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适当调控的关键组成部分 表情。近年来，人们对许多基本特征的了解迅速扩大，这些基本特征 定义基因组如何在细胞内的空间中组织，包括识别A/B等特征 隔室、拓扑关联结构域和染色质环。此外，有证据表明， 改变3D基因组结构的突变可能会导致人类疾病。对于一个班级来说，这是最明显的 被称为结构变异的突变，包括易位、倒置、串联复制和 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，例如 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，以及表型后果。这样的影响在两个方面都观察到了 导致发育和躯体综合征障碍的生殖系结构变异的背景 可能导致癌症的结构变异。虽然已经很明显，结构变体可以改变3D 基因组组织和基因表达，更多的最新研究全面检查了结构 变异和基因表达表明它们之间的关系要复杂得多。具体地说，仅在 少数情况下，结构变异确实会导致邻近基因表达的变化。因此，为什么 结构变异会对3D基因组结构和基因表达产生戏剧性的影响 目前尚不清楚具体情况，但不包括其他情况。这项提案将调查结构之间的关系 变异体、3D基因组组织和癌症基因组中的基因表达 结构变异在何时何地实际上会导致基因表达的变化，这可能有助于 致癌作用。特定目标1将测试是否只有特定的集合基因对诱导的结构变异敏感 通过检测3D基因组结构和基因的变化来研究增强子-启动子通信的变化 在单倍型分辨的人类肿瘤样本中表达。特定目标2将使用CRISPR/Cas9基因组 工程学评估结构变异的伙伴区域对癌基因表达诱导的影响。 具体目标3将评估肿瘤内异质性在结构变异对3D的影响上的作用 用新的多组学方法分析DNA甲基化和三维基因组结构 同时在从患者肿瘤样本中提取的单个细胞内。这些目标的成功实现将 从而更深入地理解结构变异、3D基因组组织和 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 来自结构变异和3D基因组结构对判断患者预后和识别的作用 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.