Integration Analysis of Differential Expressed Genes Regulated by Differential Methylated Regions for Predicting Prognosis in Human Colon Cancer

Abstract Background Colon cancer is a leading cause of cancer-associated death globally, and numerous evidences show that different expressed gens (DEGs) regulated by differential methylated regions (DMRs) act an important role in tumor biology. However, the specific regulatory mechanism of DEGs related to DERs in colonic carcinogenesis is still unclear.Materials and methods RNA sequencing data and DNA methylation data of 455 colon adenocarcinoma (COAD) cases and 41 normal controls were downloaded from The Cancer Genomic Atlas (TCGA) to investigate the significant DEGs and DMRs. Gene ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by DAVID database. To identify the hub genes regulated by methylation, univariate cox and multivariate cox regression analyses were concluded. Furthermore, Riskscore and nomogram were built to identify the prognosis prediction power of the hub genes in colon cancer patients. Results A total of 133 DEGs regulated by DMRs were identified through analyzing RNA-seq data and DNA methylation data from TCGA; GO functional enrichment and KEGG pathway enrichment analysis showed that the genes involved in the initiation and progression of colon cancer. Univariate cox regression analysis and multivariate cox regression analysis focused on the 7 hub genes associated with overall survival, whose expression negatively correlated with their methylated level; Riskscore and nomogram model showed that the hub gens served as potential biomarker for the prognosis prediction of colon cancer patient. Conclusion Our funding suggests that the DEGs regulated by DMRs involve in the carcinogenesis and development of colon cancer, and the aberrant methylated DEGs associated with overall survival of patients may be potential diagnosis and therapeutic targets for colon cancer.