Identification of Novel Mosaic Variants in Focal Epilepsy-Associated Patients' Brain Lesions

Abstract

Focal cortical dysplasia type III (FCDIII) is a rare and complex condition associated with drug-resistant epilepsy and often characterized by cortical lamination abnormalities, along with a variety of neoplasms and vascular abnormalities.

Objectives: This study aimed to elucidate the genetic architecture underlying FCDIII through the use of whole-exome sequencing (WES) of brain and peripheral blood samples from 19 patients who had been diagnosed with FCDIII.

Methods: Variants were identified through a series of machine-learning-based detection and functional prediction methods and were not previously associated with FCDIII. Mosaic fraction scores of these variants validated the variants' pathogenicity, and in silico and gene ontology enrichment analyses demonstrated that these variants had severe destabilizing effects on protein structure.

Results: We reported ten novel pathogenic somatic missense and loss of function variants across eight genes, including CNTNAP2, ACY1, SERAC1, and BRAF. Genetic alterations were linked to clinical manifestations, such as encephalopathies and intellectual disabilities, thereby emphasizing their role as molecular drivers of FCDIII.

Conclusions: We demonstrated that next-generation sequencing-based mosaic variant-calling pipelines are useful for the genetic diagnosis of FCDIII, opening up avenues for targeted therapies, yet further research is required to validate these findings and examine their therapeutic implications.

Keywords: epilepsy; focal cortical dysplasia type III; somatic variants; whole-exome sequencing.

Figure 1

Somatic variants filtering pipeline through WES in FCDII patients. (A) Stepwise process and filtering criteria for somatic variants; (B) Eight patients from eight distinct pedigrees were diagnosed with focal cortical dysplasia type III (FCDIII). MRI neuroimaging of these patients revealed brain lesions, indicated by red arrows in each image.

Figure 2

Novel disease-causing somatic variants identified in focal cortical dysplasia patients. (A) The red arrow highlights the WES-selected patients in each family. Identified novel somatic variants are displayed below each pedigree, with missense variants shown in red and frameshift variants in blue. (B) The identified variants are mapped to specific brain regions, including the temporal, frontal, and multilobar areas. (C) Visualization of the damaging effects of these variants, along with their mutant allele fraction (MAF) values; the error bar shows a 95% binomial confidence interval.

Figure 3

Identified somatic missense variants and their association with disease-related gene ontology through gene enrichment analysis. (A) Gene ontology enrichment analysis using MetaScape highlights the functional roles of each novel gene variant associated with the disease condition. (B) In Metascape, enrichment analyses scores and significance are reported as −log₁₀ (p-value). Larger values indicate stronger enrichment to account for multiple comparisons.

Figure 4

Somatic pathogenic variants destabilize the protein structure. The pathogenic impacts of somatic variants on the protein structures of CNTNAP2 p.Asn407Ser: −0.56 kcal/mol, ACY1 p.Glu233Asp: −1.25 kcal/mol, SERAC1, p.Ile30Thr: −0.22 kcal/mol, ZNF479, Cys325Tyr: −0.91 kcal/mol, BRAFp.Val600Glu: −0.84 kcal/mol, and PIGO, p.Arg811Gln: −0.44 kcal/mol were assessed. The damaging effect was quantified in terms of binding energy change, measured in kcal/mol.