Identification of hub genes and pathways in the development of gastric cancer by gene co-expression network analysis

There are many risk factors for gastric cancer (GC), including chronic atrophic gastritis, which involves multiple genes and signaling pathways. Weighted gene co-expression network analysis (WGCNA) was performed on GSE111762 to construct free-scale gene co-expression network and identified four significant modules that consisted of blue, dark orange, dark red and dark violet. In each module, genes with the most connectivity were selected as hub genes, including G antigen 12J (GAGE12J) in blue, proline, histidine and glycine rich 1 (PHGR1) in dark orange, DNA polymerase gamma 2, accessory subunit (POLG2) in dark red and collagen type XXI alpha 1 chain (COL21A1) in dark violet. The transcription COL21A1 and GAGE12J was up-regulated in atrophic gastritis vs normal gastric mucosa, but down-regulated in GC vs atrophic gastritis. PHGR1 was consistently down-regulated from normal gastric mucosa to GC, while POLG2 was up-regulated. Gene set enrichment analysis (GSEA) was then conducted to study the biological functions of hub genes in the development of GC. It showed that multiple tumorigenesis-related pathways were enriched, including peroxisome, DNA repair and KRAS signaling pathway in COL21A1, IL6-JAKSTAT3, epithelial mesenchymal transition (EMT) and TNF alpha-NF-kappa B signaling pathway in PHGR1, MYC targets, E2F targets and angiogenesis in POLG2 and peroxisome, Notch signaling pathway and androgen response in GAGE12J. The identified four genes, especially for COL21A1, PHGR1 and POLG2, were important in GC tumorigenesis and affected many cancer-related pathways.