Remodeling of 3D chromatin in B cell acute leukemia and its impact on clinical outcome

摘要 虽然儿童急性淋巴细胞白血病(ALL)的预后在过去的几年中有了显著的改善 过去40年，主要挑战仍然存在，包括传统疗法的负担和在以下方面进展较慢 主要亚群使其成为导致儿童癌症死亡的主要原因之一。因此，有针对性的，更有效的- 迫切需要对症治疗。目前的项目建立在我们最近涉及表观基因组的研究的基础上 在转变和对治疗的反应中。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组织的理解，并提供了全新的见解- 细节层次凹陷。几项研究已经确定了DNA-DNA接触图中的生物相关结构， 例如A/B隔间、拓扑关联区域(TADS)和绝缘邻域，并具有 阐明了染色质结构在基因调控和维持细胞特性中的作用。一小撮 我们实验室和其他实验室最近的研究表明，异常的TAD激活或重新连接启动子- 增强子的相互作用可以促进癌症的生长。然而，目前还没有研究解决Chro-2的干扰。 癌症患者全基因组范围内的配对组织，或者这种干扰如何改变启动子- 导致白血病启动、治疗耐药和复发的增强子格局。这项研究的目的是- 通过比较B ALL样本和正常B前体细胞中的染色质景观来填补这些缺口 确定与变化相关的染色质结构，并绘制地形变化的演变图 从诊断到复发，使用配对样本来发现与肿瘤进展相关的3D变化。在……里面 根据初步数据，我们已经分析了诊断/复发样本匹配的12名患者的一小部分试点队列。 在这个小队列中，我们已经在多个水平上确定了染色质重组事件：间隔室 开关，TAD内染色质相互作用的变化，增强子-启动子环的建立和结构 直接影响3D拓扑的更改。这些变化将在临床前模型中得到验证，使用基因 体外和体内的工程细胞系以及患者来源的异种移植(PDX)。最后，为了研究 启动子-增强子环的亚克隆组成我们将使用单细胞DNA/RNA FISH，并将使用相同的 跟踪PDX模型演变的方法。

ABSTRACT While the outcomes for children with acute lymphoblastic leukemia (ALL) have improved dramatically over the past four decades, major challenges remain including the burden of conventional therapy and less progress in major subgroups making ALL one of the leading causes of cancer death in children. Thus, targeted, more effec- tive therapies are urgently needed. The current project builds on our recent studies implicating the epigenome in transformation and response to therapy. Recent advances in chromatin conformation capture techniques have revolutionized our understanding of chromatin organization and have provided novel insights at an unprece- dented level of detail. Several studies have identified biologically-relevant structures in DNA-DNA contact maps, such as A/B compartments, topologically-associating domains (TADs), and 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 chro- matin organization on a genome-wide scale in cancer patients or how such disruptions modify the promoter- enhancer landscape leading to leukemia initiation and therapy resistance and relapse. This study aims to ad- dress these gaps by comparing the chromatin landscape in B ALL samples and normal B precursor cells to identify chromatin architecture associated with transformation and to chart the evolution of topographic changes from diagnosis to relapse using paired samples to discover 3D alterations associated with tumor progression. In preliminary data, we have analyzed a small pilot cohort of 12 patients with matched diagnosis/relapse samples. In this small cohort, we have already identified chromatin reorganization events at multiple levels: compartment switches, changes in intra-TAD chromatin interactions, establishment of enhancer-promoter loops and structural alterations that directly affect 3D topology. Such changes will be validated in preclinical models using genetically engineered cell lines in vitro and in vivo as well as patient derived xenografts (PDX). Finally, to examine the subclonal composition of promoter-enhancer loops we will use single cell DNA/RNA FISH and will use the same methodology to track evolution in PDX models.