Live-Cell Chromatin Imaging and Biology: Application to Extrachromosomal DNA

活细胞染色质成像和生物学：在染色体外 DNA 中的应用

基本信息

批准号：
10685017
负责人：
Liangqi Xie
金额：
$ 144.9万
依托单位：
CLEVELAND CLINIC LERNER COM-CWRU
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-09-01 至 2026-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10685017
关键词：
Address Automobile Driving Biochemical Biology Cells Chromatin Chromatin Structure Chromosomes Disease Disease Management Dissection Drug resistance Ensure Foundations Gene Expression Gene Expression Regulation Genetic Genetic Transcription Genome Genome engineering Genomic approach Genomics Health Health Promotion Human Image Label Malignant Neoplasms Measurement Methods Microscopy Mitosis Modernization Molecular Monitor Names National Cancer Institute Oncogenes Optics Organ Organism Outcome Patients Physiological Process Regulation Regulatory Element Resolution Time Tissues Visualization cancer genome cancer type design extrachromosomal DNA genetic approach high reward high risk improved innovation molecular dynamics novel strategies population based programs segregation spatiotemporal stem technology development tool tumor heterogeneity

Address Automobile Driving Biochemical Biology Cells Chromatin Chromatin Structure Chromosomes Disease Disease Management Dissection Drug resistance Ensure Foundations Gene Expression Gene Expression Regulation Genetic Genetic Transcription Genome Genome engineering Genomic approach Genomics Health Health Promotion Human Image Label Malignant Neoplasms Measurement Methods Microscopy Mitosis Modernization Molecular Monitor Names National Cancer Institute Oncogenes Optics Organ Organism Outcome Patients Physiological Process Regulation Regulatory Element Resolution Time Tissues Visualization cancer genome cancer type design extrachromosomal DNA genetic approach high reward high risk improved innovation molecular dynamics novel strategies population based programs segregation spatiotemporal stem technology development tool tumor heterogeneity

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项目摘要

PROJECT SUMMARY Genome regulation is the prime mechanism that governs the precise spatiotemporal gene expression program that, in turn, establishes and maintains the cellular states in tissues and organs in multicellular organisms. In humans, genomic changes that alter this regulation can cause a wide range of diseases such as cancer. Demystifying genome regulation has become a central task of modern biology in the post-genomic era and is the foundation for effective disease management and promotion of health. Homeostatic genome regulation ensures precise spatiotemporal chromosomal gene regulation in properly insulated chromatin structures, in the cis-configuration (same chromosome), and through faithful symmetric segregation during mitosis. In stark contrast, these rules are broken in human cancers particularly in the form of extrachromosomal DNA (ecDNA) that enables insulation crossover, trans regulation, and asymmetric inheritance. Named as a 2021 Cancer Grand Challenge by the National Cancer Institute, megabase-sized circular ecDNA typically contains common oncogenes and regulatory elements present in major human cancer types, driving massive oncogene amplification and expression, enabling intra-tumoral heterogeneity, and conferring drug resistance and poor patient survival. The fundamental molecular mechanisms governing ecDNA expression, interaction, and propagation are largely unknown. Although powerful biochemical, genetic, and genomic approaches have laid the conceptual framework of modern understanding of genome regulation, the largely population-based, time- averaged, and sometimes out-of-context measurements are insufficient to fully describe the spatially compartmentalized, temporally dynamic, and physiologically relevant higher-order interactions in single live cells. The fundamental challenges stem from lack of chromatin tools to label the intrinsically heterogeneous chromatin, limited spatiotemporal resolution to monitor the highly concentrated and dynamic molecular transactions, and the paucity of quantitative and rigorous methods to extract fundamental physical rules underlying genome regulatory processes. In this project, we plan to overcome these primitive challenges by initiating a radically distinctive technological development of robust, efficient, and multiplexable chromatin labeling strategies for live- cell chromatin biology, which will allow us to apply them to address the fundamental regulation of ecDNA in the cancer genome. We will integrate advanced imaging, cutting-edge microscopy, modern synthetic genome engineering, and optical/genetic perturbation to systematically study the basic mechanisms by which ecDNA orchestrates massive oncogene transcription, extensive chromosomal remodeling, and asymmetric segregation hitherto intractable by conventional biochemical, genetic, or genomic methods. Positive outcome of these cutting- edge approaches and high-risk high-reward questions embedded in our proposal will have a transformative impact on mechanistic dissection of cancer genome regulation and may help us to uncover an Achilles' heel with which to target ecDNA-driven cancer, thereby affording wide-ranging positive influence on human health.

项目摘要基因组调节是控制精确时空基因表达程序的主要机制反过来，这在多细胞生物中建立并维持在组织和器官中的细胞状态。在人类，改变这种调节的基因组变化会导致多种疾病，例如癌症。脱神秘的基因组调节已成为后代后时代现代生物学的核心任务，并且是有效疾病管理和促进健康的基础。稳态基因组调节确保在正确绝缘的染色质结构中的精确时空染色体基因调节顺式配置（相同的染色体），并通过有丝分裂过程中的忠实对称分离。在斯塔克对比，这些规则在人类癌症中被打破，尤其是以外染色体DNA（ECDNA）的形式这样可以实现绝缘交叉，反式调节和不对称的遗传。被称为2021年癌症大国家癌症研究所的挑战，巨大的圆形ecdna通常包含常见主要人类癌类型中存在的癌基因和调节元素，驱动大量癌基因放大和表达，使肿瘤内异质性和耐药性和较差患者生存。控制ECDNA表达，相互作用和的基本分子机制传播在很大程度上未知。尽管有强大的生化，遗传和基因组方法已经奠定了现代理解基因组调节的概念框架，主要基于人群的时间 - 时间 - 平均，有时甚至不足的测量不足以充分描述空间在单个活细胞中，分隔，时间动态和生理上相关的高阶相互作用。基本挑战是由于缺乏染色质工具来标记本质上异质的染色质，有限的时空分辨率来监视高度浓缩和动态的分子交易，以及定量和严格的方法缺乏提取基因组基础基本规则的基本物理规则监管过程。在这个项目中，我们计划通过从根本上发起来克服这些原始挑战鲁棒，高效和多重染色质标记策略的独特技术发展细胞染色质生物学，这将使我们能够应用它们来解决ECDNA的基本调节癌症基因组。我们将整合先进的成像，尖端显微镜，现代合成基因组工程和光学/遗传扰动系统地研究eCDNA的基本机制策划大量的癌基因转录，广泛的染色体重塑和不对称隔离迄今通过常规生化，遗传或基因组方法可纠缠的棘手。这些剪裁的积极结果 - 边缘方法和我们提案中嵌入的高风险高回报问题将具有变革性对癌症基因组调节的机械解剖的影响，可能有助于我们发现阿喀琉斯的脚跟这是针对以ECDNA驱动的癌症为目标的，从而对人类健康产生了广泛的积极影响。