چکیده:
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 (GSE87473 and GSE44076) were downloaded from the Gene Expression Omnibus (GEO) database. GSE87473 contains 21 healthy samples, 27 extensive ulcerative colitis samples and 60 limited ulcerative colitis samples. GSE44076 contains 98 colon cancer samples and 98 healthy samples. GEO2R 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 <0.05 and a log(2) fold change <-2. 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<0.05 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, 95,69 and 635 under-expressed genes with adjusted p-value<0.05 and log(2) fold change<-2 were detected respectively. Using Cytoscape software, the genes with degree> 15 including CLCA1, SLC26A3, SI, KIT, HPGDS, NR1H4, ADIPOQ, PPARGC1A, GCG, MS4A12, GUCA2A and FABP1 were screened as hub under-expressed genes in colon cancer. In extensive ulcerative colitis, the genes with degree>5 including ABCB1, ABCG2, UGT1A6, CYP2B6 and AQP8 were identified as hub genes. Moreover, the genes including NR1H4, CYP2B6, ABCB1, ABCG2, UGT2A3 and PLA2G12B were detected as hub genes with degree>5 in limited ulcerative colitis. According to inclusion criteria and venn diagram, the downregulated gene NR1H4 was common gene in limited ulcerative colitis and colon cancer. The genes MS4A12 and GUCA2A were common genes in extensive ulcerative colitis and colon cancer. The genes CLCA1, SLC26A3, SI, KIT, HPGDS, ADIPOQ, PPARGC1A, PPARGC1A, GCG and FABP1 were distinctive genes in colon cancer. The genes UGT1A6 and CYP2B6 were common genes in extensive ulcerative colitis and limited ulcerative colitis, and the genes ABCB1, ABCG2, AQP8, and UGT2A3 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 P450, 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 P450, Drug metabolism, Chemical carcinogenesis and Fat digestion and absorption. According to survival analysis, CLCA1 (Calcium-activated chloride channel regulator 1), PPARGC1A (Peroxisome proliferator-activated receptor gamma coactivator 1-alph) and AQP8 (Aquaporin-8) were with poor overall survival.
The current in silico study showed that downregulation of CLCA1, PPARGC1A and AQP8 genes may increase cancer cell invasion and metastasis ability. The recent researches showed that CLCA1 overexpression inhibited colorectal cancer aggressiveness, and overexpression of AQP8 reduced cell proliferation, migration and invasion in colon cancer. The role of downregulation of PPARGC1A gene in poor survival of patients with colon cancer has not been revealed yet.