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De Novo SCN1A, SCN8A, and CLCN2 Mutations in Childhood Absence Epilepsy T

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De Novo SCN1A, SCN8A, and CLCN2 Mutations in Childhood Absence Epilepsy T Epilepsy Research 154 (2019) 55–61 Contents lists available at ScienceDirect Epilepsy Research journal homepage: www.elsevier.com/locate/epilepsyres De novo SCN1A, SCN8A, and CLCN2 mutations in childhood absence epilepsy T Han Xie, Wenting Su, Jinrui Pei, Yujia Zhang, Kai Gao, Jinliang Li, Xiuwei Ma, Yuehua Zhang, ⁎ Xiru Wu, Yuwu Jiang Department of Pediatrics, Peking University First Hospital, Beijing, China ARTICLE INFO ABSTRACT Keywords: This study aimed to identify monogenic mutations from Chinese patients with childhood absence epilepsy (CAE) Childhood absence epilepsy and summarize their characteristics. A total of 100 patients with CAE were recruited in Peking University First SCN1A Hospital from 2005 to 2016 and underwent telephone and outpatient follow-up review. We used targeted dis- SCN8A ease-specific gene capture sequencing (involving 300 genes) to identify pathogenic variations for these patients. CLCN2 We identified three de novo epilepsy-related gene mutations, including missense mutations of SCN1A (c. 5399 T > A; p. Val1800Asp), SCN8A (c. 2371 G > T; p. Val791Phe), and CLCN2 (c. 481 G > A; p. Gly161Ser), from three patients, separately. All recruited patients presented typical CAE features and good prognosis. To date, CAE has been considered a complex disease caused by multiple susceptibility genes. In this study, we observed that 3% of typical CAE patients had a de novo mutation of a known monogenic epilepsy-related gene. Our study suggests that a significant proportion of typical CAE cases may be monogenic forms of epilepsy. For genetic generalized epilepsies, such as CAE, further studies are needed to clarify the contributions of de novo or inherited rare monogenic coding, noncoding and copy number variants. 1. Introduction 2. Materials and methods Childhood absence epilepsy (CAE) is a major subtype of genetic 2.1. Patients generalized epilepsies (GGE). Previous studies classified the genes as- sociated with CAE into two groups: ion channel and non-ion channel A total of 100 patients with CAE were recruited at the Peking genes. The majority of the genes associated with CAE comprise ion University First Hospital from 2005 to 2016 and were followed up by channel genes, such as CACAN1H, GABRA1, GABRB3 and GABRG2 telephone and outpatient follow-up visits. Those with high-quality DNA (Chen et al., 2003; Peloquin et al., 2006; Liang et al., 2006; Feng et al., samples and complete clinical data were preferentially selected. All 2017). Recently, many non-ion channel genes, such as NIPA2, were subjects were diagnosed with CAE by pediatric neurologists using the discovered to be related to CAE (Jiang et al., 2012). Since these known following criteria: (1) initial onset at 4–10 years of age; (2) absence genes are identified in a minority of patients with CAE, we sought to seizures occurring multiple times per day; (3) electroencephalogram further study the genetic basis of CAE. Although most with CAE have a (EEG) during absence seizures showing bilateral, symmetric, and syn- resolution of seizures, some do not. They may develop other epileptic chronous discharge of 3 Hz spike–waves with normal background; (4) syndromes, such as juvenile absence epilepsy (JAE) and juvenile myo- normal neurological examination; (5) normal neuroradiological ex- clonus epilepsy (JME), or have comorbidities, such as attention deficit aminations. The Medical Ethics Committee of Peking University First and learning difficulties (Wirrell et al., 1996; Echenne et al., 2001). Hospital approved this study. Informed consent was obtained from the Thus, better understanding of the contribution of novel CAE-related parents of CAE patients. Clinical data (onset age, seizure frequency, genes should provide insights into better treatments. development assessment, physical examination, EEG, neuroimaging, and treatment) were recorded by pediatric neurologists. ⁎ Corresponding author. E-mail address: [email protected] (Y. Jiang). https://doi.org/10.1016/j.eplepsyres.2019.04.005 Received 21 January 2019; Received in revised form 7 April 2019; Accepted 10 April 2019 Available online 22 April 2019 0920-1211/ © 2019 Elsevier B.V. All rights reserved. H. Xie, et al. Epilepsy Research 154 (2019) 55–61 Table 1 De novo missense mutations identified from Chinese patients with CAE. Patient ID Gene Mutation Inheritance Protein Polyphen2 MutationTaster 802 SCN1A p. Val1800Asp de novo Nav1.1 Probably damaging Disease causing 695 SCN8A p. Val791Phe de novo Nav1.6 Probably damaging Disease causing 931 CLCN2 p. Gly161Ser de novo CIC-2 Probably damaging Disease causing 2.2. Targeted next-generation sequencing 3. Results Targeted next-generation sequencing (NGS) was