Cholesterol and matrisome pathways dysregulated in human APOE ε4 glia

() ε4 is the strongest genetic risk factor for Alzheimer’s disease (AD). Although its association with AD is well-established, the impact of ε4 on human brain cell function remains unclear. Here we investigated the effects of ε4 on several brain cell types derived from human induced pluripotent stem cells and human targeted replacement mice. Gene set enrichment and pathway analyses of whole transcriptome profiles showed that ε4 is associated with dysregulation of cholesterol homeostasis in human but not mouse astrocytes and microglia. Elevated matrisome signaling associated with chemotaxis, glial activation and lipid biosynthesis in ε4 mixed neuron/astrocyte cultures parallels altered pathways uncovered in cell-type deconvoluted transcriptomic data from ε4 glia and AD post-mortem brains. Experimental validation of the transcriptomic findings showed that isogenic ε4 is associated with increased lysosomal cholesterol levels and decreased cholesterol efflux, demonstrating decoupled lipid metabolism. ε4 glia also secrete higher levels of proinflammatory chemokines, cytokines and growth factors, indicative of glial activation. Thus, ε4 induces human glia-specific dysregulation that may initiate AD risk.