Clonal analysis of cancer by mitochondrial DNA barcoding

项目摘要/摘要 所有的肿瘤都含有不同细胞类型的混合物。在恶性细胞群体中，克隆性进化 导致了具有不同遗传损伤和不同生物过程形状的克隆的出现 以特定转录/表观遗传为特征的不同细胞状态的共存 风景画。这种异质性是小群肿瘤细胞通过 治疗，导致疾病复发，这是一项重大的临床挑战。为了更好地了解克隆 在原发人类肿瘤的结构和转录/表观遗传状态中，存在着尚未满足的需求 以单细胞分辨率全面描述这些模式的技术。私人侦探/私人侦探彼得 Van Galen和Vijay Sankaran率先使用线粒体DNA(MtDNA)变体作为 自然产生的细胞条形码，以重建细胞之间的克隆关系，并展示 同时分析转录(scRNA-seq)和表观遗传(scatac-seq)细胞状态。因此， 他们处于独特的地位，可以实现这些技术的潜力来照亮复杂的肿瘤 生态系统和识别不同类型的恶性细胞的脆弱性。这样做的长期目标是 研究是指导能够有效根除异质肿瘤的新的治疗方法 细胞。总体目标是建立可广泛使用的支持技术 肿瘤改变了我们对癌症生物学的理解。Van Galen博士和Sankaran博士，由 强大的合作者网络，将通过两个具体目标共同努力实现这一目标：1) 提出并验证同时解剖转录组、表观基因组、 和癌症中的克隆结构以及2)急性髓系白血病克隆的原则证明描述 随后会导致复发的诊断。在第一个目标中，调查人员将在最近的基础上 在建立优化和有效的初级保健多组体分析程序方面取得的成就 具有明确性能衡量标准的人类癌细胞。在第二个目标中，配对诊断-复发 来自定义明确的急性髓系白血病患者队列的样本将被分析以证明 转录/表观遗传细胞克隆进化纵向模式的同步解剖 国家--这项技术的关键原则证明。这种方法是创新的，通过自然地利用 出现mtDNA变异以将克隆关系层叠到当前最先进的单细胞分析方法上 分析。拟议的研究具有重要意义，因为该项目的成功完成将 为科学界配备全面的分子/细胞表征的新工具 癌症的威胁。预期的输出是一种可重复的、可靠的方法，用于初级细胞分析 人类癌细胞在三种核心模式下，产生转录、表观遗传和克隆分辨率。 这将使NCI资助的一系列肿瘤系统项目成为可能。

Project Summary/Abstract All tumors contain a mixture of different cell types. Within the malignant cell population, clonal evolution leads to the emergence of clones with different genetic lesions, and various biological processes shape the co-occurrence of different cell states that are characterized by specific transcriptional/epigenetic landscapes. This heterogeneity underlies the persistence of small populations of tumor cells through treatment, leading to disease recurrence, which is a major clinical challenge. To better understand clonal structures and transcriptional/epigenetic states in primary human tumors, there is an unmet need for technologies that comprehensively profile these modalities at single-cell resolution. The PI/PDs Peter van Galen and Vijay Sankaran have pioneered the use of mitochondrial DNA (mtDNA) variants as naturally occurring cell barcodes to reconstruct clonal relationships between cells, and demonstrate simultaneous profiling of transcriptional (scRNA-seq) and epigenetic (scATAC-seq) cell states. As such, they are uniquely positioned to realize the potential of these technologies to illuminate the complex tumor ecosystem and identify vulnerabilities of different malignant cell types. The long-term goal of this research is to guide new therapeutic approaches that can effectively eradicate heterogeneous tumor cells. The overall objective is to establish enabling technologies that can be used across a wide range of tumors to transform our understanding of cancer biology. Drs. Van Galen and Sankaran, supported by a strong network of collaborators, will jointly work towards this objective through two specific aims: 1) Advance and validate experimental methods to simultaneously dissect the transcriptome, epigenome, and clonal structures in cancer and 2) Proof-of-principle profiling of acute myeloid leukemia clones at diagnosis that subsequently drive recurrence. In the first Aim, the investigators will build on their recent accomplishments to establish optimized and validated procedures for multi-omic analysis of primary human cancer cells with clear performance measures. In the second Aim, paired diagnosis-relapse samples from a well-defined cohort of acute myeloid leukemia patients will be analyzed to demonstrate the simultaneous dissection of longitudinal patterns of clonal evolution with transcriptional/epigenetic cell states - a key proof-of-principle for this technology. The approach is innovative by leveraging naturally occurring mtDNA variants to layer clonal relationships onto current state-of-the-art assays for single-cell analysis. The proposed research is significant because the successful completion of the project would equip the scientific community with new tools for the comprehensive molecular/cellular characterization of cancer. The expected output is a repeatable, reliable approach for single-cell analysis of primary human cancer cells at three core modalities, yielding transcriptional, epigenetic, and clonal resolution. This will be enabling for NCI-funded projects in a range of tumor systems.