Research

Poison exons, or nonsense mediated decay (NMD) exons, are small exonic regions that when spliced into an RNA transcript lead to premature truncation of a protein. Inclusion of poison exons occurs during specific times in neurodevelopment and splicing occurs in a cell-specific manner. Many of the genes implicated in epilepsy harbor these poison exons, including the voltage gated sodium channels (VGSCs) SCN1A, SCN2A and SCN8A. We first identified patient-specific variants that lead to aberrant inclusion of an SCN1A poison exons in patients with a specific epilepsy subtype – Dravet Syndrome.

We are using DNA sequencing approaches to identify poison exon variants in other epilepsy genes. We also use stem cell models to identify the proteins that control splicing of these poison exons. The poison exons are potential novel targets for RNA-therapeutics.

In genetic medicine, variants of uncertain significance (VUS) have posed a significant challenge. These
variants, identified through genetic testing, are alterations in one’s DNA sequence that cannot be definitively classified as benign or pathogenic. Approximately 80% of missense variants in the ClinVar database are classified as VUS. In clinical care, a VUS result frequently prevents clinicians from providing definitive diagnoses, limits treatment options, and causes uncertainty for patients and their families. 

Multiplexed Assays of Variant Effect (MAVEs) offer a high-throughput solution to VUS resolution by assessing variant effect for thousands of variants in vitro simultaneously. In the Carvill Lab, we are developing techniques to introduce epilepsy-related variants into cells in vitro and profile cellular function at scale

Our lab seeks to understand how variants in the non-coding genome, the sequences that do not contain instructions for making a protein, lead to disease. We are learning that non-coding DNA elements play a significant role in gene regulation. 

Using patient-derived cells and genetically engineered cells, we have discovered that a deletion in lncRNA CHASERR lead to overproduction of CHD2 protein. We are continuing to study how CHASERR exactly controls CHD2 expression, and more broadly how the non-coding genome regulates neurodevelopment. 

Our lab also explores the molecular mechanisms by which non-coding structural variants (SVs) disrupt coding regions of genes. One of our studies looks at how SVs around the FOXG1 gene may increase epilepsy susceptibility by disrupting cis-regulatory elements and/or topologically associated domains. 

In the lab we are using gene-editing technologies (CRISPR-Cas9) and reprograming of patient cells to make stem cell models of genetic epilepsy, including the genes CHD2, a chromatin remodeler and CUX2, a transcription factor. We then differentiate these cells to a neuronal lineage and study how these mutations change the epigenome structure, as well as the genes and pathways that are disrupted. These studies will provide new targets for therapeutic development and testing.