DNA hypermethylation in lung tumors

肺部肿瘤中的 DNA 高甲基化

• 批准号: 10222620
• 负责人: Gerd P Pfeifer
• 金额: $ 47.68万
• 依托单位: VAN ANDEL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-23 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10222620
• 关键词: Affect; Binding; Biological Assay; CRISPR/Cas technology; Cells; Chromatin; Chromatin Remodeling Factor; Citric Acid Cycle; Clone Cells; Complex; CpG Islands; DNA; DNA Methylation; DNA Modification Methylases; DNA Sequence; Dioxygenases; Down-Regulation; EZH2 gene; Enzymes; Epigenetic Process; Epithelial Cells; Event; Family; Functional disorder; Gene Silencing; Genes; Genetic; Histone H3; Histone-Lysine N-Methyltransferase; Histones; Human; Hypermethylation; Link; Lung Adenocarcinoma; Lung Neoplasms; Malignant Neoplasms; Malignant neoplasm of lung; Metabolic; Methylation; Mutation; Normal Cell; Oxidases; Pattern; Permeability; Polycomb; Proteins; Publications; Recovery; Role; Squamous Cell Lung Carcinoma; Succinates; Tertiary Protein Structure; Testing; Zinc Fingers; alpha ketoglutarate; bisulfite sequencing; bronchial epithelium; cancer cell; epigenetic profiling; epigenome; genetic approach; genome-wide; histone methyltransferase; insight; mammalian genome; novel; protective factors; protein function; tumor; whole genome

PROJECT SUMMARY: Epigenetic dysregulation is now widely recognized as a prominent feature of cancer cells. However, mutations in epigenetic modifier genes such as DNA and histone methyltransferases or 5-methylcytosine (5mC) oxidases can explain only a limited fraction of misregulated epigenomes in cancer. A pervasive feature of cancer epigenomes is CpG island DNA hypermethylation. Despite the fact that these methylation events have been cataloged in thousands of publications and in some instances, have been used to classify tumors, we still do not understand the mechanisms how these DNA methylation changes arise. In several types of tumors, a large percentage of the cancer-associated DNA hypermethylation events at CpG islands occur at Polycomb-marked genes. Therefore, one can view the occupancy of CpG islands by Polycomb complexes as one mechanism that protects them from de novo DNA methylation. However, this is likely not the only methylation-protective mechanism that operates at CpG islands. Mammalian genomes encode a relatively small set of 12 proteins that contain a CXXC-type zinc finger domain known to tightly bind to unmethylated CpG-rich DNA sequences. All of these proteins are known or suspected chromatin modifiers. The family includes the 5mC oxidases (the TET proteins), as well as histone lysine methyltransferases and demethylases. We propose that the common function of the majority of the CXXC proteins is to protect CpG islands from DNA methylation. Furthermore, metabolic disturbances of the TCA cycle can affect the function of multiple a-ketoglutarate-dependent dioxygenase enzymes. Remarkably, 5 of the 12 CXXC proteins belong to this class of enzymes. We hypothesize that there is functional redundancy in multiple mechanisms that protect CpG islands from DNA methylation. Overall, our main hypothesis is that a breakdown of multiple CpG island protection mechanisms, including downregulation of Polycomb components and dysfunction of CXXC proteins will lead to CpG island hypermethylation in cancer. We propose to identify these protective factors by a systematic approach using gene inactivation of Polycomb components and of CXXC proteins and comprehensive chromatin mapping studies combined with genome-wide DNA methylation assays after manipulating the different CpG island binding factors. The study will use human bronchial cells and will focus on lung cancer for which we have previously established comprehensive lists of tumor-methylated CpG islands. We consider that a combined deficiency of Polycomb components and of CXXC protein function will explain the common hypermethylation of Polycomb target genes observed in tumors. The role of accumulation of TCA cycle metabolites that inhibit dioxygenases and loss of Polycomb proteins will be tested to determine if DNA methylation can be targeted in this way to resemble a prevalent cancer-like pattern. These studies will provide insights into the long- sought mechanisms of DNA hypermethylation in cancer.

项目概要： 表观遗传失调现在被广泛认为是癌细胞的一个突出特征。然而，在这方面， 表观遗传修饰基因如DNA和组蛋白甲基转移酶或5-甲基胞嘧啶的突变 (5mC)氧化酶只能解释癌症中一小部分失调的表观基因组。一个普遍 癌症表观基因组的特征是CpG岛DNA超甲基化。尽管这些甲基化 这些事件已在数千种出版物中编目，在某些情况下，已被用于 尽管我们对肿瘤进行了分类，但我们仍然不了解这些DNA甲基化变化是如何发生的。在 在几种类型的肿瘤中，癌症相关的DNA高甲基化事件的比例很大， CpG岛出现在Polycomb标记的基因上。因此，可以通过以下方式观察CpG岛的占用率： 多梳复合物作为一种机制，保护他们从从头DNA甲基化。但这 可能不是CpG岛上唯一的甲基化保护机制。哺乳动物基因组 编码一组相对较小的12种蛋白质，这些蛋白质含有一个CXXC型锌指结构域， 与未甲基化的富含CpG的DNA序列结合。所有这些蛋白质都是已知的或疑似的染色质 修饰语该家族包括5 mC氧化酶（泰特蛋白）以及组蛋白赖氨酸 甲基转移酶和脱甲基酶。我们建议，CXXC大多数成员的共同职能 保护CpG岛不受DNA甲基化的影响。此外，TCA的代谢紊乱 循环可影响多种α-酮戊二酸依赖性双加氧酶的功能。值得注意的是，5 的12 CXXC蛋白属于这类酶。我们假设有功能性的 保护CpG岛免受DNA甲基化的多种机制中的冗余。总的来说，我们的主要 一种假说认为，多个CpG岛保护机制，包括下调， CXXC蛋白的功能障碍将导致CpG岛高甲基化。 癌我们建议用基因失活的系统方法来鉴定这些保护因子 Polycomb组分和CXXC蛋白质以及综合染色质图谱研究的组合 在操纵不同的CpG岛结合因子后，用全基因组DNA甲基化测定。 这项研究将使用人类支气管细胞，并将重点放在肺癌，我们以前已经 建立了肿瘤甲基化CpG岛的全面列表。我们认为这是一个综合的缺陷 Polycomb组分和CXXC蛋白功能的研究将解释 在肿瘤中观察到的多梳靶基因。抑制TCA循环代谢物的积累的作用 将测试双加氧酶和Polycomb蛋白的损失，以确定是否可以靶向DNA甲基化。 以这种方式类似于普遍的癌症样模式。这些研究将提供深入了解长期- 寻找癌症中DNA超甲基化的机制。