DNA methylation in cancer genomes

描述(申请人提供)：肺癌是导致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甲基化生物标记物作为识别早期肺部肿瘤的分子工具具有很大的前景。只有一组有限的基因被鉴定出来，这些基因在早期肺癌中甲基化频率很高。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。甲基化CpG岛恢复试验(MIRA)选择性地富含基因组的甲基化部分，这是基于Mbd2/MBD3L1复合体对甲基化DNA的高亲和力。这种方法可以与微阵列相结合，以识别癌症全基因组的甲基化变化。在这项应用中，我们将进一步开发和应用Mira方法，基于微阵列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，任何已识别的新甲基化生物标记物都可能适合于早期检测和诊断。从不同组织类型的肺肿瘤中提取的DNA将用于在不同的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被甲基化的基因，将使用标准甲基化检测技术在更大的样本集中进行验证。这项技术将进一步发展，以适用于少数细胞(&lt；1000)和肿瘤生物标本，包括冷冻的、包埋的和福尔马林固定的石蜡包埋组织。DNA甲基化生物标记物作为识别早期肺部肿瘤的分子工具具有很大的前景。然而，在早期肺癌中只发现了有限数量的甲基化基因。我们一直在开发一种适用于癌症DNA甲基化变化的全基因组筛查的新技术。基因组的甲基化部分使用甲基化CpG岛回收试验(MIRA)选择性地浓缩。MIRA已显示出初步承诺成为一种特定和通用的甲基化检测工具，并与微阵列分析兼容。在R21的应用中，我们将进一步改进方法，并尝试应用Mira方法基于微阵列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。

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.