1. Somatic Focal Copy Number Gains of Noncoding Regions of Receptor Tyrosine Kinase Genes in Treatment-Resistant Epilepsy
- Author
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Luis Chiriboga, Matija Snuderl, Valerio Conti, Briana Zeck, Javier Hernaez Rodriguez, Adriana Heguy, Maristela L. Onozato, Claudio Forcato, Anna Maria Buccoliero, Hussein Mohamed, Sitharam Ramaswami, Marianna Garonzi, Kaicen Zhu, Jonathan Serrano, Jane A. Skok, Varshini Vasudevaraja, Eveline Teresa Hidalgo, Daniel Friedman, Aristotelis Tsirigos, Arline Faustin, A. John Iafrate, David Zagzag, Renzo Guerrini, Cristiana Pelorosso, James M. Stafford, Orrin Devinsky, Lily M. Tredwin, and John G. Golfinos
- Subjects
Adult ,Male ,Drug Resistant Epilepsy ,Adolescent ,DNA Copy Number Variations ,PDGFRA ,Receptor tyrosine kinase ,Pathology and Forensic Medicine ,Young Adult ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Epilepsy ,0302 clinical medicine ,medicine ,Humans ,Epidermal growth factor receptor ,Copy-number variation ,Child ,Gene ,In Situ Hybridization, Fluorescence ,Retrospective Studies ,030304 developmental biology ,0303 health sciences ,biology ,Brain ,Promoter ,Original Articles ,General Medicine ,DNA Methylation ,Middle Aged ,medicine.disease ,ErbB Receptors ,Neurology ,DNA methylation ,Cancer research ,biology.protein ,Female ,Neurology (clinical) ,030217 neurology & neurosurgery - Abstract
Epilepsy is a heterogenous group of disorders defined by recurrent seizure activity due to abnormal synchronized activity of neurons. A growing number of epilepsy cases are believed to be caused by genetic factors and copy number variants (CNV) contribute to up to 5% of epilepsy cases. However, CNVs in epilepsy are usually large deletions or duplications involving multiple neurodevelopmental genes. In patients who underwent seizure focus resection for treatment-resistant epilepsy, whole genome DNA methylation profiling identified 3 main clusters of which one showed strong association with receptor tyrosine kinase (RTK) genes. We identified focal copy number gains involving epidermal growth factor receptor (EGFR) and PDGFRA loci. The dysplastic neurons of cases with amplifications showed marked overexpression of EGFR and PDGFRA, while glial and endothelial cells were negative. Targeted sequencing of regulatory regions and DNA methylation analysis revealed that only enhancer regions of EGFR and gene promoter of PDGFRA were amplified, while coding regions did not show copy number abnormalities or somatic mutations. Somatic focal copy number gains of noncoding regulatory represent a previously unrecognized genetic driver in epilepsy and a mechanism of abnormal activation of RTK genes. Upregulated RTKs provide a potential avenue for therapy in seizure disorders.
- Published
- 2020