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.

项目摘要： 现在，表观遗传失调被广泛认为是癌细胞的重要特征。然而， 表观遗传修饰剂基因的突变，例如DNA和组蛋白甲基转移酶或5-甲基胞嘧啶 （5MC）氧化酶只能解释癌症中有限的不良表观基因组。普遍 癌症基因组的特征是CpG岛DNA高甲基化。尽管这些甲基化 事件已在成千上万的出版物中分类，在某些情况下已经习惯了 对肿瘤进行了分类，我们仍然不了解这些DNA甲基化如何变化的机制。在 几种类型的肿瘤，很大一部分与癌症相关的DNA高甲基化事件在 CpG岛发生在Polycomb标记的基因上。因此，可以通过 PolyComb复合物是一种保护它们免受从头DNA甲基化的机制。但是，这个 可能不是在CPG岛上运作的唯一甲基化保护机制。哺乳动物基因组 编码一组相对较小的12个蛋白质，其中包含CXXC型锌指域已知已知 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或可疑的染色质 修饰符。该家族包括5MC氧化酶（TET蛋白）以及组蛋白赖氨酸 甲基转移酶和脱甲基酶。我们建议大多数CXXC的共同功能 蛋白质是为了保护CpG岛免受DNA甲基化的影响。此外，TCA的代谢紊乱 循环会影响多个二酮戊二酸二加氧酶的功能。值得注意的是，5 在12个CXXC蛋白中，属于这类酶。我们假设有功能 保护CpG岛免受DNA甲基化的多种机制的冗余。总体而言，我们的主要 假设是多种CpG岛保护机制的分解，包括下调 CXXC蛋白的多孔成分和功能障碍将导致CpG岛高甲基化 癌症。我们建议通过使用基因失活的系统方法来识别这些保护因素 PolyComb成分和CXXC蛋白和综合染色质图研究的合并 在操纵不同的CpG岛结合因子后，全基因组DNA甲基化测定法。 该研究将使用人支气管细胞，并将重点放在我们之前的肺癌上 已建立的肿瘤 - 甲基化CPG岛的综合清单。我们认为综合缺陷 PolyComb成分和CXXC蛋白功能的函数将解释 在肿瘤中观察到的多孔靶基因。抑制TCA循环代谢产物积累的作用 将测试二加氧酶和多肉菌蛋白的丧失，以确定是否可以靶向DNA甲基化 这样，类似于普遍的癌症样模式。这些研究将为长期提供见解 寻求癌症中DNA高甲基化的机制。