The effects of Alzheimer's disease risk genes on metabolism and signaling across cell types

摘要 阿尔茨海默病(AD)是一种普遍的、令人衰弱的疾病，没有真正有效的治疗方法。 全基因组关联研究已经发现了散发性晚发性AD的风险变异，但 驱动这一风险的机制仍不清楚。两个悲伤的变种，最高 载脂蛋白E和三磷酸腺苷结合盒与阿尔茨海默病的关系 转运蛋白A7(ABCA7)，两者都参与脂类代谢。我们之前的工作 表明APOE(APOE4)的E4等位基因具有细胞类型特异性效应，包括 脂代谢的改变，但关于下游通路的重要问题仍然存在 受这个等位基因的影响。关键的是，我们不知道APOE4诱导的变化是如何与 与衰老相关的压力，导致迟发性疾病。关于ABCA7是如何 等位基因会增加阿尔茨海默病的风险。我们建议使用系统生物学的方法来发现 这些AD风险途径，响应来自NIH的NOT-AG-18-052，它指定 《人类阿尔茨海默病诱导的多能干细胞脑神经细胞的系统生物学》 一个高度优先的研究课题。我们的方法使用了诱导多能性的多组学分析 APOE4或ABCA7早产两个风险变异体的同源干细胞(IPSC)系 终止(PTC)，然后可以分化成不同的细胞类型。使用不带偏见的 我们将揭示AD风险等位基因如何改变细胞的信号、新陈代谢和状态， 它们如何影响复杂培养中的单个细胞以及细胞与细胞之间的相互作用，以及它们如何 改变细胞对急性应激的反应。在目标1中，我们将深入描述 ApoE4和ABCA7PTC在神经元、星形胶质细胞、小胶质细胞和周细胞2D培养模型中的表达 从等基因IPSC株系中区分出来，检测代谢和翻译后的变化 蛋白质的修饰(PTM)。我们将使用先进的网络优化方法来 整合不同的数据并发现链接在一起的分子相互作用网络 观察到个体组学的变化。在目标2中，我们调查了风险改变的途径 在3D培养模型中影响细胞间相互作用的等位基因，使用空间分辨的PTM- 蛋白质组学和代谢组学/脂质组学和因果计算模型。在《目标3》中，我们将 在3D中检查风险变量与环境和细胞应激源的交集 文化典范。每个目标都包括在体外对假说进行严格的测试，并通过检查 尸检样本。

Summary Alzheimer's disease (AD) is pervasive and debilitating, with no truly effective treatments. Genome wide association studies have found risk variants for sporadic, late-onset AD, but the mechanisms driving this risk are still unknown. Two of the sAD variants with the highest association with development of AD are in Apolipoprotein E (APOE) and ATP-binding cassette transporter A7 (ABCA7), both of which are involved in lipid metabolism. Our prior work demonstrates that the E4 allele of APOE (APOE4) has cell type specific effects, including alterations in lipid metabolism, but important questions remain about the downstream pathways affected by this allele. Critically, we do not know how APOE4-induced changes interact with aging-related stress, leading to late-onset disease. Even less is known about how ABCA7 alleles lead to increased risk of AD. We propose to use a systems biology approach to discover these AD-risk pathways, responding to NOT-AG-18-052 from the NIH, which designates “systems biology of brain neural cells derived from human AD induced pluripotent stem cells” as a high-priority research topic. Our approach uses multi-omic analysis of induced pluripotent stem cell (iPSC) lines that are isogenic for two risk variants, APOE4 or ABCA7 premature termination (PTC), which can then be differentiated into diverse cell types. Using an unbiased approach, we will reveal how AD-risk alleles alter signaling, metabolism, and states of the cells, how they affect individual cells as well as cell-cell interactions in complex cultures, and how they alter cellular responses to acute stress. In Aim 1 we will deeply characterize the effects of APOE4 and ABCA7 PTC in 2D culture models of neurons, astrocytes, microglia and pericytes, differentiated from isogenic iPSC lines, examining changes in metabolism and post-translational modifications (PTMs) of proteins. We will use advanced network optimization methods to integrate the disparate data and to uncover molecular interaction networks that link together changes observed in the individual omics. In Aim 2, we investigate the pathways altered by risk alleles that influence cell-cell interactions in 3D culture models, using spatially-resolved PTM- proteomics and metabolomics/lipidomics and causal computational models. In Aim 3, we will examine the intersection of risk variant with environmental and cellular stressors in the 3D culture models. Each aim includes rigorous testing of hypotheses in vitro and by examination of postmortem samples.