performed on the 3.1. Entire cohort genomic DNA of 100 CAE patients. On the basis of published literature and databases, 300 genes were selected as genes of interest (Table S1) One hundred Chinese Han CAE patients were recruited in trios from (Zhang et al., 2015; Kong et al., 2015). The genes previously reported in our pediatric neurology clinics at Peking University First Hospital. A the literature as being associated with CAE (the genes listed in the in- total of 42 patients were male, and 58 were female. Mean onset age of troduction) were included in this analysis. We designed a complete kit the patients was 6.6 years (median 6.4 years; range 4.2–9.9 years). In using the SureSelect Target Enrichment technique (Zhongguancun total, 16 CAE patients presented a history of febrile seizures, 8 patients Huakang Gene Institute, Beijing, China). After library construction, we reported a family history of febrile seizures, and 13 patients claimed a captured the coding regions, including the exon and exon–intron family history of epilepsy. Absence status epilepticus was unobserved in boundaries (1.285 Mbp), of the selected genes. Targeted NGS was the patients. subsequently performed on an Illumina GAIIx platform using paired- end sequencing of 110 bp to screen for mutations in the selected genes of 100 CAE patients and 50 controls. For these samples, clean paired- 3.2. Mutation identification end reads were aligned on the human reference genome (hg19) and annotated. Insertion–deletions (indels) and single-nucleotide poly- Using targeted next-generation sequencing for identification and morphisms (SNPs) were excluded using the Genome Analysis Tool kit Sanger sequencing for validation, de novo missense mutations, in- (GATK) and annotated by ANNOVAR. Sanger sequencing was per- cluding SCN1A (c. 5399 T > A; p. Val1800Asp), SCN8A (c. formed on DNA samples of probands and their parents to determine the 2371 G > T; p. Val791Phe), and CLCN2 (c. 481 G > A; p. Gly161Ser), parental origin and verify the results of targeted next-generation se- were identified from three independent cases among the 100 cases of quencing. clinically diagnosed typical CAE (positive rate of 3.0%). These muta- tions were not found in the 1000 Genomes database and 50 controls in this study. Table 1 shows details of the three mutations. All subjects but 2.3. Variation analysis none of their parents were heterozygous. The mutations were all pre- dicted as “probably damaging” in Polyphen2 and “disease-causing” in We used the following criteria to select possible pathogenic varia- MutationTaster. The mutations were highly conserved according to tions: (1) insertion/deletion variations; (2) termination codon varia- homology comparison. Fig. 1 shows the sequencing data of each mu- tions; (3) splice site variations involving substitution at nucleotide tation. +1/-1 of the intron; (4) missense variations predicted by Polyphen2 as The SCN1A mutation (Val1800Asp) in Patient 1 is located in the probably/possibly damaging or benign. Variations meeting any one of cytoplasmic C-terminus of Nav1.1 protein (amino acid 1786–2009). the above criteria were regarded as candidate variations for further Val1800Asp. Glu1795Lys and Val1857Leu, which are associated with a analysis (Zhang et al., 2015; Kong et al., 2015). milder phenotype, i.e., generalized epilepsy with febrile seizures plus 2 To assess evolutionary conservation, multiple sequence alignments (GEFS + 2), are located nearby (Li et al., 2010; Nagao et al., 2005). of the affected amino acids in different species were performed using a However, several mutations related to early infantile epileptic en- sequence alignment program (ClustalW; The Biology Workbench, San cephalopathy (EIEE) and intractable childhood epilepsy with general- Diego, CA, USA). The 1000 Genomes database (http://www. ized tonic-clonic seizures (ICE-GTC) (e.g., Phe1808Leu and 1000genomes.org/) and the Human Gene Mutation Database (http:// Trp1812Gly) are also found nearby (Fujiwara et al., 2003). We con- www.hgmd.org/) were applied to identify SNPs or reported pathogenic structed a model of the Val1800Asp mutation through computational mutations. After the assessment, on average, 10 possible pathogenic simulation and found no significant changes in protein structure variations were identified in each patient (Table S2). To further prior- (Fig. 2). Interestingly, our models of Glu1795Lys, Val1857Leu, itize variations, we selected heterozygous variations of genes with Phe1808Leu and Trp1812Gly all suggest that they may also not cause known autosomal or X-linked dominant disease-causing variants, significant changes in protein structure (Fig. 2). homozygous or compound heterozygous variations of genes with au- The SCN8A mutation Val791Phe in Patient 2 is located within the tosomal recessive disease-causing variants and hemizygous variations Nav1.6 segment
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