Identification of hub genes and pathways associated with bladder cancer based on co-expression network analysis

The aim of the present study was to identify hub genes and signaling pathways associated with bladder cancer (BC) utilizing centrality analysis and pathway enrichment analysis. The differentially expressed genes (DEGs) were screened from the ArrayExpress database between normal subjects and BC patients. Co-expression networks of BC were constructed using differentially co-expressed genes and links, and hub genes were investigated by degree centrality analysis of co-expression networks in BC. The enriched signaling pathways were investigated by Kyoto Encyclopedia of Genes and Genomes database analysis based on the DEGs. The hub gene expression in BC tissues was validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blotting. A total of 329 DEGs were screened, including 147 upregulated and 182 downregulated genes. The co-expression network constructed between BC and normal controls consisted of 182 nodes and 434 edges, and the two genes in each gene pair were differentially co-expressed genes. Centrality analysis of co-expression networks suggested that the top 5 hub genes with high degree included lectin, galactoside-binding, soluble, 4 (LGALS4), protein tyrosine phosphatase, receptor type N2 (PTPRN2), transmembrane protease, serine 11E (TMPRSS11E), tripartite motif containing 31 (TRIM31) and potassium voltage-gated channel subfamily D member 3 (KCND3). Pathway analysis revealed that the 329 DEGs were significantly enriched in 5 terms (cell cycle, DNA replication, oocyte meiosis, p53 signaling pathway and peroxisome proliferator-activated receptor signaling pathway). According to RT-qPCR and western blot analysis, 4/5 hub genes were significantly expressed, including LGALS4, PTPRN2, TMPRSS11E, TRIM31; however, KCND3 was not significantly expressed. In the present study, 5 hub genes were successfully identified (LGALS4, PTPRN2, TMPRSS11E, TRIM31 and KCND3) and 5 biological pathways that may be underlying biomarkers for early diagnosis and treatment associated with bladder cancer were revealed.