早期胃癌淋巴结转移差异表达基因分析

Analysis of differentially expressed genes in lymph node metastasis of early gastric cancer

目的:利用TCGA数据库早期胃癌RNA-seq数据,探讨早期胃癌淋巴结转移差异表达基因及相关生物学意义。方法:从TCGA数据库下载胃癌RNA-seq数据和临床病理数据,筛选出早期胃癌数据,并根据有无淋巴结转移进行分组对比分析。在R3.5.3环境下,加载edgeR包,筛选T 1N 1-3 M 0期与T 1N 0M 0期胃癌相比的差异表达基因。通过对差异表达基因进行GO功能和KEGG通路富集分析,分析其潜在的生物学功能。分析差异表达基因与胃癌预后的相关性。结果:早期合并淋巴结转移组胃癌中发现197个显著上调表达基因和5个显著下调表达基因。上调差异表达基因显著富集在白细胞介素-1、白细胞介素-6、肿瘤坏死因子等作用的细胞增殖相关GO功能因子,和Wnt信号通路、核转录因子κB(NF-κB)信号通路、胃癌信号通路等癌症相关信号通路上。上调和下调差异表达基因多与胃癌患者预后相关。结论:早期胃癌淋巴结结转移相关差异表达基因可能通过细胞增殖相关GO功能和Wnt信号通路、NF-κB信号通路等信号通路影响早期胃癌的生物学行为;有无淋巴结早期胃癌中的差异表达基因表达水平多与胃癌患者预后显著相关,有可能作为胃癌的诊治靶点应用于临床。

Objective:To explore differentially expressed genes and their biological significance in lymph node metastasis of early gastric cancer using RNA-seq data from TCGA database.Methods:RNA-seq data and clinicopathological data of gastric cancer were downloaded from TCGA database,and early gastric cancer data were screened out and grouped according to the presence or absence of lymph node metastasis.Under R3.5.3 environment,edgeR package was loaded to screen differentially expressed genes of T 1N 1-3 M 0 gastric cancer compared with T 1N 0M 0 gastric cancer.The potential biology function of differentially expressed genes was analyzed by GO function and KEGG pathway enrichment analysis.The correlation between differentially expressed genes and prognosis of gastric cancer was analyzed.Results:A total of 197 significantly up-regulated genes and 5 significantly down-regulated genes were screened out in early stage gastric cancer with lymph node metastasis.The up-regulated differentially expressed genes were significantly enriched in cell proliferation-related GO functions such as interleukin-1,interleukin-6,and tumor necrosis factor-α(TNF-α),and in cancer-related signaling pathways such as Wnt signaling pathway,NF-κB signaling pathway,and gastric cancer signaling pathway.Most of the up-regulated and down-regulated differentially expressed genes were significantly related to the prognosis of gastric cancer patients.Conclusions:Differentially expressed genes associated with lymph node metastasis in early gastric cancer may affect biological behavior of early gastric cancer through cell proliferation-related GO functions,Wnt signaling pathway and NF-κB signaling pathway,and so on.The levels of most differential expression genes are significantly associated with the prognosis of patients with gastric cancer,and may be used as diagnosis and treatment targets for gastric cancer.