Systems Biology Analyses for Hemodynamic Regulation of Vascular Homeostasis

血流动力学调节在内皮动态平衡中起着重要作用。在我们这个系统的头四年里 生物学奖，我们建立了内皮细胞应答的信号和转录机制 体外和体内抗动脉粥样硬化和动脉粥样硬化的剪切应力。我们一直在继续开发第一 不同剪应力调控EC转录组的广泛时间序列动力学模型 学习。通过它，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转录组调节中。这些发现使我们假设 动脉粥样硬化保护和动脉粥样硬化血流诱导组蛋白修饰和长程改变的不同变化 长非编码RNA(LncRNA)介导的DNA相互作用导致不同的转录组 内皮细胞动态平衡与功能障碍。我们进一步假设这些变化是动态调节的 导致不同的时间信号和基因表达。我们建议研究时间上的描述 信号导致染色质修饰和远距离DNA相互作用的一系列事件 然后是转录，从而引起进一步的翻译和转录后反应，最终 正常表型与疾病表型。拟议的研究将作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其生理和病理生理机制 对动脉粥样硬化性疾病的发生和发展很重要。我们的目标是探索表观遗传学 对转录的机械性细节进行调控，具体目标包括：1) 差异调控EC功能的表观遗传和调控因子的测定和鉴定 在不同剪切条件下(CHIP-SEQ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)表观遗传和转录数据的综合分析，以提供 系统生物学中剪切介导表型的机制及其动态调控网络的构建 方法)，以及4)在体外、硅胶和硅胶中测试和验证血流动力学调节的新假说 使用遗传和药物扰动方法的活体，包括对正常和病变动脉的研究 来自人类受试者的组织。我们预计这个项目的结果将提供一个全面的 正常和病理生理学的内皮细胞内流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.