Chemical Genetic Dissection of SWI/SNF Chromatin Remodeling Complex Functions in Cerebral Cortex Development

PROJECT SUMMARY/ABSTRACT Intellectual Disability (ID) and Autism Spectrum Disorders (ASD) are the most common developmental disorders, affecting 3-4% of children in the U.S, with few therapeutic options. Although insights into the mechanisms that cause these heterogeneous disorders remains very limited, genetic studies of ID/ASD have revealed a central role for mutations in genes encoding transcriptional regulatory proteins, including multiple subunits of the SWI/SNF ATP-dependent nucleosome remodeling complex (BAF complexes). For example, heterozygous loss-of-function mutations in Arid1b, the largest subunit of the canonical BAF complex (cBAF), are among the most frequent mutations observed in de novo ID/ASD cases. However, the function of ARID1B/cBAF complexes in gene regulation during normal brain development and the specific developmental processes that are disrupted by Arid1b loss-of-function mutations remain significant gaps in knowledge. Characterizing the specific functions of transcriptional regulatory complexes in cell type-specific gene regulation in the dynamic and heterogeneous cellular environment of the embryonic brain remains difficult using current model systems and experimental tools. Our long-term goal is to develop pluripotent stem cell- based model systems and experimental tools to characterize gene regulatory networks that control cell fate specification during brain development. Towards this end, my lab recently developed a robust, reproducible protocol to make forebrain organoids from mouse pluripotent stem cells. This reduced complexity model maintains key features of the developing brain and can enable experimental approaches that are not possible in vivo. Here, we propose to 1) perform the first in depth transcriptomic and epigenomic characterization of cerebral cortex development in our novel mouse organoid model using single cell genomics approaches, 2) define the impact of Arid1b loss-of-function mutations on cortical development in vivo and in organoids, 3) implement chemical genetic approaches (dTAG) to parse stage-specific effects of ARID1B loss, 4) define direct effects of ARID1B loss on gene regulation during cortical development, 5) determine which gene expression changes are reversible upon reintroduction of ARID1B into post-mitotic cortical neurons. These data will help to establish mouse cortical organoids as a model system that can complement and extend upon in vivo approaches for studying molecular and cellular mechanisms of brain development. Our findings will provide new insight into the mechanisms by which loss-of-function mutations in Arid1b give rise to changes in gene regulation during early stages of cortical neurogenesis and reveal specific genes, cell types, and developmental stages that are susceptible to reduction of cBAF complexes. Given the relevance of this complex to common developmental disorders, our findings may also reveal novel therapeutic opportunities for ID and ASD.