Integrated analyses of the epigenome to understand the molecular basis of hematopoietic malignancies

项目摘要 研究计划：造血分化过程受损是骨髓恶性肿瘤的基础， 白血病，但我们仍然缺乏对误导白血病的调节事件序列的机械理解 分化过程。由于表观基因调控模式是白血病发展的主要特征， 了解造血细胞分化过程失败（恶性）的染色质动力学有助于 定义白血病的分子基础这种理解的先决条件是一个框架， 研究造血过程中调节元件（RE）活性的进行性变化 分化单细胞CUT&Tag（scCUT&Tag）技术非常适合RE活性等研究 通过组蛋白修饰，可以以谱系特异性的方式研究谱。然而，穷 对细胞类型特异性组蛋白修饰模式的理解使得该任务具有挑战性。克服 为了应对这一挑战，我们设计了scCUT&Tag-pro，它可以同时测量细胞表面蛋白质 以及基因表达和染色质可及性的计算机集成。我将利用这种新颖的多模态 研究RE的框架和造血过程中其活性的渐进变化。首先，我将定义 用于小鼠造血的多模式参考映射框架。这个框架将允许我整合 将多个组蛋白修饰谱加到一个参考上，并比较RE的染色质状态， 组蛋白甲基转移酶（HMT）功能丧失的野生型（WT）和小鼠模型（Aim 1）。第二、 因为HMT通过RE的相互作用网络调节转录。我将定义一个染色质状态感知 地图动态链接跨越发展轨迹的可再生能源。我将使用这个框架来研究 由于HMT损失，RE相互作用的变化（目标2）。第三，由于细胞的转录状态 从潜在的基因调控网络（GRN），我将整合单细胞基因表达数据与组蛋白 修改配置文件，并将其扩展到定义GRN的染色质状态感知模型。我将比较WT和 HMT损失实验和定义差分GRN（目标3）。总而言之，这项研究计划旨在 开创了多模式单细胞组蛋白修饰综合分析的计算方法 并系统地剖析了调节回路的系统级功能的渐进变化， 使用条件性HMT功能丧失的小鼠模型， 造血区室我已经制定了一个5年的职业发展计划，以实现我的目标， 计算癌症生物学多学科领域的独立研究者。营商友导 委员会也将为我的研究和学术求职提供指导。鉴于优秀的， 纽约基因组中心在培训多名独立科学家方面有着出色的记录，它为我提供了一个理想的 环境来实现我的科学职业目标。

PROJECT SUMMARY Research Plan: An impaired hematopoietic differentiation process underlies bone marrow malignancies like leukemia, but we still lack the mechanistic understanding of the sequence of regulatory events that misleads the differentiation process. Since epigenomic regulatory patterns are major features of leukemic development, understanding the chromatin dynamics of a failed (malignant) hematopoietic differentiation process can help define the molecular basis of leukemia. A prerequisite to such an understanding is a framework that allows investigation of the progressive changes in the activity of the regulatory elements (RE) during hematopoietic differentiation. Single-cell CUT&Tag (scCUT&Tag) technology is well-suited for such studies as RE activity through histone modification profiles can be investigated in a lineage-specific manner. However, poor understanding of the cell-type-specific histone modification patterns makes the task challenging. To overcome this challenge, we designed scCUT&Tag-pro which allows simultaneous measurement of cell-surface protein and in-silico integration of gene-expression and chromatin accessibility. I will leverage this novel multimodal framework to investigate the RE and progressive changes in their activity during hematopoiesis. First, I will define a multimodal reference mapping framework for mouse hematopoiesis. This framework will allow me to integrate multiple histone modification profiles onto one reference and compare the chromatin states of the RE between a wild type (WT) and mouse model with loss of function in histone methyl transferase (HMT) (Aim 1). Second, since HMTs regulate transcription through the interaction network of RE. I will define a chromatin state aware map that dynamically links REs across developmental trajectories. I will use this framework to investigate the changes in the interaction of REs due to HMT loss (Aim 2). Third, since the transcriptional state of a cell emerges from the underlying gene regulatory network (GRN), I will integrate single-cell gene expression data with histone modification profiles and extend it to define a chromatin state aware model of GRN. I will compare the WT and HMT loss experiments and define the differential GRN (Aim 3). Altogether, this research proposal seeks to pioneer the computational methods for the integrated analyses of multimodal single-cell histone modifications and systematically dissect progressive changes in the system-level function of the regulatory circuits that misleads hematopoietic differentiation using mouse models with conditional HMT loss of function in the hematopoietic compartment. I have developed a 5-year career development plan to meet my goal of becoming an independent investigator in the multi-disciplinary field of computational cancer biology. The mentorship committee will also provide me the guidance in my research and academic job search. Given the excellent the outstanding record of training multiple independent scientists, New York Genome Center provides me an ideal environment to attain my scientific career goals.