The regional mouse microglial transcriptome during aging

Microglia are the specialised macrophages of the central nervous system parenchyma. Diversity in macrophages is increasingly apparent in tissues outside the brain however understanding is negligible for microglia. In the present study, we present the first genome-wide analysis of microglia from discrete brain regions that reveals their multiple region-dependent transcriptional identities. Differences in bioenergetic and immunoregulatory pathways are the major sources of transcriptional heterogeneity. Region-specific differences in immunophenotype suggest cerebellar and hippocampal microglia exist in a more immune vigilant state, but distinct from the conventional M1/M2 paradigm of activation. Functional responses correlate with regional transcriptional immunophenotypes. We also show that region-dependent differences in microglial immunophenotype are superimposed upon a core profile distinguishing all microglia from systemic macrophages. We suggest microglial diversity may enable microglia to accomplish their wide-ranging homeostatic functions but could also underlie region-specific sensitivity to neuroinflammatory-mediated degeneration. During ageing key findings were made regarding the reinforcement of a specific cerebellar immunophenotype and a contrasting loss in the distinction of the phenotype of the hippocampus. The present dataset provide an extensive underpinning resource for future studies to further define how microglial diversity influences the healthy, ageing and diseased brain. In this study 4, 12 and 22 month old mice were transcardially perfused with 0.9% saline. Brains were collected and dissected into 4 regions: cerebellum, cortex, hippocampus, striatum. For the extraction of microglia tissue from 8 mice was pooled for each regional replicate and the experiment was performed in quadruplicates for each region. Microglia were extracted from each region using a magnetic bead based approach. Brain regions (2 animals per region) of 4 month old animals for total RNA extraction of homogenates were snap frozen and stored at (-80C). Total RNA was immediately isolated for purified microglia and stored (-80C) until performing microarray analysis of purified microglia and regional brain homogenates (n=56).