Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Brain. 2022 Aug 27;145(8):2704-2720. doi: 10.1093/brain/awac117.
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-AKT-mTOR-signalling 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). 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 previously 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 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 focal cortical dysplasia 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.
胚胎后获得的遗传变异，或体细胞变异，在皮质发育过程中出现，已成为局灶性癫痫的重要病因，尤其是那些与皮质发育畸形有关的癫痫。在患有偏侧巨脑畸形和局灶性皮质发育不良（II 型）的个体中，已经在 PI3K-AKT-mTOR 信号通路的许多基因中发现了致病性体细胞变异，最近在 SLC35A2 中也发现了局灶性皮质发育不良（I 型）或非发育不良性癫痫皮质的个体。鉴于体细胞变异在不同的脑畸形中作用不断扩大，我们试图描绘在接受偏侧巨脑畸形或局灶性皮质发育不良手术的大量患者队列中体细胞变异的情况。我们评估了 123 名患有偏侧巨脑畸形（n=16）、局灶性皮质发育不良 I 型和相关表型（n=48）、局灶性皮质发育不良 II 型（n=44）或局灶性皮质发育不良 III 型（n=15）的儿童的样本。我们对每个病例的脑组织衍生 DNA 进行了高深度外显子测序，并鉴定了体细胞单核苷酸、插入缺失和大片段拷贝数变异。在 75%的偏侧巨脑畸形患者和 29%的局灶性皮质发育不良 II 型患者中，我们在 PI3K-AKT-mTOR 通路基因中发现了致病性变异。48 例局灶性皮质发育不良 I 型患者中有 4 例（8%）在 SLC35A2 中发现了可能的致病性变异。虽然在局灶性皮质发育不良 I 型组中没有其他基因有多个跨组致病的体细胞变异，但在该组中有 4 名患者在 CASK、KRAS、NF1 和 NIPBL 中有单个致病性或可能致病性的体细胞变异，这些基因先前与神经发育障碍有关。在 63 名神经正常对照中（P=0.017）未发现局灶性皮质发育不良 I 型患者中发现的任何神经疾病基因的罕见致病性或可能致病性的体细胞变异，提示这些新变异的作用。我们还在一名局灶性皮质发育不良 IIIa 伴海马硬化女性患者的发育不良组织中发现了已知癫痫基因 PCDH19 的一个体细胞失活变异，该变异在少数等位基因中存在。与局灶性皮质发育不良 II 型不同，局灶性皮质发育不良 I 型和 III 型均未在汇集到统一生物学途径的基因中发现体细胞变异，这表明与 II 型相比，其遗传异质性更大。重要的是，我们证明局灶性皮质发育不良 I、II 和 III 型与广泛的基因体细胞变异相关，其中许多与由种系变异引起的临床综合征中的癫痫有关，还包括一些以前与放射学上明显的皮质脑畸形无关的变异。
