KDM5B-mediated regulation of microglial reactivity as revealed by comprehensive multi-omic analysis
The biological significance of microglia are highlighted by their critical role as the resident immune cells of the central nervous system. In this capacity, microglia maintain homeostasis through various pathways that include cell migration, phagocytosis as well as secretion of immune-related and signaling factors into the extracellular environment. Microglial reactivity is associated with a variety of functional outcomes that are highly context-dependent and therefore microglia can exhibit a wide range of phenotypes. Epigenetic regulation through DNA methylation and histone modifications has recently been implicated in this complex control of microglial reactivity. Specifically, in relation to histone methylation status, the histone demethylase KDM5B has been implicated in many pathophysiological states including alcohol use disorder (AUD), cancer, and inflammatory disorders; however, the cell type-specific role of KDM5B in microglial reactivity has yet to be fully investigated. In this study, transcriptomic and proteomic analyses were used to characterize the effects of KDM5B knockdown on microglial pathways using CRISPR editing of adult-derived murine microglial cells to generate a Kdm5b knockout pool. From this multi-omic analysis, over 34,000 genes and 9,000 proteins  were identified across all replicates of wild-type (WT) and KDM5B-depleted microglia. Additionally, various stimuli including LPS, IL4, and alcohol were used to study the effects of KDM5B knockdown on immune reactivity in microglia using deep proteomic analysis. Through this deep characterization, an overall decrease in inflammatory and immune reactivity pathways was observed in KDM5B-depleted microglia, which was then functionally validated through measurement of secreted factors including TNFa, IL6, IL4, IL10, IL16, and SPP1. The results from this study has provided critical insight into KDM5B-mediated effects on microglial function as well as a molecular framework for future studies aimed to understand epigenetic regulation of microglia and implications in neurodegenerative disease pathogenesis and progression. Overall design: To determine the function of KDM5B, a CRISPR knockout pool of Kdm5b was generated in an immortalized mouse microglia cell line (IMG). RNA-seq analysis was performed in triplicate of wildtype control and Kdm5b knockout pool IMG cells.