Authors :
Presenting Author: Christian Bosselmann, MD – Cleveland Clinic
Costin Leu, PhD – Cleveland Clinic; Lucas Hoffmann, MD – Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen; Sara Baldassari, PhD – Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France; Roland Coras, MD – Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen; Katja Kobow, PhD – Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen; Hajo Hamer, MD – Epilepsy Center, EpiCARE Partner, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany; Sebastian Brandner, MD – Department of Neurosurgery, EpiCARE Partner, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany; Karl Roessler, MD – Department of Neurosurgery, EpiCARE Partner, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany; Department of Neurosurgery, EpiCARE Partner, Medical University of Vienna, Vienna General Hospital, Vienna, Austria; Christian Bien, MD – Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, Germany; Thilo Kalbhenn, MD – Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, Germany; Department of Neurosurgery (Evangelisches Klinikum Bethel), Medical School, Bielefeld University, Bielefeld, Germany; Tom Pieper, MD – Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Rosenheim, Germany; Till Hartlieb, MD – Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Rosenheim, Germany; Kerstin Becker, PhD – Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Janine Altmüller, PhD – Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany;; Lisa Ferguson, Research Coordinator – Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Robyn Busch, PhD – Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Stephanie Baulac, PhD – Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France; Peter Nürnberg, PhD – Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Imad Najm, MD – Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Ingmar Blümcke, MD – Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany;; Dennis Lal, PhD – Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA.
Rationale:
Understanding the molecular mechanisms involved in the etiology of epileptogenic malformations of cortical development (MCD) is essential to improve the treatment of drug-resistant focal epilepsy.
Methods:
We aggregated 431 MCD across multiple centers in Europe and the Cleveland Clinic (USA). Two hundred twenty four samples were previously deep ( > 350x) exome sequenced and 148 samples were deep ( > 1500x) panel sequenced for 122 candidate genes. Results were pooled with 59 external deep WES samples. All pathology samples were independently reviewed and classified according to the 2022 ILAE consensus classification of focal cortical dysplasia. We tested for somatic variant enrichment with dNdScv, a model that provides quantitative estimates for driver mutations. We used stringent Bonferroni correction after the number of genes captured by the whole-exome screens in each pathology to identify genome-wide significant somatic variant-enriched genes. Gene list enrichment analysis was done with Enrichr.
Results:
We observed that 122/431 (28.3%) samples had ≥ 1 variant in known causal genes for MCD, and a further 35/431 (8.1%) samples had validated functional cancer driver variants from the Catalogue Of Somatic Mutations In Cancer (COSMIC v98). MTOR was the most commonly affected gene (N=34 samples). Interestingly, multiple variants in shared pathways (e.g., MTOR, TSC2, DEPDC5) co-occurred in 15 samples. Somatic variant enrichment analysis confirmed two genes previously reported to be enriched with somatic variants in individuals with MCD: MTOR in 26.4% of individuals with focal-cortical dysplasia type 2 (FCD II; P=6.45x10-8) and SLC35A2 in 30.6% of individuals with mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE; P=2.22x10-9). Pathway analyses across all nominal enrichments showed an overrepresentation of the PI3K-Akt signaling (KEGG; Padj=7.49x10-7) and autophagy pathways (GO:0016242; Padj=1.12x10-6) in FCD II.
Conclusions:
Few genes contribute to large proportions of specific pathology-defined epilepsies in somatic variant enrichment analyses of MCD.
Our study suggests that the remaining unexplained lesional epilepsies are highly heterogeneous. We hypothesize that second-hit somatic variants may potentially occur at pathway-level, pending further confirmation.
Funding:
I.B. and P.N. received research funding from the German Research Foundation (DFG, grant agreement numbers BL 421/4-1 and NU 50/13-1). D.L. was supported by the National Institutes of Health (R01 NS117544). Sequencing was facilitated by the DFG-funded West German Genome Center (WGGC).