Transfer: DNA Methylation Canyons in Human Cancers: Methods, Target Genes and Functional Consequences

项目摘要/摘要 促生长癌基因的激活在很大程度上是由基因改变驱动的，是在 肿瘤发生学。同时，肿瘤不仅在基因上，而且在表观遗传学上，与它们的组织不同。 起源。然而，关于表观遗传机制能在多大程度上激活癌基因，人们知之甚少。脱氧核糖核酸 甲基化是最广为人知的表观遗传修饰，可影响细胞命运和基因 表情。例如，使肿瘤抑制基因沉默的启动子超甲基化是一种关键的表观遗传学 肿瘤发生中的事件。此外，基因体低甲基化与基因表达呈正相关， 虽然因果关系仍有待确定。最近，我们团队和任炳斌博士的团队 在甲基化区域(UMR)下独立报道了广泛的(例如&gt；3.5-kb)，称为DNA甲基化 峡谷(自然遗传学2014)或山谷(细胞2013)，在大多数情况下跨越启动子和基因体。 峡谷中几乎所有正常细胞的甲基化水平都很低(10%)。峡谷相关基因 (每种细胞类型约1,100)富含发育调节因子和同源框基因，其中许多 在正常细胞中低表达或不表达。然而，尽管有许多后续研究(即约540次引用 对于这两篇论文)，峡谷在基因表达和肿瘤发生中的功能作用仍然很差 明白了。然而，我们的初步数据表明，在正常细胞中发现的峡谷容易发生 肿瘤中的基因体，而不是启动子，高甲基化的峡谷基因令人惊讶 富含致癌基因。此外，我们的dCas9介导的DNA甲基化编辑实验显示 基因-体峡谷高甲基化在癌基因激活中的意外因果作用。因此，我们 假设我们可以使用来自公共领域的癌症DNA甲基化数据，例如癌症基因组 Atlas(TCGA)和国际人类表观基因组学联盟(IHEC)，以及强大的生物信息学 算法，在数千个肿瘤中识别癌症特异性高甲基化峡谷的基因。我们进一步 假设我们可以在细胞和动物模型中测试高甲基化峡谷的功能作用 使用dCas9介导的全基因组甲基化筛选。拟议的工作预计将确定 高甲基化的峡谷，可以激活癌基因，促进肿瘤的体外和体内生长。因此， 这项工作可以从根本上改变我们对DNA甲基化如何调控基因的理解 表达与肿瘤发生。

PROJECT SUMMARY / ABSTRACT Activation of growth-promoting oncogenes, largely driven by genetic alterations, is a key step during tumorigenesis. Meanwhile, tumors are not only genetically, but also epigenetically, distinct from their tissues of origin. Yet, little is known regarding the extent to which epigenetic mechanisms can activate oncogenes. DNA methylation is the most extensively documented epigenetic modification that can influence cell fate and gene expression. For example, promoter hypermethylation that silences tumor suppressor genes is a key epigenetic event in tumorigenesis. In addition, gene-body hypomethylation is positively correlated with gene expression, although the causal relationship remains to be established. Recently, our group and that of Dr. Bing Ren independently reported broad (e.g. >3.5-kb) under methylated regions (UMRs), termed DNA methylation canyons (Nature Genetics 2014) or valleys (Cell 2013), which in most cases span promoters and gene bodies. Canyons exhibit very low levels of methylation (<10%) in almost all normal cells. Canyon-associated genes (~1,100 in each cell type) are enriched in developmental regulators and homeobox genes, many of which exhibit low or no expression in normal cells. However, despite numerous follow-up studies (i.e., ~540 citations for both papers), the functional role of canyons in gene expression and tumorigenesis remains poorly understood. Nevertheless, our preliminary data indicated that canyons found in normal cells are prone to gene-body, but not promoter, hypermethylation in tumors, with the hypermethylated canyon genes surprisingly enriched in oncogenes. Furthermore, our dCas9-mediated DNA methylation editing experiments revealed an unexpected causal role of gene-body canyon hypermethylation in oncogene activation. Therefore, we hypothesize that we can use cancer DNA methylation data from public domains such as The Cancer Genome Atlas (TCGA) and the International Human Epigenomics Consortium (IHEC), as well as powerful bioinformatics algorithms, to identify genes with cancer-specific hypermethylated canyons in thousands of tumors. We further hypothesize that we can test the functional roles of the hypermethylated canyons in cell and animal models using a dCas9-mediated genome-wide methylation screen. The proposed work is expected to identify hypermethylated canyons that can activate oncogenes and promote tumor growth in vitro and in vivo. Thus, this work can fundamentally transform our understanding about how DNA methylation regulates gene expression and tumorigenesis.