Research team
Expertise
The genetic epilepsies and epileptic encephalopathies are seizure disorders affecting 1 in every 1000 children, caused by defects in one or more genes. Over two hundred genes have been identified in these disorders, but a specific genetic cause can only be identified in less than half of patients. Our group uses multiple modalities to further identify genetic causes, to establish molecular mechanisms underlying known causes, and to develop potential therapeutic solutions. 1) As contributors to the Epi25 Consortium, we assist in the recruitment, phenotyping, and sequencing of patients with epileptic encephalopathies, as well as the following data analysis. In this Consortium, over 20,000 patients have already undergone whole-exome sequencing, with numerous genetic variants identified, including small substitutions, insertions, deletions, and copy number changes. Our group will add to the compendium of variant information by identifying transposable elements, and conducting burden tests to determine if these elements may also be contributing to epilepsy. Additionally, we are developing a pipeline to conduct linear modeling of rare and common variants in the Epi25 dataset to improve the statistical power of variant burden analysis. 2) We work directly with the epilepsy clinic of UZA to help identify novel genetic causes of epilepsy in patients who lack a molecular diagnosis by conventional means. We are currently analyzing whole-exome and whole-genome sequencing datasets for several dozen patients. 3) Our group has conducted extensive studies of KCNQ2 epileptic encephalopathies. As part of this work, we are performing deep molecular phenotyping (electrophysiology, immunocytology) and transcriptomics (bulk RNAseq, single-cell RNA seq) of iPSC-derived neurons from KCNQ2 patients. We will later expand these techniques to additional epileptic encephalopathies. Specific expertise: Having been trained in statistics, computational genomics, and various DNA/RNA/methylation sequencing pipelines, I will be applying my expertise to the computational aspects of these aforementioned projects.
Detection of somatic mutations in brain tissue and cerebrospinal fluid of patients with non-acquired drug-resistant epilepsy.
Abstract
Somatic (non-inherited) mutations are an increasingly appreciated cause of epilepsy and neurodevelopmental disorders (NDDs). For example, somatic mutations are recurrently found in the mTOR pathway genes in brain tissue of individuals with focal epilepsy with cortical malformations. Recent evidence indicates that somatic mosaicism in the brain is also involved in epilepsy and NDDs without brain malformations. Establishing the genetic diagnosis is a crucial step in the path towards improved care for patients. In the ~30% of patients in whom a genetic diagnosis can be made, this knowledge can lead to improved, targeted use of therapies and can inform patient families on prognosis and expected comorbidities. Uncovering the genes and mutational mechanisms involved in epilepsy and neurodevelopmental disorders also furthers our understanding of these diseases and forms the basis for development of novel targeted therapies. Somatic mutations are nowadays only identified in brain tissue, but for most epileptic and NDD patients, it is not possible to access brain tissue. Several studies have attempted to overcome this challenge by analyzing cell-free DNA (cfDNA) in cerebrospinal fluid (CSF). These previous studies used droplet digital PCR (ddPCR) to successfully track known somatic mutations in these disorders. However, in most epilepsy and NDD patients who have a possible mosaic contribution, brain tissue is not accessible, and the specific pathologic somatic change is unknown, making ddPCR protocols unsuitable. In this project, we will develop a novel protocol capable of agnostically detecting somatic pathogenic variants in cfDNA in CSF using a deep-sequencing strategy. This protocol will be validated on CSF of individuals with known somatic mutations that were first identified in post-surgical brain tissue. Once validated, this protocol will form the foundation for future research where CSF, but not brain tissue, is available. For example, we will subsequently deploy this protocol on a cohort of patients that is specifically enriched for clinical presentations of presumptive genetic epilepsy that is not adequately explained by germline mutations, an important research endeavor that has never been attempted before. We anticipate that by identifying brain somatic variants using our novel and agnostic approach, more accurate and personalized genetic counseling and treatment can be provided.Researcher(s)
- Promoter: Niranjan Tejasvi
Research team(s)
Project type(s)
- Research Project