Single-cell genomic approaches to study the cellular origins of brain tumors

摘要摘要 由于脑瘤的多样性、患病率和贫乏，脑瘤造成了巨大的疾病负担。 治疗反应差，发病率和死亡率高。美国有50多万人 有原发性脑瘤或其他中枢神经系统肿瘤的人，大约有8万个新肿瘤是 每年都会确诊。然而，脑瘤的起源-即每个大脑来自的特定细胞类型 肿瘤的产生仍然是个谜，在我们对它们的生物学理解中，它是一个根本未知的东西。这 该项目将通过开发一种新的单细胞基因组学技术来解决这一重大差距，以鉴定 脑瘤的起源。动物模型表明，“起源细胞”的表型--第一个 获得启动肿瘤的基因突变-通常在确定后续肿瘤中起主要作用 表型和行为。起源细胞的表观遗传遗产可能在人脑肿瘤中发挥作用 但是，由于一项重大的技术手段，目前还不可能确定肿瘤细胞的来源。 局限性--缺乏一种系统地追踪人体组织细胞谱系的方法。我们会 通过三个相关目标应对这一研究挑战：1)开发一种新的单细胞技术，称为 Tapestry首次能够从人体组织重建高分辨率的谱系树。 Tapestry将通过选择性地捕获数十个自发发生的体细胞突变来实现这一点 数千个单细胞，同时描绘相同单细胞的转录本，从而 允许以可行的成本重建表型注释的谱系树；2)应用 Tapestry将正常大脑皮层中的祖细胞谱系分类作为参考， 然后识别该层级中单个脑肿瘤的起源细胞和早期谱系。 这一目标将集中在三种可能有不同起源细胞的肿瘤类型：胶质母细胞瘤(最常见和 最致命的恶性脑瘤)、间变性少突胶质瘤和原始神经外胚层肿瘤；3) Tapestry识别的早期肿瘤谱系的原位空间映射以了解它们是否占据 肿瘤内的特定区域以及它们是否有助于肿瘤的迁移和侵袭。总体而言，这项工作 将提供对脑肿瘤病因学中一个重要的未知因素-起源细胞-的洞察，我们 假说在肿瘤生物学中扮演着一个重要但未被充分认识的角色。识别起源细胞将 改变我们对脑瘤发生的地点和时间，其表型多样性，以及 重要的是，可以促进更早的检测，创造新的动物模型，以及血统的设计- 有针对性的治疗。此外，这里开发的技术有可能对癌症产生重大影响。 生物学和发育生物学更广泛的研究。

Summary Abstract Brain tumors are responsible for an immense burden of disease due to their diversity, prevalence, poor response to therapies, and high morbidity and mortality. More than half a million people in the United States have a primary brain tumor or other central nervous system tumor, and about 80,000 new tumors are diagnosed each year. However, the origins of brain tumors— i.e. the specific cell type from which each brain tumor arises— remains enigmatic and is a fundamental unknown in our understanding of their biology. This project will address this major gap by developing a novel single-cell genomics technology to identify the cells of origin of brain tumors. Animal models have shown that the phenotype of the “cell of origin”— the first cell that acquires the genetic mutations to initiate a tumor— often plays a major role in determining subsequent tumor phenotype and behavior. The epigenetic legacy of the cell of origin is likely at play in human brain tumors as well, but the identification of tumor cells of origin has not been possible due to a major technological limitation— the absence of a method for systematically tracing lineages of cells in human tissues. We will address this research challenge via three related aims: 1) Development of a novel single-cell technology called TAPESTRY capable of reconstructing high-resolution lineage trees from human tissues for the first time. TAPESTRY will achieve this by selectively capturing spontaneously occurring somatic mutations in tens of thousands of single cells, while simultaneously profiling the transcriptomes of the same single cells, thereby allowing reconstruction of phenotypically annotated lineage trees at feasible costs; 2) Application of TAPESTRY to catalogue the hierarchy of progenitor cell lineages in normal cerebral cortex as a reference, followed by identification of the cells of origin and early lineages of individual brain tumors within that hierarchy. This aim will focus on three tumor types with likely different cells of origin: glioblastoma (the most common and most lethal malignant brain tumor), anaplastic oligodendroglioma, and primitive neuroectodermal tumors; 3) In situ spatial mapping of the early tumor lineages identified by TAPESTRY to understand whether they occupy specific domains within tumors and whether they contribute to tumor migration and invasion. Overall, this work will provide insight into a significant unknown factor in brain tumor etiology—the cell of origin—which, we hypothesize plays a major and under-appreciated role in tumor biology. Identifying the cell of origin would transform our understanding of why brain tumors arise where and when they do, their phenotypic diversity, and importantly, could facilitate earlier detection, the creation of new animal models, and the design of lineage- targeted therapies. Moreover, the technology developed here has the potential for major impact across cancer biology and developmental biology research more generally.