Transcriptomic Analysis Divulges Differential Expressions of Microglial Genes After Microglial Repopulation in Mice

Microglia are key immune cells in the central nervous system (CNS) and maintain hemostasis in physiological conditions. Microglial depletion leads to rapid repopulation, but the gene expression and signaling pathways related to repopulation remain unclear. Here, we used RNA sequencing (RNA-Seq) analysis to profile the transcriptome of microglia-depleted tissue by taking advantage of a conditional genetic microglial depletion model (CX3CR1CreER/+ system). Differential gene expression (DGE) sequencing analysis showed that 1226 genes were differentially up- and downregulated in both groups compared to control. Our data demonstrated that many microglial genes were highly regulated on day 3 after depletion but the numbers of differentially expressed genes were reduced by day 7. Gene ontology (GO) analysis categorized these differentially expressed genes on day 3 and day 7 to the specific biological processes, such as cell proliferation, cell activation, and cytokine and chemokine production. DGE analysis indicated that specific genes related to proliferation were regulated after depletion. Consistent with the changes in transcriptome, the histological analysis of transgenic mice revealed that the microglia after depletion undergo proliferation and activation from day 3 to day 7. Collectively, these results suggest that transcriptomic changes in microglial genes during depletion have a profound implication for the renewal and activation of microglia and may help to understand the regulatory mechanism of microglial activation in disease conditions.