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

表观基因组的综合分析以了解造血系统恶性肿瘤的分子基础

• 批准号: 10360961
• 负责人: Avi Srivastava
• 金额: $ 8.97万
• 依托单位: NEW YORK GENOME CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-15 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10360961
• 关键词: Address; Awareness; Bone Marrow; Cancer Biology; Cell Differentiation process; Cell Surface Proteins; Cell physiology; Cells; Chromatin; Computer Models; Computing Methodologies; Data; Development; Development Plans; Enhancers; Environment; Epigenetic Process; Event; Gene Expression; Genetic Transcription; Genome; Goals; Grouping; Hematopoiesis; Hematopoietic; Hematopoietic Neoplasms; Histones; Impairment; Investigation; Learning; Link; Malignant - descriptor; Malignant Neoplasms; Maps; Measurement; Mentorship; Modality; Modeling; Molecular; Mus; New York; Occupations; Pattern; Peripheral Blood Mononuclear Cell; Pilot Projects; Play; Polycomb; Process; Regulator Genes; Regulatory Element; Repression; Research; Research Personnel; Research Project Summaries; Research Proposals; Role; Scientist; System; Technology; Training; Transferase; Variant; Wild Type Mouse; anti-cancer; base; career; career development; cell fate specification; cell type; computational suite; computer framework; computerized tools; design; epigenome; epigenomics; experimental study; gene regulatory network; hematopoietic differentiation; histone methylation; histone methyltransferase; histone modification; improved; in silico; leukemia; loss of function; mouse model; multidisciplinary; multimodality; novel; promoter; single cell proteins; single cell technology

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.

项目概要 研究计划：造血分化过程受损是骨髓恶性肿瘤的基础，例如 白血病，但我们仍然缺乏对监管事件序列的机制理解，从而误导了人们 分化过程。由于表观基因组调控模式是白血病发展的主要特征， 了解失败（恶性）造血分化过程的染色质动力学可能会有所帮助 定义白血病的分子基础。这种理解的先决条件是一个允许 研究造血过程中调节元件（RE）活性的渐进变化 差异化。单细胞 CUT&Tag (scCUT&Tag) 技术非常适合 RE 活性等研究 通过组蛋白修饰谱可以以谱系特异性的方式进行研究。然而，穷 了解细胞类型特异性组蛋白修饰模式使这项任务具有挑战性。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 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式联运 框架来研究造血过程中的 RE 及其活动的渐进变化。首先，我将定义 小鼠造血的多模式参考图谱框架。这个框架将使我能够整合 将多个组蛋白修饰谱分析到一个参考上，并比较 RE 之间的染色质状态 野生型 (WT) 和组蛋白甲基转移酶 (HMT) 功能丧失的小鼠模型（目标 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 动态链接各个发展轨迹的 RE 的地图。我将使用这个框架来调查 由于 HMT 损失而导致 RE 相互作用发生变化（目标 2）。第三，由于细胞的转录状态出现 从底层基因调控网络（GRN）中，我将把单细胞基因表达数据与组蛋白整合起来 修改配置文件并将其扩展以定义 GRN 的染色质状态感知模型。我将比较 WT 和 HMT 损失实验并定义差分 GRN（目标 3）。总而言之，本研究提案旨在 开创了多模式单细胞组蛋白修饰综合分析的计算方法 并系统地剖析监管电路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误导造血分化 造血室。我制定了 5 年职业发展计划，以实现成为 计算癌症生物学多学科领域的独立研究者。辅导 委员会还将为我的研究和学术求职提供指导。鉴于优秀的 培养多名独立科学家的杰出记录，纽约基因组中心为我提供了一个理想的 实现我的科学职业目标的环境。