ApoE4 disrupts intracellular trafficking and iron homeostasis in an improved iPSC-based model of human brain endothelial cells [bulk RNA-seq]

Transferrin receptor in brain endothelial cells can deliver therapeutic antibodies to the brain via transcytosis across the blood-brain barrier. Whether receptor transport remains intact in Alzheimer’s disease is still a major open question. Here, we investigated whether apolipoprotein E4 (ApoE4), the major genetic risk factor for Alzheimer’s disease, altered intracellular transport in human brain endothelial cells. To achieve this, we first developed an optimized protocol for induced pluripotent stem cells based on a defined chemical cocktail and extracellular-matrix support to differentiate brain endothelial cells (iCE-BECs). Multi-omic profiling and functional transport assays showed that iCE-BECs have a brain endothelial gene signature and recapitulate receptor-mediated transcytosis of a clinically validated BrainshuttleTM antibody against transferrin receptor. Engineered iCE-BECs homozygous for ApoE4 had altered spatiotemporal organization of early endosomes, increased transferrin receptor expression and reduced cytoplasmic iron. Our data revealed that ApoE4 can impact intracellular transport and iron homeostasis at the BBB in a cell-autonomous manner. This finding could be relevant for the brain delivery of therapeutic antibodies for Alzheimer’s disease. To assess the quality of endothelial cells culture obtained with our optimized protocol vs published protocols, we differetiated iPSC differentiated in brain endothelial cells using our improved protocol (iCE-BECs) to brain endothelial cells differentiated with already pulished protocol (iEC, Patsch-derived protocol) and the same cells treated with Rep Sox (iEC-rep). "Condition 1" corresponds to "Protocol 1"in the manuscript (iEC), "Condition 2" corresponds to "Protocol 2" in the manuscript (iEC-rep) and "Condition 3" corresponds to "Protocol 3" in the manusctipt (iCE-BECs). This Bulk RNA-seq analysis allows an evaluation of the culture.