Investigating Aberrant DNA Methylation in Pediatric Epilepsies
Abstract number :
1.378
Submission category :
12. Genetics / 12A. Human Studies
Year :
2022
Submission ID :
2203951
Source :
www.aesnet.org
Presentation date :
12/3/2022 12:00:00 PM
Published date :
Nov 22, 2022, 05:22 AM
Authors :
Christy LaFlamme, MS – St. Jude Children's Research Hospital; Edith Almanza Fuerte, BS – St. Jude Children's Research Hospital; Sophie Russ-Hall, BS – University of Melbourne; Amy Schneider, MS – University of Melbourne; Danny Miller, MD, PhD – University of Washington; Miranda Galey, MS – University of Washington; Zhaoming Wang, PhD – St. Jude Children's Research Hospital; Bekim Sadikovic, PhD – University of Western Ontario; Lynette Sadleir, FRACP, PhD – University of Otago; Samuel Berkovic, AC, FAA, FRACP, FRS – University of Melbourne; Ingrid Scheffer, AO – University of Melbourne; Heather Mefford, MD, PhD – St. Jude Children's Research Hospital
Rationale: Developmental and epileptic encephalopathies (DEEs) are a group of disorders characterized by drug-resistant seizures and developmental slowing or regression with epileptiform activity on EEG. Advances in sequencing technology have enabled Mendelian genetic diagnosis in ~50% of patients with the potential for developing targeted therapies. Those without known pathogenic DNA variants are deemed “unsolved.” DNA methylation is an important epigenetic modification implicated in various neurodevelopmental disorders, such as Fragile X syndrome. Rare differentially methylated regions (DMRs) affect gene expression and can be influenced by DNA sequence variations, such as GC-rich repeat expansions impossible to detect by standard sequencing modalities, but have not been studied in DEEs. Additionally, as a part of EpiSign analysis, distinct genome-wide “episignatures” have been derived for ~120 monogenic neurodevelopmental disorders, including >20 genetic epilepsy syndromes and DEEs. Episignatures indicate the presence of a pathogenic variant in a specific gene. Thus, a patient with unsolved DEE could display an episignature informing the gene to examine for missed or misinterpreted coding and noncoding variants. The diagnostic utility of episignature analysis for unsolved DEE is not known. We hypothesize that DNA methylation analysis can be used to uncover novel causes of DEE by (1) investigating rare DMRs as an alternative disease mechanism and (2) using recently established methylation episignatures of monogenic disorders to inform the identification of previously hidden, novel pathogenic variants.
Methods: We generated Illumina EPIC methylation array data for >400 patients with unsolved DEEs, identified rare DMRs using a robust outlier approach, and performed episignature analysis. We have validated 15 DMRs to date using targeted bisulfite sequencing and nanopore long-read sequencing. We then identified potential underlying DNA defects of DMRs and candidate pathogenic variants associated with episignatures using a combination of short and long-read sequencing.
Results: We find that patients with unsolved DEEs harbor rare outlier DMRs and episignatures that inform potentially disease causative DNA variants. To investigate the effects of DMRs and candidate pathogenic variants on gene expression, we will perform RNA-seq of patient-derived or genetically engineered cell lines.
Conclusions: Our findings will provide insights into novel epigenetic mechanisms underlying DEEs, facilitate molecular diagnoses of patients with unsolved DEE, and potentially lead to improved diagnostics and the discovery of novel therapeutic targets for these devastating disorders.
Funding: St. Jude Graduate School of Biomedical Sciences, Center for Mendelian Genomics (UW-CMG), CURE Epilepsy
Genetics