Collaborative Research: Modeling Spatiotemporal Control of EGFR-ERK Signaling in Gene-edited Cell Systems

合作研究：基因编辑细胞系统中 EGFR-ERK 信号传导的时空控制建模

• 批准号: 1906161
• 负责人: Kevin Brown
• 金额: $ 15万
• 依托单位: Oregon State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1906161&HistoricalAwards=false
• 关键词: Collaborative; Research; Modeling; Spatiotemporal; Control

In this project, the investigators will develop a new experimental and computational platform to answer the longstanding biological question of how cellular receptors generate biochemical signals as they move among various subcellular compartments. By helping to quantitatively resolve certain apparently conflicting observations that have recently been made within a biological system previously thought to be well understood, this project will add fundamentally new understanding of basic mechanisms of cell signaling that may have implications across numerous receptor systems in cell biology. Moreover, due to the broadly important role that receptors, and the biochemical signals they generate, play in virtually every biological process, the new quantitative understanding gained will ultimately impact ongoing efforts to optimally engineer receptor-mediated signaling. This project also includes a broad and detailed set of integrated educational objectives that leverage the specific scientific objectives and activities of this project to reach students at different training stages and from diverse backgrounds. These education and outreach activities involve innovation upon existing programs at the partnering institutions as well as the creation of new outreach efforts that will target larger audiences, such as a summer academy of science for high school students and a collaboration with the Museum of Science and Industry in Tampa, FL to develop a live interaction program on cell signaling. The biochemical signaling that results upon ligand binding to receptor tyrosine kinases is accompanied by receptor clustering and internalization, or endocytosis. While it has been understood for decades that endocytosis enables cells to degrade or recycle receptors, the question of how endocytosis ultimately impacts downstream signal propagation remains wide open. For example, even for the highly studied epidermal growth factor receptor (EGFR) the literature contains highly cited, yet conflicting reports that conclude that EGFR endocytosis either promotes or impedes downstream signaling through the extracellular regulated kinase (ERK) pathway. In this project, the investigators will explore the hypothesis that the intrinsic complexity of the spatiotemporal signaling regulatory mechanisms creates parameter spaces for both answers to be true depending on the cellular context. The complexity of the receptor trafficking and signaling system cannot be fully dissected, however, without integrating quantitative experimental measurements that faithfully reflect cell biology with spatiotemporal computational models. Accordingly, the overarching goal of this project is to combine novel live-cell imaging of gene-edited cell systems with mechanistic models that capture system complexity with unprecedented detail to resolve the kinds of conflicting reports previously mentioned, as well as more recent surprising observations that certain proteins conventionally thought to remain in complex during signal transduction may become physically separated through trafficking processes. Ultimately, the proposed integration of gene-edited cell systems, quantitative live-cell imaging and biochemical measurements, and a spatiotemporal computational model will lead to an entirely new quantitative platform to answer these kinds of questions for EGFR and other receptor signaling systems.

在这个项目中，研究人员将开发一个新的实验和计算平台，以回答长期存在的生物学问题，即细胞受体在各个亚细胞区室之间移动时如何产生生化信号。通过帮助定量解决最近在以前被认为很好理解的生物系统中进行的某些明显相互矛盾的观察结果，该项目将从根本上增加对细胞信号传导基本机制的新理解，这可能对细胞生物学中的众多受体系统产生影响。此外，由于受体及其产生的生化信号在几乎每个生物过程中都发挥着广泛的重要作用，因此获得的新的定量理解最终将影响正在进行的优化受体介导信号传导的努力。该项目还包括一套广泛而详细的综合教育目标，利用该项目的具体科学目标和活动来接触处于不同培训阶段和来自不同背景的学生。这些教育和外展活动涉及对合作机构现有项目的创新，以及针对更多受众开展新的外展活动，例如针对高中生的暑期科学学院以及与佛罗里达州坦帕科学与工业博物馆合作开发关于细胞信号传导的实时互动项目。配体与受体酪氨酸激酶结合产生的生化信号传导伴随着受体聚集和内化或内吞作用。虽然数十年来人们一直认为内吞作用使细胞能够降解或回收受体，但内吞作用最终如何影响下游信号传播的问题仍然悬而未决。例如，即使对于经过深入研究的表皮生长因子受体 (EGFR)，文献中也包含大量引用但相互矛盾的报告，这些报告得出的结论是 EGFR 内吞作用通过细胞外调节激酶 (ERK) 途径促进或阻碍下游信号传导。在这个项目中，研究人员将探索这样一个假设：时空信号调节机制的内在复杂性为这两个答案根据细胞环境创建了参数空间。然而，如果不将忠实反映细胞生物学的定量实验测量与时空计算模型相结合，就无法完全剖析受体运输和信号系统的复杂性。因此，该项目的总体目标是将基因编辑细胞系统的新颖活细胞成像与机械模型相结合，以前所未有的细节捕获系统复杂性，以解决前面提到的各种相互矛盾的报告，以及最近令人惊讶的观察结果，即通常认为在信号转导过程中保持复合体的某些蛋白质可能通过运输过程而物理分离。最终，基因编辑细胞系统、定量活细胞成像和生化测量以及时空计算模型的整合将产生一个全新的定量平台，以回答 EGFR 和其他受体信号系统的此类问题。

项目成果

Analysis of sloppiness in model simulations: Unveiling parameter uncertainty when mathematical models are fitted to data.

• DOI: 10.1126/sciadv.abm5952
• 发表时间: 2022-09-23
• 期刊: Science advances
• 影响因子: 13.6