Clinical and genomic features of extrachromosomal circular DNA in pediatric cancer

摘要/项目总结 染色体外环状DNA（ecDNA）是基因组的结构重排，其中1个或多个基因组DNA被重排。 区域从染色体上断裂并环化，形成100 kbp-10 Mbp的无着丝粒环状DNA序列， 长度和通常含有多个基因和调控区。这些小体只存在于肿瘤细胞中 并且与异常恶性的癌症有关。尽管自2004年以来，在肿瘤组织中已经观察到了ecDNA。 20世纪60年代，最近的工作强调了ecDNA在癌基因扩增中的中心作用，并作为癌基因内的贡献者。 肿瘤异质性肿瘤内异质性是治疗抗性的主要决定因素之一， 治疗失败和癌症患者总体生存率低的主要原因之一。然而，功能 ecDNA作为儿科癌症中肿瘤异质性和耐药性驱动因素的相关性已经落后于进展 在成人肿瘤中。我们假设ecDNA是肿瘤发生、转移和对肿瘤细胞耐药的常见分子驱动因素。 儿科癌症的治疗。我们建议通过以下具体目标来检验这一假设： 目的1：确定髓母细胞瘤中ecDNA的基因组、临床和分子特征。我们将描述 多机构髓母细胞瘤患者队列和患者来源异种移植物的ecDNA结构 模型为了更好地了解ecDNA驱动的恶性肿瘤的分子机制，我们将进行全面的研究。 MB中ecDNAs的多组序列分析。 目的2：在单细胞分辨率下表征ecDNA赋予的肿瘤内拷贝数异质性。因为 由于ecDNAs缺乏着丝粒，肿瘤在每次细胞分裂时都可能获得肿瘤内拷贝数的异质性。我们 将开发检测单细胞中ecDNA的方法，并将其应用于表征成对细胞中的ecDNA异质性。 患者肿瘤和患者来源的异种移植物模型。 目的3：调查儿科癌症类型中ecDNA的基因组，临床和分子特性。我们将筛选 通过部署用于ecDNA的计算工具， 检测到大型儿科癌症基因组数据平台。我们还将利用高质量的突变 这些肿瘤已经有注释，以找到ecDNA的基因组相关性。 在这个项目完成后，我们将建立儿科癌症中ecDNA状态的预后相关性 类型，并开发了开源软件来分解单细胞水平的ecDNA异质性。

ABSTRACT/PROJECT SUMMARY Extrachromosomal circular DNA (ecDNA) is a structural rearrangement of the genome whereby 1 or more genomic regions breaks from the chromosomes and is circularized, forming an acentric circular DNA sequence 100kbp-10Mbp in length and generally containing multiple genes and regulatory regions. These bodies are found exclusively in tumor cells and are associated with exceptionally malignant cancers. Although ecDNA has been observed in tumor tissue since the 1960s, recent work has highlighted the central role of ecDNA in oncogene amplification and as a contributor to intra- tumoral heterogeneity. Intra-tumoral heterogeneity is one of the leading determinants of therapeutic resistance and treatment failure and one of the main reasons for poor overall survival in cancer patients. However, the functional relevance of ecDNA as a driver of tumor heterogeneity and drug resistance in pediatric cancers has lagged behind advances in adult tumors. We hypothesize that ecDNA is a frequent molecular driver of tumorigenesis, metastasis and resistance to treatment in pediatric cancer. We propose to test this hypothesis by the following specific aims: Aim 1: Establish the genomic, clinical, and molecular properties of ecDNA in medulloblastoma. We will characterize ecDNA structures across a multi-institutional cohort of medulloblastoma patients and patient-derived xenograft models. To better understand molecular mechanisms of ecDNA-driven malignancy, we will perform comprehensive multi-omic sequence analysis of ecDNAs in MB. Aim 2: Characterize intratumoral copy-number heterogeneity conferred by ecDNA at single-cell resolution. Because ecDNAs lack centromeres, a tumor may acquire intratumoral copy-number heterogeneity with every cell division. We will develop methods to detect ecDNA in single cells, and apply them to characterize ecDNA heterogeneity in a paired patient tumor and patient derived xenograft model. Aim 3: Survey the genomic, clinical and molecular properties of ecDNA across pediatric cancer types. We will screen for ecDNA across thousands of patients from 22 pediatric cancer types by deploying computational tools for ecDNA detection to large pediatric cancer genomic data platforms. We will also leverage the high-quality mutation annotations already available for these tumors to find genomic correlates of ecDNA. Upon completion of this project, we will have established the prognostic relevance of ecDNA status across pediatric cancer types, and developed open-source software to decompose ecDNA heterogeneity at the single-cell level.