CAREER: Signal processing in the Erk pathway: dynamics, decisions, and development

现代生物学中最令人兴奋和最具挑衅性的想法之一是细胞可以被重新编程并被设计成执行所需的功能。然而，操纵细胞反应的能力在两个关键方面仍然相当有限。首先，研究人员还没有破译细胞用来做出特定反应的指令。其次，即使研究人员完全知道要提供哪些指令，他们也缺乏工具，无法在不影响其邻居的情况下，在准确的时间将这些指令传递给特定的感兴趣细胞。这项研究将通过研究一种名为ERK的蛋白质来解决这两个关键挑战，ERK在所有多细胞生物体中发挥着组织细胞决策的基础作用。该项目将依靠尖端工具的组合：活细胞生物传感器来测量自然的ERK反应，以及经过工程的光敏蛋白质来改变组织中精确的时间和位置的ERK活性。这种对ERK活动模式如何在细胞、组织和整个生物体尺度上控制反应以及如何改变这些模式以控制细胞命运的全面理解。这些研究将与培养下一代定量生物学家的教育计划相结合，并培养历史上代表性不足的学生早期接触研究。研究人员实验室的长期目标是解决细胞系统生物学中的两个基本问题。少数高度保守的信号通路如何在不同的细胞类型和生物体中重新定位，以编码有关外部世界的信息？这些通路发出的信号的哪些特征足以确定细胞、组织和生物体水平的表型？实现这两个目标将有助于弥合从静态基因型到复杂多细胞表型的差距，并定义由共同处理细胞信息的蛋白质组进行的计算。该研究计划的重点是一个被广泛研究的信号通路，即ERK通路，它在真核生物中发挥着至关重要的作用。虽然组成该途径的单个蛋白质已经通过遗传和生化方法进行了彻底的研究，但活细胞ERK生物传感器最近揭示了精细的时空活动模式：单个细胞中的振荡，跨组织传播的波，以及胚胎发育期间快速连续的空间模式。这项工作将使用定量测量和高度受控的光遗传输入相结合的方法来剖析这些华丽的模式，这些输入可以用来在任何空间或时间模式中激活ERK信号。特别是，这项研究试图：(1)在表皮的实验室模型中剖析产生Erk活性脉冲的机制；(2)确定Erk动力学如何控制表皮细胞中的基因表达和细胞命运；以及(3)揭示Erk信号如何影响发育中的苍蝇胚胎的组织形态发生，其中精致的信号模式随着时间的推移出现在整个有机体的3D空间中。这项研究还得到了一项教育计划的补充，该计划旨在扩大本科生，特别是历史上代表性不足的学生的早期研究机会，并将数量生物学和光遗传学的工具传播给下一代细胞和发育生物学实习生。该项目由分子和细胞生物科学和综合组织系统联合资助，并由理事会的生命规则风险基金提供额外支持。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

One of the most exciting and provocative ideas in modern biology is the notion that cells can be "reprogrammed" and engineered to perform a desired function. Yet the ability to manipulate cellular responses is still quite limited in two key ways. First, researchers have not deciphered the instructions used by cells to adopt a particular response. Second, even if researchers perfectly knew which instructions to provide, they lack the tools to deliver them to a particular cell of interest, at a precise time, without affecting its neighbors. This research will address both of these key challenges by studying a protein, Erk, that plays a fundamental role in organizing cell decisions in all multicellular organisms. This project will rely on a combination of cutting-edge tools: live-cell biosensors to measure natural Erk responses and engineered, light-sensitive proteins to alter Erk activity at precise times and locations in a tissue. This comprehensive understanding of how Erk activity patterns control responses at the cell, tissues, and whole organism scales and how one can alter those patterns to control cell fate. These studies will be integrated with an education plan to train the next generation of quantitative biologists and to foster early exposure to research for historically underrepresented students.The long-term goal of the researcher's lab is to address two fundamental problems in cellular systems biology. How are a small number of highly conserved signaling pathways repurposed in different cell types and organisms to encode information about the external world? Which features of the signals sent by these pathways are sufficient to specify cell-, tissue-, and organism-level phenotypes? Fulfilling these two aims will help to bridge the gap from a static genotype to complex multicellular phenotypes and define the computations that are carried out by the groups of proteins that work together to process cellular information. The research plan is focused on an extensively studied signaling pathway, the Erk pathway, which plays essential roles across eukaryotic organisms. Although the individual proteins comprising the pathway have been thoroughly studied by genetic and biochemical approaches, live-cell Erk biosensors have recently revealed exquisite spatiotemporal patterns of activity: oscillations in individual cells, propagating waves across tissues, and a fast succession of spatial patterns during embryogenesis. The work will dissect these ornate patterns using a combination of quantitative measurements and highly controlled optogenetic inputs that can be used to activate Erk signaling in any spatial or temporal pattern. In particular, the research seeks to: (1) dissect the mechanism that generates pulses of Erk activity in a laboratory model of the epidermis; (2) determine how Erk dynamics control gene expression and cell fate in epidermal cells; and (3) unravel how Erk signaling affects tissue morphogenesis in the developing fly embryo, where exquisite signaling patterns appear over time and in 3D space throughout the organism. The research is complemented by an education plan directed at broadening the early-stage research opportunities available to undergraduates, particularly historically underrepresented students, and at disseminating the tools of quantitative biology and optogenetics to the next generation of cell and developmental biology trainees.The Project is jointly funded by Molecular and Cellular Biosciences and Integrative Organismal Systems, with additional support provided by the Directorate's Rule of Life Venture Fund.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.