A systems biology approach to neural crest development: The role of noise in fate choice from bipotent precursors.

人体所有不同类型的细胞都来自干细胞或其他前体细胞。这些前体是多能的，具有发展成多种工作细胞（如神经元、血液或皮肤细胞）中的任何一种的灵活性。发育生物学的一个主要问题是了解这些前体如何保持灵活性，从而能够产生非常不同的细胞类型，同时，一旦开始选择采用的细胞类型，它们就会发育成那种类型的稳定细胞。到目前为止，试图剖析这个过程中涉及的遗传和非遗传成分，即所谓的分化，已经被证明是困难的。尽管该领域取得了许多进展，但多能干细胞的灵活性和分化状态的稳定性之间的微妙平衡机制仍然是一个谜。在这个项目中，我们采用系统生物学的方法来研究这个问题。系统生物学的方法依赖于数学建模技术和实验的结合，以使我们对所研究的系统的理解取得进展。在这个框架内，我们计划收集各种能够提供详细动态模型的实验数据，这些模型将用于进行实验测试的预测，然后迭代改进。特别是，我们假设，与直觉相反，帮助干细胞产生不同命运的一个重要因素是“噪音”——生物过程中的随机波动。噪音起源于基因表达和其他细胞活动的生物学的许多方面，并解释了我们在所有生物系统中看到的大部分可变性。虽然我们想象遗传成分的结构已经进化到最小化噪音的负面影响，并使生物系统在噪音存在的情况下仍然健壮，但最近的理论提出了一个意想不到的假设，即噪音实际上是帮助驱动命运选择所需的重要因素。在细胞分化过程的背景下，我们将研究两种重要的色素细胞系统，黑色黑色素细胞和闪亮虹膜细胞，从一个共同的祖细胞，在斑马鱼。斑马鱼是一个非常有用的模型系统，因为胚胎是透明的，很容易通过显微镜技术进行视觉检查，因为我们可以很容易地改变基因活性，看看这对色素细胞有什么影响。我们将使用遗传学来辨别这种色素细胞祖细胞发育的关键基因相互作用。然后，我们将使用最先进的技术对分化过程中不同时间点相关基因的不同活动进行详细测量。同时，我们将把这些信息与基因相互作用的数学模型结合起来。实验研究和建模将并行进行，并根据彼此的结果进行通知，以便重建负责从祖细胞选择色素细胞的基因调控网络。我们还将测量影响该网络组成部分的噪声量，从这些信息中，我们将能够更深入地了解导致不同命运选择和稳定分化为这两种细胞类型的机制。特别是，我们将能够首次在活胚胎中评估系统中的噪声在多大程度上有助于或阻碍细胞分化。理解这些过程的意义远远超出了我们在这里学习的基础生物学。特别是，在医学背景下，干细胞在不同细胞类型之间进行选择的过程以及这些细胞类型的稳定过程对于理解健康的身体以及它在衰老和疾病中是如何出错的至关重要。因此，它将揭示先天性疾病和癌症的潜在机制。

All the body's different cell types derive from stem or other precursor cells. These precursors are multipotent, having the flexibility to develop into any one of many types of working cells (such as neurons, blood or skin cells). A major problem in developmental biology is to understand how these precursors maintain flexibility and are thus able to generate very different cell types, while at the same time, once the choice of cell-type to adopt has been initiated, they then develop into stable cells of that type. So far, trying to dissect the genetic and non-genetic components involved in this process, known as differentiation, has proven difficult. Despite many advances in the field, the mechanism allowing the fine balance between flexibility of the multipotent stem cell and stability of the differentiated state remains mysterious. In this project we adopt a Systems Biology approach to investigate this issue. Systems Biology approaches rely on the combination of mathematical modelling techniques and experiments, to make progress towards our understanding of the system under study. Within this framework, we plan to collect a variety of experimental data capable of informing detailed dynamical models, which will be used to make predictions to be tested experimentally, and then iteratively refined. In particular we hypothesize that, counter-intuitively, an important factor helping to create alternative fates in the stem cell is 'noise' - random fluctuations in biological processes. Noise originates in many aspects of the biology of gene expression, and of other cellular activities, and accounts for much of the variability that we see in all biological systems. While we imagine that the architecture of genetic components has evolved so as to minimize any negative impact of noise, and make biological systems robust despite its presence, recent theory suggests the unexpected hypothesis that noise is an important factor that is actually required to help drive fate choice. In the context of the cell differentiation process, we will investigate a system of two important pigment cells, black melanocytes and shiny iridophores, descending from a common progenitor cell, in zebrafish. The zebrafish is a very useful model system, because the embryo is transparent and readily allows a visual inspection by using microscope techniques, and because we can readily alter gene activity and see what effects this has on the pigment cells. We will use genetics to discern the key gene interactions underlying development of this pigment cell progenitor. Then we will make detailed measurements using state-of-the-art techniques of the different activities of the relevant genes at different time-points during differentiation. At the same time we will combine this information with a mathematical model of the gene interactions. The experimental studies and the modelling will be developed in parallel and with each informed by the results of the other, so as to reconstruct the gene regulatory network responsible for pigment cell choice from the progenitor. We will also measure the amount of noise affecting the components of this network, and from this information we will be able to develop a deeper understanding of the mechanisms leading to the choice of different fates and the stable differentiation into these two cell types. In particular, we will be able to assess for the first time in the living embryo, the degree to which noise in the system helps or hinders cell differentiation. Understanding these processes has implications well beyond the basic biology we are studying here. In particular, it is important in a medical context, in that this process of stem cells choosing between different cell-types, and the process of stabilisation of these cell-types, is of fundamental importance to understanding the healthy body and how it goes wrong in ageing and in disease. It thus will shed light on the mechanisms underlying congenital diseases and cancer.