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Background: One of the most prominent genetic risk factors for Alzheimer's Disease (AD) is the Apolipoprotein E (APOE) ε4 allele. Unlike the "neutral" ε3 variant, or the protective ε2variant, the ε4 variant is strongly associated with late‐onset AD, albeit by mechanisms that are not well‐understood. Methods: To shed light on the biology of APOE in the development of AD, as part of the IMI (Innovative Medicines Initiative) consortium "ADAPTED", we acquired two human induced pluripotent stem cell (hiPSC) lines, that were isogenically modified to carry the alleles ε2/ε2, ε3/ε3, ε3/ε4, ε4/ε4, as well as a knockout line. Neurons and the phagocytic cells of the CNS, the microglia were differentiated from all ten lines and subjected to thorough phenotyping, including RNA‐seq and proteomics analysis. Results: Cortical neurons do not secrete apoE under normal conditions and treatment of these cells with microglia‐enriched factors and apoE increased their overall Abeta secretion, without significant differences between the various genotypes. Microglia, on the other hand, secrete large amounts of apoE in varying quantities depending on the APOE genotype. Additionally, microglia carrying the ε4/ε4 genotype have a significantly reduced phagocytic capacity compared to their ε3/ε3 counterparts. These observations were supported by whole transcriptome sequencing, which revealed major differences in inflammatory and phagocytic activity‐related gene expression between the different APOE genotypes. Conclusions: This unique set of ten isogenic hiPSC lines enabled us to assess the cellular phenotypes in functional human neuronal cells. Microglia omics show changes in an array of AD‐relevant pathways, and being the main producers of apoE, these changes need to be understood in depth. Follow‐up experiments will validate candidate genes that might help design new therapies for APOE ε4 AD patients. Disclosure: This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 115975. This Joint Undertaking receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA. This study was sponsored by AbbVie Deutschland GmbH & Co. KG. AbbVie contributed to the study design, research, and interpretation of data, writing, reviewing, and approving the abstract. Some authors are currently employed by AbbVie and may own AbbVie stock. [ABSTRACT FROM AUTHOR]

Background: Apolipoprotein E (APOE) genotype is the main genetic risk factor for Alzheimer's disease (AD). APOE ε2 haplotype is protective, APOE ε3 is neutral, and APOE Ɛ4 is associated with the highest risk to develop the disease. APOE highly is conserved in vertebrates, but homology between human and mouse sequence is low (73.4% for peptide and 78.7% for the genetic sequences). To better understand the contribution of each APOE allele to the pathophysiology of AD it is necessary to generate preclinical models that recapitulate the molecular and biochemical properties of this complex gene. Within ADAPTED (Alzheimer's Disease Apolipoprotein Pathology for Treatment Elucidation and Development) project we have generated and characterized human iPSC‐derived brain cells to fill this important gap. Method: All ADAPTED isogenic iPSC‐lines were differentiated into clinically relevant cell types (neurons, astrocytes and microglia) that were characterized using unbiased methodologies (transcriptomics, metabolomics and proteomics) and functional assays such as neuronal activity, cytokine release and phagocytosis. We performed all possible comparisons across genotypes, and mostly focused on results that were replicated across the two sets. Result: We prioritized the study of iPSC‐derived glial cells based on expression levels of apoE and their critical role in brain function and AD pathophysiology. Our strategy led to the identification of APOE allele‐specific molecular signatures and pathways that partially replicates clinical findings (e.g. inflammatory response and metabolic properties). Functional assays revealed genotype differences that were also replicated in different genetic backgrounds. Conclusion: Systematic comparison of relevant cells types stratified by APOE genotypes revealed key signatures and mechanisms that have been associated to AD. Data generated from iPSC‐derived cells proves this model as a reliable tool to further study the human biology of APOE, providing one step further in our understanding of AD and the potential identification of more effective therapies. iPSC lines generated within ADAPTED are globally available to the scientific community via EBiSC repository. [ABSTRACT FROM AUTHOR]