Revanna, J. S.; Wessendorf-Rodriguez, K.; Xiao, Q.; Sabedot, T. S.; Cuoco, M. S.; Sarkar, S.; Zhou-Yang, L.; Lim, C. K.; Prozapas, V. N.; Wooldridge, R. S.; Chadarevian, J. P.; Pratt, J. M.; Steiner, S. C.; Katz, A.; Mertens, J.; Kelly, J. W.; Sole-Domenech, S.; Melchior, J. T.; Metallo, C. M.; Jones, J. R.; Gage, F. H.

While Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for late-onset Alzheimer's disease, its mechanistic role in the brain-resident macrophage, microglia, remains elusive. Microglia are important in the clearance of pathology in disease, heavily relying on lysosome functionality; therefore, we sought to understand the impact of APOE4 on microglial function. APOE44 microglia have been shown to have lipid accumulation, yet the mechanisms leading to this accumulation are unknown. Using induced pluripotent stem cell-derived microglia, we found that the APOE4 haplotype resulted in transcriptional state shifts in microglia, suppressing activated-response microglia (ARMs) and promoting a G2 senescent-like state. We found that APOE44 microglia accumulate cholesterol esters and provide less lipid support to fibroblast-induced neurons, decreasing their synaptic connections. APOE44 microglia secrete significantly less lipoproteins, leading to the accumulation of lipoproteins within the cells including the lysosomes. APOE44 microglia exhibit impaired lysosomal acidification and degradation capacity. Further, our results elucidated that APOE44 microglia are proinflammatory and shift away from fatty acid oxidation towards glycolysis, due to dysfunctional mitochondria. Taken together, our findings indicate that a loss-of-function in lipoprotein secretion drives intracellular lipid accumulation, including within lysosomes, ultimately disrupting the lysosome-endoplasmic reticulum-mitochondrial axis. This drives a proinflammatory and metabolically compromised microglial phenotype with impaired neuro-supportive functions.