Functional epigenomic dissection of genetic generalized epilepsies

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Genetic generalized epilepsies (GGEs) represent the most common form of genetically determined epilepsies. Up to date, the genetic basis of common GGE syndromes remains largely unsolved due to their prominent polygenic predisposition and extensive genetic heterogeneity. Heritability analyses implicate that at least 35% of GGE susceptibility is determined by single nucleotide polymorphisms (SNPs). Genome-wide association studies (GWASs) have identified only few GGE-risk loci mainly in non-coding genomic regions, suggesting cis-acting regulatory effects of the causal SNPs on gene expression. This project aims to dissect regulatory SNPs (rSNPs) conferring risk of GGE by epigenomic profiling of candidate SNPs derived from GWAS risk loci of GGE and candidate genes implicated in epileptogenesis. Candidate rSNPs will be prioritized in silico by their genomic intersection with binding sites of transcription factors, miRNAs and lncRNAs located within brain- and cell type-specific epigenetic elements regulating gene expression. Functional validation of the most promising candidate rSNPs will evaluate the cis-regulatory quantitative effects of rSNPs on gene expression (expression quantitative trait locus, eQTL) and CpG methylation (methylation QTL, meQTL) in human hippocampal biopsies, and in vitro gene expression analyses in primary neurons using luciferase reporter assays. Subsequently, intraventricular in utero electroporation (IUE)-mediated transgenic mouse reporter assays will explore the allelic effects of gene promoter rSNPs by in vivo molecular imaging. Initially, functional validation methods will be established for candidate rSNPs predicted to affect the promoter activity of two known epilepsy genes (CaV3.2/CACNA1H, PIGP). Together, epigenomic profiling of GGE-associated rSNPs will gain critical insights into temporospatial neurobiological processes of epileptogenesis. Predictive modeling of key pathways of epileptogenesis and delineation of individual epigenomic risk profiles of GGE may be of relevance towards precision medicine.