Germline and somatic mutations in STXBP1 with diverse neurodevelopmental phenotypes

Abstract

Objective: To expand the clinical phenotype associated with STXBP1 gene mutations and to understand the effect of STXBP1 mutations in the pathogenesis of focal cortical dysplasia (FCD).

Methods: Patients with STXBP1 mutations were identified in various ways: as part of a retrospective cohort study of epileptic encephalopathy; through clinical referrals of individuals (10,619) with developmental delay (DD) for chromosomal microarray; and from a collection of 5,205 individuals with autism spectrum disorder (ASD) examined by whole-genome sequencing.

Results: Seven patients with heterozygous de novo mutations affecting the coding region of STXBP1 were newly identified. Three cases had radiologic evidence suggestive of FCD. One male patient with early infantile epileptic encephalopathy, DD, and ASD achieved complete seizure remission following resection of dysplastic brain tissue. Examination of excised brain tissue identified mosaicism for STXBP1, providing evidence for a somatic mechanism. Cell-type expression analysis suggested neuron-specific expression. A comprehensive analysis of the published data revealed that 3.1% of severe epilepsy cases carry a pathogenic de novo mutation within STXBP1. By contrast, ASD was rarely associated with mutations in this gene in our large cohorts.

Conclusions: STXBP1 mutations are an important cause of epilepsy and are also rarely associated with ASD. In a case with histologically proven FCD, an STXBP1 somatic mutation was identified, suggesting a role in its etiology. Removing such tissue may be curative for STXBP1-related epilepsy.

Figure 1. MRI of patient 1 with fluid-attenuated inversion recovery signal

(A) Axial MRI of patient 1 demonstrating diffuse cortical/subcortical high fluid-attenuated inversion recovery (FLAIR) signal confined to the anterior left superior temporal gyrus and mesial temporal structures (white boxes). (B–C) Subtle increased FLAIR signal in the anterior temporal lobes of patients 2 and 3, respectively, suggestive of possible cortical dysplasia.

Figure 2. Histopathology of surgically excised dysplastic brain tissue (patient 1)

Circled areas of the left temporal lobe juxtacortical demonstrate linear neuronal heterotopia on (A) hematoxylin and eosin (H&E) and (B) NeuN stains, highlighting neurons; superior temporal gyrus nodular heterotopia are seen in boxes with (C) NeuN and (D) H&E stains, highlighting likely immature neurons; (E) Copy number variant mosaicism quantification using (ddPCR) within focal cortical dysplasia (red) and normal (black) tissue. The standard error bar shows the inferred copy number of approximately 20,000 droplets generated from each tissue type by the ddPCR; (F) single expression profile of the STXBP1 gene in primary brain cell types. RNA-seq reads were obtained (GEO GSE67835) for STXBP1 gene expression from 6 primary brain cell types (astrocytes, endothelial, microglia, neurons, oligodendrocytes, and oligodendrocyte progenitor cells [OPCs]). The bar showing lower 25th and upper 75th percentiles of the data, and the dots represent the outliers. Each color represents each cell types.

Figure 3. Mapping of mutations within the STXBP1 gene

(A) Mutations mapped within the 3 protein domains (cyan— domain 1, green—domain 2, and red—domain 3a/b) of the STXBP1 gene; (B) percentage of male and female cases reported to carry a pathogenic mutation for the STXBP1 gene. (C) Clinical spectrum associated with de novo STXBP1 mutations reported for early infantile epileptic encephalopathy (EIEE), focal cortical dysplasia (FCD), Ohtahara syndrome (OS), West syndrome (WS), Dravet syndrome, infantile spasms (ISs), neonatal refractory seizures, autism spectrum disorder, developmental delay, nonsyndromic intellectual disabilities (IDs), and atypical Rett syndrome.