Identifying tandem repeat expansion-mediated mechanisms of autism-risk genes

Project Summary Autism spectrum disorder (ASD) is a set of neurodevelopmental conditions that affect communication and social interactions with restricted interests and repetitive behaviors. Although ASD has one of the highest heritability rates of all complex disorders, and hundreds of genes are known to confer a risk for this condition, most ASD

cases remain idiopathic. A critical barrier to progress in the field is to identify additional ASD-risk genes. Since most of the known ASD variants are biased toward coding regions, an unmet need is to evaluate the contribution of noncoding sequences in ASD etiology, including tandem repeats (TRs) that account for ~5% of the human

genome. Recently two independent large-scale genome studies uncovered previously undetected and predominantly noncoding TR mutations that have been suggested to account for ~4% of idiopathic ASD cases. Although these studies opened uncharted territory by revealing numerous TR expansion mutations (TRexp) in

ASD, they were underpowered to adopt the required statistical rigor to select gene candidates for further mechanistic studies. To overcome this critical barrier to progress in the field, we designed a framework to investigate the contribution of noncoding TRexp in ASD etiology. Based on our considerable expertise in complex

TRexp disease mechanisms, we propose to test the central hypothesis that ASD-associated noncoding TRexp contribute to ASD etiology by inducing pathogenic gene regulatory mechanisms that have been documented in other TRexp disorders. We will test our central hypothesis by: (i) identifying high-confidence ASD-risk genes with

TRexp enriched in the ASD population (Aim 1); (ii) selecting TRexp based on their propensity to perturb high- confidence ASD-risk gene transcript processing (Aim 2); (iii) testing the hypothesis that intronic TRexp alter specific regulatory steps during ASD-risk gene RNA processing (Aim 3). The results of this proposal will

transform our understanding of ASD by addressing important problems underpinning critical barriers to progress in the field by: (i) providing a new approach to identify high-confidence ASD-risk genes from underpowered studies; (ii) developing specialized criteria to estimate TRexp propensity to perturb ASD-risk gene expression and

RNA processing patterns; (iii) spanning the bridge between genomic TRexp findings in the ASD population and their mechanistic basis. In addition, this proposal is designed to: (iv) provide a high number of underrepresented students with the opportunity to participate in high-quality computational and molecular biology research

including study execution, analysis, and reporting; (v) substantially strengthen our research environment by enhancing the PI’s research productivity and program development. Therefore, this proposal addresses the requirements listed for the SuRE-First Award (PAR-21-173) and also falls within the areas of priority detailed in

the NIMH Strategic Plan and the NIMH Strategic Research Priorities.