Signaling Logic Underlying Mammalian Germ Layer Differentiation

所有生物体都是从一个单细胞开始生命的，然后生长、分裂、分化成各种不同类型的细胞，形成身体的器官。这是如何发生的是生物学中最基本的问题之一，也是理解我们自己的起源以及地球上各种生命形式的关键。现在已经知道，细胞可以通过细胞外蛋白的交流来协调它们向特化细胞命运的分化，细胞外蛋白是由一个细胞分泌的，然后由它的邻居接收，从而影响它们分化的结果。细胞通过多种途径同时经历信号传递，其结果取决于这些多种信号如何被接收和解释的动态。了解细胞如何处理在决定细胞命运时接收到的动态信息是发育生物学的一个核心问题。解决这个问题的一个关键挑战是这些信号的复杂性和细胞用来解释它们的调节网络。在这个项目中，我们将使用干细胞实验和一个新的数学框架来研究胚胎细胞在开始分化为最终形成大脑、心脏、肺和其他器官的细胞类型时所做的第一个决定。研究人员希望这些结果能够揭示这些决定的基本机制，并产生一个模型，可以用来预测细胞命运的不同信号动力学的结果，这将最终提高我们指导干细胞走向任何给定命运的能力。作为该项目的一部分，研究人员将培养从本科生到博士后水平的不同科学家群体，并将参与干细胞主题的公共宣传和教育。他们将承担一个项目，通过编辑维基百科上有关干细胞研究的文章来改善科学教育的一个关键公共资源。研究人员还将为干细胞动力学的数学建模和实验研究提供资源，这些资源将与科学界广泛共享。在哺乳动物胚胎中，胚胎内部最初的细胞命运决定发生在原肠胚期。三个信号通路的级联，BMP， Wnt和Nodal对原肠胚形成至关重要。每一个都通过转录激活其配体来启动下一个途径，这些途径中的任何一个丢失都会导致原肠胚形成失败。众所周知，细胞命运的决定是由这三种途径的动态活动组合而成的，然而，由于在哺乳动物胚胎中难以操纵和测量信号和细胞命运，每种途径与下一种途径之间的关系以及它们如何组合以产生细胞命运仍然未知。在这里，研究人员建议使用胚胎干细胞（ESCs）作为平台，结合活细胞成像、定量分析和数学建模来研究这些问题。我们将定量表征和建模BMP如何诱导Wnt，然后Wnt如何诱导Nodal，以及细胞命运如何是这些多个信号动态的函数。然后，他们将生成一个综合模型，说明这三种途径是如何控制命运决定的。由于这个问题的复杂性，他们不会试图直接建立基因调控网络的模型，而是使用景观模型，这是沃丁顿景观概念的数学形式化，其中一个分化的细胞被设想为一个球，从山上滚到山谷，代表稳定的细胞命运。研究人员和其他人最近已经成功地使用这个框架来定量地拟合数据，并对发展系统做出预测，在这里，我们将扩展它，并将其应用于发展的这个关键阶段。他们希望这能揭示细胞决定命运的过程，为这一重要问题提供基本的见解，并作为干细胞分化预测控制的工具。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

All organisms begin life as a single cell which then grows, divides, and specializes into all of the diverse cell types which form the organs of the body. How this occurs is one of the most fundamental questions in biology and is key to understanding our own origins as well as the diverse forms of life on earth. It is now known that cells can coordinate their differentiation to specialized cell fates by communicating using extracellular proteins which are secreted by a cell and then received by its neighbors, influencing the outcome of their differentiation. Cells experience signaling through multiple pathways simultaneously, and the outcome depends on the dynamics of how these multiple signals are received and interpreted. Understanding how a cell processes the dynamic information received in making a cell fate decision is a central question in developmental biology. A key challenge in solving this question is the complexity of these signals and the regulatory networks which cells use to interpret them. In this project, we will use experiments with stem cells together with a novel mathematical framework to investigate the first decisions that embryonic cells make as they begin to specialize into the cell types that will ultimately form the brain, heart, lungs and other organs. The investigators expect the results to reveal fundamental mechanisms by which these decisions are made, as well as to yield a model which can be used to predict the outcome of different signaling dynamics on cell fate, which will ultimately improve our ability to direct stem cells to any given fate. As part of the performance of this project, the investigators will train a diverse group of scientists from the undergraduate to the postdoctoral level, and will engage in public outreach and education on the topic of stem cells. They will undertake a project to improve a key public resource for science education by editing the articles dealing with stem cell research on Wikipedia. The investigators will also generate resources for both mathematical modeling and experimental studies of stem cell dynamics which will be widely shared with the scientific community. In mammalian embryos, the initial cell fate decisions within the embryo proper occur at gastrulation stage. A cascade of three signaling pathways, BMP, Wnt, and Nodal is essential for gastrulation. Each one initiates the next pathway by transcriptionally activating its ligand, and loss of any of these pathways leads to a failure in gastrulation. It is known that cell fate decisions are made combinatorially as a function of the dynamic activity of these three pathways, however, the relationship between each pathway and the next and how they combine to generate cell fates remains unknown, because of the difficulty of manipulating and measuring signaling and cell fate in the mammalian embryo. Here the investigators propose to use embryonic stem cells (ESCs) as a platform for investigating these questions using a combination of live-cell imaging, quantitative analysis, and mathematical modeling. We will quantitatively characterize and model how BMP induces Wnt and then how Wnt induces Nodal, and how cell fate is a function of the dynamics of these multiple signals. They will then generate a synthesized model for how these three pathways control fate decisions. Due to the complexity of this problem, they will not attempt to model the gene regulatory network directly but will use landscape models, a mathematical formalization of the concept of the Waddington landscape in which a differentiating cell is envisioned as a ball rolling down a hill to valleys which represent stable cell fates. The investigators and others have recently had success in using this framework to quantitatively fit data and to make predictions about developmental systems, and here we will extend it and apply it to this key phase of development. They expect this to reveal the landscape in which cells make fate decisions, providing fundamental insight into this important problem as well as serving as a tool for predictive control over stem cell differentiation.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.