Systems Biology Analyses for Hemodynamic Regulation of Vascular Homeostasis

血流动力学调节在内皮稳态中是重要的。在这个系统的头四年里， 生物学基金，我们建立了内皮细胞应答的信号和转录机制， 在体外和体内的动脉粥样硬化保护和动脉粥样硬化剪切应力。我们继续发展第一个 EC转录组受不同剪切力调控的扩展时间序列动力学模型 study.通过这些，我们已经确定了表观遗传修饰的重要作用，特别是 染色质重塑，在EC转录调控。这些发现使我们假设， 动脉粥样硬化保护和atheroprone流量诱导组蛋白修饰和长程 由长链非编码RNA（lncRNA）介导的DNA相互作用导致不同的转录组， 内皮稳态与功能障碍。我们进一步假设这些变化是动态调节的 从而导致不同的时间信号和基因表达。我们建议研究的时间划定的 信号传导导致染色质修饰和长距离DNA相互作用的事件序列 随后是转录，从而引起进一步的翻译和转录后反应，并最终 正常与患病表型。这项研究将成为第一个多尺度系统研究， 内皮细胞对切应力的反应，以阐明生理和病理生理机制 对动脉粥样硬化疾病的发生和发展很重要。我们的目标是探索 转录调控的机制细节，具体目标包括：1） 测量和鉴定差异调节EC功能的表观遗传和调节因子 在不同剪切条件下（ChIP-seq方法），2）EC上染色质结构和拓扑结构的研究 剪切流下的功能（4C方法），3）综合分析表观遗传和转录数据，以提供 机制，并建立EC中剪切介导表型的动态调控网络（系统生物学 方法），以及4）在体外、计算机模拟和体内测试和验证血液动力学调节的新假设。 体内使用遗传和药理学扰动方法，包括对正常和患病动脉的研究 人体组织。我们预计，该项目的结果将提供一个全面的 正常和病理生理学的EC中流动介导的功能后果的多尺度模型。

Hemodynamic regulation is important in endothelium homeostasis. In our first four years of this systems biology grant, we established the signaling and transcription mechanisms of endothelial cell response to atheroprotective and atheroprone shear stresses in vitro and in vivo. We have continued to develop the first dynamical model of EC transcriptome regulated by different shear stresses with an extensive time-series study. Through which, we have established the significant role of epigenetic modifications, particularly chromatin remodeling, in EC transcriptome regulations. These findings lead us to hypothesize that atheroprotective and atheroprone flows induce differential changes in histone modifications and long-range DNA interactions mediated by long non-coding RNA (lncRNA) to lead to distinct transcriptome underlying endothelial homeostasis vs. dysfunction. We further hypothesize that these changes are dynamically regulated to result in distinct temporal signals and gene expression. We propose to study the temporal delineation of the sequence of events in which signaling leads to chromatin modifications and long-range DNA interaction followed by transcription, thus causing further translational and post-transcriptional responses, and eventually normal vs. diseased phenotype. The proposed research will serve as the first multiscale systems study of endothelial response to shear stress to elucidate the physiological and pathophysiological mechanisms important for the onset and progression of atherosclerotic diseases. Our goal is to explore the epigenetic regulation of transcription in mechanistic details, and the specific objectives include the following: 1) measurement and identification of epigenetic and regulatory factors that differentially regulate EC function under different shearing conditions (ChIP-seq method), 2) study of chromatin structure and topology on EC function under shear flows (4C method), 3) integrative analysis of epigenetic and transcriptional data to provide mechanisms and build dynamical regulatory networks of shear-mediated phenotypes in EC (systems biology methods), and 4) testing and validation of novel hypotheses of hemodynamic regulation in vitro, in silico and in vivo using genetic and pharmacological perturbation methods, including studies on normal and diseased artery tissues from human subjects. We anticipate that the results from this project will provide a comprehensive multiscale model of flow-mediated functional consequences in ECs for normal and pathophysiology.