CRISPRi-based screen of Autism Spectrum Disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and uptake of synaptic material
Autism Spectrum Disorders (ASD) are a set of neurodevelopmental disorders with complex biology. The identification of ASD risk genes from exome-wide association studies and de novo variation analyses has enabled mechanistic investigations into how ASD-risk genes alter development. Most functional genomics studies have focused on the role of these genes in neurons and progenitor cells. However, roles for ASD risk genes in other cell types are largely uncharacterized. There is evidence from postmortem tissue that microglia, the resident immune cells of the brain, appear activated in ASD. Here, we systematically assess the impact of ASD-risk gene knock-down on microglial uptake of synaptic material. We developed both an iPSC-derived microglia-neuron coculture system and high-throughput flow cytometry readout for synaptic uptake to enable CRISPRi-based screening. Our screen identified ADNP, one of the high-confidence ASD risk genes, amongst others as a modifier of microglial synaptic uptake. Transcriptomic, proteomic, and functional analyses revealed that ADNP plays a role in endocytosis, cell surface remodeling, and motility in microglia. Through this focused investigation into the role of ADNP in microglia, we also found preliminary evidence for WNT signaling coordinating microglial uptake of synaptic material.