Autism spectrum disorders (ASDs) affect 1% of the general population, and epilepsy (EPI) is observed in atleast one-third of ASD individuals. ASDs with epilepsy (ASD-EPI) are typically more severe and treatmentdelay has a negative impact on outcome. The frequent association between epileptic and autistic phenotypes suggests that they share predisposing genes. Indeed, in recent years it has become clear that genesimplicated in ASD and EPI, as well as other neurodevelopmental disorders, are interconnected in functionalnetworks. Strikingly, there is a considerable overlap in the networks affected in each disorder, raising questionson how disruptions of these common networks can give rise to such phenotypical diversity.Despite ongoing large-scale efforts to identify risk genes for ASD, and to a lesser extent for pediatric EPI, thediagnostic yield remains low and most causal genes and risk variants are yet to be identified. New cohorts arealso needed to discover additional variants in previously identified candidate genes and elevate them to thestatus of ASD-EPI risk genes. Our study differs from previous efforts by focusing on a set of 550 families with aspecific ASD-EPI sub-phenotype that will result in less phenotypic heterogeneity to increase power to findvariants in this specific subtype. For each family we will sequence the complete exome, as well as noncodingregulatory regions near genes with strong prior evidence for association with ASD and/or EPI. We will performburden analysis of rare de novo and inherited gene-disruptive events in ASD-EPI, and correlate with clinicalphenotype variables (early vs late-onset epilepsy, gender, IQ, and MRI abnormalities), and incorporate this intoexisting ASD/EPI datasets for gene-set and network analyses, as well as integrating SNVs and CNVs in acommon framework (Aim 1). We will also identify risk variants in noncoding regulatory elements, including cis-regulatory elements near implicated, high confidence, and/or candidate genes for ASD and EPI (ASD/EPI-relevant genes), intronic RBFOX binding targets, and miRNA binding targets, using a new statistical frameworkfollowed by burden analyses (Aim 2). Finally, we will functionally characterize 8 high-impact variants, which willbe introduced by CRISPR genome editing into isogenic human induced pluripotent stem cells (iPSCs) andfurther differentiated into forebrain neuronal progenitor cells (NPCs) and neurons. Functional assays will includeRNA-Seq, neuronal connectivity and morphology, as well as activity using Multi-Electrode Arrays (Aim 3). Theidentification and functional characterization of additional mutations will help prioritize genes and reveal novelcomponents of the pathways underlying ASD-EPI, and provide mechanistic insight into how they relate to eachother. Our systematic approach also provides the opportunity to classify molecular subtypes of ASD/EPI and todistinguish how the genetic subnetworks underlying ASD-EPI differ from the framework of pathwaysassociated with each disorder, as necessary steps toward tailored intervention and treatment. Our proposal willset a standard for rapid and large-scale screening for ASD and related neurodevelopmental disorders.
Interagency Autism Coordinating Committee (IACC)
Autism Research Database (AFD)
