There and Back Again: Epigenetic Reinforcement of Cellular Signaling States - Overall

描述(申请人提供)：这个项目的首要目标是测试这样一个假设，即响应扰动而调节磷酸化介导的信号事件可以通过改变细胞的表观遗传格局来建立新的细胞状态。为了实现这一目标，我们建议进行基于质谱仪(MS)的蛋白质组分析，该分析专门针对细胞中15,000个扰动条件下的磷信号和染色质修饰的定量读数。这些扰动将集中在小分子和基因失活对信号级联和表观遗传标记的调制上。我们将研究几种不同的细胞模型系统，包括全面研究从人类胚胎干细胞开始的神经元谱系分化。我们建议建立一个中心，以开发必要的基础设施、管道、数据管理和分析，以执行迄今为止最大的一组MS蛋白质组读出相关实验。我们还将探索下一代MS获取技术，以建立一个公众可访问的永久可开采的MS数据资源。我们将把产生的数据和工具提供给基于网络的细胞标志库(LINCS)计划，目的是通过磷酸蛋白质组和染色质修饰特征与其他中心提供给LINCS的其他数据类型相结合，在不同的扰动之间建立联系。由此产生的分析将有助于确定新的治疗机会和协同效应，因为磷信号和表观遗传系统的失调是在越来越多的遗传、发育和环境疾病中发现的两种最常见的分子病因。在项目描述的这一部分中，我们描述了该中心的总体愿景，用粗略的笔触描绘了我们的科学目标、逻辑实践、数据分析战略、社区协作计划和行政职能。

DESCRIPTION (provided by applicant): The overarching goal of this project is to test the hypothesis that modulation of phosphorylation-mediated signaling events in response to perturbations can establish new cellular states by altering their epigenetic landscapes. To achieve this goal, we propose performing mass spectrometry (MS)-based proteomic assays that specifically target quantitative readouts of phosphosignaling and chromatin modifications in cells on > 15,000 perturbational conditions. These perturbations will focus on modulation of signaling cascades and epigenetic marks by small molecules and gene inactivations. We will study several different cellular model systems, including comprehensive studies neuronal lineage differentiation starting from human embryonic stem cells. We propose to establish a center in order to develop the necessary infrastructure, pipelines, data management, and analytics required to perform what would be the largest set of related experiments with MS proteomic read outs to date. We will also explore next-generation MS acquisition technologies to establish a permanently minable MS data resource that will be accessible to the public. We will contribute the resulting data and tools to the Library of Integrated Network-based Cellular Signatures (LINCS) program for the purpose of making connections among disparate perturbations through phosphoproteomic and chromatin modification signatures in concert with other data types to be contributed to LINCS by other centers. The resulting analyses will help identify novel therapeutic opportunities and synergies, as dysregulation of phosphosignaling and epigenetic systems are two of the most common molecular etiologies identified in a growing number of genetic, developmental, and environmental diseases. In this component of the project description we describe the overall vision for the center, painting in broad strokes our scientific goals, logistcal practices, data analysis strategies, community collaboration plans, and administrative functions.