Resubmission: Systems for Exploring Pathogenicity in Clinical Variants of a Presynaptic Protein Involved in Epilepsy

Nemametrix, Inc., Eugene OR

Investigators

Linked publications, trials & patents

Abstract

Technical Summary Epilepsy is a large health problem affecting 1% of the human population. Genetic alterations in STXBP1 represents one of the most common causes of severe Early Infantile Epileptic Encephalopathy and many patients with pathogenic variations in STXBP1 are resistant to standard anti­epileptic treatment. Genome wide DNA sequencing is now being adopted in clinical practice and an increasing number of variants are identified in epilepsy­associated genes, yet the clinical interpretation of the new variants is challenging. Some of the variants are known to be either pathological or benign, yet a majority of the gene variations remain unknown for their functional consequence. A large number of Variant of Uncertain Significance (VUS) are becoming commonplace in genes for human diseases, providing a significant barrier in making diagnoses and implementing therapies. Bioinformatic approaches can provide some insight into pathogenic probability of VUS alleles, but functional studies in animal model systems are often needed to make definitive of pathogenicity assignments. The expense and long timelines of mouse models production make the use of alternative small animal models attractive. In this proposal, the C. elegans nematode is used as an alternative model capable of fast high­throughput production and screening. Human genes are installed as gene­swap replacements of the native disease­gene homologs. In preliminary work, gene­swap humanization of STXBP1 in the unc­18 locus rescued severe locomotion and behavior defects present in the gene KO animals. Further, installation of two pathogenic variants into the gene­swap locus lead to significant disruption of activity. In this proposal, a larger set of clinically­observed variants are installed as a gene­swap humanized STXBP1 locus, then function deviations are measured with various behavioral and physiological assays. In Aim 1 of proposal, a set of pathogenic variants are installed and measured capacity to exhibit detectable defects of function. In Aim 2, a set of known benign variants are installed and measured for presence of functional defects. In Aim 3, a set of VUS alleles are installed and activity is compared to the known pathogenic and benign variants. Achieving all aims provides a body of data for assessing the predictive capacity of humanized STXBP1 strains to support or refute the remaining variants for capacity to be pathogenic. In additional future phase II work, once pathogenic behavior of a variant is detected as deviant activity in the functional assays, the system can then be used to screen for compounds that lead to reversal of activity back towards wild type. As a result, success of the phase I work, create a platform for probing variant biology and drug discovery. Applied to other targets, similar discovery systems can be developed for many of the 6000+ disease associated genes of the human genome.