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、准确和经济等方面具有很大的优势。该方法结合了酶催化DNA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，以描述基因组甲基化模式。我们将确定一组来自乳腺癌的细胞系和一组在组织病理学和分子标记表达方面具有良好特征的原发性乳腺癌的基因组中的去甲基化和新生甲基化位点。2个导管癌和邻近正常组织的DNA全基因组甲基化谱已经完成，乳腺癌细胞系MCF7的完整甲基化谱也已经完成。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、分级和分期高度相关的甲基化异常。目标是一套诊断和预后标准，可用于开发乳腺癌的生物标志物。将开发一种诊断程序，用于检测乳腺癌中最常被发现的高甲基化序列的新生甲基化和去甲基化，并描述了一种评估活检DNA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，乳腺癌中常见的甲基化异常可能反映了一个系统（甲基化自杀系统）的运作，该系统杀死了失去生长控制的细胞。

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.