Comparative study of under-expressed prognostic biomarkers and pivotal signaling pathways in colon cancer and ulcerative colitis using integrated bioinformatics approach

Colon cancer is a prevalent gastrointestinal malignancy arising in the colon. Ulcerative colitis(UC) is one of the risk factors of colorectal cancer. The detection of under-expressed biomarkers and molecular mechanisms in UC and colon cancer can lead to effective management of colitis-associated cancer.A total of two mRNA expression datasets (GSE۸۷۴۷۳ and GSE۴۴۰۷۶) were downloaded from the Gene Expression Omnibus (GEO) database. GSE۸۷۴۷۳ contains ۲۱ healthy samples, ۲۷ extensive ulcerative colitis samples and ۶۰ limited ulcerative colitis samples. GSE۴۴۰۷۶ contains ۹۸ colon cancer samples and ۹۸ healthy samples. GEO۲R was used to screen differentially expressed genes (DEGs) between extensive ulcerative colitis samples and healthy samples, limited ulcerative colitis samples and healthy samples, and colon cancer samples and healthy samples.The inclusion criteria for DEGs included an adjusted p-value <۰.۰۵ and a log(۲) fold change <-۲. Venn diagram of DEGs was depicted for every three groups (extensive ulcerative colitis, limited ulcerative colitis and colon cancer). Protein-protein interaction (PPI) network of DEGs in every three groups was constructed using STRING online database. The DEGs of each group were imported to Cytoscape software separately and the hub genes were screened. Then, the Enrichr web server was used to perform KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses and adjusted p-value<۰.۰۵ was considered statistically significant. Furthermore, Kaplan-Meier curve in GEPIA (http://gepia.cancer-pku.cn/) was used for analyzing the overall survival (OS) of hub genes.In extensive ulcerative colitis, limited ulcerative colitis and colon cancer groups, ۹۵,۶۹ and ۶۳۵ under-expressed genes with adjusted p-value<۰.۰۵ and log(۲) fold change<-۲ were detected respectively. Using Cytoscape software, the genes with degree> ۱۵ including CLCA۱, SLC۲۶A۳, SI, KIT, HPGDS, NR۱H۴, ADIPOQ, PPARGC۱A, GCG, MS۴A۱۲, GUCA۲A and FABP۱ were screened as hub under-expressed genes in colon cancer. In extensive ulcerative colitis, the genes with degree>۵ including ABCB۱, ABCG۲, UGT۱A۶, CYP۲B۶ and AQP۸ were identified as hub genes. Moreover, the genes including NR۱H۴, CYP۲B۶, ABCB۱, ABCG۲, UGT۲A۳ and PLA۲G۱۲B were detected as hub genes with degree>۵ in limited ulcerative colitis. According to inclusion criteria and venn diagram, the downregulated gene NR۱H۴ was common gene in limited ulcerative colitis and colon cancer. The genes MS۴A۱۲ and GUCA۲A were common genes in extensive ulcerative colitis and colon cancer. The genes CLCA۱, SLC۲۶A۳, SI, KIT, HPGDS, ADIPOQ, PPARGC۱A, PPARGC۱A, GCG and FABP۱ were distinctive genes in colon cancer. The genes UGT۱A۶ and CYP۲B۶ were common genes in extensive ulcerative colitis and limited ulcerative colitis, and the genes ABCB۱, ABCG۲, AQP۸, and UGT۲A۳ were common genes in three groups. According to KEGG enrichment analysis, hub under-expressed genes in colon cancer were enriched in the pathways including Pancreatic secretion, Mineral absorption, Drug metabolism, Metabolism of xenobiotics by cytochrome P۴۵۰, Arachidonic acid metabolism, Bile secretion, PPAR signaling pathway, Adipocytokine signaling pathway and cAMP signaling pathway. The hub genes in extensive and limited ulcerative colitis were enriched in Bile secretion, ABC transporters, Steroid hormone biosynthesis, Retinol metabolism, Metabolism of xenobiotics by cytochrome P۴۵۰, Drug metabolism, Chemical carcinogenesis and Fat digestion and absorption. According to survival analysis, CLCA۱ (Calcium-activated chloride channel regulator ۱), PPARGC۱A (Peroxisome proliferator-activated receptor gamma coactivator ۱-alph) and AQP۸ (Aquaporin-۸) were with poor overall survival. The current in silico study showed that downregulation of CLCA۱, PPARGC۱A and AQP۸ genes may increase cancer cell invasion and metastasis ability. The recent researches showed that CLCA۱ overexpression inhibited colorectal cancer aggressiveness, and overexpression of AQP۸ reduced cell proliferation, migration and invasion in colon cancer. The role of downregulation of PPARGC۱A gene in poor survival of patients with colon cancer has not been revealed yet

Keywords:

biomarker , signaling pathway , overall survival , ulcerative colitis , colon cancer