Constructing Key LncRNA Networks Related To Gastric Cancer Progression By WGCDA

Objective: Gastric cancer is a malignant tumor originated from gastric mucosa epithelium.Worldwide,the morbidity and mortality rate of gastric cancer are very high.The mortality rate of gastric cancer is among the top three.In the treatment of gastric cancer,as early as last century,gastric cancer resection was widely used to treat gastric cancer patients.However,advanced gastric cancer has the characteristics of metastasis.After gastric cancer resection,there will still be recurrence symptoms,and the postoperative survival rate is very low.Long non-coding RNA(Lnc RNA)was previously considered as useless "junk genes".However,with the deepening of research,it has been found that Lnc RNA plays a very important role in cell life activities.It not only plays a role in the level of gene replication,but also plays a significant role in gene transcription,protein translation and other aspects.In addition,there may be many other ways in which Lnc RNAs are involved in cellular life.However,studies have shown that Lnc RNA is involved in cell invasion,metastasis,proliferation,autophagy and other aspects.In addition,Lnc RNA plays a role as a prognostic marker and a biomarker for cancer in most cancers,providing great help for the diagnosis and treatment of cancer.Weighted gene co-expression network analysis(WGCNA)is a method that combines gene expression data with clinical traits.In recent years,we found that a large number of studies used Gene Expression Omnibus chip data or TCGA(The Cancer Genome Atlas)sequencing data for Gene analysis,combining genes with clinical phenotypic characteristics for analysis.Research methods: WGCNA algorithm was used to analyze the gene expression information of 375 patients with gastric cancer,and the differential genes will be divided into different modules,combined with clinical data,the gene modules related to clinical phenotype were selected to construct network.The molecular functions and participating signaling pathways of gene modules were analyzed through Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG).In addition,the role of Lnc RNA in the gene network is determined by survival analysis and Receiver operating characteristic curve(ROC)plotting.In the gene network,the centrality of the nodes in the network determines the key of the genes.Results: The gene expression data of 32 normal samples and 375 tumor samples were analyzed,and 8,184 up-regulated genes and 3,632 down-regulated genes were obtained.Among them,the first 50 genes were selected for visualization,and the heat map was drawn to represent the gene expression in 32 normal tissue samples and 375 cancer tissue samples.Through WGCNA analysis of the expression data and clinical phenotype data of11816 differentially expressed genes,we found that the red module was related to gastric cancer metastasis(M,metastasis stage),lymphnodes(N,node stage)and number of positive lymphnodes;module midnightblue is associated with primary tumor(T,tumor stage)and pylori infection.Module cyan is associated with primary tumor and helicobacter pylori infection.The module floralwhite is related to M;The module sienna3 was related to M(p < 0.05).Through GO analysis,it is found that the main function of the module midnightblue is involved in the regulation of cell receptors and ligands.The main function of module cyan is to participate in the structure of extracellular matrix.The main function of the floralwhite module is to catalyze DNA polymerase activity.Through KEGG analysis,red module was mainly involved in gastric acid secretion.The module nightblue is mainly involved in the interaction of cytokine-cytokine receptor and osteoclast differentiation.Module cyan is mainly involved in protein digestion and absorption,and PI3K-Akt signaling pathway.By analyzing the survival of these gene modules,we found that there were 4 Lnc RNAs with significant significance for the prognosis.Through ROC analysis of Lnc RNAs in the module,we found that 9 Lnc RNAs had potential biomarker function(AUC>0.8,p<0.05).At the same time,we use Cytoscape software to visualize the network information of relevant modules and construct the network about Lnc RNAs-m RNAs.Conclusion: By combining the RNA-seq data of gastric cancer patients in TCGA with the clinical data of gastric cancer patients,WGCNA analysis was conducted to screen out the gene modules related to clinical traits.Through the gene survival analysis,GO analysis and KEGG analysis of the genes in the modules,important gene modules and important Lnc RNAs were found.Finally,it is found that DLGAP1-AS5,LINC01929,LINC01310 and LINC02182 have guiding significance for the prognosis diagnosis and treatment ofgastric cancer patients.It was found that LINC02345,LINC02073,MMP25-AS1,LINC01614,GORAB-AS1,LINC01235,LINC02544,LINC01050 and TMEM220-AS1 had specific expressions in gastric cancer tissues compared with normal tissues,which may be potential biomarkers for the diagnosis and treatment of gastric cancer.The expression of Lnc RNAs in gastric cancer cell lines was further determined by real-time quantitative PCR(QPCR).The identification and screening of Lnc RNAs related to the progression of gastric cancer in this study can provide a reference for the diagnosis and treatment of gastric cancer.