5-hydroxymethylcytosine in human cancer

描述(申请人提供)：细胞分化、重新编程和恶变是以表观基因组显著变化为特征的重大事件，涉及DNA甲基化模式的重塑。在癌症组织中，DNA甲基化模式与正常组织截然不同。观察到了两个主要事件，(I)癌症中以重复DNA序列为主的全球DNA低甲基化，(Ii)影响数百个基因的CpG岛的基因特异性高甲基化。这些与癌症相关的DNA甲基化模式如何产生的机制在很大程度上尚不清楚。2009年，据报道，第六个DNA碱基5-羟甲基胞嘧啶在某些类型的哺乳动物细胞中大量存在。5-羟甲基胞嘧啶(5HmC)是由5-甲基胞嘧啶(5mC)通过Tet家族蛋白质的酶促氧化反应生成的。一种模型认为，5hmC是DNA去甲基化的中间产物。我们的假设是，5mC氧化途径的缺陷是导致人类肿瘤DNA甲基化模式改变的原因。我们已经建立了5mC和5hmC的精确定量和全基因组图谱的方法学。我们的目标是确定5HmC在正常人体组织和恶性肿瘤中的水平和基因组分布。这些数据将直接与5mC在相同组织中的分布进行比较。我们将主要关注两种肿瘤类型：(1)人类II/III级星形细胞瘤，因为这些肿瘤经常包含异柠檬酸脱氢酶(IDH1或IDH2)突变，这种酶活性可能影响5mC氧化途径；以及(2)骨髓增生异常综合征(MDS)，因为这种恶性肿瘤的特征通常是Tet基因之一TET2的突变。第三个目标将集中在Tet和Tet相关蛋白的功能研究以及它们在癌症中的异常。

DESCRIPTION (provided by applicant): Cell differentiation, reprogramming and malignant transformation are major events characterized by remarkable changes in the epigenome and involve remodeling of DNA methylation patterns. In cancer tissues, DNA methylation patterns are drastically different from those in normal tissues. Two major events are observed, (i) global DNA hypomethylation in cancer affecting predominantly repetitive DNA sequences, and (ii) gene-specific hypermethylation of CpG islands affecting hundreds of genes. The mechanisms how these cancer-associated DNA methylation patterns arise are largely unknown. In 2009, it was reported that a sixth DNA base, 5-hydroxymethylcytosine, is present in substantial amounts in certain mammalian cell types. 5-hydroxymethylcytosine (5hmC) is created from 5-methylcytosine (5mC) by enzymatic oxidation carried out by the TET family of proteins. One model proposes that 5hmC is an intermediate in DNA demethylation. Our hypothesis is that defects in the 5mC oxidation pathway are responsible for altered DNA methylation patterns in human tumors. We have established methodology for precise quantification and genome-wide mapping of 5mC and 5hmC. Our goal is to determine the level and the genomic distribution of 5hmC in normal human tissues and in malignant tumors. These data will be compared directly with the distribution of 5mC in the same tissues. We will focus primarily on two tumor types: (1) human grade II/III astrocytomas, because these tumors frequently contain mutations in isocitrate dehydrogenases (IDH1 or IDH2), an enzymatic activity potentially impacting on the 5mC oxidation pathway; and (2) myelodysplastic syndrome (MDS), because this malignancy often is characterized by mutations in one of the TET genes, TET2. The third Aim will focus on functional studies of TET and TET-associated proteins and their aberrations in cancer.