Association of ultra-rare genetic variants with epilepsy

Epilepsy represents a wide spectrum of phenotypes with various etiologies and comorbidities. Genetic predisposition to epilepsy is conferred by rare variants and common risk alleles. Ultra-rare variants (URVs) – those not seen in healthy population controls – are thought to underlie a substantial part of the risk mediated by coding variants. In this dissertation, the role of URVs was studied in several cohorts of individuals with common epilepsy syndromes, aiming to identify new genetic etiologies underlying epileptogenesis. Multiple approaches based on whole exome sequencing were utilized, scaling from studies of single families to populations and from genes to gene sets. First, five closely consanguineous Sudanese families, in which multiple siblings (whose parents are cousins) were diagnosed with a genetic epilepsy, were examined to touch upon the role of rare bi-allelic coding variation in familial epilepsies. There was no evidence to support a key role for recessive inheritance in less severe epilepsies. However, the results expanded the phenotypic spectrum of biallelic ultra-rare PRRT2 variants, previously linked to movement disorders, to include mild self-limited epilepsy. Second, sequencing data from individuals diagnosed with genetic generalized epilepsy (GGE; n = 1,928 cases vs. 8,578 ancestry-matched controls of European descent) were analyzed using gene and gene set collapsing approaches to identify key URV associations. Separate analyses of familial GGE (n = 945 cases vs. 8,626 controls) or sporadic GGE (n = 1,005 cases vs. 8,621 controls) were also performed. URVs in GABRG2 showed an association with familial GGE (approaching study-wide significance) but not with sporadic GGE. Additionally, a higher enrichment of URVs affecting genes encoding GABAA receptors and GABAergic pathway genes was seen in familial vs. sporadic GGE. Third, the burden of URVs in a comprehensive range of gene sets was studied in the exomes of individuals diagnosed with GGE (n = 3,064), non-acquired focal epilepsy (NAFE; n = 3,522) or developmental and epileptic encephalopathy (DEE; n = 1,003), compared to 3,962 ancestry-matched controls. In GGE, the burden of URVs in constrained genic regions – those devoid of variations in the general population – was higher in gene sets important for inhibitory signaling vs. in gene sets representative of excitatory signaling. Conversely, there was a relatively higher burden in excitatory vs. inhibitory gene sets in NAFE. In summary, this dissertation presents novel findings pertaining to the role of ultra-rare coding variation in epileptic disorders, providing new insights into the spectrum of key genes and gene sets related to epileptogenesis

Association of ultra-rare coding variants with genetic generalized epilepsy : A case–control whole exome sequencing study

Publisher Copyright: © 2022 The Authors. Epilepsia published by Wiley Periodicals LLC on behalf of International League Against Epilepsy.Objective: We aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with familial and sporadic GGE. Methods: We performed a case–control whole exome sequencing study in unrelated individuals of European descent diagnosed with GGE (previously recruited and sequenced through multiple international collaborations) and ancestry-matched controls. The association of ultra-rare variants (URVs; in 18 834 protein-coding genes) with epilepsy was examined in 1928 individuals with GGE (vs. 8578 controls), then separately in 945 individuals with familial GGE (vs. 8626 controls), and finally in 1005 individuals with sporadic GGE (vs. 8621 controls). We additionally examined the association of URVs with familial and sporadic GGE in two gene sets important for inhibitory signaling (19 genes encoding γ-aminobutyric acid type A [GABAA] receptors, 113 genes representing the GABAergic pathway). Results: GABRG2 was associated with GGE (p = 1.8 × 10−5), approaching study-wide significance in familial GGE (p = 3.0 × 10−6), whereas no gene approached a significant association with sporadic GGE. Deleterious URVs in the most intolerant subgenic regions in genes encoding GABAA receptors were associated with familial GGE (odds ratio [OR] = 3.9, 95% confidence interval [CI] = 1.9–7.8, false discovery rate [FDR]-adjusted p =.0024), whereas their association with sporadic GGE had marginally lower odds (OR = 3.1, 95% CI = 1.3–6.7, FDR-adjusted p =.022). URVs in GABAergic pathway genes were associated with familial GGE (OR = 1.8, 95% CI = 1.3–2.5, FDR-adjusted p =.0024) but not with sporadic GGE (OR = 1.3, 95% CI =.9–1.9, FDR-adjusted p =.19). Significance: URVs in GABRG2 are likely an important risk factor for familial GGE. The association of gene sets of GABAergic signaling with familial GGE is more prominent than with sporadic GGE.Peer reviewe

EBV Associated Breast Cancer Whole Methylome Analysis Reveals Viral and Developmental Enriched Pathways

Background: Breast cancer (BC) ranks among the most common cancers in Sudan and worldwide with hefty toll on female health and human resources. Recent studies have uncovered a common BC signature characterized by low frequency of oncogenic mutations and high frequency of epigenetic silencing of major BC tumor suppressor genes. Therefore, we conducted a pilot genome-wide methylome study to characterize aberrant DNA methylation in breast cancer.Results: Differential methylation analysis between primary tumor samples and normal samples from healthy adjacent tissues yielded 20,188 differentially methylated positions (DMPs), which is further divided into 13,633 hypermethylated sites corresponding to 5339 genes and 6,555 hypomethylated sites corresponding to 2811 genes. Moreover, bioinformatics analysis revealed epigenetic dysregulation of major developmental pathways including hippo signaling pathway. We also uncovered many clues to a possible role for EBV infection in BC.Conclusion: Our results clearly show the utility of epigenetic assays in interrogating breast cancer tumorigenesis, and pinpointing specific developmental and viral pathways dysregulation that might serve as potential biomarkers or targets for therapeutic interventions

Loss-of-function variants in the KCNQ5 gene are implicated in genetic generalized epilepsies

Summary Background De novo missense variants in KCNQ5, encoding the voltage-gated K+ channel KV7.5, have been described to cause developmental and epileptic encephalopathy (DEE) or intellectual disability (ID). We set out to identify disease-related KCNQ5 variants in genetic generalized epilepsy (GGE) and their underlying mechanisms. Methods 1292 families with GGE were studied by next-generation sequencing. Whole-cell patch-clamp recordings, biotinylation and phospholipid overlay assays were performed in mammalian cells combined with homology modelling. Findings We identified three deleterious heterozygous missense variants, one truncation and one splice site alteration in five independent families with GGE with predominant absence seizures; two variants were also associated with mild to moderate ID. All missense variants displayed a strongly decreased current density indicating a loss-of-function (LOF). When mutant channels were co-expressed with wild-type (WT) KV7.5 or KV7.5 and KV7.3 channels, three variants also revealed a significant dominant-negative effect on WT channels. Other gating parameters were unchanged. Biotinylation assays indicated a normal surface expression of the variants. The R359C variant altered PI(4,5)P2-interaction. Interpretation Our study identified deleterious KCNQ5 variants in GGE, partially combined with mild to moderate ID. The disease mechanism is a LOF partially with dominant-negative effects through functional deficits. LOF of KV7.5 channels will reduce the M-current, likely resulting in increased excitability of KV7.5-expressing neurons. Further studies on network level are necessary to understand which circuits are affected and how this induces generalized seizures. Funding DFG/FNR Research Unit FOR-2715 (Germany/Luxemburg), BMBF rare disease network Treat-ION (Germany), foundation ‘no epilep’ (Germany)