Microarray-based Method for Detecting Methylation Changes of P16(Ink4a) Gene 5'-CpG Islands in Gastric Carcinomas

Overview

Journal World J Gastroenterol

Publisher Baishideng Publishing Group

Specialty Gastroenterology

Date 2004 Nov 10

PMID 15534905

Citations 3

Authors

Peng Hou

Jia-Yao Shen

Mei-Ju Ji

Nong-Yue He

Zu-Hong Lu

Affiliations

Soon will be listed here.

Abstract

Aim: Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so far been hampered by the lack of high-throughput approach for analyzing DNA methylation. The aim of this study was to describe a microarray-based method for detecting changes of DNA methylation in cancer.

Methods: This method used bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. Therefore, the amplified product might contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status. Nine sets of oligonucleotide probes were designed to fabricate a DNA microarray to detect the methylation changes of p16 gene CpG islands in gastric carcinomas. The results were further validated by methylation-specific PCR (MSP).

Results: The experimental results showed that the microarray assay could successfully detect methylation changes of p16 gene in 18 gastric tumor samples. Moreover, it could also potentially increase the frequency of detecting p16 methylation from tumor samples than MSP.

Conclusion: Microarray assay could be applied as a useful tool for mapping methylation changes in multiple CpG loci and for generating epigenetic profiles in cancer.

Citing Articles

Identification of Key Genes in Gastric Cancer by Bioinformatics Analysis.

Chong X, Peng R, Sun Y, Zhang L, Zhang Z Biomed Res Int. 2020; 2020:7658230.

PMID: 33015179 PMC: 7525308. DOI: 10.1155/2020/7658230.

Identification of driver and passenger DNA methylation in cancer by epigenomic analysis.

Kalari S, Pfeifer G Adv Genet. 2010; 70:277-308.

PMID: 20920752 PMC: 2951285. DOI: 10.1016/B978-0-12-380866-0.60010-1.

Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: an emphasis on fetal-based adult diseases.

Ho S, Tang W Reprod Toxicol. 2007; 23(3):267-82.

PMID: 17317097 PMC: 2055548. DOI: 10.1016/j.reprotox.2007.01.004.

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