Functional Analysis of 3q29 Microdeletion Syndrome Driver Genes

PROJECT SUMMARY Pathogenic copy number variants (pCNVs) are strongly associated with neurodevelopmental and neuropsychiatric disorders, including autism spectrum disorders and schizophrenia, yet identifying the genes or combinations of genes within pCNVs that drive syndromic phenotypes remains a central challenge. Cumulative data from our team and others has shown that the 3q29 deletion is associated with a high neurodevelopmental and neuropsychiatric illness burden, including a 40-fold increase in schizophrenia risk. We identified reduced cerebellar volume as a core phenotype that correlates with greater phenotypic severity including lower IQ. However, the individual genes driving these phenotypes remain unknown. In this proposal, we will use a highly innovative approach that capitalizes on the unique features of zebrafish to rapidly screen the function of genes and combinations of genes in the 3q29 deletion in the developing vertebrate brain. Our central goal is to identify the driver genes and/or gene combinations that are associated with neurodevelopmental phenotypes. Our central hypothesis is that individual driver genes in the 3q29 deletion interval act alone or in smaller subsets to cause reduction in cerebellar volume, growth deficits, and behavioral dysfunction. This hypothesis is based on accumulating evidence supporting the presence of driver genes for specific phenotypes in pCNVs, as well as the high expression level of multiple genes in the 3q29 interval in the cerebellum. To test this hypothesis, we will perform in vivo screens of individual 3q29 genes in zebrafish using a novel CRISPR-F0 method that allows us to rapidly assess the effects of gene loss of function. We will assess the consequences of loss of function of individual genes on body size, brain structure, and cerebellar volume using a custom whole-brain mapping pipeline (Aim 1) and basic arousal and sensory processing behaviors using automated, high-throughput assays (Aim 2), and assess the effect of disrupting combinations of genes on these phenotypes (Aim 3). The expected outcome of this research is to identify driver genes and/or gene combinations in the 3q29 deletion that contribute to a range of neurodevelopmental phenotypes. The broader impact of this research is that it will provide a path forward for the identification of driver genes and gene interactions that is generalizable across pCNVs associated with neurodevelopmental and neuropsychiatric disorders.