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， 该中心重点关注癌症中染色质的时空动态和信息传递。全部 细胞的功能最终由细胞核控制，基因在细胞核中表达，在精心设计的条件下 监管控制。染色体和底层染色质的分子组织对于 基因调控。存在多少基因拷贝，转录因子的结合模式是什么 基因调控元件，哪些区域受到异染色质化的严重抑制，以及哪些区域 携带表观遗传标记的基因都在控制基因表达中发挥着核心作用。在癌症中，这些因素通常是 – 通常同时出现 – 失调，伴有细胞核结构异常和 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 检验了由一系列初步数据支持的假设，即 癌细胞中染色体和细胞核的物理组织和力学发生了改变。这将是 使用细胞核和染色体的微机械研究以及主要的荧光成像进行测试 染色体和细胞核组织蛋白，以及核的部分波谱测量 紊乱（PWS，一项由提议的纳米细胞计数核心支持的技术）。将进行实验 其他项目正在研究一系列致瘤和非致瘤细胞类型。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细胞系中开发的想法 （由拟议的 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 将 Aim 1 和 Aim 2 与 Hi-C 数据相结合，建立中期数学模型 染色体和间期细胞核组织。目标 3 将关注染色质纤维本身的性质 在单染色质纤维组装和力学实验中，不同细胞类型的物理变化 目标 1 和 2 中研究的细胞核提取物，主要目标是关联“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，癌细胞中染色质和染色体发生了重塑，其研究将是 通过对相同细胞系的平行研究、使用物理分析与项目 1 和项目 2 紧密相连 项目 3 中开发的，并通过合作开发 siRNA 和 CRISPR 方法学。