Systems Analysis of BMP Regulation in Developing Zebrafish Embryos

斑马鱼胚胎发育中 BMP 调控的系统分析

• 批准号: 8719149
• 负责人: David Michael Umulis
• 金额: $ 29.64万
• 依托单位: PURDUE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-09 至 2018-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8719149
• 关键词: Affect; Biochemical; Bone Morphogenetic Proteins; Cell Differentiation process; Cell Nucleus; Cells; Complex; Data; Data Sources; Development; Dorsal; Embryo; Experimental Designs; Family; Feedback; Gastrula; Gene Expression Profile; Gene Expression Profiling; Genes; Goals; Image; Image Analysis; Individual; Injury; Knowledge; Measurement; Measures; Mediating; Methods; Modeling; Molecular; Neoplasm Metastasis; Organogenesis; Outcome; Pathway interactions; Pattern; Pattern Formation; Reference Standards; Regulation; Role; Signal Transduction; Specific qualifier value; Stem cells; System; Systems Analysis; Testing; Time; Tissues; Vertebrates; Zebrafish; angiogenesis; base; blastocyst; bone morphogenetic protein 5; cell growth; cell type; chordin; data integration; design; disorder control; extracellular; fitness; gastrulation; human disease; information processing; mathematical model; model development; morphogens; mutant; predictive modeling; prospective; protein distribution; public health relevance; research study; spatiotemporal; tissue regeneration

DESCRIPTION (provided by applicant): Bone Morphogenetic Proteins (BMPs) act in developmental pattern formation as a paradigm of extracellular information that is spatially distributed in a gradient as a morphogen, specifying distinct cell types via morphogen levels. In vertebrate dorsal-ventral (DV) axial pattern formation the function, molecular partners, and role of each BMP component are fairly well understood, but the mechanism by which the combined function of the components form a robust BMP gradient is complex and still poorly understood. The field is at an impasse to go beyond the current paradigms and solve the mechanism by which the extracellular factors and multiple feedback loops interact and regulate each other's' activity spatially and temporally to generate a gradient that patterns the embryo. The zebrafish system is sufficiently well defined now to allow effective and testable mathematical models to be generated that could move this field forward. Moreover, we know very little about how BMP regulators modulate the actual signaling gradient. The objective is to discover and discriminate mechanisms of BMP regulation by utilizing quantitative image acquisition and analysis, geometrically accurate mathematical models of early zebrafish embryo DV patterning, and mixed-quality constraint based optimization. In Aim 1 the spatiotemporal formation of the BMP signaling gradient will be quantitatively investigated by measuring phospho-Smad 1/5 levels IN TOTO in wild-type and BMP component mutant zebrafish embryos, segment all nuclei in each embryo, and register the data to a standard embryo. These studies will provide the first-ever (semi)-quantitative data that can be used to discern the spatial and quantitative differences and similarities of individual BMP extracellular modulators to understand their roles in BMP signaling gradient formation. In Aim 2 networks for BMP-mediated signaling control will be identified by developing, optimizing, and analyzing 3D spatiotemporal models. An image-based zebrafish late blastula- gastrula embryo BMP pattern formation model will be developed and tested for multiple alternative mechanisms of BMP regulation that guide pattern formation dynamics. In aim 3 we will use Model-Based Optimal Design of Experiments to reduce the complexity of factorial design required for comprehensive analysis of multiple-component networks. Additionally, we will determine the mechanism of Cvl2, Tsg1, and Chd regulation of dynamic BMP signaling to test the model's predictive ability and delineate the action of this important network. The goal of this aim is to carry out simultaneous gene perturbation experiments that will provide the greatest amount of information pertaining to BMP regulation. Understanding the mechanism of BMP-mediated patterning in vertebrates will provide the basis for tightly controlling BMP signaling in tissue regeneration and other prospective treatments of human disease.

描述（由申请人提供）：骨形态发生蛋白（BMP）在发育模式形成中发挥作用，作为细胞外信息的范例，其作为形态发生素以梯度空间分布，通过形态发生素水平指定不同的细胞类型。在脊椎动物背腹 (DV) 轴向模式形成中，每个 BMP 成分的功能、分子伙伴和作用已得到相当充分的了解，但各成分的组合功能形成强大的 BMP 梯度的机制很复杂，而且仍然知之甚少。该领域陷​​入了超越当前范式并解决细胞外因子和多个反馈回路相互作用并在空间和时间上调节彼此活动以产生胚胎模式梯度的机制的僵局。斑马鱼系统现在已经足够明确，可以生成有效且可测试的数学模型，从而推动这一领域向前发展。此外，我们对 BMP 调节器如何调节实际信号梯度知之甚少。目的是通过利用定量图像采集和分析、早期斑马鱼胚胎 DV 图案的几何精确数学模型以及基于混合质量约束的优化来发现和区分 BMP 调节机制。在目标 1 中，将通过测量野生型和 BMP 成分突变斑马鱼胚胎中的磷酸化 Smad 1/5 水平来定量研究 BMP 信号梯度的时空形成，分割每个胚胎中的所有细胞核，并将数据记录到标准胚胎中。这些研究将提供有史以来第一个（半）定量数据，可用于辨别单个 BMP 细胞外调节剂的空间和定量差异和相似性，以了解它们在 BMP 信号梯度形成中的作用。在目标 2 中，将通过开发、优化和分析 3D 时空模型来识别 BMP 介导的信号控制网络。将开发和测试基于图像的斑马鱼晚期囊胚-原肠胚胚胎 BMP 模式形成模型，以用于指导模式形成动态的多种 BMP 调节替代机制。在目标 3 中，我们将使用基于模型的实验优化设计来降低多组件网络综合分析所需的因子设计的复杂性。此外，我们将确定 Cvl2、Tsg1 和 Chd 调节动态 BMP 信号传导的机制，以测试模型的预测能力并描绘这个重要网络的作用。该目标的目标是进行同步基因扰动实验，以提供有关 BMP 调控的最大量信息。了解脊椎动物中 BMP 介导的模式形成机制将为严格控制组织再生和其他人类疾病前瞻性治疗中的 BMP 信号传导奠定基础。