Development of a risk model for colon adenocarcinoma based on 3 methylation-regulated long non-coding RNA

Abstract

Objective The purpose of this study is to identify the methylation-regulated long non-coding RNA (lncRNA) in patients with colon adenocarcinoma (COAD) and its prognostic value by mining the cancer genome atlas (TCGA) and gene expression omnibus (GEO). Methods Gene expression profile data, DNA methylation data and corresponding clinical data were obtained from the TCGA. The expression profile data of GSE39582 array was downloaded from the GEO. The edgeR and limma packages were used to screen differentially expressed genes. Spearman rank correlation was used to determine the correlation between gene expression values and methylation values. Cox regression model was used to construct risk model. Results Through joint analysis of TCGA and GEO databases, 23 methylation-regulated lncRNA were identified. Univariate Cox analysis identified 4 methylation-regulated lncRNA (LINC00675, LINC01082, LINC01207, and RP1-170O19.14) associated with overall survival (OS) in COAD patients. A risk model was constructed based on stepwise Cox regression analysis, risk score=(-0.148 19×expression valueLINC01082)+(-0.120 50×expression valueLINC01207)+(-0.120 46×expression valueRP1-170O19.14). Conclusion In this study, the risk model of COAD patients are constructed based on methylation-regulated lncRNA, which could promote the individual prediction of OS in COAD patients.