Dynamic 3D chromatin remodeling in acute leukemia - Resubmission - 1

急性白血病的动态 3D 染色质重塑 - 重新提交 - 1

• 批准号: 10210969
• 负责人: Aristotelis Tsirigos
• 金额: $ 61.29万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-01 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10210969
• 关键词: 3-Dimensional; Acute; Acute Lymphocytic Leukemia; Acute T Cell Leukemia; Acute leukemia; Address; Affect; Architecture; Automobile Driving; Binding; Biological; CRISPR interference; CRISPR/Cas technology; Cancer Patient; Cell Maintenance; Child; Chromatin; Chromatin Loop; Clustered Regularly Interspaced Short Palindromic Repeats; Computing Methodologies; DNA; Diagnosis; Disease; Disease remission; Dissection; Downstream Enhancer; Drug resistance; Enhancers; Epigenetic Process; Event; Evolution; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Enhancer Element; Glioblastoma; Growth; Hi-C; Human; Hypermethylation; IGF1R gene; In Vitro; Large-Scale Sequencing; Light; MYC gene; Malignant Neoplasms; Maps; Mediating; Methods; NOTCH1 gene; Neighborhoods; Oncogenes; Oncogenic; Outcome; Pathway interactions; Patients; Pharmaceutical Preparations; Pharmacotherapy; Point Mutation; Prognosis; Property; Recurrence; Regulation; Regulator Genes; Regulatory Element; Relapse; Resistance; Role; Sampling; Structure; T-Cell Development; Techniques; Technology; Testing; Thymus Gland; Time; Transcriptional Regulation; Treatment outcome; Tumor Suppressor Proteins; Untranslated RNA; Validation; base; cancer initiation; chromatin remodeling; chromosome conformation capture; cohort; differential expression; drug relapse; genome-wide; in vivo; insight; leukemia; metaplastic cell transformation; new therapeutic target; novel; novel marker; novel strategies; pediatric acute leukemia; promoter; relapse patients; targeted treatment; therapy resistant; tool; transcription factor; treatment response

ABSTRACT Recent advances in chromatin conformation capture techniques have revolutionized our understanding of chro- matin organization and have provided novel insights at an unprecedented level of detail. Several studies have identified biologically-relevant structures in DNA-DNA contact maps, such as A/B compartments, topologically- associating domains (TADs), insulated neighborhoods, and have elucidated the role of chromatin architecture in gene regulation and maintenance of cell identity. A handful of very recent studies from our lab and others have shown that aberrant TAD activation or “rewiring” promoter-enhancer interactions can promote cancer growth. However, no study has yet addressed the disruptions of chromatin organization on a genome-wide scale in cancer patients or how such disruptions modify the promoter-enhancer landscape leading to drug resistance and relapse. Using primary acute leukemia patient samples, we have, for the first time, identified recurrent TAD disruptions in leukemia involving key oncogenes (e.g. NOTCH1, MYC) and their targets. For example, we iden- tified a recurrent disruption of 3D chromatin topology in the MYC locus at a previously uncharacterized non- coding CTCF-bound region that insulates MYC from downstream enhancers. This disruption enables chromatin interactions between the MYC oncogene and the downstream enhancers leading to an increase in MYC expres- sion. Based on our preliminary results, we propose to investigate 3D chromosomal landscape reorganization as a new mechanism of cancer initiation, progression and relapse, and to discover novel non-coding regulatory elements (enhancer 3D hubs and their TAD boundaries) that drive leukemia. To this end, we will first profile and analyze a large cohort of leukemia patients using Hi-C and H3K27ac HiChIP both at diagnosis and at relapse to identify recurrent relapse-specific 3D reorganization events. We will combine computational methods with or- thogonal CRISPR strategies to discover transcription factors and epigenetic modifiers that enable the emergence of drug resistance via the rewiring of enhancer-promoter chromatin looping. We will then focus on enhancer hubs: we and others have shown that enhancers that are densely connected with target promoters and other enhancers (i.e. enhancer hubs) are robust regulators of gene expression and their disruption can impact the regulation of multiple genes. Based on these findings, we will test whether such enhancer hubs and their 3D topology can be drivers of drug resistance by activating oncogenic loci in vitro and in vivo. Our proposed study will not only elucidate the role of 3D architecture in leukemia at diagnosis and relapse, but it will also advance our understanding of resistance to therapy and develop new approaches to overcome it.

抽象的 染色质构象捕获技术的最新进展彻底改变了我们对染色质的理解 matin 组织并以前所未有的详细程度提供了新颖的见解。多项研究已 在 DNA-DNA 接触图中识别出生物学相关的结构，例如 A/B 区室，拓扑结构 关联域（TAD）、绝缘邻域，并阐明了染色质结构在 基因调控和细胞特性的维持。我们实验室和其他实验室最近的一些研究表明 研究表明，异常的 TAD 激活或“重新布线”启动子-增强子相互作用可以促进癌症生长。 然而，尚未有研究解决全基因组范围内染色质组织的破坏问题。 癌症患者或这种破坏如何改变启动子增强子景观导致耐药性和 复发。使用原发性急性白血病患者样本，我们首次确定了复发性 TAD 涉及关键癌基因（例如 NOTCH1、MYC）及其靶标的白血病破坏。例如，我们认为—— 证实了 MYC 位点中 3D 染色质拓扑结构的反复破坏，处于先前未表征的非 编码 CTCF 结合区域，将 MYC 与下游增强子隔离。这种破坏使染色质 MYC 癌基因和下游增强子之间的相互作用导致 MYC 表达增加 锡安。根据我们的初步结果，我们建议研究 3D 染色体景观重组： 癌症发生、进展和复发的新机制，并发现新的非编码调控 驱动白血病的元素（增强子 3D 中心及其 TAD 边界）。为此，我们首先要介绍和 使用 Hi-C 和 H3K27ac HiChIP 分析一大群白血病患者的诊断和复发情况 识别复发性复发特异性 3D 重组事件。我们将把计算方法与 or- 正交 CRISPR 策略发现转录因子和表观遗传修饰剂，使出现 通过增强子-启动子染色质环的重新布线来抑制耐药性。然后我们将重点关注增强剂 中心：我们和其他人已经证明，与目标启动子和其他启动子紧密相连的增强子 增强子（即增强子中心）是基因表达的强大调节剂，它们的破坏可能会影响 多个基因的调控。基于这些发现，我们将测试此类增强器中心及其 3D 拓扑结构可以通过激活体外和体内致癌位点来驱动耐药性。我们提出的研究 不仅将阐明 3D 架构在白血病诊断和复发中的作用，而且还将推进 我们对治疗耐药性的理解并开发新的方法来克服它。