| Objective: To explore the relationship between immune infiltration and survival of patients with lung adenocarcinoma,and establish a prognostic marker based on immune-related genes,these results can provide a theoretical basis for predicting the survival of patients with lung adenocarcinoma.Methods: The subjects were collected from the TCGA-LUAD cohort of TCGA database,including 535 cases of tumor tissue,59 cases of normal tissue and 502 cases of complete clinical data.The data were standardized by log2(X+1).The immune and stromal scores of 594 samples were calculated by ESTIMATE algorithm in R language.Wilcoxon test was used to explore whether there was difference between tumor and normal tissues,whether there was difference between I/II and III/IV stages.Kaplan-Meier survival analysis was used to evaluate the relationship between immune scores or stromal scores and prognosis of patients.The differentially expressed genes were screened by LIMMA algorithm according to the median immune score(screening criteria :| log FC | > 1;P <0.05).The R packet "WGCNA" was used to cluster the genes to get the immune-related module and to find out the genes that were highly related to the phenotype and closely related to other genes in the module.The overlapping genes screened by the two methods were defined as immune-related genes.The DAVID website was used for functional analysis to reveal the immune-related biological processes involved in these genes.R packet "set.seeds" randomly divided the data into training set and verification set.The prognostic genes related to survival were obtained by univariate Cox regression analysis of immune-related genes in the training set,and significant variables were included in multivariate Cox regression to establish a prognostic model.According to the median risk score,the cohort survival analysis,time-dependent ROC curve analysis(1,3,5 years)and C-index index test were used to test the performance of the prognostic model.The content of 22 kinds of tumor infiltrating immune cell subsets in tumor microenvironment was analyzed by Ciber Sort algorithm,and the distribution of immune cells in high and low risk groups was compared by Wilcoxon test.R package "corrplot" was used to calculate the correlation between immune cells.Wilcoxon was used to detect the difference in the expression of genes related to immune checkpoint between high and low risk groups.Results: The immune score and stromal score of patients with lung adenocarcinoma were lower than those of normal tissues(P<0.001).The immune score was related to different clinical stages(P=0.0057),but the stromal score had no significant difference in different clinical stages(P=0.059).The results of survival analysis showed that patients in the high immunity score group tended to have a longer survival time(P=0.039),while there was no correlation between interstitial score and survival(P=0.061).420 up-regulated genes and 18 down-regulated genes were screened by differential expression analysis.14 modules were obtained by WGCNA cluster analysis,among which the blue module was highly correlated with immune score,and there were 133 core genes in this module.111 overlapping immune-related genes were obtained by the two methods.47 prognostic genes were screened by univariate Cox regression analysis,and a prognostic model containing 12 genes(P2RY13,CCR2,PSTPIP1,LCP1,HLA-DMB,IRF8,NCKAP1 L,CD247,TRAC,ITGAL,MNDA,BTK)was established by multivariate Cox regression.The high expression of CCR2,BTK,ITGAL and CD247 were protective factors,while the high expression of NCKAP1 L,IRF8,MNDA and TRAC were risk factors.Kaplan-Meier survival analysis showed that the prognosis of high risk group was worse than that of low risk group(P < 0.001).The area under the ROC curve of 1,3 and 5 years was 0.735 and 0.750 respectively,and the consistency index of the model was 0.69.Independent prognostic analysis showed that the model could be used as an independent predictor of prognosis in patients with lung adenocarcinoma.The validity of the model was further verified in the verification set.The results of immunocyte infiltration analysis in high and low risk groups showed that there were differences in the infiltration abundance of plasma cells,macrophage M0,macrophage M2,resting dendritic cells,resting mast cells and living chemical mast cells between the two groups(P < 0.05).The results of predicting the effect of immunotherapy showed that the expression level of target genes related to immunotherapy in the low risk group was higher than that in the high risk group(P < 0.05).Conclusion:(1)Lung adenocarcinoma patients with high immune infiltration tend to have a better prognosis.(2)A new marker based on immune-related genes can predict the prognosis of patients with lung adenocarcinoma.(3)The scoring model has potential value in predicting the efficacy of Immunocheckpoint inhibitor treatment,the low risk group has a better prognosis. |
PDF Full Text Request