Loss of function in the autism and schizophrenia-associated gene CYFIP1 in human microglia supports a role in synaptic pruning

BackgroundThe CYFIP1 gene, located in the neurodevelopmental risk locus 15q11.2, is highly expressed in microglia, but its role in human microglial function as it relates to neurodevelopment is not well understood. MethodsWe generated multiple CRISPR knockouts of CYFIP1 in patient-derived models of microglia to characterize function and phenotype. Using microglia-like cells reprogrammed from peripheral blood mononuclear cells, we quantified phagocytosis of synaptosomes (isolated and purified synaptic vesicles) from human iPSC-derived neuronal cultures as an in vitro model of synaptic pruning. We repeated these analyses in human iPSC-derived microglia, and characterized microglial development and function through morphology and motility. ResultsCYFIP1 knockout using orthogonal CRISPR constructs in multiple patient-derived cell lines was associated with statistically significant decrease in synaptic vesicle phagocytosis in microglia models derived from both PBMCs and iPSCs (p<0.0001). Morphology was also shifted toward a more ramified profile (p<0.0001), and motility was significantly reduced (p<0.0001). However, iPSC-CYFIP1 knockout lines retained the ability to differentiate to functional microglia. Conclusion: The changes in microglial phenotype and function from loss of CYFIP1 may contribute to pruning abnormalities observed in CYFIP1-associated neurodevelopmental disorders. Investigating risk genes in a range of CNS cell types may be required to fully understand the way in which common and rare variants intersect to yield neuropsychiatric disorders.