Identifying cell type specific driver genes in autism-associated copy number loci from cerebral organoids

Neuropsychiatric and neurodevelopmental disorders have been particularly challenging to study using animal models, and recently, human-derived cerebral organoids demonstrate great promise for discovering molecular processes that are important in these disorders. However, several challenges remain in achieving robust phenotyping to discover cell type specific genes. We perform RNA sequencing on 71 samples comprising of 1,420 cerebral organoids from 25 donors, and describe a framework (Orgo-Seq) to identify cell type specific driver genes, for 16p11.2 deletions and 15q11-13 duplications. We identify neuroepithelial cells as critical cell types for 16p11.2 deletions, and discover novel and previously reported cell type specific driver genes. Finally, we validated our results that mutations in KCTD13 in the 16p11.2 locus lead to imbalances in the proportion of neuroepithelial cells, using CRISPR/Cas9-edited mosaic organoids. Our work presents a quantitative discovery and validation framework for identifying cell type specific driver genes associated with complex diseases using cerebral organoids.