Clinical application of trio-based whole-exome sequencing in idiopathic generalized epilepsy

CSMD1 as a causative gene of developmental and epileptic encephalopathy and generalized epilepsies

Genetic factors are the major causes of epilepsies, such as developmental and epileptic encephalopathy (DEE) and idiopathic generalized epilepsy (IGE). However, the etiology of most patients remains elusive. This study performed exon sequencing in a cohort of 173 patients with IGE. Additional cases were recruited from the matching platform in China. The excess and damaging effect of variants, the genotype-phenotype correlation, and the correlation between gene expression and phenotype were studied to validate the gene-disease association. CSMD1 compound heterozygous variants were identified in four unrelated cases with IGE. Additional CSMD1 variants were identified in five cases with DEE featured by generalized seizures from the matching platform, including two with de novo and three with compound heterozygous variants. Two patients were refractory to antiseizure medications and all patients were on long-term therapy. The CSMD1 variants presented a significantly high excess of variants in the case-cohort. Besides de novo origination, the DEE cases had each of the paired variants located closer to each other than the IGE cases or more significant alterations in hydrophobicity. The DEE-associated variants were all absent in the normal population and presented significantly lower minor allele frequency than the IGE-associated variants, suggesting a minor allele frequency-phenotype severity correlation. Gene expression analysis showed that CSMD1 was extensively expressed throughout the brain, particularly in the cortex. The CSMD1 temporal expression pattern correlated with the disease onset and outcomes. This study suggests that CSMD1 is associated with epilepsy and is a novel causative gene of DEE and generalized epilepsies.

Role of voltage-gated chloride channels in epilepsy: current insights and future directions

Epilepsy is a prevalent chronic neurological disorder characterised by recurrent seizures caused by excessive neuronal discharge. Disruptions in chloride ion homeostasis significantly affect neuronal excitability, and play a crucial role in the pathophysiology of this disorder. This review highlights the emerging importance of chloride voltage-gated channels in epilepsy, which has been largely underappreciated compared to cation channels. Recent studies have suggested that genetic alterations in chloride channels, such as CLCN1, CLCN2, CLCN3, CLCN4, and CLCN6, contribute to neuronal excitability and seizure susceptibility, with variations in these channels acting more as susceptibility factors than direct causes. However, there is a significant gap in the research on other chloride channels, particularly ClC-Ka, ClC-Kb, ClC-5, and ClC-7, whose roles in epilepsy remain underexplored. Future research should focus on these channels to better understand their contribution to the pathophysiology of epilepsy. The incorporation of genetic tests for chloride channel variants in clinical practice could provide valuable insight into the aetiology of epilepsy, leading to improved diagnostic and therapeutic strategies for affected individuals.

Clinical and Genetic Characterization of Adolescent-Onset Epilepsy: A Single-Center Experience in Republic of Korea

OBJECTIVES

This study investigated the characteristics of adolescent-onset epilepsy (AOE) and conducted genetic tests on a cohort of 76 Korean patients to identify variants and expand the spectrum of mutations associated with AOE.

METHODS

Clinical exome sequencing after routine karyotyping and chromosomal microarray was performed to identify causative variants and expand the spectrum of mutations associated with AOE.

RESULTS

In cases of AOE without neurodevelopmental delay (NDD), this study identified four likely pathogenic variants (LPVs) or variants of uncertain significance (VUS) and two copy number variations (CNVs). To explore the unique features of AOE; clinical manifestations were compared between patients with and without NDD. The analysis revealed statistically significant differences in the prevalence of males and the yield of genetic testing results. AOE without NDD had a lower prevalence in males (49%) compared to AOE with NDD (60%) (p = 0.007). Genetic alterations: AOE with NDD exhibited a higher frequency of genetic alterations (35%) compared to AOE without NDD (12%) (p = 0.011). Thorough evaluation of AOE can be particularly challenging in adolescent patients. Some individuals may display genetic variations due to a phenomenon known as locus heterogeneity, where different genetic causes lead to similar clinical presentations.

CONCLUSIONS

Implementing a robust genetic workflow is crucial for accurately diagnosing AOE, even in cases with complex genetic underpinnings. This study underscores the importance of genetic testing as an essential diagnostic tool for AOE. Identifying genetic variants and understanding their clinical correlations can aid in improving diagnostic accuracy and optimizing treatment approaches for adolescent patients with epilepsy.

Gene-gene interaction network analysis indicates CNTN2 is a candidate gene for idiopathic generalized epilepsy

Twin and family studies have established the genetic contribution to idiopathic generalized epilepsy (IGE). The genetic architecture of IGE is generally complex and heterogeneous, and the majority of the genetic burden in IGE remains unsolved. We hypothesize that gene-gene interactions contribute to the complex inheritance of IGE. CNTN2 (OMIM* 615,400) variants have been identified in cases with familial adult myoclonic epilepsy and other epilepsies. To explore the gene-gene interaction network in IGE, we took the CNTN2 gene as an example and investigated its co-occurrent genetic variants in IGE cases. We performed whole-exome sequencing in 114 unrelated IGE cases and 296 healthy controls. Variants were qualified with sequencing quality, minor allele frequency, in silico prediction, genetic phenotype, and recurrent case numbers. The STRING_TOP25 gene interaction network analysis was introduced with the bait gene CNTN2 (denoted as A). The gene-gene interaction pair mode was presumed to be A + c, A + d, A + e, with a leading gene A, or A + B + f, A + B + g, A + B + h, with a double-gene A + B, or other combinations. We compared the number of gene interaction pairs between the case and control groups. We identified three pairs in the case group, CNTN2 + PTPN18, CNTN2 + CNTN1 + ANK2 + ANK3 + SNTG2, and CNTN2 + PTPRZ1, while we did not discover any pairs in the control group. The number of gene interaction pairs in the case group was much more than in the control group (p = 0.021). Taking together the genetic bioinformatics, reported epilepsy cases, and statistical evidence in the study, we supposed CNTN2 as a candidate pathogenic gene for IGE. The gene interaction network analysis might help screen candidate genes for IGE or other complex genetic disorders.