Epileptic encephalopathy (EE) is an umbrella-term for a class of severe epilepsies characterized by debilitating seizures. Epileptic activity often begins in early adolescence, contributing to developmental, cognitive, and behavioral abnormalities. Identification of genetic mutations in EE-patients has implicated >50 genes, with clinical diagnostic labs reporting a molecular diagnosis in 24-40% of cases. Current EE gene discovery focuses primarily on identifying de novo mutations in genomic coding regions, which alter the amino acid sequence of the resulting protein, disrupting the protein’s function and leading to neural abnormalities. A de novo mutation is not inherited from either unaffected parent; it first occurs in an affected individual, suggesting a genetic cause for the phenotype. My research focuses on identifying novel noncoding mutations in a cohort of 167 patients with EE of unknown cause. The proportion of rare diseases caused by noncoding mutations is unknown and relatively few examples of functional noncoding causative mutations exist. My goal is to identify de novo variants in intronic and untranslated genomic regions, and also to identify synonymous variants in which the resulting amino acid is unaltered. Initially, the 167-patient cohort was screened for variants in 44 established EE genes using targeted next-generation DNA sequencing. I have filtered this data for high-quality noncoding variants, which are unreported in a healthy population. I am currently screening patients’ parents for these noncoding variants to determine the mode of inheritance. Confirmed de novo variants will be followed-up with functional studies to test their molecular consequences (via mRNA, splicing, gene expression). Determining genetic causes of EE unveils molecular mechanisms behind phenotypes, allowing for precise diagnoses, and leading to treatment of severe epilepsies based on their causes. I hope to identify causative noncoding variants in epilepsy genes to expand epigenetic analysis of EE, and contribute to a better understanding of EE genotype-phenotype relationship.

The Mefford lab is identifying the genetic mutations that cause early-onset epileptic encephalopathies. This is a rare class of epilepsy that is characterized by refractory seizures that often begin in infancy and carry a poor prognosis for the patient. We accomplish this by identifying de novo mutations in affected children using Sanger sequencing to compare the children’s DNA to that of their unaffected parents. This approach, however, lacks the sensitivity to detect genetic mosaicism. A mosaic mutation occurs post-fertilization and causes one’s body to contain cells with different genotypes from one another. These mutations can be difficult to identify with Sanger sequencing because they are often present at very low levels. However, recent advances in gene-sequencing technology has enabled us to detect mosaicism in patients at increasingly lower levels via deep sequencing using smMIPs (single-molecule molecular inversion probes), a technique that allows us to quantify the number of alleles assayed. Recent studies have reported that 1.7% - 10% of alleged de novo mutations were actually inherited from a mosaic parent, inspiring us to find the rate of falsely identified de novo mutations in our own research. We re-sequenced the parents in our cohort of 50 solved de novo cases using smMIPs to investigate how often the mutation had actually come from a mosaic parent. This revealed 10 parents as candidate mosaic carriers. We are still performing further testing on those parents and are adding more families to the study. Knowing the origin of a mutation is crucial for genetic counselors, and knowing whether a child’s epilepsy came from a de novo or a mosaic mutation in the parent can have huge effects on the recurrence risk of the disease. The data from this study will also help other researchers assess the accuracy of their research on disease inheritance as well.

Epileptic encephalopathies (EEs) are devastating childhood epilepsies characterized by multiple seizure types that are usually refractory to medication. Next-generation sequencing has revealed the prominent role of de novo mutations in causing EEs with clinical diagnostic labs reporting a molecular diagnosis in as many as 24-40% of cases. Despite this significant progress, the majority of cases are unexplained. Exome sequencing, a next-generation sequencing technique, allows one to look at all the protein coding regions of an individual’s genome, offering an affordable and unbiased approach to gene discovery. Using exome sequence data for 50 trios (proband and unaffected parents), in which the child had seizure onset in the first 2 years of life, we identified 76 candidate genes, of which 37 are confirmed de novo variants through Sanger sequencing. Notably, 2 affected individuals were identified to have a de novo variant in the guanine nucleotide-binding protein (G-protein) beta1 subunit, GNB1. This was a statistically significant finding (p=0.005), and in collaboration with colleagues we have now identified 13 patients with neurodevelopmental delays with and without seizures. This previously unrecognized genetic condition is characterized by global developmental delays (13/13), hypotonia (11/13), seizures (10/13), ocular manifestations (8/13) and growth delay (6/13). These genetic findings will have immediate impact to clinicians and families when discussing diagnosis and prognosis, and hopefully guide future studies of finding effective therapies for these patients. Future work will screen for genetic variants in the candidate genes identified by exome sequencing using a targeted sequencing approach in a cohort of 600 patients with EE of unknown etiology.

3 million Americans and 65 million people worldwide have been diagnosed with epilepsy. In two-thirds of these patients, the causes of epilepsy, and therefore the therapeutic targets, are unknown. Recently, de novo mutations in the EEF1A2 gene, which encodes for a protein translation regulator, were found in several individuals with pediatric epilepsy and intellectual disability. In order to study how a mutation in this gene causes the neurological defects, we generated mutant eef1a2 zebrafish using the CRISPR/Cas9 method. Zebrafish models to study diseases have gained momentum due to their genetic similarity to humans, large amount of offspring in each generation, easy genetic manipulation and amenability to large-scale drug screens. Our initial in situ hybridization studies showed that eef1a2 has a limited expression pattern in the developing zebrafish that includes neurons involved in movement and escape behavior. To understand whether the mutation causes observable behavioral dysfunction or seizures, we tracked wild type (WT) zebrafish and heterozygous and homozygous mutants in various behavioral assays and genotyped tracked fish using Sanger sequencing. We are expecting that the mutants to have defect in movement and escape response. In a future study, the electrophysiology of the forebrain will be recorded to determine whether eef1a2 mutants reveal abnormal electrical discharge characteristic of a seizure. These studies with the zebrafish model will provide more insight about the EEF1A2 protein and its neurological function, and may lead to a better understanding of epilepsy etiology and the design of targeted therapeutic approaches.