Immune microenvironment correlates with clinical characteristics of patients with cervical cancer
The gene expression profiles and corresponding clinical data of 307 patients were obtained from TCGA datasets. The youngest patients were 20 years old, the oldest 88 years old, and the median was 46 years old.
We used the ESTIMATE algorithm to calculate the immunescore ranging from -1209.74 to 3419.323, stromalscore ranging from -2437.40 to 804.22 and ESTIMATEScore ranging from -3262.05 to 4002 of all patients (13). This data indicated that the higher the ESTIMATEScore, the less the proportion of tumor cells. In order to study the potential relationship between clinical overall survival of patients and their immunescores or stromalscores, we divided the 307 patients into high- and low-score groups according to immunescore or stromalscore, then evaluated their relationship with Kaplan-Meier survival analysis. The results showed that there was a statistically significant difference between the high immunescore group and the low immunescore group. And the low immunescore group had shorter lifetimes than the high scores group (P = 0.035, Fig. 1A). However, there was no significant difference between the high stromalscore group and low stromalscore group for nearly 15 years. (P = 0.391, Fig. 1B)
Furthermore, according to the clinical TMN stage of the tumor, patients with cervical cancer were classified into two groups: M1 and M0 stage. We analyzed the relationship between M1/M0 stage and their corresponding immune score or stromal score. As shown in Figure 1C,D, the immunescore and stromalscore in M0 stage group were significantly higher than those in M1 stage group (P=0.048,P=0.027).
Identification of DEGs based on immunescore and stromalscore
The expression profile data for all 307 patients with cervical cancer from TCGA was investigated to screen for DEGs between the high score and low score groups. A total of 1067 and 946 DEGs in cervical cancer sample cells based on immunescores and stromalscores, respectively. The heat map for DEGs of immune/stromal score groups was shown that DEGs were classified into 2 clusters. Genes in cluster with blue bar were belonged to high score group, while genes in cluster with pink bar were belonged to low score group in cervical cancer samples (Fig. 2A,B). Among them, we identified 408 up-regulated genes and 17 down-regulated genes in Fig. 2C,D from both immunescore groups and stromalscore groups.
GO and KEGG pathway enrichment analyses
In order to study the enrichment analysis of DEGs, we completed the enrichments of GO, including BP, CC, and MF. KEGG enrichment analysis of DEGs using the R package. DEGs in the BP category were mainly associated with T cell activation, regulation of lymphocyte activation, regulation of T cell activation and lymphocyte differentiation. For CC, DEGs were frequently enriched in the GO term of external side of plasma membrane, plasma membrane receptor complex, immunological synapse and T cell receptor complex. With regard to MF, DEGs were primarily enriched in cytokine receptor activity, cytokine receptor binding and immunoglobulin binding (Fig. 3A). Subsequently, the KGEE enrichment analysis of DEGs was completed and found mainly clustered in the cytokine–cytokine receptor interaction, chemokine signaling pathway, cell adhesion molecules and the intestinal immune network for IgA production (Fig.3B,C).
Construction of PPI Network and module analysis
PPI network of DEGs for cervical cancer was constructed with 150 nodes and 282 edges based on the STRING network tool and Cytoscape software (Fig. 4A). We selected the top twelve DEGs with the number of nodes, including CXCL10(15), CXCL9(14), CCL5 (13), CD4(13), CCL19(12), CCL21(12), CCR5(12), CD3E(12), CXCL11(12), IL10(12), ITGB2(12)and TYROBP(12) (Fig. 4D).
Cytotype MCODE software was used to analyze Clustering analysis of the PPI network based on the above-mentioned PPI network. The two significant modules based on the degree of importance were selected. The module 1 contained 11 nodes and 48 edges, including aforementioned CXCL10, CXCL11, CXCL9, CCL21,CCR5, CCL19, CCL5 (Fig. 4D). Another one, module 2 contained 6 nodes and 15 edges, including CD4, CD3D, CD3E, CD3G, ITK, LCP2(Fig. 4C).
Survival analysis
We investigated the potential value between DEGs and overall survival in patients with cervical cancer using Kaplan-Meier survival curves. 149 DEGs were significantly correlated with the overall survival of patients among the 425 commonly DEGs according to the log-rank test (P < 0.05). As shown in Fig. 5, several representative genes are represented (p < 0.001).