Whole genome MBD-seq and RRBS analyses reveal that hypermethylation of gastrointestinal hormone receptors is associated with gastric carcinogenesis

Abstract

DNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis. In this study, we focused on differentially methylated promoters (DMPs) that could be directly associated with gene expression. We detected 2,761 and 677 DMPs between the GT and GM by MBD-seq and RRBS, respectively, and for a total of 3,035 DMPs. Then, 514 (17%) of all DMPs were detected in the IM genome, which is a precancer of GC, supporting that some DMPs might represent an early event in gastric carcinogenesis. A pathway analysis of all DMPs demonstrated that 59 G protein-coupled receptor (GPCR) genes linked to the hypermethylated DMPs were significantly enriched in a neuroactive ligand–receptor interaction pathway. Furthermore, among the 59 GPCRs, six GI hormone receptor genes (NPY1R, PPYR1, PTGDR, PTGER2, PTGER3, and SSTR2) that play an inhibitory role in the secretion of gastrin or gastric acid were selected and validated as potential biomarkers for the diagnosis or prognosis of GC patients in two cohorts. These data suggest that the loss of function of gastrointestinal (GI) hormone receptors by promoter methylation may lead to gastric carcinogenesis because gastrin and gastric acid have been known to play a role in cell differentiation and carcinogenesis in the GI tract.

ONECUT2 upregulation is associated with CpG hypomethylation at promoter‐proximal DNA in gastric cancer and triggers ACSL5

“…Previously, we identified 174 hypomethylated differentially methylated promoters (DMPs) using methylome data from laser‐capture microdissected GM, IM, and GC cells from a single patient with IGC . These included 91 GC‐specific and 83 early‐onset DMPs.…”

“…Total RNA was isolated from GC cells or tissues using the RNeasy kit (Qiagen, Valencia, CA), treated with DNase I (Promega), and reverse‐transcribed with Superscript II reverse transcriptase (Invitrogen) as previously described . RT‐PCR for OC2 was performed as follows: 94°C for 5 min, followed by 35 cycles of 94°C for 30 sec, 64°C for 30 sec and 72°C for 30 sec, with a final cycle of 72°C for 7 min.…”

Predicting Carcinogenic Mechanisms of Non-Genotoxic Carcinogens via Combined Analysis of Global DNA Methylation and In Vitro Cell Transformation

“…RRBS is an efficient and high-throughput technique for analyzing genome-wide methylation profiles at a single nucleotide level [25]. In addition, RRBS has been used to study several human diseases, including cancer [47], neurodegenerative diseases [48], aging [49], and immunological diseases [50]. Ten test articles selected as NGTXCs in this study were also predicted to be negative through Derek/Sarah analysis.…”

A novel multi-scale bioinformatics strategy for identifying the molecular mechanism by insighting into ceRNA network integrating WGCNA and meta-analysis: compound kushen injection for treating gastric carcinoma as a proof

“…Whole-genome analysis showed that PTGER3 is abnormally low in gastric cancer. PTGER3 can inhibit the secretion of gastric parietal cells and gastric acid [61]. The lack of PTGER3 leads to abnormal secretion of gastrin and gastric acid and accelerates the occurrence of gastric cancer [62].…”