Research

The goal of our lab is to determine the genetic causes of epilepsy, as well as study how pathogenic variants in these genes affect how the brain develops and functions, and ultimately find ways to intervene.

The Genetic Causes of . . .

Pediatric epilepsy

The implementation of massively parallel sequencing has led to an explosion in the number of genes implicated in epilepsy, and there are now mutations in over 100 genes that can cause this disorder. Despite these progresses 30-70% of severe early onset pediatric epilepsies remain of unknown etiology. Our work focuses on finding new genes in pediatric patients with unexplained epilepsy. In addition to hunting for new genes for epilepsy, we are also interested in the ‘other 99% of the genome’. Only about 1% of our genome contains DNA sequences that contain the code to make proteins – the other 99% is known as non-coding DNA. One of the functions of these regions of DNA is to control the expression of other genes. In the lab we use a range of epigenetic techniques and genome sequencing to identify non-coding variants implicated in epilepsy

 

Adult epilepsy

Most epilepsy genetics research has focused on pediatric patients, in contrast, genetic causes in adult patients are relatively unknown. We are also interested in using our knowledge of the genetic architecture of pediatric patients, as well as DNA sequencing approaches, to understand the role of genetics in adult patients with epilepsy. To achieve this, we’ve formed a multi-disciplinary team to develop the Adult Epilepsy Genetics Program at Northwestern. This program is co-directed by Dr. Zoe Gerard, a clinical epileptologist, and Dr. Carvill along with Senior Genetic Counselor, Lisa Kinsley (MS, CGC) and clinical research associate support from Irena Bellinski. Dr. Gerard and Lisa Kinsley see patients clinically with suspected genetic causes of epilepsy, and we recruit interested patients and families in research studies to find genetic causes of epilepsy as well as study these variants in cellular models, in particular many of the variants we have identified occur in genes of the mTOR pathway.

New approaches to genetic diagnosis. . .

Somatic Mosaicism and cell-free DNA

It has been hypothesized that some of the unexplained cases of epilepsy may be attributed to somatic mosaicism. Somatic mosaicism occurs when a DNA mutation is introduced during embryonic development; as a result, the somatic cells of the body are of more than one genotype. However, by and large these potentially disease-causing variations go undetected due to the inability to sample the affected tissue, the brain. We hypothesize that cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) and plasma may be a source for detecting these variants, as the cfDNA may originate from dying cells in the brain as a result of seizures. We are characterizing the origins of cfDNA in CSF and plasma in mouse models of epilepsy and humans using epigenomic profiling. We aim to use this approach to identify disease-causing brain-specific variants in the cfDNA in patients with epilepsy. In the future we aim to develop cfDNA as biomarker for epilepsy diagnosis, prognosis and seizure management. This work is sponsored by the high-risk, high-reward, NIH New Innovator Award. 

Understanding pathogenic mechanisms. . .

Stem Cell Models

We have noted that many of these genes that can cause epilepsy control the expression of other genes. In other words, they are responsible for switching certain genes ‘on’ or ‘off’ during the development and/or functioning of the brain. This switching is dependent on the 3D structure of DNA – called the epigenome. A class of genes called chromatin remodelers, change this 3D structure, while another class of genes – transcription factors, bind the DNA regions that are now accessible and can promote the expression of the target genes. 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.

Poison exons and alternative splicing

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.