MD/PhD Trainee Sanford Consortium for Regenerative Medicine, United States
Abstract: The development of the cerebral cortex is one of the most intricate processes in neurobiology. Disruptions to this complex and highly regulated process are central to neurodevelopmental disorders (NDDs), which collectively impact an estimated 317 million individuals globally. Recent work suggests that post-transcriptional modifications, such as A-to-I RNA editing mediated by ADAR enzymes, may contribute to the diverse etiologies of NDDs. Cortical organoids recapitulate key human-specific aspects of corticogenesis and provide a powerful platform to study these modifications in a controlled environment. However, the suitability of organoids as a model for A-to-I RNA editing remains unproven, and current computational approaches cannot fully capture the intricate editing dynamics across diverse cell types in organoid cultures. To this end, we used our recently published algorithm, MARINE (Multi-core Algorithm for Rapid Identification of Nucleotide Edits), to map the A-to-I editome of human fetal brain and cortical organoids at single-cell resolution over an extended developmental time course. This approach enabled a comprehensive analysis of RNA editing dynamics across various stages of corticogenesis. Our findings revealed remarkable concordance between fetal brain and organoid datasets, demonstrating distinct temporal and cell type-specific patterns of A-to-I editing. We also observed significant variation in editing frequency and site specificity across different cell types and developmental timepoints. Additionally, our analysis identified unique expression profiles of co-factors associated with high and low editing activity, suggesting that certain cellular states may predispose cells to enhanced RNA editing. Given the established dysregulation of A-to-I editing in NDDs such as Fragile X syndrome, we leveraged MARINE to compare the A-to-I editome between healthy control cortical organoids and isogenic NDD variant organoids. Despite overall similarities in editing patterns, we noted significant alterations in ADAR expression and editing site variance in FMR1 KO organoids. This study represents the largest investigation of A-to-I RNA editing dynamics in the developing brain and in human-derived model systems of NDD-linked diseases within an isogenic background.
Funding Source: NIH/NIMH Human Isogenic Organoid Models of Genetic Forms of Autism to Identify Convergent and Divergent Patho-mechanisms in Autism (MPI) R01 MH131907
