载脂蛋白E (APOE) 基因是阿尔茨海默病 (Alzheimer's disease, AD) 的最强遗传风险因素，然而它如何调节脑内稳态尚不清楚。apoE蛋白是脑内主要的脂质载体，可在不同脑细胞类型间转运胆固醇等脂质。我们通过人类iPSC亲本细胞系和成为APOE缺失 (APOE-/-) 的等基因iPSC细胞系培养出三维（3-D）脑器官样体。为了阐明APOE缺失对脑器官样体中细胞类型特异性影响，我们在亲本和APOE-/-脑器官样体中的第90天进行了单细胞RNA测序（scRNA-seq）实验。我们的研究显示，APOE缺失对人类iPSC源脑器官样体中脑脂质稳态产生影响，并通过调节多条细胞和分子通路实现。通过单细胞RNA测序的分子标记揭示，APOE缺失通过调控真核起始因子2 (EIF2) 信号通路改变等基因脑器官样体的细胞组成。这些事件在综合应激反应阻滞剂 (ISRIB) 的处理下得到缓解。APOE缺失还导致胶质细胞中Wnt/β-连环蛋白信号通路的激活，同时伴随着分泌的肿瘤疱疹相关蛋白1 (SFRP1) 表达的减少。值得注意的是，在APOE删除的脑器官样体中，apoE在细胞类型特异性脂质稳态中起到关键作用，兴奋性神经元中胆固醇合成上调，星形胶质细胞中脂质过度积累。与人类AD相关，APOE4脑器官样体在神经发生和胆固醇代谢方面显示出差异，与APOE3相比。我们的研究证明了apoE在脑内稳态中的关键作用，并提供了与APOE4相关病理机制的重要见解。© 2023 BioMed Central Ltd., Springer Nature的一部分。

The apolipoprotein E (APOE) gene is the strongest genetic risk factor for Alzheimer's disease (AD); however, how it modulates brain homeostasis is not clear. The apoE protein is a major lipid carrier in the brain transporting lipids such as cholesterol among different brain cell types.We generated three-dimensional (3-D) cerebral organoids from human parental iPSC lines and its isogenic APOE-deficient (APOE-/-) iPSC line. To elucidate the cell-type-specific effects of APOE deficiency in the cerebral organoids, we performed scRNA-seq in the parental and APOE-/- cerebral organoids at Day 90.We show that APOE deficiency in human iPSC-derived cerebral organoids impacts brain lipid homeostasis by modulating multiple cellular and molecular pathways. Molecular profiling through single-cell RNA sequencing revealed that APOE deficiency leads to changes in cellular composition of isogenic cerebral organoids likely by modulating the eukaryotic initiation factor 2 (EIF2) signaling pathway as these events were alleviated by the treatment of an integrated stress response inhibitor (ISRIB). APOE deletion also leads to activation of the Wnt/β-catenin signaling pathway with concomitant decrease of secreted frizzled-related protein 1 (SFRP1) expression in glia cells. Importantly, the critical role of apoE in cell-type-specific lipid homeostasis was observed upon APOE deletion in cerebral organoids with a specific upregulation of cholesterol biosynthesis in excitatory neurons and excessive lipid accumulation in astrocytes. Relevant to human AD, APOE4 cerebral organoids show altered neurogenesis and cholesterol metabolism compared to those with APOE3.Our work demonstrates critical roles of apoE in brain homeostasis and offers critical insights into the APOE4-related pathogenic mechanisms.© 2023. BioMed Central Ltd., part of Springer Nature.