression reduction of Haplotype 2, 3, 4 and 5 was measured

Figure 3

distribution of different cognitive outcome scores between patients with and without variants in the promoter‐region of their unaffected SCN1A allele

Figure 4

distribution of age at seizure onset between patients with and without variants in the promoter‐region of their unaffected SCN1A allele

Figure 5

distribution of onset of developmental delay between patients with and without variants in the promoter‐region of their unaffected SCN1A allele

Figure 6

distribution of age at first afebrile seizure between patients with and without variants in the promoter‐region of their unaffected SCN1A allele

Figure 7

distribution of IQ/DQ scores after five years of disease between patients with and without variants in the promoter‐region of their unaffected SCN1A allele

Figure 8

Family tree I‐IV. Orange box indicates mild epilepsy phenotype with normal cognitive functioning. Light red box indicates a mild DS, or borderline DS/GEFS+ phenotype. Dark red boxes indicate severe DS. Numbers in the boxes correspond to promoter haplotype number or wildtype haplotype from Figure 2