Rare genetic factors in epileptogenesis

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The factors contributing to genetic generalized epilepsies (GGE) are largely uncharted and known factors explain only a minor component of its high heritability. Possible explanations are large numbers of not yet identified contributing rare variants and also more common risk-conferring variants. Common variants are addressed in project P3. Here, we will run the complete gamut of gene discovery for rare variants, from analysing the largest assembled collection of exome sequences – 6400 GGE and 3200 epileptic encephalopathies (EE) cases – to functional interpretation in the context of epileptogenesis. To this end, we will use a broad spectrum of methods, from omics data modeling to validation of genes and variants in cellular and animal models. Firstly, substantially increased sample sizes of whole-exome sequences from global collaborations will put us in a position to identify new variants from hypothesis-free analyses. The identification of rare variants will be run by state-of-the-art statistical models as burden or collapsing tests. The heterogeneity of epilepsies is undoubtedly contributing to prior failures in gene discovery and burden tests are not able to utilize information on the severity of the phenotype. We will therefore explore pleiotropic models for analysing GGE addressing phenotype details but also including EE as well as focal epilepsies (FE) in comparison to GGE. Secondly, we will search for gene networks mediating epileptogenesis in GGE by integration of protein-protein interactions, gene expression and enrichment of genetic variants. New data from single-cell RNA-seq experiments will allow us to take variant interpretation to individual cell types. In a systems biology approach, predicted key genes of such networks will be validated in cooperation with other projects, e.g. in zebrafish. Thirdly, physiological testing of genetic variants in cellular and mouse models will be performed to complete our understanding of their impact. Automated screening in Xenopus oocytes and patch clamp studies in mammalian cell lines will identify biophysical consequences of variants in ion channels and receptors. Causal variants in genes not yet involved in GGE, such as KCNA2, KCNQ5, and KCND2, will be investigated. A knock-in (KI) mouse which we generated carrying a human GGE-associated mutation in GABRA5 will allow assessing modifying effects by cross-breeding with other epilepsy mouse models. In this multifaceted, concerted way, the project will lead to the identification of new and validated susceptibility variants and an in-depth qualitative understanding of GGE epileptogenesis.