A family study implicates GBE1 in the etiology of autism spectrum disorder

Abstract

Autism spectrum disorders (ASD) are neurodevelopmental disorders with an estimated heritability of >60%. Family-based genetic studies of ASD have generally focused on multiple small kindreds, searching for de novo variants of major effect. We hypothesized that molecular genetic analysis of large multiplex families would enable the identification of variants of milder effects. We studied a large multigenerational family of European ancestry with multiple family members affected with ASD or the broader autism phenotype (BAP). We identified a rare heterozygous variant in the gene encoding 1,4-ɑ-glucan branching enzyme 1 (GBE1) that was present in seven of seven individuals with ASD, nine of ten individuals with the BAP, and none of four tested unaffected individuals. We genotyped a community-acquired cohort of 389 individuals with ASD and identified three additional probands. Cascade analysis demonstrated that the variant was present in 11 of 13 individuals with familial ASD/BAP and neither of the two tested unaffected individuals in these three families, also of European ancestry. The variant was not enriched in the combined UK10K ASD cohorts of European ancestry but heterozygous GBE1 deletion was overrepresented in large ASD cohorts, collectively suggesting an association between GBE1 and ASD.

Keywords: autism spectrum disorder; broader autism phenotype; genetics; glycogen branching enzyme; linkage; whole exome sequencing.

Figure 1:

De-identified and scrambled pedigree of Family B showing the unilineal Core family utilised for linkage analysis in this study and the excluded bilineal branch (indicated by the dashed box). The phenotyping key for ASD, BAP, unassessed and unaffected (assessed) individuals is indicated, as are the molecular studies performed on each sample and GBE1 p.Ile59Thr variant status.

Figure 2:

Genome-wide linkage analysis plot for Core Family B (A) and chromosome 3 linkage plot (B). Data generated using the lm bayes function in MORGAN identified a region with a LOD score of 2.9 on chr3. (C) ClustalW alignment of the GBE1 amino acid sequence demonstrated evolutionary conservation of isoleucine at amino acid position 59.

Figure 3:

De-identified and scrambled pedigrees of Family C (A), Family D (B) and Family E (C). The phenotyping key for ASD, BAP, unassessed and unaffected (assessed) individuals is indicated, as are the molecular studies performed on each sample and GBE1 p.Ile59Thr variant status.

Figure 4.

HEK293 cells transfected with constructs encoding wildtype and variant GBE1 were grown in the absence or presence of 10 mM MG-132 for 14 hours. Total protein was isolated and analyzed by SDS-PAGE and immunoblotting with antibodies directed against GBE1 and β-actin. A representative image is shown, with approximate sizes in kDa indicated. UT=untransfected cells, EV=empty vector control.

Figure 5.

CNV analysis. (A). Screenshot of UCSC Genome Browser displaying custom track of results of GBE1 CNVs in a cohort of children with neurodevelopmental delay (top) and controls (bottom); deletions are indicated in red, duplications in blue (B). Screenshot of UCSC Genome Browser displaying custom track of results of GBE1 deletions (green) in the AGP cohort.