It is estimated that at least 30 percent of simplex autism spectrum disorder (ASD) arises from de novo disruptive, missense or copy number variation, thus supporting the hypothesis that rare variants with a large effect size contribute to disease etiology in ASD. However, the identification of causal genes in ASD has been historically difficult due to both genotypic and phenotypic heterogeneity among patients. The study of sporadic ASD families by whole exome sequencing has provided many strong candidate genes. Deep clinical phenotyping has further defined some of these genes as putative ‘genetic subtypes’ of ASD. Although the genetics in these cases are very convincing, better therapeutics cannot be developed without understanding the biology underlying these mutations.

Currently, the ASD community has very little understanding of the role deleterious mutations (nonsense, frameshift, splice-site) have on disease etiology. To address this issue, Holly Stessman and her colleagues at Creighton University Medical School are developing stable human cell line models for nine of the top candidate ASD genes—NAA15, WAC, TRIP12, ASH1L, CUL3, DDX3X, PAX5, SETD5 and SMC3. For each gene, two independent, ultra-rare de novo mutations that show a conserved patient phenotype are being engineered using CRISPR/Cas9 technology. The functional consequences of these mutations are being assessed on cell growth, replication, morphology, differentiation and gene expression using firstly an established isogenic human cell line and secondly human induced pluripotent stem cell (iPSC) lines. Where available, iPSCs from patients carrying known mutations are being used to both confirm in vitro phenotypes and for rescue experiments.

Stessman’s team aims to use this model system to bridge the gap between genetics and function. The identification of distinct, well-characterized genetic subtypes of ASD will not only have diagnostic value, but it will also facilitate the development of new targeted therapies and contribute to the understanding of early neurodevelopment.