Identification and evaluation of oxidative phosphorylation-related genes regulated by METTL3 in gastric cancer based on proteomics and m6A methylomes

METTL3-mediated RNA N6-methyladenosine (m6A) is the most prevalent modification participates in tumor initiation and progression via regulating expression of their target genes in cancers. However, its role in tumor cell metabolism remains poorly appreciated. In this study, we conducted a multi-omics analysis including m6A microarray and quantitative proteomics to explore the potential effect and mechanism of METTL3 on the metabolism in gastric cancer cells. Our results found that significant alterations in the protein and m6A modification profile which induced by METTL3 overexpression in GC cells. Gene Ontology (GO) enrichment results showed that down-regulated proteins were significantly enriched in intracellular mitochondrial oxidative phosphorylation (OXPHOS), and the Protein-Protein Interaction (PPI) network analysis found that these differentially expressed proteins were significantly associated with OXPHOS. Subsequently, a prognostic model constructed based on the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and the high-risk group showed a worse prognosis in GC patients. Meanwhile, the Gene Set Enrichment Analysis (GSEA) showed a significant enrichment in the energy metabolism signaling pathway. Then, combined with the results of the m6A microarray analysis, the intersection molecules of DEPs and differential methylation genes (DMGs) were significantly correlated with the genes involved in OXPHOS. Besides, there were also significant differences in prognosis and GSEA enrichment between the two clusters of GC patients classified according to consensus clustering algorithm. Finally, we focused on highly expressed, highly methylated molecules regulated by METTL3 and identified three (AVEN, DAZAP2, DNAJB1) genes that were significantly associated with poor prognosis in patients with GC. These results indicated that METTL3-regulated DEPs in GC cells were significantly associated with OXPHOS. After combined with m6A microarray analysis, the results suggested that these proteins might be involved in cell energy metabolism through m6A modifications thus influencing the prognosis of GC patients. Overall, our study revealed that METTL3 involved in cell metabolism through an m6A-dependent mechanism in GC cells, and indicated a potential biomarker for prognostic prediction in GC.

METTL3介导的RNA N6-甲基腺苷（m6A）是最普遍的RNA修饰类型，可通过调控癌症中靶基因的表达参与肿瘤的发生与进展。然而，其在肿瘤细胞代谢中的作用仍未得到充分阐明。本研究通过整合m6A微阵列与定量蛋白质组学的多组学分析，探究METTL3对胃癌（Gastric Cancer, GC）细胞代谢的潜在影响与作用机制。研究结果显示，胃癌细胞中METTL3过表达会显著改变蛋白质组与m6A修饰谱。基因本体（Gene Ontology, GO）富集分析结果显示，下调的差异表达蛋白显著富集于细胞内线粒体氧化磷酸化（mitochondrial oxidative phosphorylation, OXPHOS）通路；蛋白质相互作用（Protein-Protein Interaction, PPI）网络分析则发现，这些差异表达蛋白（differentially expressed proteins, DEPs）与OXPHOS通路显著相关。随后，本研究基于癌症基因组图谱（Cancer Genome Atlas, TCGA）与基因表达综合数据库（Gene Expression Omnibus, GEO）构建了胃癌预后预测模型，其中高风险亚组的胃癌患者预后更差。与此同时，基因集富集分析（Gene Set Enrichment Analysis, GSEA）结果显示，能量代谢信号通路显著富集。结合m6A微阵列分析结果，差异表达蛋白与差异甲基化基因（differential methylation genes, DMGs）的交集分子与OXPHOS通路相关基因显著相关。此外，通过一致性聚类算法对胃癌患者进行分组后，两个亚组在预后与GSEA富集结果上均存在显著差异。最后，本研究聚焦于METTL3调控的高表达、高甲基化分子，筛选出3个与胃癌患者不良预后显著相关的基因（AVEN、DAZAP2、DNAJB1）。上述结果表明，胃癌细胞中METTL3调控的差异表达蛋白与OXPHOS通路显著相关。结合m6A微阵列分析结果，本研究提示这些蛋白可能通过m6A修饰参与细胞能量代谢，进而影响胃癌患者的预后。综上，本研究揭示了METTL3通过m6A依赖的调控机制参与胃癌细胞的能量代谢，并为胃癌患者的预后预测提供了潜在的生物标志物。