DNA methylation status of a distinctively different subset of genes is associated with each histologic Lauren classification subtype in early gastric carcinogenesis

Abstract

Abstract. DNA methylation change is known to play a crucial role in early gastric carcinogenesis. The present study aimed to identify and validate the correlation between differentially methylated regions (DMRs) and the subtypes of early gastric cancers (EGCs). Illumina Infinium methylation assay (IIMA; 450K BeadChip kit) was performed on fresh tumor and non-tumor tissues of 12 EGCs to screen the methylation status of 450,000 CpG sites. To evaluate the significance of DNA methylation in each histologic subtype, pyrosequencing assay (PA) was performed on 38 EGCs (18 intestinal-, 12 mixed-and 8 diffuse-type) using 12 genes selected from the screening. Between tumors of the intestinal-type (n=6), and diffuse-(n=4) plus mixed-types (n=2), 169 regions showed significant differences (intensity >3,000, Δβ >0.2) in IIMA. Hierarchical clustering using the 169 DMRs revealed distinct separation between the two groups. In PA using 12 selected genes from the IIMA results, the aberrant methylation statuses of DVL2 (p=0.0186) and ETS1 (p=0.0222) were significantly related to diffuse-and mixed-types rather than the intestinal-type, while C19orf35 (p=0.019) and CNRIP1 (p=0.0473) were related to the diffuse-type rather than intestinal-type, and GAL3ST2 (p=0.0158) and ITGA3 (p=0.0273) were related to the mixedtype rather than the other two types. The methylation of other genes, CLIP4, XKR6, CCDC57, MAML3 and SDC2, was related with age, tumor location, or Helicobacter infection rather than the histologic subtype. Aberrant DNA methylation of certain genes may be independently involved in each histologic subtype of EGC. Furthermore, mixed-type EGCs may be a distinctive histologic subtype based on the different subset of DMRs compared to those of other subtypes. IntroductionDespite its decreasing trend, gastric cancer (GC) still remains one of the most troublesome malignant diseases worldwide. It is the fourth most common cancer and the second leading cause of cancer-related death worldwide (1-3). In Asian countries such as Japan and Korea, it has the highest incidence among all malignancies although its overall survival rate has improved during the last few decades due to extensive screening programs (3,4). Due to the poor prognosis and limited treatment options of advanced GC, it remains a challenging task to determine effective molecular-pathological markers for early diagnosis with appropriate histological classification (5).Lauren classification, which subgroups GCs mainly as two types, intestinal and diffuse, was first introduced in 1965 and has been generally accepted as a distinct and simple histological classification of GCs by most pathologists (6). Since the two major types show distinctively different phenotypic, epidemiologic and biologic characteristics, it is believed that different genetic alterations may be implicated in each histologic type of the classification (7). However, a considerable number of GCs accounting for 10-15% of cases, share the histologic features of these two types and are designated as mixed-type ...

Colorectal adenoma and cancer detection based on altered methylation pattern of SFRP1, SFRP2, SDC2, and PRIMA1 in plasma samples

“…62 Another study showed that SDC2 was hypermethylated in tumor tissue samples of gastric cancer patients compared with the corresponding non-tumor mucosa (CNM). 63 As the first step in our study, the SDC2 promoter was found to be strongly hypermethylated by pyrosequencing both in colonic adenoma and CRC samples compared with unmethylated healthy controls. These results have inspired us to analyze the methylation pattern of SDC2 using ML assays in cell-free DNA fraction.…”

Clinicopathological Significance of Elevated PIK3CA Expression in Gastric Cancer

“…Furthermore, a recent study revealed that each Lauren classification subtype (diffuse, mixed, and intestinal) exhibited a unique DNA methylation signature during early gastric carcinogenesis. 27 These findings suggested that the morphological characteristics of gastric cancer are induced by a variety of unique genetic or epigenetic alterations. Therefore, we concluded that different PIK3CA expression levels among the histological subgroups can partially explain their morphological features, including tumor differentiation.…”

Early detection of gastric cancer using global, genome-wide and IRF4, ELMO1, CLIP4 and MSC DNA methylation in endoscopic biopsies

“…Shin et al reported the promoter methylation of MOS, DCC, CRK , and PTPN6 in gastric cancer [76]. Epigenome-wide DNA methylation arrays have also identified the role of DVL2 and ETS1 methylation in diffuse- and mixed-types of early gastric cancers [77]. On the other hand, C19orf35 and CNRIP1 were related to the diffuse type rather than intestinal type, and GAL3ST2 and ITGA3 were related to the mixed-type rather than the other two types [77].…”

“…Epigenome-wide DNA methylation arrays have also identified the role of DVL2 and ETS1 methylation in diffuse- and mixed-types of early gastric cancers [77]. On the other hand, C19orf35 and CNRIP1 were related to the diffuse type rather than intestinal type, and GAL3ST2 and ITGA3 were related to the mixed-type rather than the other two types [77]. The methylation of other genes, CLIP4, XKR6, CCDC57, MAML3 and SDC2 , was related with one or more of the following variables: age, tumor location, and Helicobacter pylori infection, rather than with the histologic subtype [77].…”