The Challenge of Somatic Variants in Focal Cortical Dysplasia

Joana Jesus-Ribeiro; Luís Miguel Pires; Ilda Patrícia Ribeiro; Olinda Rebelo; Ricardo Pereira; Francisco Sales; Isabel Santana; António Freire; Joana Barbosa Melo

The Challenge of Somatic Variants in Focal Cortical Dysplasia

Innov Clin Neurosci. 2023 Dec 1;20(10-12):35-39. eCollection 2023 Oct-Dec.

Authors

Joana Jesus-Ribeiro^{1

2}, Luís Miguel Pires^{2

3}, Ilda Patrícia Ribeiro^{2

3}, Olinda Rebelo⁴, Ricardo Pereira⁵, Francisco Sales⁶, Isabel Santana^{7

8}, António Freire^{8

9}, Joana Barbosa Melo^{2

3}

Affiliations

¹ Dr. Jesus-Ribeiro is with Neurology Department, Centro Hospitalar de Leiria in Leiria, Portugal.
² Drs. Jesus-Ribeiro, Ribeiro, and Melo and Mr. Pires are with Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment, Genetics, and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra in Coimbra, Portugal.
³ Drs. Ribeiro and Melo and Mr. Pires are also with Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra in Coimbra, Portugal.
⁴ Dr. Rebelo is with Neuropathology Laboratory, Neurology Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal.
⁵ Dr. Pereira is with Neurosurgery Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal.
⁶ Dr. Sales is with Epilepsy and Sleep Monitoring Unit, Neurology Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal.
⁷ Dr. Santana is with Neurology Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal.
⁸ Drs. Santana and Freire are with Faculty of Medicine, University of Coimbra in Coimbra, Portugal.
⁹ Dr. Freire is also with Neurology Department, Luz Hospital in Coimbra, Portugal.

PMID: 38193103
PMCID: PMC10773600

Abstract

Objective: The advent of next-generation sequencing (NGS) enabled the detection of low-level brain somatic variants in postsurgical tissue of focal cortical dysplasia (FCD). The genetic background of FCD Type I remains elusive, while the mammalian target of rapamycin (mTOR) pathway seems to have a relevant role in the pathogenesis of FCD Type II. Our goal was to uncover information on the molecular basis of FCD, performing whole genome sequencing (WGS) in postsurgical tissue to detect candidate brain-specific somatic variants, and evaluate their clinical significance.

Design: WGS was performed using paired peripheral venous blood and postsurgical pathological brain deoxyribonucleic acid (DNA) samples. Libraries were prepared using the Roche KAPA HyperPrep polymerase chain reaction (PCR) free library preparation kit. Paired-end 150bp reads were generated on the Illumina NovaSeq platform. The FASTQ files were processed using the nf-core sarek pipeline (version 3.0) to call somatic variants, which were then annotated with ANNOVAR. A screening strategy was applied to obtain relevant variants.

Results: Two female patients with drug-resistant epilepsy due to FCD who underwent surgical treatment were included. Regarding neuropathological diagnosis, one patient had FCD Type Ia and the other had FCD Type IIa. Five somatic nonsynonymous single nucleotide variants (SNVs) were detected using WGS, three in FCD Ia tissue (WDR24 p.Trp259Gly; MICAL1 p.Lys1036Arg; and KATNB1 p.Leu566Ile) and two in FCD IIa tissue (MATN4 p.Phe91Val and ANKRD6 p.His386Gln). All variants were predicted to be potentially pathogenic by at least two different tools. However, they were classified as variants of uncertain significance (VUS) according to the American College of Medical Genetics and Genomics (ACMG) criteria.

Conclusion: Brain-specific somatic missense variants were identified by NGS in new candidate genes (WDR24, MICAL1, KATNB1, MATN4, and ANKRD6) using postsurgical FCD tissue, which may contribute to further understanding of the genetic background of FCD. All the reported genes were previously related to epilepsy and/or malformations of central nervous system (CNS) and cortical development. However, the pathogenicity assessment of these variants and, consequently, their impact on clinical practice still poses an important challenge.

Keywords: Focal cortical dysplasia; drug-resistant epilepsy; missense variant; next-generation sequencing; somatic variant.

Publication types

Case Reports