Gong Zhiyuan, Bi Chunxia, Liu Wen, Luo Bing
Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
Department of Clinical Laboratory, Qingdao Municipal Hospital, Qingdao, Shandong, China.
Biochem Genet. 2025 Feb;63(1):67-84. doi: 10.1007/s10528-024-10702-y. Epub 2024 Feb 27.
An important feature of EBV-associated gastric cancer (EBVaGC) is extensive methylation of viral and host genomes. This study aims to analyze DNA methylation-driven genes (DMDG) in EBVaGC through bioinformatics methods, providing an important bioinformatics basis for the differential diagnosis and treatment of potential methylation biomarkers in EBVaGC. We downloaded the mRNA expression profiles and methylation datasets of EBVaGC and EBV-negative gastric cancer (EBVnGC) through the TCGA database to screen methylated-differentially expressed genes (MDEGs). DNA methylation-driver genes were identified based on MethylMix algorithm and key genes were further identified by LASSO regression and Random Forest algorithm. Then, we performed gene enrichment analysis for key genes and validated them by GEO database. Gene expression differences in EBVaGC and EBVnGC cell lines was determined by quantitative real-time PCR (qRT-PCR) and western blotting and in GT38 cell and SNU719 cell which all treated by 5-Aza-CdR. Finally, the effect of key gene on the migration and proliferation capacity of EBVaGC cells was determined by Transwells assay and Cell counting Kit-8 (CCK-8) assay. We obtained a total of 687 hypermethylation-low expression genes (Hyper-LGs) and further obtained 53 DNA methylation-driver genes based on the MethylMix algorithm. A total of six key genes (SCIN, ETNK2, PCDH20, PPP1R3C, MATN2, and HOXA5) were identified by LASSO regression and Random Forest algorithm. Among them, SCIN expression was significantly lower in EBVaGC cell lines than in EBVnGC cell lines, and its expression was significantly recovered in EBVaGC cell lines treated with 5-Aza-CdR. Overexpression of SCIN can promote the proliferation and migration capacity of EBVaGC cells. Our study will provide some bioinformatics basis for the study of EBVaGC-related methylation. SCIN may be used as potential methylation biomarkers for the diagnosis and treatment of EBVaGC.
EB病毒相关胃癌（EBVaGC）的一个重要特征是病毒和宿主基因组的广泛甲基化。本研究旨在通过生物信息学方法分析EBVaGC中DNA甲基化驱动基因（DMDG），为EBVaGC潜在甲基化生物标志物的鉴别诊断和治疗提供重要的生物信息学依据。我们通过TCGA数据库下载了EBVaGC和EBV阴性胃癌（EBVnGC）的mRNA表达谱和甲基化数据集，以筛选甲基化差异表达基因（MDEG）。基于MethylMix算法鉴定DNA甲基化驱动基因，并通过LASSO回归和随机森林算法进一步鉴定关键基因。然后，我们对关键基因进行基因富集分析，并通过GEO数据库进行验证。通过定量实时PCR（qRT-PCR）和蛋白质免疫印迹法测定EBVaGC和EBVnGC细胞系中的基因表达差异，并在经5-氮杂-2'-脱氧胞苷（5-Aza-CdR）处理的GT38细胞和SNU719细胞中进行测定。最后，通过Transwell实验和细胞计数试剂盒-8（CCK-8）实验确定关键基因对EBVaGC细胞迁移和增殖能力的影响。我们共获得687个高甲基化低表达基因（Hyper-LGs），并基于MethylMix算法进一步获得53个DNA甲基化驱动基因。通过LASSO回归和随机森林算法共鉴定出6个关键基因（SCIN、ETNK2、PCDH20、PPP1R3C、MATN2和HOXA5）。其中，SCIN在EBVaGC细胞系中的表达明显低于EBVnGC细胞系，在用5-Aza-CdR处理的EBVaGC细胞系中其表达明显恢复。SCIN的过表达可促进EBVaGC细胞的增殖和迁移能力。我们的研究将为EBVaGC相关甲基化的研究提供一些生物信息学依据。SCIN可能作为EBVaGC诊断和治疗的潜在甲基化生物标志物。
