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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: Alzheimer's Disease (AD) is the most common cause of dementia in the elderly and affects over 35 million people worldwide, imposing increasing social and economic burden as the population ages. While it is widely known that the most prominent genetic risk factor for AD is the presence of the Apolipoprotein E (APOE) ε4 allele, the effects of APOE in the development of AD is still poorly understood. As part of the IMI ADAPTED consortium, we aim to clarify the role of APOE as a risk factor in the development of AD. Here we present an in‐depth analysis of the effect of the APOE genotype on the transcriptome of brain cells derived from human‐induced pluripotent stem cells (hiPSCs). Method: Isogenic hiPSC lines were modified to carry different APOE genotypes: ε3/ε3, ε4/ε4, ε3/ε4, ε2/ε2, as well as an APOE knock‐out (KO) cell line. Lines carrying each of these genotypes were differentiated into distinct cell types. Differential gene expression (DGE) and protein expression (DPE) was calculated, followed by gene set enrichment. Clustering approaches were used to identify shared and differing gene signatures across genotypes. We further applied upstream regulator and network analysis on the individual cell‐type results and integrated these results across cell types. The results were compared with DGE and DEP results from an APOE mouse model. Finally, the identified genes and mechanisms were combined with the results of data from postmortem human brain samples of AD cases and controls. Results: The observed transcriptional changes confirmed phenotypic observations made for the hiPSCs and refined the insight of genes identified human brain OMICS data. Several genes and pathways were identified, which showed consistent gene expression on transcriptome and proteome level. Further, shared patterns of expressions of genes across genotypes and potential mechanisms involved in this were detected. Conclusions: In depth transcriptomics and proteomics analysis of APOE modified hiPSCs enabled to study cell type specific effects and contributed with this to the understanding of mechanisms affected by different APOE genotypes. [ABSTRACT FROM AUTHOR]

Background: While being the most prominent genetic risk factor for AD, the effects of APOE variants on biology and the development of AD is still poorly understood. The IMI ADAPTED consortium strives to illuminate the mechanisms underlying the effect of APOE with several approaches. Complementing the reanalysis of the publicly available human data, hiPSC lines with different APOE genotypes (ε3/ε3, ε4/ε4, ε3/ε4, ε2/ε2), differentiated into distinct brain cell types provide a tool to study cell‐type level effects of the APOE genotype. Further, OMICS data of human APOE modified mouse model (ε2/ε2, ε3/ε3, ε4/ε4) allowed cross species comparison and model validation. Method: For multiple brain cell types differentiated from the APOE modified isogenic hiPSC (neurons, astrocytes, microglia and macrophages) and mice transcriptomics and proteomics data were generated. Differential gene expression (DGE) and protein expression (DPE) was calculated, followed by gene set enrichment. Clustering approaches were used to identify shared and differing gene signatures across genotypes. We further applied upstream regulator and network analysis on the individual cell‐type results and integrated these results across cell types. The results were compared with DGE and DPE results from the humanized APOE mouse model. Finally, the identified genes and mechanisms were combined with the results of the integrated analysis of data from postmortem human brain samples of AD cases and controls. Results: The observed transcriptional changes confirmed and extended the phenotypic observations and refined the insight of genes identified in the integrated analysis of APOE genotype stratified human OMICS data. Several genes/proteins and pathways were consistently identified on transcriptome and proteome level. Further, shared patterns of expressions of genes across genotypes and potential mechanisms involved in this were detected. Conclusions: In depth transcriptomics and proteomics analysis of APOE modified hiPSCs‐derived cells enabled to study cell type and genotype specific effects and contributed with this to the understanding of mechanisms affected by different APOE genotypes. The findings in hiPSC we be compared with human blood and CSF OMICS analysis to be potentially used as biomarker for AD and AD progression. [ABSTRACT FROM AUTHOR]