Transcriptional regulation of homeostatic and disease‐associated‐microglial genes by IRF1, LXRβ, and CEBPα

Abstract

Microglia transform from homeostatic to disease‐associated‐microglia (DAM) profiles in neurodegeneration. Within DAM, we recently identified distinct pro‐inflammatory and anti‐inflammatory sub‐profiles although transcriptional regulators of homeostatic and distinct DAM profiles remain unclear. Informed by these studies, we nominated CEBPα, IRF1, and LXRβ as likely regulators of homeostatic, pro‐inflammatory and anti‐inflammatory DAM states and performed in‐vitro siRNA studies in primary microglia to identify roles of each transcriptional factor (TF) in regulating microglial activation, using an integrated transcriptomics, bioinformatics and experimental validation approach. Efficient (>70%) silencing of TFs in microglia revealed reciprocal regulation between each TF specifically following pro‐inflammatory activation. Neuroinflammatory transcriptomic profiling of microglia coupled with qPCR validation revealed distinct gene clusters with unique patterns of regulation by each TF, which were independent of LPS stimulation. While all three TFs (especially IRF1 and LXRβ) positively regulated core DAM genes (Apoe, Axl, Clec7a, Tyrobp, and Trem2) as well as homeostatic and pro‐inflammatory DAM genes, LPS, and IFNγ increased pro‐inflammatory DAM but suppressed homeostatic and anti‐inflammatory DAM gene expression via an Erk1/2‐dependent signaling pathway. IRF1 and LXRβ silencing suppressed microglial phagocytic activity for polystyrene microspheres as well as fAβ42 while IRF1 silencing strongly suppressed production of pro‐inflammatory cytokines in response to LPS. Our studies reveal complex transcriptional regulation of homeostatic and DAM profiles whereby IRF1, LXRβ, and CEBPα positively regulate both pro‐ and anti‐inflammatory DAM genes while activating stimuli independently augment pro‐inflammatory DAM responses and suppress homeostatic and anti‐inflammatory responses via Erk signaling. This framework can guide development of therapeutic immuno‐modulatory strategies for neurodegeneration.