Genome-wide profiling of methylated promoters in pancreatic adenocarcinoma
Genome-wide profiling of methylated promoters in pancreatic adenocarcinoma
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DOI：
10.4161/cbt.7.7.6208
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发表时间：
2008-07-01
影响因子：
3.6
通讯作者：
Goggins, Michael
中科院分区：
文献类型：
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作者：
Omura, Noriyuki;Li, Chung-Pin;Goggins, Michael
许多基因在人类癌症中经历异常甲基化，微阵列平台能够更全面地分析异常DNA甲基化模式。结果：88k启动子阵列上的87,922个探针（606个基因）中，有1,010个探针在胰腺癌系Panc-1中比在非肿瘤性胰管系HPDE中具有更高的信号（log(2) > 2）。使用这个截止点，亚硫酸氢盐测序和/或MSP证实了MCA阵列预测的所有27个基因（66个探针）的差异甲基化。通过表达阵列分析，半数以上Panc-1异常高甲基化的基因在胰管（HPDE）中不表达。使用244k CpG岛阵列，与正常胰腺相比，MiaPaca2中有1968个CpG岛甲基化差异。MCA方法比甲基化敏感限制性内切酶的混合物更容易识别CpG岛内的超甲基化。使用10 μ g DNA的DNA甲基化谱与使用5 μ g DNA的DNA甲基化谱高度相关（R2 = 0.98）。使用MSP分析57例胰腺癌和34例正常胰腺，发现MDFI、hsa-miR-9-1、ZNF415、CNTNAP2和ELOVL4在96%、89%、86%、82%和68%的癌症中甲基化，而在正常胰腺中分别为9%、15%、6%、3%和9%。方法：我们使用甲基化CpG岛扩增（MCA）和Agilent启动子和CpG岛微阵列来鉴定胰腺癌与正常胰腺DNA甲基化模式的差异。我们检查了MCA阵列的可重复性，将其与使用甲基化敏感限制性内切酶鸡尾酒获得的甲基化谱进行了比较，并检查了甲基化基因的基因表达。结论：启动子和CpG岛阵列分析发现胰腺癌细胞中数百个启动子和CpG岛甲基化异常。
Many genes undergo aberrant methylation in human cancers, and microarray platforms enable more comprehensive profiling of aberrant DNA methylation patterns.Results: 1,010 of 87,922 probes on the 88 K promoter array ( 606 genes) had a higher signal ( log(2) > 2) in the pancreatic cancer line, Panc-1 compared to the non-neoplastic pancreatic duct line, HPDE. Using this cut-off, bisulfite sequencing and/or MSP confirmed differential methylation of all 27 genes ( 66 probes) predicted to be methylated by the MCA array. More than half of the genes aberrantly hypermethylated in Panc-1 were not expressed in the pancreatic duct ( HPDE) by expression array analysis. Using the 244 K CpG island array, 1,968 CpG islands were differentially methylated in MiaPaca2 compared to normal pancreas. The MCA method was more likely to identify hypermethylation within CpG islands than a cocktail of methylation sensitive restriction enzymes. DNA methylation profiles using 10 ng of DNA were highly correlated with those obtained using 5 mu g of DNA ( R2 = 0.98). Analysis of 57 pancreatic cancers and 34 normal pancreata using MSP identified MDFI, hsa-miR-9-1, ZNF415, CNTNAP2 and ELOVL4 as methylated in 96%, 89%, 86%, 82% and 68% of the cancers vs. 9%, 15%, 6%, 3% and 9% of normal pancreata, respectively.Methods: We used methylated CpG island amplification ( MCA) and Agilent promoter and CpG island microarrays to identify differential DNA methylation patterns in pancreatic cancer vs. normal pancreas. We examined MCA array reproducibility, compared it to methylation profiles obtained using a cocktail of methylation-sensitive restriction enzymes and examined gene expression of methylated genes.Conclusion: Promoter and CpG island array analysis finds aberrant methylation of hundreds of promoters and CpG islands in pancreatic cancer cells.