Identification of G0S2 as a gene frequently methylated in squamous lung cancer by combination of in silico and experimental approaches
Identification of G0S2 as a gene frequently methylated in squamous lung cancer by combination of in silico and experimental approaches
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DOI：
10.1002/ijc.24947
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发表时间：
2010-04-15
影响因子：
6.4
通讯作者：
Takai, Daiya
中科院分区：
文献类型：
--
作者：
Kusakabe, Masashi;Kutomi, Tomoko;Takai, Daiya
表观遗传学改变可导致癌症中基因的异常表达，已有报道在非小细胞肺癌(NSCLC)中有几个基因具有异常的启动子DNA甲基化。我们通过计算机和实验相结合的方法鉴定了非小细胞肺癌中的异常甲基化基因。我们首先应用了生物信息学，并从微阵列数据集中选择了与癌症相关的低表达和功能基因。接下来，对10例合并切除的肺癌组织进行亚硫酸氢盐联合限制性内切酶分析，以筛选异常甲基化的基因，并通过甲基化等位基因的定量分析来定量甲基化比率(从癌症组织样本提取的DNA中甲基化DNA的比例)。我们发现了8个在非小细胞肺癌中未见报道的甲基化基因(ARPC1B、DNAH9、FLRT2、G0S2、IRS2、PKP1、SPOCK1和UCHL1)。对101例手术切除的肺癌组织标本进行甲基化分析，发现肺癌组织整体甲基化程度较低，甲基化后的肺癌组织甲基化比率几乎不到30%，且经系统聚类法2年随访，与预后无明显相关性。鳞癌G0S2基因甲基化频率(n=18，平均甲基化比：15%)显著高于非鳞癌(n=83，平均甲基化比：2.6%)(Mann-Whitney U检验，p<；0.001)。G0S2基因甲基化可作为鳞癌的重要生物标志物。
Epigenetic changes can lead to abnormal expression of genes in cancer, and several genes have been reported to have aberrant promoter DNA methylation in non-small-cell lung cancer (NSCLC). We identified aberrantly methylated genes in NSCLC by combination of in silico and experimental approaches. We first applied bioinformatics, and from microarray datasets, we selected genes with low expression and having functions related to cancer. Next, combined bisulfite restriction analysis was carried out in 10 pooled resected lung cancer tissues to screen for genes that were aberrantly methylated, and the methylation ratio (the fraction of methylated DNA in extracted DNA from a cancer tissue sample) was quantified using quantitative analysis of methylated alleles. We identified 8 methylated genes (ARPC1B, DNAH9, FLRT2, G0S2, IRS2, PKP1, SPOCK1 and UCHL1) previously unreported in NSCLC. Analyses of methylation profiles of 101 resected lung cancer tissue samples revealed quantitatively low methylation in whole, methylation ratios were almost less than 30% even in the methylated samples, and no significant correlation to prognosis after 2 years of follow-up using hierarchical clustering. DNA methylation of G0S2 gene was significantly more frequent in squamous lung cancer (n = 18, mean of methylation ratios: 15%) compared with nonsquamous lung cancer (n = 83, mean of methylation ratios: 2.6%) (Mann-Whitney U test, p < 0.001). DNA methylation of G0S2 can be an important biomarker for squannous lung cancer.