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.

项目摘要 /摘要 癌症的破坏世界主要源自肿瘤细胞进化的能力。转移， 免疫进化，耐药性甚至肿瘤发生本身就是进化过程。我们的 对肿瘤演化的理解是不完整的，某些癌症能够进化的能力证明 快速响应治疗而不是与经典遗传学兼容。更全面的分子 了解肿瘤演化如何改善癌症治疗的关键。 最近的工作表明，牙外DNA（ECDNA）上的癌基因扩增是主要的 肿瘤进化的驱动因素，治疗性耐药性和患者的预后不佳。这些圆形DNA是 敏感，长期以来一直认为在细胞分裂上不对称地分离，导致肿瘤内 异质性。我们最近证明了情况，但是我们对确切机制的理解 eCDNA驱动肿瘤进化仍然有限。在这个项目中，约翰·罗斯（John Rose）博士旨在进步 我们通过前所未有的良好控制实验研究对癌症进化中的ECDNA的理解 ecdna。首先，通过一种新颖的方法来对活细胞中的每个ECDNA进行映射，我将描述ecdna 在将这些发现扩展到Organoid之前 ECDNA+患者样品的模型和分析（AIM 1B）。其次，我将确定影响eCDNA的基因， 使用高通量CRISPR筛选策略，促进或抑制肿瘤细胞中的核心 （目标2）。最后，我将表征EcdNA独特可访问的染色质结构的开发， 阐明其病因（目标3）。这些研究将大大改善我们对ecdna的理解 在肿瘤演化中，同时确定了用于治疗干预的推定途径。 这项工作将在斯坦福大学的世界一流培训环境中进行 霍华德·张博士（Howard Chang）博士是癌症研究的专家，博士 保罗·米歇尔（Paul Mischel），牙外DNA的专家。由领导人组成的咨询委员会 肿瘤进化，计算生物学，高级细胞成像，高通量CRISPR屏幕和癌症 Organoid模型将提供更多的专业知识和指导。每个目标的前半部分将完成 主要是在奖励的K99阶段，为完成R00的目标提供了一个平台 阶段。

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