APOE4 genotype confers transcriptomic and functional alterations to primary mouse microglia

Relative to E3 microglia, E4 microglia exhibit altered morphology, increased numbers of endosomes and lysosomes, increased cytokine/chemokine production, and increased lipid accumulation at baseline. These changes were accompanied by increased activation of kinases that mediate global repression of translation. In a subsequent phagocytosis assay, E4 microglia exhibited increased accumulation of a variety of substrates when compared to E3 microglia. While transcriptomic profiling of myelin-challenged microglia revealed a largely overlapping response profile across genotypes, differential regulation of several pathways including interferon-related signaling, translation-related processes was identified in E4 versus E3 microglia both at baseline and following myelin challenge. Here we identify and describe several important functional alterations in E4 relative to E3 microglia. Together, our results suggest E4 genotype confers elevated levels of baseline stress to microglia relative to E3 genotype, even prior to treatment with exogenous stimuli. This work provides insight into the molecular mechanisms by which E4 genotype may increase risk for AD. Overall design: The major genetic risk factor for AD is Apolipoprotein E (APOE) genotype, with the e4/e4 genotype increasing risk for AD by ten fold compared to the most common e3/e3 genotype. However, the impact of APOE genotype on microglial function has not been thoroughly investigated. To address this, we cultured primary microglia from mice in which both alleles of the mouse Apoe gene have been humanized to encode either human APOE e3 (E3) or APOE e4 (E4). Using a combination of immunocytochemistry, immunoblotting, and flow cytometry we profiled functional differences in the endolysosomal system, lipid accumulation, phagocytosis, and cytokine secretion across E3 and E4 microglia both at baseline and in response to an acute (~3 hour) myelin challenge. RNA sequencing was used to assess differences in transcriptional profiles across genotypes and treatment conditions.