Mammary Carcinoma and Genomic Methylation Patterns

描述（由申请人提供）：我们开发了一种新技术，可提供全基因组甲基化图谱。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。该方法结合了一种新的方法，酶法分馏的DNA成甲基化和非甲基化的车厢和新兴技术的应用，在高通量DNA测序的基因组甲基化模式。我们将确定一组来源于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物表达方面具有良好的特征。已完成2个导管癌和邻近正常组织的DNA的全基因组甲基化谱，乳腺癌细胞系MCF7的完整甲基化谱也已完成。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的类型，级别和阶段高度相关的甲基化异常。目标是一套诊断和预后标准，可用于乳腺癌生物标志物的发展。将开发一种诊断程序，将测试从头甲基化和去甲基化的序列发现最经常高甲基化的乳腺癌，并描述了一种简单而新颖的方法，用于评估活检DNA中的甲基化异常。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系统（甲基化自杀系统）的运作，该系统杀死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.