Somatic Ras/Raf/MAPK Variants Enriched in the Hippocampus in Drug-Resistant Mesial Temporal Lobe Epilepsy
Authors: Khoshkhoo Sattar , Wang Yilan , Chahine Yasmine , Erson-Omay E. Zeynep , Robert Stephanie , Kiziltug Emre , Damisah Eyiyemisi C. , Nelson-Williams Carol , Zhu Guangya , Kong Wenna , Huang August Yue , Stronge Edward , Phillips H. Westley , Chhouk Brian H. , Bizzotto Sara , Chen Ming Hui , Adikari Thiuni N. , Ye Zimeng , Witkowski Tom , Lai Dulcie , Lee Nadine , Lokan Julie , Scheffer Ingrid E. , Berkovic Samuel F. , Haider Shozeb , Hildebrand Michael S. , Yang Edward , Gunel Murat , Lifton Richard P. , Richardson R Mark , Blümcke Ingmar , Alexandrescu Sanda , Huttner Anita , Heinzen Erin L. , Zhu Jidong , Poduri Annapurna , DeLanerolle Nihal , Spencer Dennis D. , Lee Eunjung Alice , Walsh Christopher A. , Kahle Kristopher T. 
Published: December 2022

AbstractImportanceMesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy subtype and is often refractory to anti-seizure medications. While most MTLE patients do not have pathogenic germline genetic variants, the contribution of post-zygotic (i.e., somatic) variants in the brain is unknown.ObjectiveTo test the association between pathogenic somatic variants in the hippocampus and MTLE.DesignThis case-control genetic association study analyzed the DNA derived from hippocampal tissue of neurosurgically-treated patients with MTLE and age- and sex-matched neurotypical controls. Participants were enrolled from 1988 through 2019 and clinical data was collected retrospectively. Whole-exome and gene-panel sequencing (depth>500X) were used to identify candidate pathogenic somatic variants. A subset of novel variants were functionally evaluated using cellular and molecular assays.SettingLevel 4 epilepsy centers, multi-center study.ParticipantsNon-lesional and lesional (mesial temporal sclerosis, focal cortical dysplasia, and low-grade epilepsy-associated tumors) drug-resistant MTLE patients who underwent anterior medial temporal lobectomy. All patients with available frozen tissue and appropriate consents were included. Control brain tissue was obtained from neurotypical donors at brain banks.ExposuresDrug-resistant MTLE.Main Outcomes and MeasuresPresence and abundance of pathogenic somatic variants in the hippocampus versus the unaffected temporal neocortex.ResultsSamples were obtained from 105 MTLE patients (52 male, 53 female; age: MED [IQR], 32 [26-44]) and 30 neurotypical controls (19 male, 11 female; age: MED [IQR], 37 [18-53]). Eleven pathogenic somatic variants, enriched in the hippocampus relative to the unaffected temporal neocortex (MED [IQR], 1.92 [1.5-2.7] vs 0.3 [0-0.9], p<0.05), were detected in MTLE patients but not in the controls. Ten of these variants were inPTPN11, SOS1, KRAS, BRAF, andNF1, all predicted to constitutively activate Ras/Raf/MAPK signaling. Immunohistochemical studies of variant-positive hippocampal tissue demonstrated increased Erk1/2 phosphorylation, indicative of Ras/Raf/MAPK activation, predominantly in glial cells. Molecular assays showed abnormal liquid-liquid phase separation for thePTPN11variants as a possible dominant gain-of-function mechanism.Conclusions and RelevanceHippocampal somatic variants, particularly those activating Ras/Raf/MAPK signaling, may contribute to the pathogenesis of sporadic, drug-resistant MTLE. These findings may provide a novel genetic mechanism and highlight new therapeutic targets for this common indication for epilepsy surgery.