A multi-omics approach to understanding pediatric epilepsies - PROJECT SUMMARY/ABSTRACT Developmental and epileptic encephalopathies (DEEs) are severe pediatric neurological disorders with a strong genetic link characterized by drug-resistant seizures and developmental delays. To develop precision therapies in the era of genomic medicine, one must first obtain a precise molecular diagnosis. Sequencing technologies can now identify genetic etiologies of DEEs in about 50% of patients, but the remaining 50% have genetically “unsolved” DEEs. Furthermore, understanding how these genetic alterations lead to disease underlies important aspects of basic biology and is paramount for moving effective therapies into the clinic. We have recently established the diagnostic utility of genome-wide DNA methylation analysis to uncover causal and candidate etiologies in DEEs. By investigating DNA methylation arrays for >500 individuals with unsolved DEEs, we determined that rare differentially methylated regions are accompanied by underlying rare CG-rich tandem repeat expansions (TREs) and other structural variants. We also diagnosed a subset of individuals by leveraging DNA methylation signatures (“episignatures”), which are clinically validated biomarkers of >100 neurodevelopmental disorders, including epilepsies. Our work represents a significant advance towards solving the unsolved and opens further questions regarding genomic discoveries in DEEs and functional investigations of episigantures, each of which is highly applicable to hundreds of genetic disorders. In the F99 phase of this proposed research, I will utilize our growing cohorts of short- and long-read genome sequencing data from individuals with unsolved DEEs and their parents to investigate rare TREs more broadly as potential novel etiologies of DEEs and RNA-seq data to probe TRE function. I will harness overlapping epigenomic and transcriptomic datasets to investigate episignatures in brain-relevant cell types using CHD2- encephalopathy as a model. Individuals with loss-of-function variants in CHD2 harbor a robust episignature in the blood, but no work has been done to characterize these episignatures in brain-relevant cell types, such as neuronal progenitor cells and 2D neurons. I will characterize episignatures and correlations with gene expression for CHD2 in these cell types and determine if restoration of CHD2 is sufficient to alter episignatures back to normal. This will determine whether episignatures can serve as biomarkers for therapeutic development. In the K00 phase of this proposed research, I will continue to use cutting-edge sequencing technologies to understand human genetic variation and how alterations lead to disease phenotypes. I will expand on my bioinformatics skills by developing software solutions to address new technologies and growing datasets. I will use these tools on large, diverse datasets to understand disease biology and translate my findings into the clinic. The proposed work will yield novel genomic, epigenomic, and transcriptomic discoveries that will increase our understanding of pediatric epilepsies, their etiologies and how those etiologies lead to disease. Ultimately, this work has diagnostic, prognostic, and therapeutic implications relevant for hundreds of genetic disorders.
