Investigating the role of APOE: limitations of human pluripotent stem cell-derived cerebral organoids

Apolipoprotein E (APOE) is the most important susceptibility gene for late onset of Alzheimers disease, with the presence of APOE-{varepsilon}4 associated with increased risk of developing Alzheimers disease. Here, we reprogrammed human fibroblasts from individuals with different APOE-{varepsilon} genotypes into induced pluripotent stem cells, and generated isogenic lines with different APOE profiles. We then differentiated these into cerebral organoids for six months and assessed the suitability of this in vitro system to measure APOE, {beta} amyloid, and Tau phosphorylation levels. We identified intra- and inter-variabilities in the organoids cell composition. Using the CRISPR-edited APOE isogenic lines, we observed more homogenous cerebral organoids, and similar levels of APOE, {beta} amyloid, and Tau between the isogenic lines, with the exception of one site of Tau phosphorylation which was higher in the APOE-{varepsilon}4/{varepsilon}4 organoids. These data describe that pathological hallmarks of AD are observed in cerebral organoids, and that their variation is mainly independent of the APOE-{varepsilon} status of the cells, but associated with the high variability of cerebral organoid differentiation. It demonstrates that the batch-to-batch and cell-line-to-cell-line variabilities need to be considered when using cerebral organoids.