Clonal analysis of cancer by mitochondrial DNA barcoding

通过线粒体 DNA 条形码对癌症进行克隆分析

• 批准号: 10612155
• 负责人: Vijay Ganesh Sankaran
• 金额: $ 46.3万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-11 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10612155
• 关键词: ATAC-seq; Acute Myelocytic Leukemia; Architecture; Bar Codes; Biological Assay; Biological Process; Blood Cells; Cancer Biology; Cancer Patient; Cell Lineage; Cell division; Cells; Cessation of life; Chromatin; Chronic Lymphocytic Leukemia; Clinical; Clonal Evolution; Clone Cells; Communities; Complex; DNA; Development; Diagnosis; Disease Progression; Dissection; Ecosystem; Epigenetic Process; Evolution; FLT3 gene; Funding; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Generations; Genetic; Genetic Transcription; Goals; Head and Neck Cancer; Heterogeneity; Human; Individual; Knowledge; Lesion; Lifting; Malignant - descriptor; Malignant Neoplasms; Malignant neoplasm of pancreas; Measures; Messenger RNA; Methods; Mission; Mitochondrial DNA; Modality; Molecular; Mutate; Mutation Analysis; Myeloproliferative disease; Nuclear; Outcome; Output; Patients; Pattern; Performance; Population; Positioning Attribute; Procedures; Production; Public Health; Recurrence; Recurrent disease; Relapse; Research; Research Personnel; Resistance; Resolution; Sampling; Shapes; Solid Neoplasm; Structure; System; Technology; Tumor Biology; United States National Institutes of Health; Variant; Work; anticancer research; cancer cell; cancer therapy; cell type; cohort; driver mutation; epigenome; epigenomics; experience; heteroplasmy; improved; in vitro Assay; in vitro Model; innovation; insight; leukemia; mRNA Expression; multiple omics; neoplastic cell; novel therapeutic intervention; programs; single cell analysis; single cell sequencing; therapy resistant; tool; transcriptome; transcriptome sequencing; tumor; tumor eradication

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.

项目摘要/摘要 所有肿瘤都包含不同细胞类型的混合物。在恶性细胞种群中，克隆进化 导致具有不同遗传病变的克隆的出现，各种生物学过程形成 具有特定转录/表观遗传学特征的不同细胞状态的共发生 风景。这种异质性是通过 治疗，导致疾病复发，这是一个主要的临床挑战。更好地了解克隆 原发性人类肿瘤中的结构和转录/表观遗传态，对 以单细胞分辨率全面介绍这些方式的技术。 pi/pds彼得 Van Galen和Vijay Sankaran率先使用线粒体DNA（mtDNA）变体作为 天然存在的细胞条形码以重建细胞之间的克隆关系，并证明 转录（SCRNA-SEQ）和表观遗传（SCATAC-SEQ）细胞状态的同时分析。像这样， 它们是独特的位置，可以意识到这些技术照亮复杂肿瘤的潜力 生态系统并确定不同恶性细胞类型的漏洞。这个长期目标 研究是指导可以有效消除异质肿瘤的新治疗方法 细胞。总体目的是建立可以在各种范围内使用的能力技术 肿瘤改变了我们对癌症生物学的理解。博士。范·盖伦（Van Galen）和桑卡兰（Sankaran），由 强大的合作者网络将通过两个具体目标共同致力于这一目标：1） 提前和验证实验方法同时剖析转录组表观基因组， 癌症中的克隆结构和2）急性髓样白血病克隆的原则分析证明 诊断随后驱动复发。在第一个目标中，调查人员将以他们最近的作用为基础 成就建立优化和经过验证的程序，以进行主要分析 人类癌细胞采取明确的性能度量。在第二个目标中，配对的诊断 - 释放 将分析来自明确定义的急性髓样白血病患者的样本以证明 与转录/表观遗传细胞的克隆进化的纵向模式的同时解剖 国家 - 该技术的主要原则证明。通过自然利用这种方法是创新的 发生mtDNA变体以将克隆关系分层到单细胞的当前最新测定 分析。拟议的研究很重要，因为该项目的成功完成将 为科学界配备用于综合分子/细胞表征的新工具 癌症。预期的输出是一种可重复的可靠方法，用于单细胞分析原主 人类癌细胞的三种核心方式，产生转录，表观遗传和克隆分辨率。 这将为NCI资助的一系列肿瘤系统中的项目启用。