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

摘要 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构象的理解。 马丁组织，并提供了新颖的见解，在一个前所未有的细节水平。几项研究 在DNA-DNA接触图中识别生物相关结构，如A/B区室，拓扑学- 关联结构域（TADs），绝缘的邻居，并阐明了染色质架构的作用， 基因调控和维持细胞特性。我们实验室和其他人最近的一些研究表明， 显示异常的启动子激活或“重新连接”启动子-增强子相互作用可以促进癌症生长。 然而，还没有研究在全基因组范围内解决染色质组织的破坏， 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， 复发使用原发性急性白血病患者样本，我们首次发现了复发性白血病。 涉及关键癌基因（如NOTCH 1、MYC）及其靶点的白血病破坏。例如，我们认为- 证实了MYC基因座中3D染色质拓扑结构的反复破坏， 编码CTCF结合区域，其将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， 锡永。基于我们的初步结果，我们建议研究3D染色体景观重组， 癌症发生、发展和复发的新机制，并发现新的非编码调控基因， 驱动白血病的元素（增强子3D枢纽及其边界）。为此，我们将首先分析和 分析在诊断和复发时使用Hi-C和H3 K27 ac HiChIP的白血病患者的大队列， 鉴定复发性复发特异性3D重组事件。我们将联合收割机的计算方法与或- 双基因CRISPR策略来发现转录因子和表观遗传修饰因子， 通过增强子-启动子染色质环的重新连接来产生耐药性。然后我们将专注于增强剂 hubs：我们和其他人已经表明，与靶启动子和其他启动子紧密连接的增强子， 增强子（即增强子枢纽）是基因表达的稳健调节剂，并且它们的破坏可以影响基因表达。 多基因调控。基于这些发现，我们将测试这种增强器枢纽及其3D 拓扑结构可以通过在体外和体内激活致癌基因座而成为耐药性的驱动因素。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，而且还将推动 我们对治疗耐药性的理解，并开发新的方法来克服它。

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.