Rare coding variants in genes encoding GABA receptors in genetic generalised epilepsies: an exome-based case-control study.

Authors:
Patrick May Simon Girard Merle Harrer Dheeraj R Bobbili Julian Schubert Stefan Wolking Felicitas Becker Pamela Lachance-Touchette Caroline Meloche Micheline Gravel Cristina E Niturad Julia Knaus Carolien De Kovel Mohamad Toliat Anne Polvi Michele Iacomino Rosa Guerrero-López Stéphanie Baulac Carla Marini Holger Thiele Janine Altmüller Kamel Jabbari Ann-Kathrin Ruppert Wiktor Jurkowski Dennis Lal Raffaella Rusconi Sandrine Cestèle Benedetta Terragni Ian D Coombs Christopher A Reid Pasquale Striano Hande Caglayan Auli Siren Kate Everett Rikke S Møller Helle Hjalgrim Hiltrud Muhle Ingo Helbig Wolfram S Kunz Yvonne G Weber Sarah Weckhuysen Peter De Jonghe Sanjay M Sisodiya Rima Nabbout Silvana Franceschetti Antonietta Coppola Maria S Vari Dorothée Kasteleijn-Nolst Trenité Betul Baykan Ugur Ozbek Nerses Bebek Karl M Klein Felix Rosenow Dang K Nguyen François Dubeau Lionel Carmant Anne Lortie Richard Desbiens Jean-François Clément Cécile Cieuta-Walti Graeme J Sills Pauls Auce Ben Francis Michael R Johnson Anthony G Marson Bianca Berghuis Josemir W Sander Andreja Avbersek Mark McCormack Gianpiero L Cavalleri Norman Delanty Chantal Depondt Martin Krenn Fritz Zimprich Sarah Peter Marina Nikanorova Robert Kraaij Jeroen van Rooij Rudi Balling M Arfan Ikram André G Uitterlinden Giuliano Avanzini Stephanie Schorge Steven Petrou Massimo Mantegazza Thomas Sander Eric LeGuern Jose M Serratosa Bobby P C Koeleman Aarno Palotie Anna-Elina Lehesjoki Michael Nothnagel Peter Nürnberg Snezana Maljevic Federico Zara Patrick Cossette Roland Krause Holger Lerche

Lancet Neurol 2018 08 17;17(8):699-708. Epub 2018 Jul 17.

Background: Genetic generalised epilepsy is the most common type of inherited epilepsy. Despite a high concordance rate of 80% in monozygotic twins, the genetic background is still poorly understood. We aimed to investigate the burden of rare genetic variants in genetic generalised epilepsy.

Methods: For this exome-based case-control study, we used three different genetic generalised epilepsy case cohorts and three independent control cohorts, all of European descent. Cases included in the study were clinically evaluated for genetic generalised epilepsy. Whole-exome sequencing was done for the discovery case cohort, a validation case cohort, and two independent control cohorts. The replication case cohort underwent targeted next-generation sequencing of the 19 known genes encoding subunits of GABA receptors and was compared to the respective GABA receptor variants of a third independent control cohort. Functional investigations were done with automated two-microelectrode voltage clamping in Xenopus laevis oocytes.

Findings: Statistical comparison of 152 familial index cases with genetic generalised epilepsy in the discovery cohort to 549 ethnically matched controls suggested an enrichment of rare missense (Nonsyn) variants in the ensemble of 19 genes encoding GABA receptors in cases (odds ratio [OR] 2·40 [95% CI 1·41-4·10]; p=0·0014, adjusted p=0·019). Enrichment for these genes was validated in a whole-exome sequencing cohort of 357 sporadic and familial genetic generalised epilepsy cases and 1485 independent controls (OR 1·46 [95% CI 1·05-2·03]; p=0·0081, adjusted p=0·016). Comparison of genes encoding GABA receptors in the independent replication cohort of 583 familial and sporadic genetic generalised epilepsy index cases, based on candidate-gene panel sequencing, with a third independent control cohort of 635 controls confirmed the overall enrichment of rare missense variants for 15 GABA receptor genes in cases compared with controls (OR 1·46 [95% CI 1·02-2·08]; p=0·013, adjusted p=0·027). Functional studies for two selected genes (GABRB2 and GABRA5) showed significant loss-of-function effects with reduced current amplitudes in four of seven tested variants compared with wild-type receptors.

Interpretation: Functionally relevant variants in genes encoding GABA receptor subunits constitute a significant risk factor for genetic generalised epilepsy. Examination of the role of specific gene groups and pathways can disentangle the complex genetic architecture of genetic generalised epilepsy.

Funding: EuroEPINOMICS (European Science Foundation through national funding organisations), Epicure and EpiPGX (Sixth Framework Programme and Seventh Framework Programme of the European Commission), Research Unit FOR2715 (German Research Foundation and Luxembourg National Research Fund).

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http://dx.doi.org/10.1016/S1474-4422(18)30215-1DOI Listing
August 2018
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