AbstractBackgroundApolipoprotein E4 (APOE4) is an established AD risk gene, while APOE2 is considered protective. Recently, several studies demonstrated that APOE4 can induce AD‐related pathological phenotypes including tau phosphorylation (p‐tau), neuroinflammation, and tau‐mediated neurodegeneration in both mouse models and human neurons. However, the underlying mechanism of APOE4 in AD pathology and how other APOE isoforms affect the molecular and cellular phenotypes associated with AD are not well understood in human cells. In this study, we used isogenic human induced pluripotent stem cell (iPSC)‐derived neurons to explore the differential effects of APOE isoforms on AD‐related pathology.MethodsIsogenic human APOE2/2, APOE3/3, APOE4/4 and APOE knock‐out (APOE‐/‐ ) iPSC lines were generated by CRISPR‐Cas9 editing and characterized by immunocytochemistry. Functional excitatory neurons were induced from isogenic iPSCs by overexpressing neural fate‐driven gene neurogenin2, and tested for the expression of AD and neuroinflammation‐related genes, p‐tau, and neuronal firing and synchrony in vitro.ResultsFour isogenic iPSC lines were successfully differentiated into functional excitatory neurons with >99% purity. We found significantly reduced gene expression of C4A and C4B, which have been implicated in AD pathology, in APOE2/2 neurons compared to APOE3/3 (p=0.0377) or APOE‐/‐ neurons (p=0.0284). We also observed an upregulated expression of PPP2CB in APOE‐/‐ neurons compared to three other APOE isogenic neurons (one‐way ANOVA, F=3.863, p=0.0249), suggesting a possible APOE‐dependent suppression of PPP2CB expression. Further, the ratio of the level of p‐tau at both Thr 231 and Thr 181 sites to total tau was significantly lower in APOE3/3 neurons than APOE4/4 or APOE‐/‐ neurons (Thr 231: APOE3/3 vs APOE4/4, p<0.0001; APOE3/3 vs APOE‐/‐ , p=0.0033; Thr 181: APOE3/3 vs APOE4/4, p=0.0071; APOE3/3 vs APOE‐/‐ , p=0.0115). The expression of C4A/B but not PPP2CB was found inversely correlated with the level of p‐tau at the Thr 231 site. Finally, APOE3/3 neurons showed significantly higher neuronal firing activity and synchronization compared to other APOE isogenic neurons, which were resistant to excess glutamate treatment.ConclusionOur findings in isogenic iPSC‐derived neurons describe the differential effects of APOE on the expression of AD‐related genes, p‐tau and neuronal functions, which provide new insights into the potential role of the APOEvariants in AD.