Quantitative models for controlling collective cell fate selection in stem cells

控制干细胞集体细胞命运选择的定量模型

• 批准号: 8416032
• 负责人: Matthew W. Thomson
• 金额: $ 31.51万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-25 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8416032
• 关键词: Accounting; Behavior; Biochemical; Biological Models; Biomedical Research; Cell Cycle; Cell division; Cell model; Cell physiology; Cells; Cellular Structures; Color; Communication; Communities; Complex; Data; Data Analyses; Decision Making; Development; Disease; Environment; Fibrinogen; Gene Expression; Genomics; Germ Layers; Goals; Homeostasis; Human; Human body; Image; In Vitro; Individual; Kinetics; Laboratories; Learning; Left; Libraries; Life; Light; Maps; Measurement; Measures; Methods; Microscopy; Modeling; Molecular; Mus; Muscle; Neurons; Pathway interactions; Pattern; Physics; Physiology; Population; Process; Proteins; Protocols documentation; Regenerative Medicine; Reporter; Research; Resolution; Route; Signal Pathway; Signal Transduction; Signaling Molecule; Signaling Protein; Stem cells; Structure; System; Systems Biology; Techniques; Testing; Time; Tissues; Work; cell motility; cellular imaging; design; embryonic stem cell; genome-wide; human disease; human tissue; in vitro Model; information processing; insight; light gated; mathematical model; models and simulation; neural circuit; neural model; notch protein; optogenetics; predictive modeling; reconstitution; relating to nervous system; repaired; response; single cell analysis; small molecule; stem cell differentiation; stem cell fate; stem cell population; tissue repair; tool; transcription factor

DESCRIPTION (provided by applicant): An important biomedical research goal is to reconstitute human tissues from induced pluripotent cells for in vitro interrogation of human disease states. However, our ability to coax stem cells to form complex multi- cellular structures is currently limited by deep conceptual and technical challenges. While high-throughput gene expression and biochemical measurements allow us to reconstruct the molecular circuits that control stem cell fate, these circuits are enormously complex, and the maps produced by genomics are static. Therefore, we do not understand how individual stem cells dynamically integrate signals from their environment while communicating with other cells to coordinate and construct multi-cellular tissues. The major goal of my research is to combine high-throughput single cell imaging and mathematical modeling to derive reduced, predictive models of cell fate circuits and to exploit these models with new optogenetic tools to manipulate stem cell fate with spatial and temporal control. In this application, I use mouse Embryonic Stem (ES) cell differentiation as a powerful model system for quantitative single cell analysis of fate selection n a stem cell population. In response to Wnt and Fgf signals, ES cells leave the pluripotent state and select between two alternate germ layer cell fates. A complex network of transcription factors controls the ES cell, but, in previous research, I showed that a circuit of just two transcription factors, Oct4 and Sox2, controls germ layer fate selection. Now, I use Oct4 and Sox2 as the essential nodes in a quantitative and predictive model of germ layer fate selection that incorporates both single cell information processing and inter-cellular communication. First, I will perform high-throughput single cell time lapse imaging of Oct4 and Sox2 protein levels to quantify the ES cell's response to a large array of Wnt and Fgf inputs. With statistical analysis, will reduce these measurements to a predictive dynamical systems model of signal integration. Second, to determine the impact of inter-cellular communication on ES cell fate selection, I will quantify the spatial and temporal propagation of differentiation signals through the Wnt, Fgf, and Notch pathways in ES cell populations and construct a population level model of cell fate selection. Third, I will combine the model with new optogenetic tools to modulate the single cell response to Wnt and Fgf in order to direct germ layer differentiation with spatial control. Since germ layer differentiation is a foundational process of both mammalian development and in vitro differentiation, optogenetic control of this process would provide a platform for in vitro construction of complex multi-cellular structures from germ layer derivatives. Together, these aims will provide conceptual insight into how stem cells communicate to execute multi-cellular processes like tissue development, homeostasis, and repair. Further, my application will provide a proof of principle for optogenetic light-gated control of in vitro embryonic stem cell differentiation to synthetically generate tissues for studies of human disease. PUBLIC HEALTH RELEVANCE: The goal of this application is to develop mathematical models of stem cell differentiation and to use these models to guide stem cells to form complex multi-cellular structures like muscle tissue and neural circuits in the laboratory. By controlling stem cell differentiation, we might establish in vitro models of human physiology and disease and learn how millions of individual cells in the body work together to form and repair tissues.

描述（由申请人提供）：一个重要的生物医学研究目标是从诱导多能细胞重建人体组织，用于体外询问人类疾病状态。然而，我们诱导干细胞形成复杂的多细胞结构的能力目前受到深刻的概念和技术挑战的限制。虽然高通量基因表达和生化测量使我们能够重建控制干细胞命运的分子回路，但这些回路非常复杂，基因组学产生的图谱是静态的。因此，我们不了解单个干细胞如何动态地整合来自其环境的信号，同时与其他细胞通信以协调和构建多细胞组织。我研究的主要目标是将联合收割机高通量单细胞成像和数学建模相结合，以推导出细胞命运回路的简化预测模型，并利用这些模型与新的光遗传学工具来操纵干细胞的命运与空间和时间控制。在这个应用中，我使用小鼠胚胎干（ES）细胞分化作为一个强大的模型系统定量单细胞分析的命运选择在干细胞群体。响应于Wnt和Fgf信号，ES细胞离开多能状态并在两种交替的胚层细胞命运之间进行选择。一个复杂的转录因子网络控制着ES细胞，但是，在以前的研究中，我发现只有两个转录因子Oct4和Sox 2的电路控制着胚层的命运选择。现在，我使用Oct4和Sox 2作为胚层命运选择的定量和预测模型中的重要节点，该模型结合了单细胞信息处理和细胞间通信。首先，我将对Oct4和Sox 2蛋白水平进行高通量单细胞延时成像，以量化ES细胞对大量Wnt和Fgf输入的反应。通过统计分析，将这些测量结果简化为信号集成的预测动态系统模型。第二，为了确定细胞间通讯对ES细胞命运选择的影响，我将量化ES细胞群中通过Wnt、Fgf和Notch途径的分化信号的空间和时间传播，并构建细胞命运选择的群体水平模型。第三，我将联合收割机与新的光遗传学工具相结合，以调节单细胞对Wnt和Fgf的反应，从而通过空间控制来指导胚层分化。由于胚层分化是哺乳动物发育和体外分化的基础过程，因此该过程的光遗传学控制将为从胚层衍生物体外构建复杂的多细胞结构提供平台。总之，这些目标将为干细胞如何通信以执行多细胞过程（如组织发育，稳态和修复）提供概念性见解。此外，我的申请将为体外胚胎干细胞分化的光遗传学光门控控制提供原理证明，以合成产生用于人类疾病研究的组织。 公共卫生关系：该应用程序的目标是开发干细胞分化的数学模型，并使用这些模型指导干细胞在实验室中形成复杂的多细胞结构，如肌肉组织和神经回路。通过控制干细胞分化，我们可以建立人体生理和疾病的体外模型，并了解体内数百万个细胞如何共同形成和修复组织。