DNA hypermethylation in lung tumors

项目总结： 表观遗传失调现在被广泛认为是癌细胞的一个显著特征。然而， 表观遗传修饰基因突变，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一小部分调控不当的表观基因组。无处不在的 肿瘤表观基因组的特征是CpG岛DNA高甲基化。尽管这些甲基化 数以千计的出版物对事件进行了编目，在某些情况下，事件被用来 对于肿瘤的分类，我们仍然不清楚这些DNA甲基化变化是如何产生的机制。在……里面 几种类型的肿瘤中，很大比例的癌症相关DNA超甲基化事件发生在 CpG岛出现在多梳标记基因上。因此，可以通过以下方式查看CpG岛屿的占有率 多梳复合体是保护它们免受从头DNA甲基化的一种机制。不过，这个 很可能不是在CpG岛上运行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种蛋白质，含有已知紧密结合的CXXC型锌指结构域 结合未甲基化的富含CpG的DNA序列。所有这些蛋白质都是已知的或可疑的染色质 修饰符。该家族包括5mC的氧化酶(Tet蛋白)，以及组蛋白赖氨酸 甲基转移酶和去甲基酶。我们建议CXXC大多数成员的共同职能 蛋白质是为了保护CpG岛免受DNA甲基化的影响。此外，三氯乙酸的代谢紊乱 循环可以影响多种a-酮戊二酸依赖的双加氧酶的功能。值得注意的是，5 在12种CXXC蛋白中，CXXC属于这类酶。我们假设有一个功能性的 保护CpG岛免受DNA甲基化的多种机制中的冗余。总体而言，我们的主要 假设是多种CpG岛保护机制的崩溃，包括下调调控 多梳组成成分和CXXC蛋白功能障碍将导致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。 结合多梳组分和CXXC蛋白以及全面的染色质图谱研究 在操纵不同的CpG岛结合因子后进行全基因组DNA甲基化检测。 这项研究将使用人类支气管细胞，并将重点放在我们以前治疗过的肺癌上 建立了肿瘤甲基化CpG岛的全面清单。我们认为这是一种综合缺陷。 多梳状成分和CXXC蛋白功能的差异将解释常见的 在肿瘤中观察到的多梳靶基因。TCA循环代谢产物的积累对抑制 将测试双加氧酶和多梳蛋白的丢失，以确定DNA甲基化是否可以作为靶点 以这种方式类似于一种流行的类似癌症的模式。这些研究将提供对长期- 探索癌症中DNA高甲基化的机制。

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.