Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis

Recent studies have identified a large number of high confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses have consistently implicated excitatory neurogenesis. However, the extent to which hcASD genes are involved in this process has not been explored systematically nor have the underlying biological pathways. Here, we leveraged CROP-Seq to repress 87 hcASD genes in an in vitro model of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cell state characterized by disruptions in proliferation and differentiation, cell cycle occupancy, mitotic spindle and microtubule biology, and RNA-binding proteins (RBPs). We also identified over 3,000 differentially expressed genes, 286 of which have expression profiles correlated with changes in developmental trajectory. Collectively, these genes again highlight microtubule biology and RBPs. Overall, we uncover transcriptional disruptions downstream of hcASD gene perturbations and correlate these disruptions with distinct differentiation phenotypes, while reinforcing neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD. iPSC derived neural progenitor cells and neurons expressing the CRISPRi machinery were sequenced using 10X Chromium v3 using a CROP-seq protocol at three timepoints during differentiation (D0, D2, D4). The 10X labeled sequencing reads are the transcriptomic data and the PCR labeled reads are the sgRNA enrichment PCR reads used to assign sgRNAs to cell barcodes.