DNA methylation in cancer genomes

描述（由申请人提供）：肺癌是癌症死亡的主要原因，在美国每年有超过15万人死于肺癌。由于早期肺癌可以通过手术切除治愈，因此努力开发有效的早期疾病筛查方法。DNA甲基化生物标志物作为识别早期肺肿瘤的分子工具具有很大的前景。只有一组有限的基因被确定在早期肺癌中甲基化的频率很高。我们已经开始开发适用于癌症DNA甲基化变化的全基因组分析的新技术。利用甲基化cpg岛恢复试验（MIRA）选择性富集基因组的甲基化部分，这是基于MBD2/MBD3L1复合物对甲基化DNA的高亲和力。这种方法可以与微阵列相结合，以确定癌症中全基因组甲基化的变化。在这项应用中，我们将进一步开发和应用MIRA方法，以微阵列为基础筛选正常肺组织和早期肺肿瘤之间的全基因组DNA甲基化差异。关注早期阶段的原因是，任何鉴定出的新的甲基化生物标志物都可能适合于早期检测和诊断。从不同组织学类型的肺肿瘤中分离的DNA将在不同的CpG岛和启动子微阵列平台上进行杂交。通过微阵列分析确定在早期肺肿瘤中甲基化的基因，将在更大的样本集中使用标准甲基化检测技术进行验证。该技术将进一步发展，适用于少量细胞（<1000）和肿瘤生物标本，包括冷冻、包埋、福尔马林固定、石蜡包埋组织。DNA甲基化生物标志物作为识别早期肺肿瘤的分子工具具有很大的前景。然而，只有有限数量的基因在早期肺癌中被甲基化。我们一直在开发一种适用于癌症DNA甲基化变化全基因组筛选的新技术。使用甲基化cpg岛恢复试验（MIRA）选择性地富集基因组的甲基化部分。MIRA已经显示出作为一种特定的和通用的甲基化检测工具的初步承诺，并与微阵列分析兼容。在本R21应用中，我们将进一步完善方法，并尝试将MIRA方法应用于正常肺组织和早期肺肿瘤之间基于微阵列的全基因组DNA甲基化差异筛选。

DESCRIPTION (provided by applicant): Lung cancer is the leading cause of death from cancer and kills over 150,0000 people each year in the United States. Since early stage lung cancer can be cured by surgical resection, efforts are made to develop effective screening approaches for early stage disease. DNA methylation biomarkers hold great promise as molecular tools to identify early stage lung tumors. Only a limited panel of genes has been identified that are methylated at a high frequency in early stage lung cancers. We have begun to develop new technology applicable for genome-wide analysis of DNA methylation changes in cancer. The methylated fraction of the genome is selectively enriched using the methylated-CpG island recovery assay (MIRA), which is based on the high affinity of the MBD2/MBD3L1 complex for methylated DNA. This approach can be combined with microarrays to identify genome-wide methylation changes in cancer. In this application, we will further develop and apply the MIRA approach for microarray-based screening of genome-wide DNA methylation differences between normal lung tissue and early stage lung tumors. The reason for focusing on early stages is that any identified new methylation biomarker may be appropriate for early detection and diagnosis. DNA isolated from different histological types of lung tumors will be used for hybridization on different CpG island and promoter microarray platforms. Genes identified as being methylated in early stage lung tumors by microarray analysis, will be verified in a larger set of samples using standard methylation detection techniques. The technology will be further developed to be applicable to small numbers of cells (<1000) and to tumor biospecimens including frozen, embedded, and formalin-fixed, paraffin embedded tissues. DNA methylation biomarkers hold great promise as molecular tools to identify early stage lung tumors. However, only a limited number of genes have been identified that are methylated in early stage lung cancers. We have been developing a new technology applicable to genome- wide screening of DNA methylation changes in cancer. The methylated fraction of the genome is selectively enriched using the Methylated-CpG Island Recovery Assay (MIRA). MIRA has shown initial promise to be a specific and general methylation detection tool and is compatible with microarray analysis. In this R21 application, we will further refine the methodology and attempt to apply the MIRA approach for microarray-based screening of genome-wide DNA methylation differences between normal lung tissue and early stage lung tumors.