Abstract 421: Differences of DNA methylation patterns according to histologic subtypes of early gastric carcinomas

• Published in: Cancer research (Chicago, Ill.) Ill.), 2014-10, Vol.74 (19_Supplement), p.421-421
• Main Authors: Mia-Jan, Khalilullah, Ryu, Hoon, Lee, Mi-Ra, Ji, Sun-Young, Cho, Mee-Yon
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2014-421

Background: The DNA methylation change is known to play a crucial role in early gastric carcinogenesis. However, its association with the histologic subtypes of EGCs has not been fully elucidated. In this study, we aim to know whether the subtypes of early gastric carcinomas (EGCs) are related to the differences of DNA methylation or not using genome wide methylation assay. Materials and Method: The comprehensive methylation analysis was performed by Illumina Infinium methylation assay (IIMA, 450K BeadChip kit) covering 450,000 sites on 12 tumors and 12 matched non-tumor mucosa from 12 patients with EGC. Hisytologically, the EGCs were devided into intestinal type (group A, n=6) and non-intestinal type (group B, diffuse=4 and mixed=2). The CpG sites in 450K microarray chip are classified into CpG islands, shores (2kb), shelves (2kb∼4kb) and open sea (>4kb) by CpG content and neighborhood context. According to the functional genomic distribution they are classified into promoter, body, 3′UTR and intergenic. To determine DMRs, average β-values were computed with β-values in signal intensity of over 3000. The Δβ-value was a result substracted average β-value of one from the other. When Δβ is over 0.2 or below -0.2, it was considered to be meaningful and refered to differentially methylated regions (DMRs) . Results: There were 484 DMRs in group A tumor and 208 DMRs in group B. The pattern of DMRs were different between two groups. In group A tumor, most of DMRs (97.73%) were hypermethylated and 75.26% were in CpG island. On the other hand, the group B tumors showed that 63.94% of DMRs were hypermethylated and only less than half of them (48.87%) were in CpG island. In terms of functional genomic distribution of DMRs, promoter (38.66%) was the most common site in group A while body (54.14%) was in group B. On Hierarchical clustering analysis, the clear grouping was made by 208 DMRs in three cases, two of them being mixed-type, by both correlation and Euclidean methods. However, no distinct grouping was found with DMRs in group A. Hierarchical clustering analysis of non-tumor mucosa showed a distinct separation between group A and B. Conclusions: DNA methylation pattern was distinctively different between the histologic subtype of EGCs. In the intestinal type of EGCs, the DNA methylation seems to be started in non-tumor mucosa. Citation Format: Khalilullah Mia-Jan, Hoon Ryu, Mi-Ra Lee, Sun-Young Ji, Mee-Yon Cho. Differences of DNA methylation patterns according t