Regulators of Cancer-Specific DNA Hypermethylation.

癌症特异性 DNA 高甲基化的调节因子。

• 批准号: 8713421
• 负责人: Jean-Pierre J. Issa
• 金额: $ 30.8万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-21 至 2017-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8713421
• 关键词: Affect; Algorithms; Area; Beryllium; Binding Sites; Bioinformatics; CCCTC-binding factor; Cancer Model; Cancer cell line; Cell Line; Cell model; ChIP-seq; Chromatin; Chromatin Structure; Code; Colon; Colorectal Cancer; CpG Islands; DNA; DNA Binding; DNA Methylation; DNA-Binding Proteins; Data; Development; Direct Repeats; Elements; Engineering; Enzymes; Epigenetic Process; Epithelial Cells; Evaluation; Event; Experimental Models; Gene Targeting; Genes; Genetic; Genetic Transcription; Genomic Imprinting; Genomics; Goals; Head and Neck Squamous Cell Carcinoma; Head and neck structure; Hematopoietic; Histones; Human; Hypermethylation; Indium; Individual; Knock-out; Knowledge; Laboratories; Large Intestine Carcinoma; Lead; Luciferases; Malignant Neoplasms; Measures; Methylation; Modeling; Modification; Myelogenous; Myeloid Leukemia; Neoplasms; Normal Cell; Normal tissue morphology; Oncogenes; Pathway interactions; Pattern; Polycomb; Predictive Factor; Predisposition; Primary Neoplasm; Process; Proteins; RIL Gene; Refractory; Repetitive Sequence; Reporter Genes; Repression; Research; Resistance; Resolution; Retrotransposon; Role; Sampling; Series; Short Interspersed Nucleotide Elements; Site; Sp1 Transcription Factor; Statistical Models; Susceptibility Gene; System; Systems Integration; Tail; Testing; Tetanus Helper Peptide; Tetracyclines; Time; Transcription Initiation Site; Transgenes; Tumor Suppressor Proteins; USF1 gene; Validation; X Inactivation; base; bisulfite; cancer cell; cancer therapy; cancer type; density; embryonic stem cell; epigenomics; gene repression; genome-wide; genome-wide analysis; histone modification; human ZNF45 protein; insight; interest; knock-down; mathematical model; novel; programs; promoter; site-specific integration; tool; transcription factor; tumor; tumorigenesis

DESCRIPTION (provided by applicant): In normal cells, DNA methylation is rare in promoter-associated CpG islands but important to X-inactivation, genomic imprinting and repression of repetitive elements. During tumorigenesis hundreds to thousands of genes gain methylation in promoter-associated CpG islands, affecting many pathways including tumor- suppressor pathways. The causes of this massive switch in DNA methylation remain mysterious. Interestingly, some genes are refractory to abnormal de-novo methylation in cancer while others are frequently targeted. Deciphering the differences between CpG islands sensitive or resistant to aberrant methylation will lead to a better understanding of the cellular factors that modulate cancer-specific DNA hypermethylation. Based on preliminary data, our central hypothesis to explain this difference is that an interplay between local sequence features (repeat elements, recognition sites for DNA binding proteins) and baseline chromatin states (histone modifications) related to developmental transcription programs modulates CpG island methylation in cancer. To test this hypothesis, we propose the following specific aims: (1) Identify baseline genetic and epigenetic features which segregate genes with propensity to become de-novo methylated in cancer from genes protected from de-novo methylation; and (2) use cellular models of DNA methylation induction to validate the individual and cooperative action of candidate genetic and epigenetic features. In specific aim 1, we propose (a) to measure the propensity of promoter-associated CpG islands to DNA hypermethylation in myeloid leukemia and colorectal carcinomas) and (b) to identify the genomic (transcription factor binding sites, retrotransposons, short direct repeats) and epigenomic (histone modifications in normal cells) factors that distinguish methylation-prone versus methylation-resistant CpG islands. Significant features will be entered in a mathematical model to reveal individual and cooperative activity in modulating methylation in cancer, and the model will be validated in other samples and tumor types. The most significant features and known factors associated with differential predisposition to DNA methylation (the transcription factor Sp1, LINE/SINE retrotransposons and the insulator proteins CTCF, USF1/2 and VEZF1) will be tested in specific aim 2. For this testing we will use a series of cellular models developed in our laboratory where engineered transgenes can be inserted in specific genomic loci, and later on moved in and out of repressive contexts due to the presence of tetracycline-induced repressors. We expect that the successful development of our research will bring novel insights in how abnormal DNA methylation is targeted to specific genes while sparing others, and will also result in the identification of multiple targets for epigenetic-based therapies.

描述（由申请人提供）：在正常细胞中，DNA甲基化在与启动子相关的CpG岛中很少见，但对重复元件的X灭活，基因组印迹和抑制至关重要。在肿瘤发生期间，数百至数千个基因在启动子相关的CpG岛中获得甲基化，影响了包括肿瘤抑制途径在内的许多途径。 DNA甲基化这种大规模开关的原因仍然是神秘的。有趣的是，某些基因对癌症异常的脱诺沃甲基化是难治性的，而其他基因经常是针对性的。解解CpG岛对异常甲基化敏感或抗性的差异将使人们更好地理解调节癌症特异性DNA高甲基化的细胞因子。基于初步数据，我们解释这种差异的中心假设是，局部序列特征（重复元素，DNA结合蛋白的识别位点）之间的相互作用与与发育转录程序有关的基线染色质状态（组蛋白修饰）调节癌症中CPG岛甲基化。为了检验这一假设，我们提出了以下特定目的：（1）鉴定基线遗传和表观遗传特征，这些特征将基因隔离，其倾向是在癌症中被甲基化的甲基化甲基化的基因，免受保护脱诺沃甲基化的基因； （2）使用DNA甲基化诱导的细胞模型来验证候选遗传和表观遗传特征的个体和合作作用。在特定目标1中，我们建议（a）测量促启动子相关的CpG岛对髓样白血病和大肠癌中的DNA高甲基化的倾向和（b）以识别基因组（转录因子结合位点，逆转转跨反转换，短直接重复）和隔离式（Espementy actional）的基因组（转录因子结合位点）的正常因子（均为基型）。抗甲基化的CPG岛。将在数学模型中输入重要的特征，以揭示调节癌症甲基化的个体和合作活动，并且该模型将在其他样品和肿瘤类型中进行验证。 The most significant features and known factors associated with differential predisposition to DNA methylation (the transcription factor Sp1, LINE/SINE retrotransposons and the insulator proteins CTCF, USF1/2 and VEZF1) will be tested in specific aim 2. For this testing we will use a series of cellular models developed in our laboratory where engineered transgenes can be inserted in specific genomic loci, and later on moved in and out of由于存在四环素引起的阻遏物而引起的压制背景。我们预计，我们的研究的成功发展将带来新的见解，即在保留他人的同时如何将异常的DNA甲基化靶向特定基因，并且还将导致鉴定基于表观遗传学的疗法的多个靶标。