Hypermethylation of N-Acetyltransferase 1 Is a Prognostic Biomarker in Colon Adenocarcinoma

Abstract

Background: The N-acetyltransferase 1 (NAT1) gene is downregulated in several cancers and associated with patient survival. In this study, we sought to examine the prognostic value and clinical significance of NAT1 methylation in colon adenocarcinoma (COAD). Methods: Data relating to NAT1 mRNA expression and methylation and clinicopathological features of COAD were extracted from the database of The Cancer Genome Atlas. We compared the mRNA expression and methylation of NAT1 between COAD and normal tissues and performed correlation analysis to assess the association between NAT1 mRNA expression and methylation. Furthermore, we assessed patient survival based on CpG sites in the promoter region of NAT1 and analyzed the association between the NAT1 mRNA expression and CpG site methylation and clinicopathological features. An independent Gene Expression Omnibus (GEO) dataset was used to validate the results. Results: We found that the expression of NAT1 mRNA was reduced in COAD compared with normal tissues and that mean methylation of the eight CpG sites in the promoter region of NAT1 was higher in COAD tissues than in normal tissues. Furthermore, five CpG sites were demonstrated to be significantly negatively correlated with NAT1 mRNA expression in COAD. Survival analysis indicated that NAT1 mRNA expression and the cg15797286 and cg18509990 sites were associated with the overall survival of COAD patients. Combined survival analysis revealed that combinations of NAT1 mRNA expression with five CpG sites were significantly associated with the overall survival of COAD patients. Both NAT1 mRNA and cg15797286 were associated with the T, N, and clinical stages of COAD. The GEO data indicated that cg15797286 was hypermethylated in recurrent colorectal adenomas. Conclusions: Methylation of NAT1 is associated with the development of COAD, and may serve as prognostic and treatment biomarkers for COAD.

Keywords: N-acetyltransferase 1; The Cancer Genome Atlas; colon adenocarcinoma; methylation; prognosis.

Figure 1

(A) Genomic position and functional annotation of N-acetyltransferase 1 (NAT1) gene from the University of California Santa Cruz genome browser; (B) Comparison of NAT1 mRNA in cancers and corresponding normal tissues; (C) The mean methylation of NAT1 in promoter region of COAD and normal tissues; (D) Heatmap of methylation CpG sites of NAT1 in COAD. *p < 0.05.

Figure 2

(A) Correlation analysis of N-acetyltransferase 1 (NAT1) mRNA with the mean methylation of promoter region; (B–G) Correlation analysis of NAT1 mRNA with cg04241863, cg07470176, cg15138846, cg15797286, cg21172319, cg21298408.

Figure 3

(A) Kaplan–Meier curve of N-acetyltransferase 1 (NAT1) mRNA expression in COAD; (B) Kaplan–Meier curve of cg15797286 in COAD; (C) Kaplan–Meier curve of cg18509990 in COAD.

Figure 4

Kaplan–Meier curve of combination of N-acetyltransferase 1 (NAT1) mRNA with CpG sites in COAD. (A) NAT1 mRNA with cg07470176; (B) NAT1 mRNA with cg15138846; (C) NAT1 mRNA with cg15797286; (D) NAT1 mRNA with cg18509990; (E) NAT1 mRNA with cg21172319; (F) NAT1 mRNA with cg21298408; (G) NAT1 mRNA with cg22904102.

Figure 5

(A) Comparison of mean CpG value of N-acetyltransferase 1 (NAT1) in colorectal adenomas and normal tissues; (B) Comparison of methylation of CpG sites in colorectal adenomas and normal tissues.