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 that enables the systematic elucidation of functional consequences of genetic alterations in human iPSC-derived microglia. We developed a protocol based on the inducible expression of six transcription factors, which generates microglia-like cells in an efficient eight-day protocol which was confirmed by bulk RNA sequencing. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the “druggable genome” that uncovered genes controlling microglia survival, activation and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identifies regulators of these states. A disease-associated state characterized by SPP1 expression is selectively depleted by CSF1R inhibition.Thus, our platform can systematically uncover regulators of microglia states, enabling their functional characterization and therapeutic targeting. Overall design: QuantSeq bulk RNA-sequencing of iTF-Microglia (Day 0, Day 8 (non-targeting and PFN1 CRISPRa sgRNAs), Day 9 +/- LPS treatment, Day 15) and Brownjohn-iMicroglia (Brownjohn et al., 2018, Day 9 +/- LPS treatment); Paired-end RNA-sequencing of iTF-Microglia (D14 +/- LPS treatment); and CROP-seq, single cell RNA-sequencing of Day 8 iTF-Microglia infected with a library of sgRNAs targeting 38 genes performed on four lanes of the 10X platform.