High-throughput Functional Analysis of Autism Risk Genes

PROJECT SUMMARY There is a critical need to advance from gene discovery to the identification of actionable biological mechanisms in autism spectrum disorders (ASDs). Despite considerable progress in the identification of high confidence genes that are strongly associated with risk, advancing from ASD genes to biologically relevant cellular and circuit mechanisms remains a central challenge. We established a high-throughput zebrafish system for the in vivo functional analysis of multiple ASD genes in parallel. Our analysis of 10 ASD genes in zebrafish mutants revealed novel points of convergence at multiple neurodevelopmental levels and uncovered ASD gene subgroups with shared functional effects. As a critical next step, we will leverage the zebrafish system to analyze the function of 50 ASD genes in parallel at the whole-brain transcriptomic, structural, and circuit levels and translate our findings to human induced pluripotent stem cells (hiPSCs). Our central objectives are to: (1) identify convergent molecular signatures resulting from ASD gene LoF; (2) elucidate novel cellular and circuit mechanisms contributing to whole-brain structural and activity phenotypes; and (3) uncover highly conserved pharmacological pathways downstream of ASD genes. We hypothesize that ASD genes converge on shared molecular, cellular, and circuit mechanisms in the developing vertebrate brain, which will allow us to define novel ASD gene subgroups. This hypothesis is based on compelling evidence for biological convergence across ASD genes from our group and others. To test this hypothesis, we perform molecular phenotyping of ASD gene mutants using whole-brain single nuclear RNA-seq (Aim 1); identify cellular phenotypes contributing to circuit deficits by combining in vivo imaging and cell-type-specific labeling (Aim 2); and conduct parallel pharmacological screens to identify novel phenotypic suppressors in zebrafish and hiPSCs (Aim 3). The expected outcomes of this research are to (1) define convergent molecular, cellular, and circuit phenotypes downstream of ASD genes in the developing vertebrate brain; and (2) leverage the identification of biologically relevant ASD gene subgoups with shared mechanisms to uncover novel pharmacological pathways with translational relevance.