5-hydroxymethylcytosine in human cancer

5-羟甲基胞嘧啶在人类癌症中的作用

• 批准号: 8292990
• 负责人: Gerd P Pfeifer
• 金额: $ 34.86万
• 依托单位: BECKMAN RESEARCH INSTITUTE/CITY OF HOPE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-04-01 至 2017-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8292990
• 关键词: Affect; Astrocytoma; Brain; Brain Neoplasms; Cell Differentiation process; Cells; CpG Islands; Cytosine; DNA; DNA Methylation; DNA Sequence; Data; Defect; Dependence; Dysmyelopoietic Syndromes; Epigenetic Process; Event; Exons; Gene Expression Profile; Genes; Genome; Genomics; Goals; Human; Hypermethylation; Isocitrate Dehydrogenase; Malignant - descriptor; Malignant Neoplasms; Mammalian Cell; Maps; Methodology; Methylation; Modeling; Modification; Mononuclear; Mutate; Mutation; Normal tissue morphology; Oxidases; Pathway interactions; Pattern; Protein Family; Protein Isoforms; Proteins; Reporting; Role; Stem cells; Techniques; Tertiary Protein Structure; Tissues; base; cell type; demethylation; genome-wide; human tissue; mutant; nerve stem cell; next generation; novel; oxidation; tumor; tumorigenesis

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. PUBLIC HEALTH RELEVANCE: DNA cytosine-5 methylation patterns in cancer are aberrant and are characterized by frequent hypermethylation of CpG islands. It is unknown how these changes in tumors are initiated. Recently, it has been shown that 5-methylcytosine can be oxidized enzymatically to 5-hydroxymethylcytosine. In this application, we propose that changes in 5-hydroxymethylcytosine patterns are hallmarks of malignant transformation and are related to the aberrant DNA cytosine methylation patterns seen in tumors. We will analyze this novel epigenetic mark as well as 5-methylcytosine in normal and malignant tissues. We will also investigate if and how mutations affecting the 5- methylcytosine oxidation pathway have an effect on genomic methylation patterns in human tumors. Functional studies of 5-methylcytosine oxidases (TET proteins) and their associated factors will support these studies so that a comprehensive picture of the importance of this pathway in human tumorigenesis can be obtained.

描述（申请人提供）：细胞分化、重编程和恶性转化是表观基因组发生显著变化的重大事件，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中的DNA甲基化模式截然不同。观察到两个主要事件，(i)癌症中主要影响重复DNA序列的整体DNA低甲基化，以及（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甲基化模式产生的机制在很大程度上是未知的。2009年，有报道称，在某些哺乳动物细胞中大量存在第六种DNA碱基，5-羟甲基胞嘧啶。5-羟甲基胞嘧啶（5hmC）是由5-甲基胞嘧啶（5mC）通过TET家族蛋白的酶氧化作用产生的。一种模型提出5hmC是DNA去甲基化的中间体。我们的假设是，5mC氧化途径中的缺陷是导致人类肿瘤中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定位的方法。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在同一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）的突变，这是一种可能影响5mC氧化途径的酶活性；(2)骨髓增生异常综合征（MDS），因为这种恶性肿瘤通常以TET基因之一TET2突变为特征。第三个目标将集中在TET和TET相关蛋白及其在癌症中的畸变的功能研究。