Characterization of extrachromosomal DNAs in tumors through computational analysis of single-cell and bulk sequencing data

通过单细胞和批量测序数据的计算分析来表征肿瘤中的染色体外 DNA

• 批准号: 10302738
• 负责人: Roel GW Verhaak
• 金额: $ 40.61万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-23 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10302738
• 关键词: Address; Affect; Automobile Driving; Basic Cancer Research; Behavior; Biology; Cancer Etiology; Cancer Patient; Cell Line; Cell division; Cells; Centromere; Chromosomal Rearrangement; Chromosome Structures; Chromosome abnormality; Chromosomes; Clinical; Clinical Research; Collection; Complex; Computer Analysis; DNA; DNA Sequence; DNA Structure; DNA sequencing; Data; Data Set; Detection; Development; Diagnostic; Double Minutes; Evolution; Genetic; Genome; Genomics; Glioblastoma; Growth; Individual; Investigation; Knowledge; Light; Machine Learning; Malignant Neoplasms; Methods; Modeling; Molecular; Molecular Evolution; Molecular Profiling; Molecular Structure; Mutation; Normal Cell; Oncogenes; Patient-Focused Outcomes; Patients; Process; Public Domains; Recurrence; Resistance; Resolution; Sampling; Structure; Supervision; Testing; Therapeutic; Time; Treatment Failure; anticancer research; base; cancer therapy; cancer type; cohort; computerized tools; cost; daughter cell; design; exome; exome sequencing; extrachromosomal DNA; frontier; genetic variant; genome sequencing; improved; insight; learning classifier; neoplastic cell; novel; predictive modeling; pressure; research study; response; single cell analysis; targeted cancer therapy; therapy development; tool; transcriptome sequencing; tumor; tumor growth; tumor heterogeneity; tumor progression; whole genome

PROJECT SUMMARY Extrachromosomal DNAs (ecDNAs) are found in 40% of tumors but rarely found in normal cells. Importantly, they contain and express amplified oncogenes derived from chromosomal sequences. In contrast to the chromosomes, ecDNAs segregate unequally to daughter cells during cell division and thus can accumulate at high copy numbers in individual cells within a tumor. This contributes to intratumor heterogeneity (ITH), which can give subsets of tumor cells a selective growth advantage and enable resistance to cancer treatment. While previous studies have focused on how ITH of chromosomal mutations contributes to tumor evolution, little is known about how ecDNAs might impact tumor evolution and patient outcomes. To address how ecDNAs contribute to ITH and tumor evolution, Aim 1 will determine the ITH of ecDNAs for cell lines derived from patient-matched primary and recurrent glioblastoma tumors for which single-cell DNA sequencing (scDNA-seq) and standard bulk short-read whole-genome sequencing (WGS) data have been previously generated. To overcome the technical challenge of detecting individual ecDNAs in scDNA-seq data, we will employ an alternative supervised approach of using `breakpoints' between high-copy number segments in the scDNA-seq data as surrogates for the ecDNA breakpoints and intersect these with the identified ecDNA breakpoint sequences in the reference sets. This approach will enable us to study ecDNA-driven ITH and evolution in single cells between the cell lines derived from the longitudinal glioblastoma tumors. We will also apply this approach to existing scDNA-seq datasets to assess the presence of ecDNAs. Current computational tools used to predict ecDNAs in standard bulk short-read WGS data have limited ability to determine the ecDNA breakpoints in single cells; thus, we anticipate that our proposed approach, while conceptually simple, will have a major impact on improving our understanding of how ecDNAs evolve within the cells of a tumor. In Aim 2, a large cohort of publicly available tumor bulk WGS datasets representing multiple cancer types will be leveraged to more broadly characterize ecDNAs and their effects on tumor evolution. We will perform integrative analysis of ecDNAs and other genomic features using a large number of tumors to characterize ecDNAs and to infer the potential molecular mechanisms underlying their formation. We will build a machine learning classifier that can predict the presence of ecDNAs using non-WGS data (i.e. whole-exome and RNA sequencing) that have been a primary strategy for sequencing patient tumors, and therefore, are more widely available than WGS. We will also systematically analyze a large number of single-time point and longitudinal tumor samples to characterize the effects of ecDNAs on evolutionary selection pressures in tumors. Overall, completion of these Aims will greatly advance our understanding of ecDNAs in tumor evolution, thereby shedding light on how ecDNAs impact patient outcomes and ultimately establishing a basis for novel cancer therapeutics.

项目摘要 染色体外DNA（ecDNAs）在40%的肿瘤中发现，但在正常细胞中很少发现。重要的是， 它们含有并表达来自染色体序列的扩增的癌基因。相对于 染色体，ecDNAs在细胞分裂过程中不平等地分离到子细胞，因此可以在染色体上积累。 肿瘤内单个细胞的高拷贝数。这有助于肿瘤内异质性（ITH）， 可以使肿瘤细胞亚群具有选择性生长优势，并能够抵抗癌症治疗。而 以前的研究集中在染色体突变的ITH如何有助于肿瘤的演变，很少有 了解ecDNAs如何影响肿瘤演变和患者预后。为了解决ecDNAs 有助于ITH和肿瘤演变，Aim 1将决定来源于 患者匹配的原发性和复发性胶质母细胞瘤肿瘤，单细胞DNA测序（scDNA-seq） 和标准批量短读全基因组测序（WGS）数据已经在之前产生。到 为了克服在scDNA-seq数据中检测单个ecDNAs的技术挑战，我们将采用 在scDNA-seq中高拷贝数片段之间使用“断点”的另一种监督方法 数据作为ecDNA断裂点的替代物，并将这些数据与鉴定的ecDNA断裂点相交 序列在参考集中。这种方法将使我们能够研究ecDNA驱动的ITH和进化， 来源于纵向胶质母细胞瘤肿瘤的细胞系之间的单个细胞。我们也将应用这一点 使用现有的scDNA-seq数据集来评估ecDNAs的存在。当前的计算工具 用于预测标准批量短读WGS数据中的ecDNA的方法具有有限的确定ecDNA的能力 单细胞中的断点;因此，我们预计，我们提出的方法，而概念上简单，将有 这对提高我们对ecDNAs在肿瘤细胞内如何进化的理解产生了重大影响。在目标2中，a 代表多种癌症类型的公开可用的肿瘤块WGS数据集的大队列将被 更广泛地描述了ecDNA及其对肿瘤演变的影响。我们将执行 使用大量肿瘤来表征ecDNAs和其他基因组特征的综合分析 并推断其形成的潜在分子机制。我们要造一台机器 学习分类器，其可以使用非WGS数据（即全外显子组和RNA）预测ecDNA的存在 测序），其已经是用于对患者肿瘤进行测序的主要策略，并且因此，更广泛地应用于肿瘤细胞。 比WGS更好。我们还将系统地分析大量的单时间点和纵向 肿瘤样本，以表征ecDNAs对肿瘤中进化选择压力的影响。总的来说， 这些目标的完成将极大地推进我们对ecDNAs在肿瘤演变中的理解，从而 阐明了ecDNAs如何影响患者的预后，并最终为新型癌症奠定了基础。 治疗学