Bilateral NSF/BIO-BBSRC: The design logic of Hedgehog-based pattern formation

生物学的一个关键挑战是了解细胞如何相互交流和反应。这在胚胎发育中尤其重要，在胚胎发育中，细胞通讯负责组织和创造细胞类型的模式，这些细胞类型是形成功能器官的模板。在过去的几十年里，在识别组织发育中涉及的基因和所谓的“信号通路”方面取得了快速进展。然而，我们对这些途径的设计逻辑和动力学知识相对较少，并且通常以可预测的方式干扰或控制这些途径的能力有限。这些途径是如何工作的，它们提供了什么能力？而且，我们如何预测它们对扰动的反应，或者用它们来控制细胞行为？为了实现对这些问题的更根本的理解，需要从定性分子观点到定量系统分析的方法转变。获得洞察力是必要的，以了解，例如，如何实现精确性和可重复性的发展模式，并最终了解如何控制这些过程时，他们出错或工程新的tissues.In本提案中，我们的目标是了解的设计原则，产生的动力学和基因反应的刺猬途径。这一途径提供了一个实验上易处理的例子，一个发育重要的信号通路参与不同的发育过程和病理。然而，尽管我们对通路中的蛋白质、相互作用和反馈回路了解很多，但我们对通路为什么具有这种结构、它在单个细胞中的动态行为以及它的动态如何确保适当的组织发育知之甚少。一个关键的限制是缺乏在单个细胞水平上直接读出和控制途径活性，以及将这些数据与组织水平测定相关联的能力。为了解决这一缺陷，我们计划联合收割机结合我们实验室的专业知识，并在明确定义的细胞模型系统中使用定量单细胞和发育生物学方法的组合。Elowitz实验室在开发和分析来自一系列生物系统的单细胞定量数据方面具有专业知识;而Elowitz实验室拥有分析神经组织中Hedgehog信号传导的经验和试剂，在神经组织中Hedgehog信号传导负责产生不同的神经元亚型。该项目将开发试剂和方法，为Hedgehog途径提供新的定量理解。获得该通路的系统水平视图将提供对信号如何在发育组织中通信的洞察，并揭示Shh通路的哪些特征支持这一点。这些设计原则很可能是相关的理解不仅刺猬，但参与不同的发展过程中的其他信号通路。更一般地说，将定量和系统生物学的见解引入发育和干细胞生物学将推动该领域的发展，并有助于巩固其在药物发现，疾病临床前模型和最终临床应用中的未来用途。

A key challenge in biology is to understand how cells communicate and respond to one another. This is particularly important in developing embryos where cell communication is responsible for organizing tissues and creating the patterns of cell types that are the template for the formation of functioning organs. Over the last few decades rapid progress has been made in identifying the genes and so-called 'signaling pathways' involved in tissue development. However we have relatively little knowledge of the design logic and dynamics of these pathways, and usually limited ability to perturb or control these pathways in a predictable way. How do these pathways work, and what capabilities do they provide? And, how can we predict their response to perturbations or use them to control cellular behaviors? To achieve a more fundamental understanding of these issues requires a shift in approach from a qualitative molecular view to a quantitative systems analysis. Gaining insight is necessary in order to understand, for instance, how precision and reproducibility of developmental patterning is achieved and ultimately in order to understand how to control these processes when they go wrong or to engineer new tissues.In this proposal we aim to understand the design principles that produce the dynamics and gene responses of the Hedgehog pathway. This pathway provides an experimentally tractable example of a developmentally important signaling pathway involved in diverse developmental processes and pathologies. However, although we know a lot about the proteins, interactions and feedback loops in the pathway we have little understanding of why the pathway has this architecture, how it behaves dynamically in an individual cell, and how its dynamics ensure proper tissue development. A key limitation has been the lack of direct readout and control of pathway activity at the level of individual cells, and the ability to link these data to tissue level assays. To address this deficiency we plan to combine the expertise of our labs and use a combination of quantitative single-cell and developmental biology approaches in well-defined cellular model systems. The Elowitz lab has expertise in developing and analyzing single cell quantitative data from a range of biological systems; whereas the Briscoe lab has experience and reagents to analyse Hedgehog signaling in neural tissue, where it is responsible for generating different neuronal subtypes. The project will develop reagents and methods that provide a new quantitative understanding of the Hedgehog pathway. Obtaining this systems level of view of the pathway will provide insight into how signals are communicated in developing tissues and reveal what features of the Shh pathway support this. These design principles are likely to be relevant for understanding not only Hedgehog but other signaling pathways involved in diverse developmental processes. More generally, introducing insights from quantitative and system biology to developmental and stem cell biology will advance the field and help underpin its future use in drug discovery, preclinical models of disease, and ultimately clinical applications.