IBIS-iPSC: Organoid modeling of cortical surface area hyperexpansion in autism spectrum disorder

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Project Summary/Abstract Many individuals with monogenic and idiopathic forms of autism spectrum disorder (ASD) exhibit brain enlargement early in life. However, the underlying cellular and molecular mechanisms leading to early brain overgrowth in ASD are unknown. To identify the mechanisms leading to brain overgrowth, we will use an appropriate model system, iPSC-derived organoids, from a well-powered, deeply phenotyped cohort with multiple control groups, the Infant Brain Imaging Study (IBIS). IBIS is the largest longitudinal neuroimaging study of infants (>250 participants) at high familial risk for autism by virtue of having an older sibling/proband with ASD. Importantly, IBIS participants have previously undergone longitudinal neuroimaging at multiple time points in infancy (between 6-24 months of age) and school age, extensive behavioral assessments at these time points, as well as rare and common variant genotyping. The extensive phenotypic data generated in this cohort make it an ideal population from which to generate iPSC-derived organoid models and relate in vitro phenotypes to in vivo brain growth and behavioral trajectories. Our study also represents a unique opportunity to evaluate how well organoid phenotypes model the in vivo brain growth trajectories of the individual from whom they were derived. In this proposal, we will derive and validate iPSCs from blood for participants from high risk families who developed ASD (HR+), high risk participants who did not develop ASD (HR-), and low risk individuals without ASD (LR-) totaling 99 participants. We will differentiate the iPSC lines to cortical organoids to model inter- individual differences in brain development. We will use single cell (sc)RNA-seq to identify cell types, cell cycle states, and differentiation trajectories in each participant-derived organoid across two time points modeling the period of cortical neurogenesis, totaling 2.38M sequenced cells. We will validate cell type counts and states using tissue clearing followed by lightsheet microscopy of the cortical organoids. We will identify cell types, fate decisions, and cell cycle states that correlate with both cross-sectional and longitudinal cortical surface area growth and ASD symptoms and cognitive ability over time. Leveraging this unique, deeply characterized clinical cohort, we will determine both the in vivo relevance of cortical organoids and the cellular and molecular mechanisms underlying brain overgrowth in ASD.