Transcriptional regulation of disease-relevant microglial activation programs

Summary Microglia, the brain’s 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 microglia activation states, we conducted CRISPR interference screens in iPSC-derived microglia for inhibitors and activators of six microglial states. We characterized 31 regulators at the single-cell transcriptomic and cell-surface proteome level in two distinct iPSC-derived microglia models, uncovering new protein markers of relevant states. We functionally characterized several multi- state regulators. ZNF532 and PRDM1 knockdown drive disease-associated, lipid-rich signatures and enhance phagocytosis while showing opposing effects on antigen-presentation signatures. 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. Highlights CRISPRi screening reveals novel regulators of six microglia activation states Multi-modal single-cell screens highlight new markers of microglial states Different iPSC-microglia models show different landscapes of activation states at baseline Loss of DNMT1 leads to widespread DNA demethylation, promoting some states but limiting the interferon-response state Loss of PRDM1 or ZNF532 drives the microglial disease-associated state