Decoding glioma evolution and progression by multi-dimensional single-cell profiling

项目总结/摘要 研究计划：肿瘤演变是癌症治疗的根本障碍，因为恶性细胞适应 治疗和进展期间的变化。了解这些适应性不仅是识别 脆弱的基因靶点，但也在最佳时间窗口期间进行干预， 不明显花瓣绘制这种进化的图表需要了解驱动或 伴随疾病进展，但这些在许多恶性肿瘤中很大程度上是未映射的。一个恰当的例子是扩散 神经胶质瘤是一种无法治愈的脑癌，由不同的细胞状态组成，这些细胞状态在相对 在神经胶质瘤进展过程中的丰度，最终改变对治疗的反应。解码神经胶质瘤的努力 进化是有限的：虽然我们已经描述了不同的胶质瘤细胞状态，但我们还没有发现它们的特征。 遗传和表观遗传驱动因素或测量这些因素如何影响整个进展过程中的细胞状态丰度。到 为此，我们开发了新颖的单细胞技术，以同时在同一细胞中进行分析，i） 转录组和表观基因组（具体地，DNA甲基化）和ii）转录组和基因组（DNA 突变）以前所未有的检测率。 首先，通过结合基因型和细胞状态数据，我将定义体细胞突变如何失调 转录模式，导致细胞状态（目的1a），并表征体细胞突变如何决定 胶质瘤谱系结构（Aim 1b）。通过结合我的博士后工作-描述表观遗传如何 多样化有助于转录组的多样性-我将创建第一个神经胶质瘤的多维模型 进化第二，我将使用我们的方法来测量单细胞DNA甲基化和转录谱， 从同一患者身上纵向采集的样本。这将检验一个假说，即表观遗传失调 模式有助于胶质瘤的进展，它不仅将提供胶质瘤的多维模型， 进展，但也将提供表观遗传标记，以跟踪临床进展（目标2）。最后要 通过设计一种推断细胞状态组成、进展和 基于来自常规进行的批量DNA甲基化测定的数据， 诊所（目标3）。这些研究将为新型胶质瘤治疗，准确诊断和最佳治疗铺平道路。 治疗的时机。 职业发展计划：我已经制定了一个5年的职业发展计划，以实现我成为一名 癌症生物学独立研究者，专注于肿瘤进展的内在决定因素， 对治疗的反应我已经组建了一个由该领域领导人组成的指导委员会，我将与他们一起培训 填补多组学进化中剩余的知识空白，以及如何利用我的研究结果来支持临床 在乎最后，布罗德研究所是实现我的科学和职业目标的理想环境， 鉴于其杰出的研究社区和培训独立科学家的记录。

PROJECT SUMMARY / ABSTRACT Research Plan: Tumor evolution is a fundamental obstacle to cancer treatment, as malignant cells adapt to treatment and change during progression. Understanding these adaptations is key to not only identifying vulnerable gene targets, but also intervening during the optimal time window, before the targets become obsolete. Charting this evolution requires understanding the genetic and epigenetic events that drive or accompany disease progression, but these are largely unmapped in many malignancies. A case in point is diffuse glioma, an incurable brain cancer composed of distinct cellular states that dramatically change in relative abundance during glioma progression, ultimately changing the response to treatment. Efforts to decode glioma evolution have been limited: while we have characterized the distinct glioma cell states, we have not found their genetic and epigenetic drivers or measured how these affect cell states abundance throughout progression. To this end, we have developed novel single-cell technologies to concurrently profile in the same cell i) the transcriptome and epigenome (specifically, DNA methylation) and ii) the transcriptome and genome (DNA mutations) at an unprecedented detection rate. First, by combining genotype with cellular state data, I will define how somatic mutations dysregulate transcriptional patterns, resulting in cellular states (Aim 1a), and characterize how somatic mutations dictate glioma lineage structure (Aim 1b). By combining this with my postdoctoral work – characterizing how epigenetic diversification contributes to transcriptomic diversity – I will create the first multi-dimensional model of glioma evolution. Second, I will use our method to measure single-cell DNA methylation and transcriptional profiles in samples taken longitudinally from the same patients. This will test the hypothesis that dysregulated epigenetic patterns contribute to glioma progression, and it will not only provide a multi-dimensional model of glioma progression, but will also provide epigenetic markers to track progression in the clinic (Aim 2). Finally, I will improve diagnosis in the clinical setting by designing a tool that infers cell state composition, progression and likely response to treatment based on data from the bulk DNA methylation assay that is routinely done in the clinic (Aim 3). These studies will pave the way towards novel glioma treatments, accurate diagnoses and optimal timing of treatment. Career Development Plan: I have outlined a 5-year career development plan to meet my goal of becoming an independent investigator in cancer biology who focuses on intrinsic determinants of tumor progression and response to treatment. I have assembled a Mentorship Committee of leaders in the field, with whom I will train to close remaining knowledge gaps in multi-omics evolution and how to leverage my results to support clinical care. Finally, the Broad Institute constitutes the ideal environment for attaining my scientific and career goals, given their outstanding research communities and track records of training independent scientists.