Microglial transcription profiles in mouse and in human are driven by APOE4 and sex

Summary Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for sporadic Alzheimer’s disease (AD). APOE4 is known to affect the function of microglia, but to what extent this gene drives microglial gene expression has thus far not been examined. Using a transgenic mouse model of AD that expresses human APOE, we identify a unique transcriptional profile associated with APOE4 expression. We also show a sex and APOE interaction, such that both female sex and APOE4 drive expression of this gene profile. We then confirm these findings in human cells, using microglia derived from induced pluripotent stem cells. Moreover, we find that these interactions are driven in part by genes related to metal processing, and we show that zinc treatment has APOE genotype-dependent effects on iMGL. These data identify a sex- and APOE4-associated microglial transcription profile and highlight the importance of considering interactive risk factors such as sex and environmental exposures.