Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays.
Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays.
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DOI：
10.1186/bcr2121
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发表时间：
2008
期刊：
影响因子：
--
通讯作者：
Chambers AF
中科院分区：
文献类型：
--
作者：
Rodenhiser DI;Andrews J;Kennette W;Sadikovic B;Mendlowitz A;Tuck AB;Chambers AF
乳腺癌转移是一个复杂的、多步骤的生物学过程。基因突变沿着DNA甲基化模式和组蛋白修饰形式的表观遗传学改变，导致转移相关基因表达变化和基因组不稳定。到目前为止，这些表观遗传对乳腺癌转移的贡献还没有得到很好的表征，对这些表观遗传改变影响的功能机制只有有限的了解。此外，尚未进行全基因组评估以确定转移背景下改变的DNA甲基化模式及其对特定功能途径或基因网络的影响。我们已经使用人类基因启动子平铺微阵列平台来分析由低转移性MDA-MB-468 GFP人类乳腺癌细胞系及其高转移性变体（468 LN）组成的淋巴结转移的细胞系模型。确定了与转移相关的基因网络和途径，并就DNA甲基化对基因表达的影响验证了与上皮-间质转化相关的靶基因。我们将来自平铺微阵列的数据与通过Influencity Pathways Analysis软件鉴定的靶点相结合，并观察了与上皮-间充质转化和肿瘤细胞迁移有关的基因的表观遗传变异。我们在这些细胞中鉴定了广泛的基因组高甲基化和低甲基化事件，并通过定量实时PCR证实了甲基化状态与CDH 1，CST 6，EGFR，SNAI 2和ZEB 2基因表达之间的功能相关性。我们的数据还表明，癌细胞中存在的复杂的基因组重组可能与负责基因特异性表达变化的启动子特异性甲基化事件叠加。这是第一个全基因组方法，以确定全基因组和基因特异性表观遗传改变，以及这些变化的功能后果，在乳腺癌转移到淋巴结的背景下。这种方法允许转移的表观遗传特征的开发与基因组特征同时使用，以改善转移不断变化的分子格局的绘图，并允许翻译方法靶向与转移进展相关的表观遗传调节分子途径。
Breast cancer metastasis is a complex, multi-step biological process. Genetic mutations along with epigenetic alterations in the form of DNA methylation patterns and histone modifications contribute to metastasis-related gene expression changes and genomic instability. So far, these epigenetic contributions to breast cancer metastasis have not been well characterized, and there is only a limited understanding of the functional mechanisms affected by such epigenetic alterations. Furthermore, no genome-wide assessments have been undertaken to identify altered DNA methylation patterns in the context of metastasis and their effects on specific functional pathways or gene networks. We have used a human gene promoter tiling microarray platform to analyze a cell line model of metastasis to lymph nodes composed of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). Gene networks and pathways associated with metastasis were identified, and target genes associated with epithelial–mesenchymal transition were validated with respect to DNA methylation effects on gene expression. We integrated data from the tiling microarrays with targets identified by Ingenuity Pathways Analysis software and observed epigenetic variations in genes implicated in epithelial–mesenchymal transition and with tumor cell migration. We identified widespread genomic hypermethylation and hypomethylation events in these cells and we confirmed functional associations between methylation status and expression of the CDH1, CST6, EGFR, SNAI2 and ZEB2 genes by quantitative real-time PCR. Our data also suggest that the complex genomic reorganization present in cancer cells may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes. This is the first whole-genome approach to identify genome-wide and gene-specific epigenetic alterations, and the functional consequences of these changes, in the context of breast cancer metastasis to lymph nodes. This approach allows the development of epigenetic signatures of metastasis to be used concurrently with genomic signatures to improve mapping of the evolving molecular landscape of metastasis and to permit translational approaches to target epigenetically regulated molecular pathways related to metastatic progression.
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