Abstract
BackgroundThe recent discovery of cancer/tissue specificity of miRNA has indicated its great potential as a therapeutic target. In Epstein–Barr virus-associated gastric cancer (EBVaGC), host genes are affected by extensive DNA methylation, including miRNAs. However, the role of methylated miRNA in the development of EBVaGC and immune cell infiltration has largely remained elusive.ResultsAfter crossmatching the DNA methylation and expression profile of miRNA and mRNA in the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas Research Network (TCGA), we discovered that miR-129-2-3p was significantly suppressed due to hypermethylation on its enhancer in EBVaGC. The differentially expressed genes (DEGs) added up to 30, among which AKAP12 and LARP6 were predicted to be the target genes of miR-129-2-3p and negatively correlated with patients’ survival. Accordingly, miR-129-2-3p was significantly down-regulated in tumor samples in 26 (65%) out of 40 cases in our cohort (P < 0.0001). The proliferation, migration and invasion functions of GC cells were significantly promoted when transfected with miR-129-2-3p inhibitor and suppressed when transfected with mimics or treated with 5-aza-2′-deoxycytidine. Moreover, a comprehensive regulation network was established by combining the putative transcription factors, miRNA-mRNA and protein–protein interaction (PPI) analysis. Pathway enrichment analysis showed that cytokine activity, especially CCL20, was the most prominent biological process in EBVaGC development. Immune cell infiltration analysis demonstrated CD4+ T cell, macrophage and dendritic cell infiltrates were significantly enriched for the prognostic-indicated hub genes.ConclusionThis study has provided a comprehensive analysis of differentially expressed miRNAs and mRNAs associated with genome-wide DNA methylation by integrating multi-source data including transcriptome, methylome and clinical data from GEO and TCGA, QPCR of tumor samples and cell function assays. It also gives a hint on the relationships between methylated miRNA, DEGs and the immune infiltration. Further experimental and clinical investigations are warranted to explore the underlying mechanism and validate our findings.
Highlights
The recent discovery of cancer/tissue specificity of miRNA has indicated its great potential as a therapeutic target
Identification of methylated differentially expressed miRNAs in Epstein–Barr virus-associated gastric cancer (EBVaGC) The procedure for data analysis was compiled into a flowchart (Fig. 1)
To further delineate the DEmiRNAs in EBVaGC due to methylation, we again integrated the results of Methylated differentially expressed gene (MDEG) from Gastric cancer (GC) and Epstein–Barr virus (EBV) datasets and found miR-129-2-3p to be the only one gene that was down-regulated due to hypermethylation in EBVaGC (Additional file 1: Fig. S1a)
Summary
The recent discovery of cancer/tissue specificity of miRNA has indicated its great potential as a therapeutic target. In Epstein–Barr virus-associated gastric cancer (EBVaGC), host genes are affected by extensive DNA methylation, including miRNAs. the role of methylated miRNA in the development of EBVaGC and immune cell infiltration has largely remained elusive. The EBV-associated gastric cancers (EBVaGC) are attracting much attention recently, since they are often correlated with increased lymphocytic infiltration with high expression of PD-L1, demonstrating higher sensitivity to immune checkpoint therapies [3]. It has been reported that EBVaGCs are abundant with DNA methylation, little is known of the role of EBV infection during the development of GC and its effect on the efficacy of immune checkpoint therapy. Epigenetic alterations are reversible and have immense therapeutic potential They could be seen as surrogate markers for exposure to environmental factors, such as infections and hypoxia. Since the heterogeneity of immune infiltration might be a trait intrinsic of tumor cells [12], epigenetic changes such as DNA methylation could serve as a dynamic marker for the immune infiltration profile
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