To determine whether the AD-related pathologies in apoE4/4 neurons are specifically induced by apoE4, we used gene editing to generate an isogenic apoE3/3-hiPSC line from the apoE4/4-hiPSC-A line (Supplementary Fig. 6a)29. As in the parental line, the isogenic apoE3/3-hiPSC line (iE3/3) had normal expression of pluripotency genes (Supplementary Fig. 6b,c) and a normal karyotype (Supplementary Fig. 6d), and it generated normal neural stem cells, which expressed Sox2, nestin, and FoxG1 (Supplementary Fig. 6e,f) and developed into mature neurons (Supplementary Fig. 6g). Importantly, DNA sequencing analyses revealed no off-target effects of the gene-editing at least on some major AD-related genes (Supplementary Table 2).
