AbstractBackgroundDown syndrome (DS) is among the most common forms of familial Alzheimer’s disease (AD), resulting from triplication of the amyloid precursor protein (APP) gene on chromosome 21 which leads to increased amyloid beta (Aβ) peptide accumulation in the brain. As a result, all people with DS will develop Aβ plaques and tau tangles by the age of 40, and the majority will eventually develop AD‐related cognitive decline. Carrying the e4 allele of the apolipoprotein E gene (APOE), APOE4, because it catalyzes the formation of neurotoxic Aβ oligimers. The combination of APOE4 and trisomy 21 results in a very high risk for DS associated AD. APOE4 has also been shown to drive altered microglial activity in the AD brain, leading to increased neuroinflammation, neurodegeneration and cognitive decline. Studying mechanisms underlying APOE4‐microglial interactions could lead to identification of new therapeutic targets for DS‐AD treatments. Microglia‐containing cerebral organoids (MCOs) derived from human induced pluripotent stem cells (hiPSCs) with both trisomy 21 and APOE4 would offer a distinct advantage over prior models.MethodIsogenic hiPSC disomic or trisomic for chromosome 21 from an individual mosaic for trisomy 21 and carrying the APOE3/3 genotype and CRISPR‐Cas9 gene editing was then used to generate hiPSCs with the APOE4/4 genotype. hiPSCs were then differentiated into hematopoetic progenitor cells (HPCs) and neural progenitor cells (NPCs) and co‐cultured at a 7:3 ratio (NPCs:HPCs) to form MCOs.ResultControl cerebral organoids (COs) lacking HPCs were reduced in size compared to age‐matched MCOs, suggesting the successful integration of HPCs with NPCs during co‐culture. Immunohistochemical analysis showed neural rosettes characteristic of COs and shows that neurons, astrocytes and microglia were all present in MCOs throughout development.ConclusionWe have developed a novel model for DS‐AD that will be critical for identifying APOE4‐microglial interactions as a therapeutic target in DS‐AD. These MCOs may be used in pre‐clinical testing of potential therapies, which may lead to treatment for the highly vulnerable population of APOE4 carriers with DS‐AD.