| Background and Objectives:Colon cancer is one of the most common malignant tumors of digestive system in China.Metastasis and recurrence are the main causes of death in most patients with colon cancer.Techniques such as surgery and neoadjuvant chemotherapy have been widely used to treat colon cancer.However,due to the insidious onset of colon cancer and asymptomatic progress,some colon cancer patients were already in the middle and late stage when they sought treatment,and surgical resection could not prolong the survival time of these patients.At present,clinicians mainly judge the prognosis of colon cancer patients by disease progression and tumor stage at the time of diagnosis.However,traditional methods are insufficient to accurately evaluate the prognosis of patients with colon cancer.Therefore,it is important to accurately evaluate the prognosis of patients with colon cancer.In this study,differentially expressed genes related to the prognosis of colon cancer were screened from the TCGA database to construct a prognostic gene model for colon cancer,and key genes in the Wnt signaling pathway regulating the occurrence and development of colon cancer were screened,which is expected to provide a theoretical basis for prognosis management and individualized precision treatment of colon cancer patients.Methods:1.Access the Cancer Genome Atlas(TCGA)database,download the RNA expression data and clinical information of colon cancer patients,and analyze and screen the differentially expressed genes between colon cancer samples and normal tissues by R software edgeR package.2.Univariate Cox and multivariate Cox regression analysis of differentially expressed genes was conducted based on Cox proportional risk regression model,and prognostic genes related to overall survival were screened.The optimal prognostic gene model was constructed by coxph()function fitting of the Survival package in R language,and a risk scoring formula was formed.3.According to the median risk score,colon cancer patients were divided into high risk group and low risk group,and the predictive performance of prognostic gene model was evaluated by Kaplan-Meier survival analysis and ROC curve.4.The survival package of R language was used to analyze the relationship between the prognostic gene model and various clinical traits,and to evaluate whether the model can be used as an independent prognostic factor in patients with colon cancer.The predictive performance of the model in different populations was evaluated.5.Combined with the expression of each gene in the model and clinical information,the 5-year survival rate of patients with high and low gene expression groups was calculated by using the Survival package and Log-rank test in R software.The "ggpubr" package and Kruskal-Wallis test were used to analyze the relationship between gene expression and clinical data.6.KEGG signaling pathway analysis of differentially expressed genes was conducted by using the package of "clusterProfiler" in R language to screen the key genes involved in the Wnt signaling pathway of colon cancer.The "ggpubr" package and Kruskal-Wallis test were used to analyze the relationship between the expression of key genes and clinical data.Results:1.A total of 5544 differentially expressed genes were screened by TCGA database,among which 4152 genes were up-regulated and 1392 genes were down-regulated.2.Eleven genes including GABRD,FAM132B,LRRN4,RP11-400N13.2,RP11-108K3.2,RNU6-403P,RP11-429J17.8,LINC01296,RP11-190J1.3,AC002076.10,and CTC-573N18.1 were screened out by univariate and multivariate Cox regression analysis,and the optimal progress-gene model of colon cancer was constructed.Riskscore=GABRD ×0.40835+FAM132B ×0.29934+LRRN4×0.11695+RP11-400N13.2×0.14548+RP11-108K3.2×0.34000+RNU6-403P×0.17471+RP11-429J17.8×0.14123+LINC01296× 0.11822+RP11-190J1.3×0.12992+AC002076.10×0.26846+CTC-573N18.1 ×0.22879.3.Patients were divided into high and low risk groups according to the cut-off point of the median risk score of 0.9404.The 5-year overall survival rate was 39.5%(CI 29.5%-53%)in the high-risk group and 89.6%(CI 82.2%-97.7%)in the low-risk group.The results showed that with the increase in risk score,the number of deaths in the high-risk group was significantly higher than that in the low-risk group.The area under the ROC curve(AUC)of 1-year,3-year and 5-year overall survival rates of colon cancer patients was 0.796,0.839 and 0.827,respectively,indicating that the model had good prediction effect on short-term survival time and long-term survival time of colon cancer patients.4.By exploring the relationship between the prognostic gene model and various clinical traits,the results showed that the prognostic gene model(HR=1.112 95%CI 1.077-1.147 P<0.001)could independently predict the overall survival of patients with colon cancer,and was an independent predictor of the overall survival time of patients with colon cancer.Clinical grouping analysis showed that in different clinical stages(Ⅰ+Ⅱ,Ⅲ+Ⅳ),distant metastases(M0,M1)or lymph node metastases(N0,N1+2),the survival rate of high-risk patients was significantly lower than that of low-risk patients,indicating that the model could be used for prognosis analysis of colon cancer patients with different TNM stages.5.The 5-year survival rate of patients with high expression of GABRD,FAM132B,Rp11-400N13.2,Rp11-108K3.2,Rnu6-403P,Rp11-429J17.8,LINC01296,Rp11-190J1.3,AC002076.10,CTC-573N18.1 was lower than that of patients with low expression.The expression of GABRD,LINC01296,AC002076.10 and LRRN4 increased with the clinical stage and TNM stage.The expression of RP11-400N13.2 increased with the progression of clinical stages or lymph node metastasis.The expression of RP11-108K3.2 in patients with distant metastasis was significantly higher than that in patients without distant metastasis.6.Thirty-three differentially expressed genes in colon cancer Wnt signaling pathway were obtained by KEGG enrichment analysis,among which 26 genes were up-regulated and 7 genes were down-regulated.The top 10 key proteins were further screened by protein-protein interaction network,and the coding genes were Wnt11,Wnt7A,RNF43,Wnt3A,RSPO1,FZD10,Wnt2,Wnt3,Wnt7B,and Wnt8B.The expression of Wnt11 and Wnt7A increased with the clinical stage and TNM stage.The expression level of RNF43 in patients with distant metastasis was significantly higher than that in patients without distant metastasis.The expression of Wnt3A in patients with lymph node metastasis was significantly higher than that in patients without distant metastasis.Conclusions:A prognostic gene model for predicting the risk of colon cancer was established based on the data of patients with colon cancer from the Cancer Genome Atlas Database.At the same time,this model has been proved to be able to identify the risk of death in patients with colon cancer,and can effectively predict the survival rate of patients with colon cancer,and can be used as an independent influencing factor to evaluate the prognosis of patients with colon cancer.Explore the relationship between prognostic genes,key genes of Wnt signaling pathway and clinical traits in this model,which will help to understand the molecular mechanism of the occurrence and development of colon cancer,and provide theoretical reference for prognosis evaluation and targeted therapy of colon cancer. |
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