Project 3: Mechanics of Nuclei, Chromosomes and Chromatin in Cancer

项目 3：癌症中细胞核、染色体和染色质的力学

• 批准号: 8866972
• 负责人: JOHN F MARKO
• 金额: $ 39.95万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-19 至 2020-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8866972
• 关键词: Address; Affect; Automobile Driving; Binding; Biological; Biological Assay; Cell Cycle; Cell Extracts; Cell Line; Cell Nucleus; Cell physiology; Cells; Cellular biology; Characteristics; Chemicals; Chromatin; Chromatin Fiber; Chromatin Loop; Chromatin Structure; Chromosome Structures; Chromosome abnormality; Chromosomes; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Crowding; Data; Development; Disease; Electron Microscopy; Engineering; Epigenetic Process; Excision; Feedback; Fiber; Fractals; Gene Expression; Gene Expression Regulation; Genes; Goals; Higher Order Chromatin Structure; Histones; Human; Image; Immunofluorescence Immunologic; Interphase; Interphase Chromosome; Ions; Label; Lead; Link; Magnetism; Maintenance; Malignant Neoplasms; Measurement; Mechanics; Metals; Metaphase; Methodology; Methods; Mitosis; Mitotic Chromosome; Modeling; Molecular; Molecular Models; Mutation; Normal Cell; Nuclear; Nuclear Envelope; Nuclear Extract; Nuclear Structure; Oncogenic; Patients; Pattern; Phenotype; Physics; Play; Polymers; Positioning Attribute; Post-Translational Protein Processing; Property; Prophase; Proteins; Reagent; Regulatory Element; Relative (related person); Research; Research Personnel; Research Project Grants; Resources; Role; Small Interfering RNA; Spectrum Analysis; Statistical Mechanics; Structure; Techniques; Technology; Testing; Time; Variant; Xenograft procedure; base; cancer cell; cell type; cohesin; fluorescence imaging; histone modification; mathematical model; molecular modeling; optical imaging; protein distribution; research study; simulation; single molecule; statistics; tool; transcription factor; tumor progression; tumorigenic

ABSTRACT (RESEARCH PROJECT 3) Project 3 aims to understand organization and function of chromosomes and the nucleus in cancer cells, engaging the Center's focus on spatio-temporal dynamics of chromatin and information transfer in cancer. All functions of the cell are ultimately controlled by the nucleus, in which genes are expressed, under elaborate regulatory control. The molecular organization of chromosomes and the underlying chromatin is central to gene regulation. How many copies of genes are present, what patterns of transcription factors are bound to gene regulatory elements, which regions are heavily repressed by heterochromatinization, and which regions carry epigenetic marks all play a central role in controlling gene expression. In cancer, these factors are often – and usually in combination – dysregulated, with concomitant aberrant structure of the nucleus and chromosomes. Project 3 seeks to analyze the variation in chromatin structure – from the fiber level to chromosomes to the whole cell nucleus – using physical tools in combination with state-of-the-art cell biological approaches. Aim 1 of the project examines the hypothesis, supported by an array of preliminary data, that the physical organization and mechanics of chromosomes and nuclei are altered in cancer cells. This will be tested using micromechanical studies of nuclei and chromosomes, combined fluorescence imaging of major chromosome- and nucleus-organizing proteins, and partial-wave spectroscopy measurements of nuclear disorder (PWS, a technology supported by the proposed Nanocytometry Core). Experiments will be carried out in a range of tumorigenic and non-tumorigenic cell types being studied in the other Projects. Experiments using patient-derived xenografts (PDX) will test ideas developed in cell lines in a patient disease context (supplied by the proposed PDX Core). Aim 2 will test how removal of specific chromosome-organizing proteins (using siRNA and CRISPR methods) affects chromosome and nuclear structure, and then will use the results of both Aim 1 and Aim 2 in combination with Hi-C data to develop mathematical models of metaphase chromosome and interphase nucleus organization. Aim 3 will focus on how chromatin fibers themselves are physically altered in different cell types, in single-chromatin-fiber assembly and mechanics experiments using nuclear extracts from cells studied in Aims 1 and 2, a primary goal being to correlate “open” or “soft” chromatin states with specific histone modifications. The result of Project 3 will be a comprehensive study of how chromatin and chromosomes are remodeled in cancer cells relative to normal cells, and its research will be tightly linked to Project 1 and Project 2 via parallel studies of the same cell lines, use of the physical assays developed in Project 3, and through cooperation on development of siRNA and CRISPR methodologies.

摘要（研究项目3） 项目3旨在了解癌细胞中染色体和细胞核的组织和功能， 参与该中心对染色质时空动力学和癌症信息传递的关注。所有 细胞的功能最终由细胞核控制，基因在细胞核中表达， 监管控制。染色体和染色质的分子组织是 基因调控基因有多少拷贝，转录因子的模式是什么 基因调控元件，哪些区域被异染色质化严重抑制，哪些区域 携带表观遗传标记的基因在控制基因表达方面都起着重要作用。在癌症中，这些因素通常 - 并且通常是组合的-失调，伴随着细胞核的异常结构， 染色体项目3旨在分析染色质结构的变化-从纤维水平到 染色体到整个细胞核-使用物理工具结合最先进的细胞生物学 接近。该项目的目标1审查了一系列初步数据支持的假设，即 在癌细胞中染色体和细胞核的物理组织和力学发生改变。这将是 使用细胞核和染色体的微机械研究进行测试，结合主要细胞的荧光成像， 染色体和细胞核组织蛋白，以及核组织蛋白的分波光谱测量 无序（PWS，由提议的纳米细胞计数核心支持的技术）。将进行实验 在其他项目中正在研究的一系列致瘤性和非致瘤性细胞类型中。实验 使用患者来源的异种移植物（PDX）将测试在患者疾病背景下的细胞系中开发的想法 （由提议的PDX核心提供）。目标2将测试如何去除特定的染色体组织蛋白 （使用siRNA和CRISPR方法）影响染色体和核结构，然后将使用结果 目的1和目的2的数学模型结合Hi-C数据建立中期的数学模型 染色体和间期核组织。目标3将集中在如何染色质纤维本身是 在不同的细胞类型中，在单染色质纤维组装和力学实验中， 目的1和2中研究的细胞核提取物，主要目标是将“开放”或“软”染色质 具有特定组蛋白修饰的状态。项目3的结果将是全面研究如何 相对于正常细胞，癌细胞中的染色质和染色体被重塑，其研究将是 通过对相同细胞系的平行研究，使用物理测定，与项目1和项目2紧密相关 在项目3中开发，并通过合作开发siRNA和CRISPR方法。