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Comparative Study
. 2008 Mar 7;14(9):1333-8.
doi: 10.3748/wjg.14.1333.

Isolation and bioinformatics analysis of differentially methylated genomic fragments in human gastric cancer

Ai-Jun Liao  1 , Qi Su, Xun Wang, Bin Zeng, Wei Shi
Affiliations
Comparative Study

Isolation and bioinformatics analysis of differentially methylated genomic fragments in human gastric cancer

Ai-Jun Liao et al. World J Gastroenterol. .

Abstract

Aim: To isolate and analyze the DNA sequences which are methylated differentially between gastric cancer and normal gastric mucosa.

Methods: The differentially methylated DNA sequences between gastric cancer and normal gastric mucosa were isolated by methylation-sensitive representational difference analysis (MS-RDA). Similarities between the separated fragments and the human genomic DNA were analyzed with Basic Local Alignment Search Tool (BLAST).

Results: Three differentially methylated DNA sequences were obtained, two of which have been accepted by GenBank. The accession numbers are AY887106 and AY887107. AY887107 was highly similar to the 11th exon of LOC440683 (98%), 3' end of LOC440887 (99%), and promoter and exon regions of DRD5 (94%). AY887106 was consistent (98%) with a CpG island in ribosomal RNA isolated from colorectal cancer by Minoru Toyota in 1999.

Conclusion: The methylation degree is different between gastric cancer and normal gastric mucosa. The differentially methylated DNA sequences can be isolated effectively by MS-RDA.

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Figures

Figure 1
Figure 1
Schematic diagram of MS-RDA experimental strategy.
Figure 2
Figure 2
Amplicons of gastric cancer and normal gastric mucosa. M: DNA marker; 1: Gastric cancer amplicon; 2: Normal gastric mucosa amplicon.
Figure 3
Figure 3
A: Results after the third cycle of competitive hybridization. B: After a second cycle of competitive hybridization. M: DNA marker; 1: differentially methylated fragment of approximately 400 bp; 2: Two differentially methylated fragments, one is approximately 400 bp and the other lies between 200-300 bp.
Figure 4
Figure 4
PCR results. M: DNA marker; 1: Differ-entially methylated fragment of approximately 400 bp; 2: Differentially methylated fragment of approximately 200-300 bp.
Figure 5
Figure 5
AY887106 (A) and AY887107 (B) sequencing.
See this image and copyright information in PMC

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