A miR-151 binding site polymorphism in the 3′-untranslated region of the cyclin E1 gene associated with nasopharyngeal carcinoma

Genetic alterations in nasopharyngeal carcinoma (NPC) have been reported in previous works. However, it remains unclear whether polymorphisms within the miRNA-target binding sites are associated with individual NPC risk. In this study, new experimental and computational approaches were developed to assess the polymorphism frequency distribution within the miRNA sites in NPC patients, and to explore its association with NPC risk. We focused on 220 single-nucleotide polymorphisms (SNPs) in the 3′-untranslated regions (3′UTRs) of 32 genes carrying putative miRNA-binding sites by specialized algorithms. A total of 9 candidate genes were selected for further investigation, which were reportedly overexpressed in NPC, including EGFR, COX2, CCNE1, hTERT, MMP2, MMP9, NF-κB VEGF, and WNT3. SNPs in 3′UTRs were genotyped by direct polymerase chain reaction sequencing of the genomic DNA of 24 cases and 24 controls. Then, EGFR rs884225, CCNE1 rs3218073, and MMP2 rs7201 were screened with large samples. Based on the analysis of a series of 167 NPC cases and 171 controls from Guangdong Province, statistically significant associations were found between NPC risk and variant genotypes of CCNE1 rs3218073 for TC + TT (OR = 1.585; 95% CI = 1.023–2.458; P = 0.046) and for T-allele (OR = 1.464; 95% CI = 1.012–2.118; P = 0.042). In addition, a significant association among rs3218073 genotype TC (OR = 1.959, P = 0.043), T-allele (OR = 2.123, P = 0.006), and primary tumor (T3–T4) was retrieved. Genotype TC (OR = 1.959, P = 0.043) and T-allele (OR = 2.123, P = 0.006) of rs3218073 were correlated with increased risk of higher NPC stage (III to IV). In support of the postulation that the 3′UTR SNP directly affected miRNA-binding site, luciferase reporter assay indicated that CCNE1 was a direct target of miR-151, and the rs3218073 T > C change resulted in altered regulation of CCNE1 expression. By contrast, no statistically significant association with NPC risk was found for MMP2 rs7201 and EGFR rs884225 polymorphisms (P > 0.05). In conclusion, our data demonstrate that CCNE1 rs3218073 polymorphism located at miRNA-151 binding site is associated with NPC susceptibility and is correlated with NPC stage. These results suggest that CCNE1 rs3218073 polymorphism can be exploited as a novel biomarker for future NPC diagnosis and prognosis. ⺠rs3218073 is associated with NPC risk and pathologic stage. ⺠rs3218073 C > T change interfered in the interaction between CCNE1 and miR-151. ⺠CCNE1 is overexpressed in NPC tissues of individuals carrying the T-allele.