| Literature DB >> 34221961 |
Ruoyue Tan1,2,3, Guanghui Zhang1,2, Ruochen Liu1,2, Jianbing Hou1,2, Zhen Dong1,2, Chaowei Deng1,2, Sicheng Wan1,2, Xiaodong Lai4, Hongjuan Cui1,2,3.
Abstract
Stomach adenocarcinoma (STAD) is a leading cause of cancer deaths, and the outcome of the patients remains dismal for the lack of effective biomarkers of early detection. Recent studies have elucidated the landscape of genomic alterations of gastric cancer and reveal some biomarkers of advanced-stage gastric cancer, however, information about early-stage biomarkers is limited. Here, we adopt Weighted Gene Co-expression Network Analysis (WGCNA) to screen potential biomarkers for early-stage STAD using RNA-Seq and clinical data from TCGA database. We find six gene clusters (or modules) are significantly correlated with the stage-I STADs. Among these, five hub genes, i.e., MS4A1, THBS2, VCAN, PDGFRB, and KCNA3 are identified and significantly de-regulated in the stage-I STADs compared with the normal stomach gland tissues, which suggests they can serve as potential early diagnostic biomarkers. Moreover, we show that high expression of VCAN and PDGFRB is associated with poor prognosis of STAD. VCAN encodes a large chondroitin sulfate proteoglycan that is the main component of the extracellular matrix, and PDGFRB encodes a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor (PDGF) family. Consistently, Gene Ontology (GO) analysis of differentially expressed genes in the STADs indicates terms associated with extracellular matrix and receptor ligand activity are significantly enriched. Protein-protein network interaction analysis (PPI) and Gene Set Enrichment Analysis (GSEA) further support the core role of VCAN and PDGFRB in the tumorigenesis. Collectively, our study identifies the potential biomarkers for early detection and prognosis of STAD.Entities:
Keywords: TCGA; WGCNA; biomarkers; early diagnosis; prognosis; stomach adenocarcinoma (STAD)
Year: 2021 PMID: 34221961 PMCID: PMC8249817 DOI: 10.3389/fonc.2021.636461
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 6.244
Figure 1A total of 407 STAD and normal samples were obtained from the TCGA database, and 3,746 DEGs were identified. (A) 30 samples was randomly used to test the standardized results. (B) Heatmap of 3,746 DEGs (FDR<0.01, LogFC<-1 and LogFC>1).
Figure 2GO enrichment analysis and KEGG pathway analysis were performed on 3,746 DEGs in STAD. (A) GO biological process (BP) enrichment results. (B) GO cellular component (CC) enrichment results. (C) GO molecular function (MF) enrichment results. (D) KEGG pathway enrichment results.
Figure 3The WGCNA method was used to analyze STAD and to find out the modules that are significantly related to traits. (A) Scale-free topology fitting graph. (B) Cluster modules dendrogram of STAD (up) and the colored bands (down) each dendrogram indicate the module color. (C) Clustering dendrogram of genes, with dissimilarity based on topological overlap, together with assigned module colors. (D) Module–Clinical Trait Relationships of consensus module eigengene and different stages of STAD. Each row in the table corresponds to an ME (module eigengene), and each column to a clinical parameter. The cells are colored by the correlation according to the color legend. Intensity and direction of correlations are indicated on the right side of the heatmap (red, positively correlated; green, negative correlated).
Figure 4Candidate gene expression and verification. (A) LY9. (B) MS4A1. (C) THBS2. (D) VCAN. (E) PDGFRB. (F) KCNA3. (G) FCRL5. (H) ARHGAP25. (I) FLI1. (J) TRAF3IP3. (K) Candidate biomarkers in the STAD volcano map. (L) Candidate biomarkers in the verification set GSE116312 volcano map. *P<0.05, **P<0.01, ***P<0.001 and ns, not significant.
Figure 5Gene set variation analysis and survival analysis. (A) Heat map of gene set GSVA enrichment score. (B) Gene set GSVA enrichment score box plot. (C) Orange gene set survival analysis. (D) Blue gene set survival analysis. (E) Black gene set survival analysis. (F) Lightyellow gene set survival analysis. (G) Darkgrey gene set survival analysis. (H) Cyan gene set survival analysis. (I) PDGFRB Kaplan-Meier survival analysis. (J) VCAN Kaplan-Meier survival analysis. (K) THBS2 Kaplan-Meier survival analysis.
Figure 6The expression of PDGFRB and VCAN was significantly improved in the tumor tissues compared with the normal adjacent tissues. (A) IHC results of 20180919 samples with PDGFRB antibody. (B) IHC results of 20180919 samples with VCAN antibody. (C) IHC results of 20190120 samples with PDGFRB antibody. (D) IHC results of 20190120 samples with VCAN antibody (C indicates tumor tissue while N means adjacent normal tissue, and samples with same numbers are from the same STAD patients). *P<0.05, **P<0.01.
Figure 7Co-expression network and protein interaction network analysis. (A) Co-expression network of VCAN and PDBFRB. (B) The linear correlation analysis between VCAN and PDGFRB was performed using the ggstatsplot R package (R2 = 0.71, P=2.04e-104). (C) The protein interaction analysis involving VCAN and PDGFRB was conducted by String online database.
Figure 8Gene set enrichment analysis results. (A) High expression of PDGFRB gene can up-regulate the focal adhesion kinase signaling pathway. (B) High expression of VCAN gene can up-regulate the focal adhesion kinase signaling pathway. (C) High expression of VCAN will lead the PDGF pathway up-regulate.