利用甲基化芯片及转录组测序方法筛选哈萨克族食管癌DNA异常甲基化谱

doi:10.3969/j.issn.1004-616x.2014.02.003

Abstract

Abstract:

OBJECTIVE: To screen the aberrant methylation genes in esophageal squamous cell carcinoma for Kazakh ethnic group in Xinjiang. The aberrant methylation pattern would provide a clue for in-depth study on esophageal squamous cell carcinoma mechanism. METHODS：We used Illumina Human Methylation 450K chip to carry out the genome-wide methylation screening on 6 cancer tissues and 6 adjacent normal tissues of esophageal squamous cell carcinoma in Kazakh people， to explore aberrant the methylation genes. Genome-wide sequencing were carried out on 2 cancer tissues and 2 adjacent normal tissues by Hiseq2000. Meanwhile，mRNA database was established. With the association study between the methylation profile and expression profile，aberrant DNA methylation genes were identifed and were uploaded to the GoMiner and the KEGG database，completing the bioinformatic analysis. RESULTS：There were 227 hypermethylated genes and 6 hypomethylated genes in cancer tissue，mRNA expression varied from 0.031 2 to 8 192 in cancer tissues and from 0.031 2 to 1 024 in adjacent normal tissues. The association study indicated that there were 10 loci，10 down-regulated genes hypermethylated in promoter region in the negative group. Additionally，there were 11 loci，10 up-regulated genes in the negative group. Using GoMiner to do GO analysis on aberrant DNA methylation genes，revealed that ALDH1L1 ralated to folinic acid catabolism and CAPN1 was associated with positive regulation of cell proliferation. During pathyway analysis，we found that ALDH1L1 was involved in one carbon metabolism and CAPN1 participated in the apoptosis process. CONCLUSION：The aberrant DNA methylation profiles were estabilsed and provided a clue for further studies on ESCC of Kazakh ethnic group.

Key words: DNA methylation, ESCC, Kazakh ethnic group, bioinformmatic analysis

CHEN Yan，DENG Yan-chao，LI Lei. Screening aberrant methylation in esophageal squamous cell carcinoma for Kazakhs by methylation chip and transcription group sequencing[J]. Carcinogenesis, Teratogenesis & Mutagenesis, doi: 10.3969/j.issn.1004-616x.2014.02.003.

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Screening aberrant methylation in esophageal squamous cell carcinoma for Kazakhs by methylation chip and transcription group sequencing

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