Potentially functional genetic polymorphisms of USP45 and PRFP19 in the NER pathway genes predict HBV-related hepatocellular carcinoma survival

Abstract

Abstract Nucleotide excision repair (NER) is an important DNA damage repair pathway involved in prognosis of cancer. The aim of this study was to investigate the association between genetic variants in NER pathway genes and overall survival (OS) of hepatocellular carcinoma (HCC) patients. Cox proportional hazards regression analyses was performed to investigate the associations between single nucleotide polymorphism (SNPs) in candidate genes and OS of 866 patients with operable hepatitis B virus (HBV) related HCC. The relationship between SNPs and corresponding genes was estimated by GTEx database and 1000 Genomes project. Online biological information databases were used for functional annotation of SNPs. Gene expression was calculated using data obtained from The Cancer Genome Atlas (TCGA). Kaplan-Meier plotter was used to evaluate the relationship between gene expression and OS in HBV-HCC patients. cBioPortal database was applied to observe the mutation rate of genes in HCC tumor tissues. We identified two independent functional SNPs were significantly associated with OS of HBV-HCC patients [USP45 rs4840048 T > C: Hazard ratio (HR) = 0.64, 95% confidence interval (CI) = 0.48–0.86, P = 0.003) and PRPF19 rs7116665 C > A: HR = 1.31, 95%CI = 1.13–1.53, P < 0.001). Besides, rs4840048 T allele was significantly correlated with higher USP45 mRNA expression levels (P = 0.010), while rs7116665 A allele was significantly correlated with decreased PRPF19 mRNA expression levels (P = 0.003). In the TCGA database, high expression of USP45 and PRPF19 was associated with poorer survival in HCC patients (P = 0.026 and P < 0.001, respectively). Our finding indicated that the two SNPs in NER pathway genes may be novel biomarkers of the survival in HBV-HCC patients.