Epstein‐Barr virus‐positive gastric cancer involves enhancer activation through activating transcription factor 3

Abstract

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. AbstractEpstein-Barr virus (EBV) is associated with particular forms of gastric cancer (GC).We previously showed that EBV infection into gastric epithelial cells induced aberrant DNA hypermethylation in promoter regions and silencing of tumor suppressor genes. We here undertook integrated analyses of transcriptome and epigenome alteration during EBV infection in gastric cells, to investigate activation of enhancer regions and related transcription factors (TFs) that could contribute to tumorigenesis. Formaldehyde-assisted isolation of regulatory elements (FAIRE) sequencing (-seq) data revealed 19 992 open chromatin regions in putative H3K4me1 + H3K4me3 − enhancers in EBV-infected MKN7 cells (MKN7_EB), with 10 260 regions showing increase of H3K27ac. Motif analysis showed candidate TFs, eg activating transcription factor 3 (ATF3), to possibly bind to these activated enhancers. ATF3 was considerably upregulated in MKN7_EB due to EBV factors including EBV-determined nuclear antigen 1 (EBNA1), EBV-encoded RNA 1, and latent membrane protein 2A. Expression of mutant EBNA1 decreased copy number of the EBV genome, resulting in relative downregulation of ATF3 expression. Epstein-Barr virus was also infected into normal gastric epithelial cells, GES1, confirming upregulation of ATF3. Chromatin immunoprecipitation-seq analysis on ATF3 binding sites and RNA-seq analysis on ATF3 knocked-down MKN7_EB revealed 96 genes targeted by ATF3-activating enhancers, which are related with cancer hallmarks, eg evading growth suppressors. These 96 ATF3 target genes were significantly upregulated in MKN7_EB compared with MKN7 and significantly downregulated when ATF3 was knocked down in EBVpositive GC cells SNU719 and NCC24. Knockdown of ATF3 in EBV-infected MKN7, SNU719, and NCC24 cells all led to significant decrease of cellular growth through | 1819 ASAKAWA et Al.

DNA Methylation and Genetic Aberrations in Gastric Cancer

“…EBV infection causes enhancer activation and repression, which may be associated with gastric carcinogenesis [31]. A recent study suggested that enhancer activation through ATF3 might be involved in carcinogenesis [32]. Our latest study has revealed that interaction of episomal EBV genome may directly rewire the host chromatin structure to aberrantly activate proto-oncogenes and promote gastric carcinogenesis [17].…”

Activation of EHF via STAT3 phosphorylation by LMP2A in Epstein‐Barr virus–positive gastric cancer

“…The dynamics of histone alterations usually cooperate with transcription programs to interact with genes through master transcription factors (TFs) by binding specific enhancer regions 21,22 . It has been reported that one of the master TFs, ATF3, induces aberrant enhancer activation after EBV infection in GC 23 . Other studies have also implied that EBV infection can induce enhancer rewiring by chromatin structural aberrations, contributing to EBV‐positive GC tumorigenesis 24 .…”

Inhibitory role of ATF3 in gastric cancer progression through regulating cell EMT and stemness

“…Genetic studies indicated the complexity of gastric cancer exits in different subtypes such as Epstein-Barr virus (EBV), microsatellite instability (MSI), and so on [ 30 ]. In the study by Asakawa et al [ 31 ], upregulation of ATF3 is linked with aberrant enhancer activation in EBV infected gastric epithelial cells (e.g. SNU719 and NCC24), and enhances proliferation of these gastric cells.…”