Transcriptional regulation of disease-relevant microglial activation programs

Microglia, the brains innate immune cells, can adopt a wide variety of activation states relevant to health and disease. Dysregulation of microglial activation occurs in numerous brain disorders, and driving or inhibiting specific states could be therapeutic. To discover regulators of microglial activation states, we conducted CRISPR interference screens in iPSC-derived microglia for inhibitors and activators of six microglial states. We identified transcriptional regulators for each of these states and characterized 31 regulators at the single-cell transcriptomic and cell-surface proteome level in two distinct iPSC-derived microglia models. Finally, we functionally characterized several regulators. STAT2 knockdown inhibits interferon response and lysosomal function. PRDM1 knockdown drives disease-associated and lipid-rich signatures and enhanced phagocytosis. DNMT1 knockdown results in widespread loss of methylation, activating negative regulators of interferon signaling. These findings provide a framework to direct microglial activation to selectively enrich microglial activation states, define their functional outputs, and inform future therapies. HighlightsO_LICRISPRi screening reveals novel regulators of six microglia activation states C_LIO_LIMulti-modal single-cell screens highlight differences between mRNA and protein level expression C_LIO_LIiPSC-microglia models show different baseline distributions of activation states C_LIO_LILoss of DNMT1 leads to widespread DNA demethylation, promoting some states but limiting the interferon-response state C_LIO_LILoss of PRDM1 drives microglial disease-associated state C_LI