The metabolic landscape of Epstein–Barr-virus-associated gastric cancer (EBVaGC) remains to be elucidated. In this study, we used transcriptomics, metabolomics, and lipidomics to comprehensively investigate aberrant metabolism in EBVaGC. Specifically, we conducted gene expression analyses using microarray-based data from gastric adenocarcinoma epithelial cell lines and tissue samples from patients with clinically advanced gastric carcinoma. We also conducted complementary metabolomics and lipidomics using various mass spectrometry platforms. We found a significant downregulation of genes related to metabolic pathways, especially the metabolism of amino acids, lipids, and carbohydrates. The effect of dysregulated metabolic genes was confirmed in a survival analysis of 3951 gastric cancer patients. We found 57 upregulated metabolites and 31 metabolites that were downregulated in EBVaGC compared with EBV-negative gastric cancer. Sixty-nine lipids, mainly ether-linked phospholipids and triacylglycerols, were downregulated, whereas 45 lipids, mainly phospholipids, were upregulated. In total, 15 metabolisms related to polar metabolites and 15 lipid-associated pathways were involved in alteration of metabolites by EBV in gastric cancer. In this work, we have described the metabolic landscape of EBVaGC at the multi-omics level. These findings could help elucidate the mechanism of EBVaGC oncogenesis.

Epstein-Barr virus remains dormant in the host cell but occasionally switches to the lytic cycle when stimulated. However, the exact molecular mechanism of this lytic induction is not well understood. In this study, we demonstrate that Epstein-Barr virus infection leads to a reduction in ceramide levels. Additionally, the restoration of ceramide levels triggers lytic replication of Epstein-Barr virus with increase in phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) and CREB. Our study suggests that the Epstein-Barr virus can inhibit lytic replication and remain latent through reduction of host cell ceramide levels. This study reports the regulation of lytic replication by ceramide in Epstein-Barr virus-positive gastric cancer.

Epstein–Barr virus (EBV)-associated gastric carcinoma (EBVaGC) represents a distinct molecular subtype characterized by extensive DNA methylation and altered cell death signaling. This study investigated the regulation and function of gasdermin E (GSDME), a key mediator of pyroptosis, in EBVaGC. Transcriptomic analysis of The Cancer Genome Atlas (TCGA) data revealed that GSDME expression was selectively suppressed in EBV-positive gastric cancer, while other gasdermin family members were upregulated. Validation in multiple cell lines confirmed that EBV infection markedly reduced GSDME expression through promoter hypermethylation, which was reversed by treatment with the DNA methyltransferase inhibitor 5-azacytidine. EBV-positive cells exhibited enhanced caspase-3 activation and increased GSDME cleavage upon paclitaxel (PTX) exposure, leading to elevated lactate dehydrogenase (LDH) release and pyroptotic morphology. Overexpression of GSDME amplified, whereas siRNA-mediated knockdown or caspase-3 inhibition suppressed, PTX-induced pyroptosis without significantly altering overall cell viability. These findings demonstrate that EBV-induced epigenetic silencing of GSDME contributes to the modulation of chemotherapy-induced cell death, and that GSDME acts as a critical effector converting apoptosis to pyroptosis through caspase-3 activation. Collectively, our results reveal a novel link between EBV-driven DNA methylation and pyroptotic cell death, suggesting that restoration of GSDME expression may enhance therapeutic responses in EBV-associated gastric cancer.

Epstein–Barr virus (EBV) infection is closely associated with gastric cancer, yet its role in m6A-dependent gene regulation remains poorly understood. In this study, we investigated how EBV infection alters the m6A methylation pattern in gastric cancer cells and examined its impact on TSC22D1 mRNA stability through interaction with the m6A reader protein YTHDF1. m6A RNA immunoprecipitation sequencing (MeRIP-seq) revealed a significant reduction in m6A methylation of TSC22D1 in EBV-infected gastric cancer cells (AGS-EBV) compared with EBV-negative cells (AGS). Moreover, YTHDF1 knockdown increased both the stability and expression of TSC22D1. These findings demonstrate that YTHDF1 binds to TSC22D1 mRNA and promotes its m6A-dependent degradation. Collectively, our results suggest that EBV infection modulates m6A modification to regulate gene stability and identify the YTHDF1–TSC22D1 axis as a potential therapeutic target in EBV-associated gastric cancer.