Quantitative analysis of the biological forces and their context in tissue patterning

组织图案中生物力及其背景的定量分析

• 批准号: 9489281
• 负责人: Je Hyuk Lee
• 金额: $ 48万
• 依托单位: COLD SPRING HARBOR LABORATORY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-19 至 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9489281
• 关键词: Address; Architecture; Biochemical; Biological; Cell Cycle; Cell Lineage; Cells; Communication; Development; Developmental Process; Dimensions; Environment; Event; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genetic; Genome; Goals; Growth Factor; Heterogeneity; Homeostasis; In Situ; Individual; Information Theory; Laboratories; Measurement; Mediating; Methods; Modernization; Molecular; Organ; Organism; Organogenesis; Pathway interactions; Pattern; Periodicity; Process; Reporter; Research; Research Personnel; Resolution; Shapes; Signal Transduction; Specific qualifier value; Stem cells; Structure; Technology; Time; Tissues; Transcription Initiation; Wound Healing; cell type; cellular imaging; driving force; gene product; genetic information; genome-wide; imaging approach; in situ sequencing; in vivo; insight; mathematical model; morphogens; novel; post-doctoral training; programs; tissue regeneration; tool; transcriptome sequencing; tumorigenesis

Rules specifying form and function of an organism are encoded in the genome. Over the years, a variety of approaches have been leveraged to elucidate the underlying programs and machinery that govern the size and form of different organs or structures. These include genetic strategies, employed to identify gene products that control developmental events, and biochemical advances that have provided molecular insights into how communication between individual cells during development is accomplished. While information theory and mathematical modeling have made inroads toward integrating genetic and molecular aspects of development, these approaches are fundamentally limited by the simple fact that most measurements that guide these applications (either genetic or biochemical) are often derived from experimental contexts that lack the spatial or temporal richness found in vivo.  My research team is prepared to address a theoretical, quantitative, and computational program at Cold Spring Harbor Laboratory (CSHL) with an emphasis on in vivo cellular imaging and in situ sequencing technologies for gene expression and cell lineage analysis during development. During my postdoctoral training, I developed an in situ RNA sequencing technology that can be generally employed to determine the spatial and informational heterogeneity of gene expression in a genome-wide manner. As an independent investigator I have adapted this technology to monitor gene expression in developing tissues. These methods enable the simultaneous measurement of gene expression patterns in thousands of single cells in the context of a developing cell lineage. While simple in concept, this major advance will allow dynamic and temporal changes in gene expression to be directly tied to three-dimensional architecture, enabling the mathematical modeling of key developmental processes in the absence of prior limitations. Initially, we will focus on understanding how oscillations in gene expression pattern, including those mediated by the cell cycle, modulate growth factor signaling. Specifically, we will determine if cyclical patterns of gene expression are sufficient to generate a morphogenic field that controls the size and shape of developing structures or how these patterns contribute to the robustness of these processes in vivo. We will also determine the molecular mechanisms of gradient-associated transcriptional initiation/elongation using direct RNA sequencing in situ. Both oscillatory gene expression and morphogen gradient-associated transcriptional initiation/elongation impact aspects of cell fate commitment stem cells (important in tissue regeneration and homeostasis) and these approaches can be used to dissect the contribution of multiple genetic pathways in vivo. In summary, we have the conceptual framework, biological questions, cutting-edge technologies, and rigorous scientific environment to better characterize the biological forces driving tissue patterning and development of form and function.   1

指定生物体的形式和功能的规则被编码在基因组中。多年来，一个 已经利用各种方法来阐明管理的基本计划和机制 不同器官或结构的大小和形式。其中包括用于识别基因的遗传策略 控制发育事件的产品以及提供分子见解的生化进展 研究发育过程中各个细胞之间的通讯是如何完成的。同时信息 理论和数学模型已经在整合遗传和分子方面取得了进展 发展中，这些方法从根本上受到一个简单事实的限制，即大多数测量 指导这些应用（遗传或生物化学）通常源自缺乏经验的实验背景 体内发现的空间或时间丰富度。  我的研究团队准备在 Cold 开展理论、定量和计算项目 斯普林港实验室 (CSHL)，重点研究体内细胞成像和原位测序 开发过程中的基因表达和细胞谱系分析技术。在我博士后期间 在培训期间，我开发了一种原位 RNA 测序技术，可普遍用于确定 全基因组范围内基因表达的空间和信息异质性。作为一个独立的 研究人员我已经采用这项技术来监测发育组织中的基因表达。这些方法 能够同时测量环境中数千个单细胞的基因表达模式 发育中的细胞谱系。虽然概念简单，但这一重大进步将允许动态和时间 基因表达的变化与三维结构直接相关，使得数学 在没有先验限制的情况下对关键发育过程进行建模。 首先，我们将重点了解基因表达模式的振荡，包括那些 由细胞周期介导，调节生长因子信号传导。具体来说，我们将确定周期性模式是否 基因表达的变化足以产生一个形态发生场，控制基因的大小和形状 开发结构或这些模式如何有助于体内这些过程的稳健性。我们将 还确定梯度相关转录起始/延伸的分子机制 直接RNA原位测序。振荡基因表达和形态发生素梯度相关 转录起始/延伸影响细胞命运定型干细胞的各个方面（在组织中很重要） 再生和稳态），这些方法可用于剖析多种因素的贡献 体内遗传途径。总之，我们有概念框架、生物学问题、前沿 技术和严格的科学环境，以更好地表征驱动组织的生物力 形式和功能的模式化和发展。   1