Somatic mutation involving diverse genes leads to a spectrum of focal cortical malformations

Abstract

Post-zygotically acquired genetic variants, or somatic variants, that arise during cortical development have emerged as important causes of focal epilepsies, particularly those due to malformations of cortical development. Pathogenic somatic variants have been identified in many genes within the PI3K-AKT3-mTOR-signaling pathway in individuals with hemimegalencephaly and focal cortical dysplasia (type II), and more recently in SLC35A2 in individuals with focal cortical dysplasia (type I) or non-dysplastic epileptic cortex. Given the expanding role of somatic variants across different brain malformations, we sought to delineate the landscape of somatic variants in a large cohort of patients who underwent epilepsy surgery with hemimegalencephaly or focal cortical dysplasia. We evaluated samples from 123 children with hemimegalencephaly (n=16), focal cortical dysplasia type I and related phenotypes (n=48), focal cortical dysplasia type II (n=44), or focal cortical dysplasia type III (n=15) classified using imaging and pathological findings. We performed high-depth exome sequencing in brain tissue-derived DNA from each case and identified somatic single nucleotide, indel, and large copy number variants. In 75% of individuals with hemimegalencephaly and 29% with focal cortical dysplasia type II, we identified pathogenic variants in PI3K-AKT-mTOR pathway genes. Four of 48 cases with focal cortical dysplasia type I (8%) had a likely pathogenic variant in SLC35A2. While no other gene had multiple disease-causing somatic variants across the focal cortical dysplasia type I cohort, four individuals in this group had a single pathogenic or likely pathogenic somatic variant in CASK, KRAS, NF1, and NIPBL, genes associated with neurodevelopmental disorders. No rare pathogenic or likely pathogenic somatic variants in any neurological disease genes like those identified in the focal cortical dysplasia type I cohort were found in 63 neurologically normal controls (P = 0.017), suggesting a role for these novel variants. We also identified a somatic loss-of-function variant in the known epilepsy gene, PCDH19, present in a very small number of alleles in the dysplastic tissue from a female patient with focal cortical dysplasia IIIa with hippocampal sclerosis. In contrast to focal cortical dysplasia type II, neither focal cortical dysplasia type I nor III had somatic variants in genes that converge on a unifying biological pathway, suggesting greater genetic heterogeneity compared to type II. Importantly, we demonstrate that FCD types I, II, and III, are associated with somatic gene variants across a broad range of genes, many associated with epilepsy in clinical syndromes caused by germline variants, as well as including some not previously associated with radiographically evident cortical brain malformations.

Comprehensive multiomic profiling of somatic mutations in malformations of cortical development

“…Notably, ATP2A1, PPFIA4 , and NIPBL were recurrently mutated, either within our cohort or with a recent report 24 (Extended Data Fig. 3a-b), occurring within the latter 3 clusters.…”

“…This nevertheless provided an opportunity to study converging functional gene networks. Thus, we performed Markov clustering with a STRING network generated from the putative MCD genes 22 , as well as recently reported novel MCD candidates ( NAV2, EEF2, CASK, NF1, KRAS, PTPN11 ) 23,24 (Fig. 2a).…”

The genomic landscape across 474 surgically accessible epileptogenic human brain lesions

“…We generated deep (>350x) whole-exome sequencing (WES) data to identify somatic SNV and whole-genome genotyping data to identify somatic CNV across surgically-resected epileptogenic brain lesions from 474 individuals with focal drug-resistant epilepsy. While other studies performed targeted sequencing of lesional brain tissue from <100 individuals 16 , or WES in <130 individuals 72 , our study sample represents the largest cohort of epilepsy-associated brain lesions analyzed through deep whole-exome analysis. Using this rich source of data, we demonstrated differential somatic variant profiles across LEAT, MCD, and HS.…”

The genomic landscape across 474 surgically accessible epileptogenic human brain lesions

“…We generated deep (>350x) whole-exome sequencing (WES) data to identify somatic SNV and whole-genome genotyping data to identify somatic CNV across surgically-resected epileptogenic brain lesions from 474 individuals with focal drug-resistant epilepsy. While other studies performed targeted sequencing of lesional brain tissue from <100 individuals 16 , or WES in <130 individuals 69 , our study sample represents the largest cohort of epilepsy-associated brain lesions analyzed through deep whole-exome analysis. Using this rich source of data, we demonstrated differential somatic variant profiles across LEAT, MCD, and HS.…”

“…individuals 69 , our study sample represents the largest cohort of epilepsy-associated brain lesions analyzed through deep whole-exome analysis. Using this rich source of data, we demonstrated differential somatic variant profiles across LEAT, MCD, and HS.…”