Expression characteristics of long non-coding RNA in colon adenocarcinoma and its potential value for judging the survival and prognosis of patients: bioinformatics analysis based on The Cancer Genome Atlas database

Abstract

Background: To investigate the expression characteristics of long non-coding RNA (lncRNA) in colon adenocarcinoma (COAD) and its potential value in predicting the prognosis of patient survival.

Methods: We downloaded COAD-related RNA sequencing (RNA-seq) data and patient survival data from The Cancer Genome Atlas (TCGA). The data were analyzed for lncRNA expression differences, subjected to Cox regression analysis for survival rate, and Kaplan-Meier (KM) survival curves were plotted to analyze the role of the key genes related to prognostic survival by pathway enrichment analysis.

Results: The data of 494 COAD clinical samples from TCGA were analyzed; 204 lncRNAs were differentially expressed, 156 were up-regulated, and 48 were down-regulated. The 10 genes with the most significant expression differences were Linc02418, Blacat1, ELFN1-AS1, CRNDE, AC002384.1, AL353801.1, LINC01645, AC073283.2, AC087379.1, and LINC00484. Cox regression analysis of 204 lncRNA genes showed that 23 lncRNA genes with significant effects on the prognosis and survival rate of COAD patients were obtained when P<0.05 was used as the threshold. With P≤0.001 as the threshold, the KM curves of 4 genes (Linc02257, Linc02474, Ac010789.1, Ac083967.1) were statistically significant (P<0.05). The gene Linc02257 was selected for Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and it was revealed that the inheritance of Linc02257-regulated gene expression was closely related to tumor development, such as collagen-containing extracellular matrix, organogenesis, activity of membrane protein receptors, and ion channel activity. The signaling pathways regulated by Linc02257 were also closely related to tumors, such as neuroactive ligand-receptor interaction, the PI3K-AKT signaling pathway, calcium signaling pathway, and protein digestion and absorption.

Conclusions: In COAD, lncRNA is differentially expressed and plays an important role in the disease regulation. It has potential application value in the diagnosis, targeted therapy, and prognosis of COAD patients.

Keywords: Long non-coding RNA (lncRNA); The Cancer Genome Atlas (TCGA); bioinformatics analysis; colon cancer.

Figure 1

Significant differential gene up-regulation and down-regulation plot. A total of 204 genes; red indicates up-regulation, blue indicates down-regulation.

Figure 2

Comparison of genes LINC02418, BLACAT1, and AL353801.1 in cancer tissues and normal tissues.

Figure 3

Twenty-three lncRNA genes that have an impact on prognostic survival. HR, hazard ratio; CI, confidence interval.

Figure 4

Twenty-three lncRNA genes that have an impact on prognostic survival. The dotted line presented the upper and lower interval of the 95% Confidential Interval along with the same color for the two compared groups. KM, Kaplan-Meier.

Figure 5

GO functional enrichment results of gene Linc02257. GO, Gene Ontology.

Figure 6

KEGG Pathway functional enrichment results for gene Linc02257. KEGG, Kyoto Encyclopedia of Genes and Genomes; ECM, extracellular matrix; TGF, transforming growth factor.