Novel approach to whole genome methylation profiling of breast cancer

描述（由申请人提供）：了解癌细胞基因组经历的甲基化异常的作用对癌症研究和治疗非常重要;然而，一个主要的限制是缺乏以快速、成本有效的方式同时分析整个基因组的甲基化模式的方法。例如，基于阵列的技术不能用于揭示重复元件的甲基化状态，这些重复元件被假设在癌细胞中发现的改变的表达模式和重排中起关键作用。特别是，甲基化在乳腺癌中的作用仍然知之甚少;肿瘤抑制基因启动子的超甲基化和基因组的整体低甲基化都被认为在早期发挥重要作用。本文提出的新方法结合了根据甲基化状态分级DNA的新技术和使用“下一代”DNA测序技术的超高通量DNA测序，以允许有效的全基因组甲基化谱分析，即使当仅可获得微克量的DNA时。我们将使用这项技术来检查一组乳腺癌样本的完整基因组甲基化状态，并研究这些模式如何与生存和复发等各种因素相关，以开发甲基化谱作为潜在的强大生物标志物。我们将利用这些数据作为一个平台，阐明甲基化作为一种调节剂在乳腺癌中所起的作用。我们将确定乳腺癌的低甲基化特征是一个随机的还是定向的过程，并检查肿瘤抑制基因高甲基化是否是乳腺癌的关键因素，或者这仅仅是一个偶发事件。我们还将研究甲基化对染色体重排热点的影响，这在乳腺癌中很常见。该项目通过全基因组甲基化分析方法，该方法是无偏见的，能够调查所有序列的甲基化状态，包括已知在乳腺癌中去甲基化的重复序列，将首次研究乳腺癌的完整甲基化景观，并提供对癌症表观遗传异常的新见解。

DESCRIPTION (provided by applicant): Understanding the role of methylation abnormalities undergone by cancer cell genomes is of great importance to cancer research and treatment; however, one major limitation has been the lack of a method for analyzing the methylation patterns of the entire genome simultaneously in a rapid, cost-effective manner. For instance, array based techniques cannot be used to reveal the methylation status of repetitive elements, which are hypothesized to play a key function in the altered expression patterns and rearrangements found in cancer cells. In particular, the role of methylation in breast cancer is still poorly understood; both hypermethylation of tumor suppressor gene promoters and global hypomethylation of the genome are thought to play significant early roles. The novel method presented here combines new techniques of fractionation of DNA according to methylation status and ultra-high throughput DNA sequencing using "Next- Gen" DNA sequencing technologies to allow efficient whole-genome methylation profiling even when only microgram amounts of DNA are available. We will use this technology to examine the complete genomic methylation status of a panel of breast cancer samples and study how these patterns correlate with various factors such as survival and recurrence to develop methylation profiles as a potentially powerful biomarker. We will use this data as a platform to elucidate the role methylation plays in breast cancer as a regulatory agent. We will determine if the hypomethylationthat characterizes breast cancer is a stochastic or directed process and examine whether tumor suppressor hypermethylation is a key factor in breast cancer or if this is solely a sporadic event. We will also examine the effects of methylation on hotspots for chromosomal rearrangements, which are commonly found in breast cancer. This project, via a whole genome methylation profiling method that is unbiased and capable of investigating the methylation status of all sequences including the repeated sequences known to be demethylated in breast cancer, will provide a first look into the complete methylation landscape of breast cancer and provide new insights into epigenetic abnormalities in cancer.