Investigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomes

摘要 三维基因组组织已经成为基因正确调控的关键组成部分， 表情近年来，人们对许多基本特征的理解迅速扩大， 定义基因组在细胞内的空间组织方式，包括识别A/B等特征 区室、拓扑相关结构域和染色质环。此外，有证据表明， 改变3D基因组结构的突变可能导致人类疾病。这对于一个类来说是最明显的 突变称为结构变异，包括易位，倒位，串联重复， 删除。当这些突变破坏了对3D基因组结构至关重要的序列特征时， 拓扑相关结构域之间的边界，这可能导致增强子-启动子重新连接， 基因表达的变化和表型的后果。这种影响在两个国家都有观察到。 生殖系结构变异的背景下，有助于综合征性疾病的发展，以及体细胞 可能导致癌症的结构变异。虽然很明显，结构变异可以改变3D 基因组组织和基因表达，最近的研究，全面审查结构 变异和基因表达表明它们的关系要复杂得多。具体而言，在一个 少数情况下结构变异导致邻近基因表达的变化。因此，为什么 结构变异可以对一些人的3D基因组结构和基因表达产生巨大的影响。 而不是其他方面目前尚不清楚。本研究将探讨结构性 变异，3D基因组组织和癌症基因组中的基因表达，目的是了解 结构变异在何时何地会导致基因表达的改变， 肿瘤发生具体目标1将测试是否只有特定的基因组对诱导的结构变异敏感 通过检查3D基因组结构和基因表达的变化， 在单体型分辨的人肿瘤样品中的表达。具体目标2将使用CRISPR/Cas9基因组 工程化以评估结构变体配偶体区域对致癌基因表达的诱导的影响。 具体目标3将评估肿瘤内异质性对结构变体对3D的影响的作用 通过使用用于分析DNA甲基化和3D基因组结构的新的多组学方法的基因组结构 同时在来源于患者肿瘤样品的单细胞内。成功实现这些目标将 导致对结构变异，3D基因组组织， 癌症基因组背景下的基因调控。从长远来看，这将促进信息的使用 从结构变异和3D基因组结构中获得，用于确定患者预后和识别 癌症的新治疗靶点。

Abstract Three-dimensional genome organization has emerged as a critical component for the proper regulation of gene expression. Recent years have seen a rapid expansion of the understanding of many of the basic features that define how genomes are organized in space inside of cells, including the identification of features such as A/B compartments, Topologically Associated Domains, and chromatin loops. Furthermore, there is evidence that mutations that alter 3D genome organization can contribute to human disease. This is most evident for a class of mutations known as structural variants, which includes translocations, inversions, tandem duplications, and deletions. When these mutations disrupt sequence features that are critical for 3D genome structure, such as the boundaries between Topologically Associating Domains, this can lead to enhancer-promoter rewiring, changes in gene expression, and phenotypic consequences. Such effects have been observed both in the context of germline structural variants that contribute to syndromic disorders of development as well as somatic structural variants that can lead to cancer. While it has become clear that structural variants can alter 3D genome organization and gene expression, more recent studies that comprehensively examined structural variants and gene expression indicate their relationship is considerably more complex. Specifically, in only a minority of instances do structural variants lead to changes in expression of neighboring genes. Therefore, why structural variants can have dramatic consequences on 3D genome structure and gene expression in some contexts but not others is currently unclear. This proposal will investigate the relationship between structural variants, 3D genome organization, and gene expression in cancer genomes with the goal of understanding where and when structural variants will actually lead to changes in gene expression that may contribute to oncogenesis. Specific aim 1 will test whether only specific sets genes are sensitive to structural variant induced changes in enhancer-promoter communication by examining changes in 3D genome structure and gene expression in haplotype resolved human tumor samples. Specific aim 2 will use CRISPR/Cas9 genome engineering to evaluate the effects of structural variant partner regions on induction of oncogene expression. Specific aim 3 will assess the role of intra-tumor heterogeneity on the effects of structural variants on 3D genome structure by using novel multi-omic methods for profiling DNA methylation and 3D genome structure simultaneously within single cells derived from patient tumor samples. Successful completion of these aims will result in a deeper understanding of the relationship between structural variation, 3D genome organization, and gene regulation in the context of cancer genomes. In the long term, this will facilitate the use of information derived from structural variants and 3D genome structure on determining patient prognosis and on identifying novel therapeutic targets in cancer.