Mammary Carcinoma and Genomic Methylation Patterns

描述（由申请人提供）：我们开发了一种提供全基因组甲基化谱的新技术。与其他方法相比，新技术在覆盖范围、简单性、准确性和经济性方面具有很大优势。该方法结合了将 DNA 酶促分离成甲基化和非甲基化区室的新方法，以及超高通量 DNA 测序中新兴技术的应用，以分析基因组甲基化模式。我们将确定一组源自乳腺癌的细胞系和一大组原发性乳腺癌的基因组中的去甲基化和从头甲基化位点，这些细胞系在组织病理学和分子标记的表达方面具有良好的特征。 2 个导管癌和邻近正常组织的 DNA 的全基因组甲基化图谱已经完成，乳腺癌细胞系 MCF7 的完整甲基化图谱也已完成。然后，我们将使用完全实现的计算方法来识别那些与乳腺癌类型、分级和阶段高度相关的甲基化异常。目标是建立一套可用于开发乳腺癌生物标志物的诊断和预后标准。将开发一种诊断程序，测试乳腺癌中最常见的高甲基化序列的从头甲基化和去甲基化，并描述一种评估活检 DNA 中甲基化异常的简单而新颖的方法。我们的初步结果，加上文献中一些长期存在的谜团，使我们提出，乳腺癌中如此常见的甲基化异常可能反映了一个杀死失去生长控制的细胞的系统（甲基化自杀系统）的运作。

DESCRIPTION (provided by applicant): We have developed a new technology that provides whole-genome methylation profiles. The new technology has large advantages in coverage, simplicity, accuracy, and economy over other methods. The approach combines a new method of enzymatic fractionation of DNA into methylated and unmethylated compartments and the application of emerging technologies in ultrahigh throughput DNA sequencing to profile genomic methylation patterns. We will determine sites of demethylation and de novo methylation in the genomes of a panel of cell lines derived from mammary carcinomas and of a large panel of primary mammary carcinomas that are well-characterized in terms of histopathology and expression of molecular markers. Whole-genome methylation profiling of DNA of 2 ductal carcinomas and adjacent normal tissues has been completed, as has a complete methylation profile of the mammary carcinoma cell line MCF7. We will then use fully-implemented computational methods to identify those methylation abnormalities that are most highly correlated with type, grade, and stage of mammary carcinomas. The goal is a set of diagnostic and prognostic criteria that can be used in the development of biomarkers for mammary carcinoma. A diagnostic procedure will be developed that will test for de novo methylation and demethylation of the sequences found to be most often hypermethylated in mammary carcinoma, and a simple and novel method for the evaluation of methylation abnormalities in biopsy DNA is described. Our preliminary results, together with some long-standing enigmas in the literature, lead us to propose that the methylation abnormalities so common in mammary carcinoma may reflect the operation of a system (the methylation suicide system) that kills cells that have lost growth control.