Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA.
Department of Pathology; Fox Chase Cancer Center; Philadelphia PA, USA.
Epigenetics. 2014 May;9(5):760-73. doi: 10.4161/epi.28078. Epub 2014 Feb 12.
The epigenetic alteration of aberrant hypermethylation in the promoter CpG island of a gene is associated with repression of transcription. In neoplastic cells, aberrant hypermethylation is well described as a mechanism of allele inactivation of particular genes with a tumor suppressor function. To investigate the role of aberrant hypermethylation in the biology and progression of urothelial cancer, we examined 101 urothelial (transitional cell) carcinomas (UC), broadly representative of the disease at presentation, with no prior immunotherapy, chemotherapy or radiotherapy, by Infinium HM27 containing 14,495 genes. The genome-wide signature of aberrant promoter hypermethylation in UC consisted of 729 genes significant by a Wilcoxon test, hypermethylated in a CpG island within 1 kb of the transcriptional start site and unmethylated in normal urothelium from aged individuals. We examined differences in gene methylation between the two main groups of UC: the 75% that are superficial, which often recur but rarely progress, and the 25% with muscle invasion and poor prognosis. We further examined pairwise comparisons of the pathologic subgroups of high or low grade, invasive or non-invasive (pTa), and high grade superficial or low grade superficial UC. Pathways analysis indicated over-representation of genes involved in cell adhesion or metabolism in muscle-invasive UC. Notably, the TET2 epigenetic regulator was one of only two genes more frequently methylated in superficial tumors and the sole gene in low grade UC. Other chromatin remodeling genes, MLL3 and ACTL6B, also showed aberrant hypermethylation. The Infinium methylation value for representative genes was verified by pyrosequencing. An available mRNA expression data set indicated many of the hypermethylated genes of interest to be downregulated in UC. Unsupervised clustering of the most differentially methylated genes distinguished muscle invasive from superficial UC. After filtering, cluster analysis showed a CpG Island Methylator Phenotype (CIMP)-like pattern of widespread methylation in 11 (11%) tumors. Nine of these 11 tumors had hypermethylation of TET2. Our analysis provides a basis for further studies of hypermethylation in the development and progression of UC.
基因启动子 CpG 岛的异常高甲基化的表观遗传改变与转录抑制有关。在肿瘤细胞中，异常高甲基化被描述为特定具有肿瘤抑制功能基因的等位基因失活的机制。为了研究异常高甲基化在尿路上皮癌生物学和进展中的作用，我们使用包含 14495 个基因的 Infinium HM27，对 101 例无免疫治疗、化疗或放疗史的广泛代表性尿路上皮（移行细胞）癌（UC）进行了研究。UC 中异常启动子高甲基化的全基因组特征由 729 个基因组成，这些基因通过 Wilcoxon 检验显著，即在转录起始位点 1kb 内的 CpG 岛中高甲基化，而在老年个体的正常尿路上皮中未甲基化。我们检查了 UC 的两个主要组之间基因甲基化的差异：75%的是浅表性的，常复发但很少进展，25%的是肌肉浸润性的，预后不良。我们进一步检查了高级别或低级别、浸润性或非浸润性（pTa）以及高级别浅表性或低级别浅表性 UC 的病理亚组之间的两两比较。通路分析表明，在肌肉浸润性 UC 中，细胞黏附或代谢相关基因的过度表达。值得注意的是，TET2 表观遗传调节剂是在浅表性肿瘤中甲基化频率更高的仅有的两个基因之一，也是低级别 UC 中唯一的一个基因。其他染色质重塑基因 MLL3 和 ACTL6B 也表现出异常高甲基化。代表性基因的 Infinium 甲基化值通过焦磷酸测序得到验证。可用的 mRNA 表达数据集表明，感兴趣的大多数高甲基化基因在 UC 中下调。最具差异甲基化基因的无监督聚类可区分肌肉浸润性和浅表性 UC。经过过滤后，聚类分析显示 11 例（11%）肿瘤存在广泛甲基化的 CpG 岛甲基化表型（CIMP）样模式。这 11 例肿瘤中有 9 例 TET2 发生高甲基化。我们的分析为进一步研究 UC 发展和进展中的异常高甲基化提供了基础。
