Single-cell transcriptome sequencing to investigate mechanisms of epileptogenesis in genetic mouse models and human brain biopsy tissue

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Despite the identification of a steadily increasing number of epilepsy genes and elucidation of molecular mechanisms of disease-causing mutations in simple expression systems, the exact mechanisms as to how epilepsy develops as a consequence of a genetic defect is poorly understood. Specifically, it remains elusive how genetic mutations and epileptogenesis are interconnected in the development of an epileptic phenotype in genetic epilepsy syndromes as well as at which time-points epileptic seizures start. Using state of the art sequencing techniques we, therefore, intend to investigate in four separate projects of our DFG-funded research unit 2715 (RU FOR 2715) brain region- and time-specific RNA expression in distinct neuronal subpopulations of a conditional knock-in mouse model (Scn1a) and global knock-in epilepsy mouse models (Scn2a, Kcna2). Transcriptomic signatures of epileptogenesis will be identified by single-cell RNA sequencing of hippocampal (CA1 and CA3), cortical (S1), and thalamic (nRT) neurons. In addition, we will dissect regulatory SNPs (rSNPs) conferring increased risk of generalized genetic epilepsies (GGE) by epigenomic profiling of candidate SNPs derived from GWAS risk loci of GGE and candidate genes implicated in epileptogenesis in human hippocampal (University of Bonn) and cortical (University of Tübingen) biopsies. The efforts will be performed within the framework of the already established RU FOR 2715 projects and a close collaboration of the PIs from Tübingen, Köln and Bonn with Prof. P. Nürnberg, Cologne Center for Genomics (CCG), which is already established. The generated data of the single cell sequencing related to epileptogenesis will not only be used to further deepen our understanding of the developmental contribution in epilepsy syndromes, but also utilized in the Research unit to guide its human genetic projects to identify new genes causing epilepsy.