Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis

Abstract

Gastric cancer has remained in the top five cancers for over ten years, both in terms of incidence and mortality due to the shortage of biomarkers for disease follow-up and effective therapies. Aiming to fill this gap, we performed a bioinformatics assessment on our data and two additional GEO microarray profiles, followed by a deep analysis of the 40 differentially expressed genes identified. PPI network analysis and MCODE plug-in pointed out nine upregulated hub genes coding for proteins from the collagen family (COL12A1, COL5A2, and COL10A1) or involved in the assembly (BGN) or degradation of collagens (CTHRC1), and also associated with cell adhesion (THBS2 and SPP1) and extracellular matrix degradation (FAP, SULF1). Those genes were highly upregulated at the mRNA and protein level, the increase being correlated with pathological T stages. The high expression of BGN (p = 8 × 10^-12), THBS2 (p = 1.2 × 10^-6), CTHRC1 (p = 1.1 × 10^-4), SULF1 (p = 3.8 × 10^-4), COL5A1 (p = 1.3 × 10^-4), COL10A1 (p = 5.7 × 10^-4), COL12A1 (p = 2 × 10^-3) correlated with poor overall survival and an immune infiltrate based especially on immunosuppressive M2 macrophages (p-value range 4.82 × 10^-7-1.63 × 10^-13). Our results emphasize that these genes could be candidate biomarkers for GC progression and prognosis and new therapeutic targets.

Keywords: biomarkers; cell adhesion; collagens; extracellular matrix; survival; targeted therapy.

Figure 1

Venn diagrams of upregulated and downregulated genes in all three GC microarray datasets.

Figure 2

DAVID gene ontology enrichment analysis for common DEGs performed for biological process, cellular component, molecular function, significant keywords, and KEEG pathway.

Figure 3

Protein–protein interaction (PPI) analysis. (A) PPI networks of the common upregulated DEGs. (B) Identification of nine hub genes according to MCODE score.

Figure 4

The expression levels of hub genes in GC. (A) The mRNA expression was correlated with pathological T stages. The asterisk represents the comparison between a specific stage and the normal group, or between different stages. * p < 0.05, ** p < 0.01, *** p < 0.001. (B) Representative western blotting for COL10A1, BGN, and FAP proteins in 4 paired gastric tumor (T) and adjacent non-tumor tissues (N) with progressive stages from T1 to T4.

Figure 5

Overall survival curves according to high and low DEG expression. High gene expression has a higher hazard ratio (HR) for poor overall survival.

Figure 6

Analysis of tumor infiltrate in GC. Correlation between hub genes and 12 immune cell types in tumor microenvironment based on Spearman’s rho.