Gene regulatory mechanisms connecting metabolism and Alzheimer’s Disease

到2050年，阿尔茨海默病（AD）将成为一种流行病，影响1380万美国人，他们将需要持续的治疗。 医疗和社会支持。迫切需要找到能够减缓或预防这种疾病的机制。 代谢、表观遗传学和基因表达在AD中起重要作用。代谢途径直接调节 在控制基因表达的顺式调节元件（克雷斯）处对染色质进行生物化学修饰。 因此，特异性克雷斯可能是代谢、基因表达和AD之间的关键界面。然而，在这方面， 在基因组中有数百万个克雷斯，寻找用于功能研究的初级克雷斯是一个挑战。我们 这项研究将定义一个重要的新的CRE亚类，它影响AD病理学并调节 代谢，基因表达和AD过程之间的联系。在未发表的研究中，我们 开发了一种创新的H3 K27 ac靶向配对PLAC-Seq + RNASeq（pPR-Seq）方法， 同时分析组织中活性克雷斯、顺式调节接触和基因表达。成人 在小鼠下丘脑中，我们发现了与多个相邻基因形成接触的超级循环克雷斯， 并起协调基因共表达的作用。我们称之为协调员克雷斯（cCREs）。我们发现 cCREs占下丘脑克雷斯的18%，在AD风险基因和基因中显著富集 与调节单个基因的典型克雷斯相比，CREs对代谢变化有反应。击倒（KO） 小鼠一个cCRE，我们发现显着的基因表达，代谢反应，行为和衰老 表型。下丘脑是AD的一个新的重要研究领域。另一些人建议， 下丘脑的神经退行性变化有助于级联代谢和稳态 导致AD进展的失调。我们的研究建立在这个想法的基础上，重点关注cCREs。目前我们 不完全了解下丘脑cCREs的功能或与AD风险基因相关的cCREs如何影响AD 大脑和行为病理学此外，人类下丘脑中cCREs的性质尚不清楚。这里我们 测试下丘脑cCREs是不成比例整合的调节中心的一般假设 与典型的克雷斯相比，代谢和神经变性信号，并调节 邻近基因，影响小鼠模型中AD病理学的进展，并显示出在 老鼠和人类目标1将确定cCREs的染色质可及性如何变化，以响应 在小鼠中的代谢和神经变性信号，并定义不同的cCREs是活跃的细胞类型。 目的2将确定cCREs调节重要AD风险位点的功能，包括Abca 7，Picalm和 Fto-Irx，以及对5xFAD小鼠中AD病理学的影响。目标3将揭示人类下丘脑中的cCREs 并确定小鼠的保护性。总之，我们的研究将定义保守的下丘脑cCREs， 作为连接代谢和AD过程的重要顺式调节枢纽发挥作用。通过了解这些 影响原发性AD风险基因和过程的基本新机制，未来的研究将能够 研究人类AD中的cCRE并设计策略来改变cCRE活性以减缓AD进展。

By 2050, Alzheimer's disease (AD) will be an epidemic affecting 13.8 million Americans, who will need ongoing medical and social support. There is an urgent need to find mechanisms that can slow or prevent the disease. Metabolism, epigenetics and gene expression have important roles in AD. Metabolic pathways directly regulate biochemical modifications to chromatin at cis-regulatory elements (CREs) that control gene expression. Therefore, specific CREs could be a critical interface between metabolism, gene expression and AD. However, there are millions of CREs in the genome and finding primary CREs for functional studies is a challenge. Our study will define an important new subclass of CRE that affects AD pathology and regulates connections between metabolism, gene expression and AD processes. In unpublished studies, we developed an innovative H3K27ac-targeted paired PLAC-Seq + RNASeq (pPR-Seq) approach to simultaneously profile active CREs, cis-regulatory contacts and gene expression in tissues. For the adult mouse hypothalamus, we uncovered super-looping CREs that form contacts with multiple neighboring genes, and function to coordinate gene co-expression. We call these coordinator CREs (cCREs). We found that cCREs make up 18% of hypothalamic CREs and are significantly enriched at AD risk genes and genes responsive to metabolic changes compared to canonical CREs that regulate single genes. In knockout (KO) mice for one cCRE, we found significant gene expression, metabolic response, behavioral and aging phenotypes. The hypothalamus is an important new area of focus in AD. Others have proposed that early neurodegenerative changes in the hypothalamus contribute to cascading metabolic and homeostatic dysregulation that drives AD progression. Our study builds on this idea with a focus on cCREs. Currently, we do not fully understand the functions of hypothalamic cCREs or how cCREs linked to AD risk genes affect AD brain and behavioral pathology. Moreover, nature of cCREs in the human hypothalamus is unknown. Here, we test the general hypothesis that hypothalamic cCREs are regulatory hubs that disproportionately integrate metabolic and neurodegeneration signals compared to canonical CREs, and regulate the co-expression of neighboring genes, affect the progression AD pathology in mouse models and show conservation between mice and humans. Aim 1 will determine how chromatin accessibility changes at cCREs in response to metabolic and neurodegeneration signals in mice and define the cell-types that different cCREs are active in. Aim 2 will determine the functions of cCREs regulating important AD risk loci, including Abca7, Picalm and Fto-Irx, and effects on AD pathology in 5xFAD mice. Aim 3 will uncover cCREs in the human hypothalamus and determine conservation with mice. In summary, our study will define conserved hypothalamic cCREs that function as important cis-regulatory hubs connecting metabolic and AD processes. By understanding these fundamental new mechanisms that affect primary AD risk genes and processes, future studies will be able to study cCREs in human AD and devise strategies to modify cCRE activity to slow AD progression.