A CRISPRi/a platform in iPSC-derived microglia uncovers regulators of disease states

Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. Here, we present a screening platform to systematically elucidate functional consequences of genetic perturbations in human iPSC- derived microglia. We developed an efficient eight-day protocol for the generation of microglia-like cells based on the inducible expression of six transcription factors. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the “druggable genome”. These screens uncovered genes controlling microglia survival, activation and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing as the readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identified regulators of these states. A disease-associated state characterized by SPP1 expression was selectively depleted by CSF1R inhibition. Thus, our platform can systematically uncover regulators of microglia states, enabling their functional characterization and therapeutic targeting. ### Competing Interest Statement MN consults for Neuron23. MN and FF participated in this work in part due to a competitively awarded consulting contract between Data Tecnica International LLC and the National Institutes of Health (USA). JKI is a cofounder of AcuraStem, Inc. and Modulo Bio, and serves on the scientific advisory board of Spinogenix. LG is a founder of Aeton Therapeutics. MK has filed a patent application related to CRISPRi and CRISPRa screening (PCT/US15/40449) and serves on the scientific advisory boards of Engine Biosciences, Casma Therapeutics, and Cajal Neuroscience. The remaining authors declare no competing interests.