Molecular dissection of extrachromosomal DNA formation, development, and evolution

染色体外 DNA 形成、发育和进化的分子解剖

• 批准号: 10640520
• 负责人: John Christopher Rose
• 金额: $ 12.64万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-03 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10640520
• 关键词: ATAC-seq; Advisory Committees; Automobile Driving; Award; Bar Codes; Behavior; Biogenesis; Biology; CRISPR screen; CRISPR/Cas technology; Cancer cell line; Cell Line; Cell Lineage; Cell division; Cells; Centromere; Chromatin; Chromatin Structure; Chromosomal Duplication; Circular DNA; Computational Biology; Coupled; DNA; Development; Dissection; Environment; Etiology; Evolution; Frequencies; Functional disorder; Generations; Genes; Genetic; Genetic Recombination; Genetic Transcription; Genomics; Goals; Haploidy; Hour; Human; Image; Immune Evasion; Investigation; Link; Maintenance; Malignant Neoplasms; Mentorship; Methods; Modeling; Molecular; Monitor; Mutation; Nature; Neoplasm Metastasis; Oncogenes; Organoids; Outcome; Patients; Phase; Population; Postdoctoral Fellow; Process; Resolution; Resources; Role; Sampling; Stains; System; Techniques; Therapeutic; Therapeutic Intervention; Time; Tissues; Training; Tumor Promotion; Universities; Work; cancer therapy; cellular imaging; epigenomics; experimental study; extrachromosomal DNA; genetic analysis; histone modification; improved; insight; interest; live cell imaging; live cell microscopy; loss of function mutation; micronucleus; neoplastic cell; novel; novel strategies; novel therapeutic intervention; particle; pharmacologic; phenomenological models; predictive modeling; pressure; response; segregation; small molecule; theories; therapy resistant; treatment response; tumor; tumor heterogeneity; tumorigenesis

PROJECT SUMMARY / ABSTRACT The devastation wrought by cancer derives primarily from the capacity of tumor cells to evolve. Metastasis, immune evasion, treatment resistance, and even tumorigenesis itself are evolutionary processes. Our understanding of tumor evolution is incomplete, evidenced by the ability of some cancers to evolve more quickly in response to treatment than is compatible with classical genetics. A more comprehensive molecular understanding of how tumors evolve is key to improving cancer treatment. Recent work has shown that oncogene amplification on extrachromosomal DNAs (ecDNAs) is a major driver of tumor evolution, treatment resistance, and poor outcomes in patients. These circular DNAs are acentric and have long been thought to asymmetrically segregate at cell division, leading to intratumoral heterogeneity. We have recently proved this to be the case, but our understanding of the precise mechanisms through which ecDNA drives tumor evolution remains limited. In this project, Dr. John Rose aims to advance our understanding of ecDNAs in cancer evolution through unprecedented, well-controlled experimental studies of ecDNA. First, through a novel approach to image every ecDNA in living cells, I will delineate ecDNA dynamics on the level of single cells and single ecDNAs (Aim 1a), before extending these findings to organoid models and analysis of ecDNA+ patient samples (Aim 1b). Second, I will identify the genes that impact ecDNA, either promoting or inhibiting their accrual in tumor cells, using a high-throughput CRISPR screening strategy (Aim 2). Finally, I will characterize the development of ecDNAs’ uniquely accessible chromatin structure, elucidating its etiology (Aim 3). Together, these studies will dramatically improve our understanding of ecDNA in tumor evolution, while identifying putative avenues for therapeutic intervention. This work will be performed in the world-class training environment at Stanford University, under the mentorship of Dr. Howard Chang, an expert in the application of epigenomics to the study of cancer, and Dr. Paul Mischel, an expert in extrachromosomal DNA. An advisory committee composed of leaders in the fields of tumor evolution, computational biology, advanced cell imaging, high-throughput CRISPR screens, and cancer organoid models will provide additional expertise and mentorship. The first half of each aim will be completed predominantly during the K99 phase of the award, providing a platform for completion of the aims in the R00 phase.

项目总结/摘要 癌症造成的破坏主要来自肿瘤细胞的进化能力。转移， 免疫逃避、治疗抗性、甚至肿瘤发生本身都是进化过程。我们 对肿瘤演变的理解是不完整的，一些癌症的演变能力证明了这一点。 对治疗的反应比经典遗传学更快。更全面的分子 了解肿瘤如何演变是改善癌症治疗的关键。 最近的研究表明，染色体外DNA（ecDNAs）上的癌基因扩增是一个主要的 肿瘤演变的驱动因素，治疗抵抗和患者的不良结局。这些环状DNA 并且长期以来被认为在细胞分裂时不对称分离，导致肿瘤内 异质性我们最近已经证明了这一点，但我们对精确机制的理解 ecDNA驱动肿瘤进化的机制仍然有限。在这个项目中，约翰·罗斯博士旨在推动 我们通过前所未有的、控制良好的实验研究， 的ecDNA。首先，通过一种新的方法来成像活细胞中的每一个ecDNA，我将描绘ecDNA， 在将这些发现扩展到类器官之前，在单细胞和单ecDNAs水平上的动力学（Aim 1a） ecDNA+患者样本的模型和分析（目标1b）。其次，我将识别影响ecDNA的基因， 使用高通量CRISPR筛选策略， (Aim 2）。最后，我将描述ecDNAs独特的染色质结构的发展， 阐明其病因（目的3）。总之，这些研究将大大提高我们对ecDNA的理解 在肿瘤演变中，同时确定治疗干预的假定途径。 这项工作将在斯坦福大学的世界级培训环境中进行， 张博士（霍华德，表观基因组学在癌症研究中的应用专家）的指导下， Paul Mischel是染色体外DNA的专家。一个咨询委员会，由以下领域的领导人组成： 肿瘤进化、计算生物学、先进细胞成像、高通量CRISPR筛选和癌症 类器官模型将提供额外的专业知识和指导。每个目标的前半部分将完成 主要是在K99阶段的奖励，为完成R 00目标提供了一个平台 相位

项目成果

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair.

染色体外 DNA 生物发生和基因组 DNA 修复的不同途径。

• DOI: 10.1101/2023.10.22.563489
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Rose,JohnC;Wong,IvyTsz-Lo;Daniel,Bence;Jones,MatthewG;Yost,KathrynE;Hung,KingL;Curtis,EllisJ;Mischel,PaulS;Chang,HowardY
• 通讯作者: Chang,HowardY