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

描述（由申请人提供）：这个项目的总体目标是测试这样一个假设，即磷酸化介导的信号事件在响应扰动时的调节可以通过改变它们的表观遗传景观来建立新的细胞状态。为了实现这一目标，我们提出了一种基于质谱（MS）的蛋白质组学分析方法，该方法专门针对细胞中磷信号和染色质修饰的定量读数，这些信号和染色质修饰在bb0 - 15,000扰动条件下进行。这些扰动将集中在信号级联和表观遗传标记的小分子和基因失活的调制。我们将研究几种不同的细胞模型系统，包括从人类胚胎干细胞开始的神经谱系分化的综合研究。我们建议建立一个中心，以便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MS蛋白质组学读出相关实验集。我们还将探索下一代MS采集技术，以建立一个永久可开采的MS数据资源，将向公众开放。我们将把结果数据和工具贡献给基于网络的综合细胞特征库（LINCS）项目，目的是通过磷蛋白质组学和染色质修饰特征，以及其他中心将贡献给LINCS的其他数据类型，在不同的扰动之间建立联系。结果分析将有助于确定新的治疗机会和协同作用，因为磷酸化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，大致描绘了我们的科学目标、后勤实践、数据分析策略、社区协作计划和管理功能。

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.