Discovery of Novel Autism-Associated Variation in Brain Miniproteins

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PROJECT SUMMARY This R03 proposal describes a two-year research plan focused on the investigation of previously unannotated miniproteins to the genetic etiology of Autism Spectrum Disorder (ASD). Rare inherited and de novo genetic variants are important causes of ASD, but explain the etiology in only ~20% of families. Furthermore, rare ASD-associated variants have been identified in noncoding regions of the genome, but the functional significance of those found is largely unknown, representing a critical knowledge gap in ASD genetics. We recently completed a study to profile the mRNA translational landscape (the “translatome”) of the human brain, identifying thousands of small open reading frames (sORFs) encoding putative miniproteins <100 amino acids, many of which are translated from annotated noncoding regions of the genome. We hypothesize that miniproteins represent an unappreciated cache of hidden genes whose role in disease is almost entirely unexplored. To address the potential role of miniproteins in ASD, we will leverage the largest whole-genome sequencing (WGS) dataset in ASD, as well as our newly created atlas of human brain miniproteins, to discover miniprotein genes associated with ASD risk based on rare inherited and de novo sequence-level and structural variants (Aim 1). Additionally, our preliminary data suggest that many miniproteins lack three-dimensional structure (intrinsically disordered) and are rich in sequence motifs that bind RNA. Traditional sequence-based analysis of proteins will perform poorly on short, highly disordered miniproteins. Therefore, in Aim 2, we will build physical feature-based analysis paradigms to predict the molecular function of ASD-associated miniproteins. This work combines expertise in developmental neuroscience, genomics, and computational protein biology. The knowledge gained from this R03, including the identification of new ASD-associated genes, will form the basis of future studies to characterize the function, cell type-specificity, and developmental regulation of miniproteins in the human brain, as well as their contribution to ASD. Our approach to incorporating previously unannotated miniproteins in genetic analysis can be applied to other neurologic and non-neurologic conditions, thereby expanding our understanding of the genetic architecture of human disease.