Loh Marie, Liem Natalia, Vaithilingam Aparna, Lim Pei Li, Sapari Nur Sabrina, Elahi Eiram, Mok Zuan Yu, Cheng Chee Leong, Yan Benedict, Pang Brendan, Salto-Tellez Manuel, Yong Wei Peng, Iacopetta Barry, Soong Richie
Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
BMC Gastroenterol. 2014 Mar 28;14:55. doi: 10.1186/1471-230X-14-55.
Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC.
The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations.
A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy.
High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.
肿瘤抑制基因启动子CpG岛的甲基化诱导沉默在人类致癌过程中起重要作用。在结直肠癌中，CpG岛甲基化表型（CIMP）被定义为广泛且升高的DNA甲基化水平，CIMP+肿瘤具有独特的临床病理和分子特征。相比之下，胃癌（GC）中类似CIMP亚型的存在尚未明确确立。为进一步研究此问题，在本研究中，我们对一系列特征明确的原发性胃癌进行了全面的DNA甲基化分析。
使用Illumina GoldenGate甲基化检测试剂盒I，对从60对胃癌肿瘤及配对的肿瘤旁胃组织中提取的DNA，检测位于768个癌症相关基因内的1421个常染色体CpG位点的甲基化状态。使用递归划分混合模型分析甲基化数据，并研究其与临床病理和分子特征的关联，包括年龄、幽门螺杆菌状态、肿瘤部位、患者生存率、微卫星不稳定性以及BRAF和KRAS突变。
肿瘤组织与配对的肿瘤旁胃组织之间共有147个基因存在差异甲基化，其中HOXA5和刺猬信号通路分别是排名最靠前的基因和信号通路。甲基化数据的无监督聚类揭示了在两个主要聚类下存在6个亚组，分别称为L（低甲基化；28%的病例）和H（高甲基化；72%）。与L组相比，H肿瘤组中女性患者比例过高（36%对6%；P = 0.024），然而在临床病理或分子特征方面没有其他明显差异。H组中高甲基化的CpG位点更频繁地位于CpG岛中，并标记有聚梳蛋白占据。
高通量甲基化分析表明参与胚胎发育和刺猬信号通路的基因与胃癌发生有关。胃癌由两种主要的甲基化亚型组成，高度甲基化组显示出一些与CpG岛甲基化表型一致的特征。
