Bioinformatics analysis of the prognosis and biological significance of VCAN in gastric cancer

Abstract

Gastric cancer (GC) is one of the most common cancers in the world, and the tumor microenvironment (TME) plays a vital role in the occurrence and development of GC. In this study, we obtained differential expressed genes in GC tissues from The Cancer Genome Atlas. After ESTIMATE and weighted correlation network analysis, we obtained differentially expressed genes (DEGs). With further screening DEGs of immune infiltration and then through Kaplan-Meier survival analysis, least absolute shrinkage and selection operator regression analysis and COX analysis, we found that VCAN was a gene positively correlated with high immune infiltration and poor prognosis of patients in GC. In addition, we selected a Gene Expression Omnibus dataset (GSE84433) to verify the effect of VCAN on the patient's prognosis, and analyzed the value of VCAN in immunotherapy through TIMER database and TISIDB. In conclusion, we hold the view that VCAN may affect the development of GC by regulating the TME, which may act as a potential therapeutic target for GC.

Keywords: VCAN; gastric cancer; immune infiltration; tumor microenvironment.

Figure 1

ESTIMATEScore in The Cancer Genome Atlas (TCGA)‐STAD and weighted correlation network analysis (WGCNA) of DEGs. (A) Hierarchical clustering analysis of differentially expressed genes in gastric cancer tissues and adjacent tissues from TCGA database. (B) The Volcano Plots showed the genes with low expression (blue) and high expression (red) in gastric cancer tissues. The screening condition was |logFC| > 1.5, p < .01. (C) Cluster Dendrogram was used for the enrichment of gene modules related to immune infiltration, stromal cell infiltration, and ESTIMATEScore. (D) The correlation between each module and immune cell, stromal cell infiltration, and ESTIMATEScore was visualized by Module‐trait relationship. (E–G) The genes in three modules (turquoise, brown, yellow) were screened with ESTIMATEScore > 0.5, module membership >0.8. DEG, differentially expressed gene

Figure 2

VCAN is associated with immune infiltration and prognosis of GC patients. (A) Immune infiltration heatmap showed the relationship between immune infiltration with tumor purity, stromal score, immune score, and ESTIMATEScore. (B, C) The violin figure and scatter diagram showed that the tumor immune infiltration was positively correlated with ESTIMATEscore. (D–F) Genes expression was significantly different between high and low immune infiltration group. (G, H) LASSO regression analysis was used to identify genes involved in survival. (I) COX analysis was used to further screen for genes that affect survival. GC, gastric cancer; LASSO, least absolute shrinkage and selection operator

Figure 3

VCAN act as a tumor promoter in gastric cancer. (A) The expression of VCAN in gastric cancer and adjacent tissues. (B) Kaplan–Meier analysis showed that the higher the expression level of VCAN, the worse the prognosis of gastric cancer patients. (C) COX analysis showed that T stage and VCAN were both poor prognostic factors. (D, E) The box diagram showed the relationship between VCAN expression and T staging in TCGA and GEO database, respectively. (F) The box diagram showed the relationship between VCAN expression and TNM stage. (G) COX analysis showed that VCAN and T staging were associated with poor prognosis. GEO, Gene Expression Omnibus; TCGA, The Cancer Genome Atlas

Figure 4

Relationship between VCAN and immune infiltration. (A) CIBERSORT was used to analyze the immune infiltration of 22 immune cells. (B) 7 immune cells (T cells CD8+, T cells CD4 memory activated, macrophages M0, macrophage M1, mast cells resting, mast cells activated, neutrophils) were supposed to have different levels of infiltration between high/low immunity group. (C–E) According to the TIMER database, 3 immune cells (T cell CD8+, macrophages M1, mast cell activated) were suggested to have a significant correlation after the adjustment of purity. (F) Macrophage M1 had significant high expression in mutated VCAN group, which indicated that mutation VCAN may induce the high immune infiltration of macrophage M1. (G, H) According the TISIDB, macrophage and mast cells were supposed to have significant correlation with VCAN expression

Figure 5

The value of VCAN in immune therapy. (A) In TISIDB, VCAN had the most high expression in TGF‐b dominant type of gastric cancer significantly (p = 9.14 × 10⁻³). (B, C) After analyzing in TISIDB, VCAN was significantly correlated with two immune biomarkers in immunotherapy (PDCD1LG2, ENTPD1). (D, E) The correlation between two biomarkers and VCAN were verified through GEPIA which demonstrated that VCAN was significantly correlated with two genes indeed. (F, G) According to the result from TIMER database, VCAN had a significant correlation with two genes after the adjustment of tumor purity. (H, I) VCAN was found to be the target of the hyaluronic acid. IFN, interferon; TGF, tumor growth factor

Figure 6

(A) The effect of VCAN on AGS migration ability of gastric cancer cells was detected by Wound healing assay. (B) Transwell detected the effect of VCAN on the invasion ability of AGS in gastric cancer cells. (C) Western blot detected the effect of VCAN on the expression of immune protein CD44. GAPDH, glyceraldehyde 3‐phosphate dehydrogenase