Genotypes, haplotypes and diplotypes of three XPC polymorphisms in urinary-bladder cancer patients

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Abstract

Purpose

The XPC gene is involved in DNA damage recognition in the nucleotide excision repair pathway (NER). We investigated the additive effects of single nucleotide polymorphisms (SNPs) in bladder-cancer patients and population controls for three XPC polymorphisms: A499V (C > T), K939Q (A > C), and poly AT (PAT, −/+).

Experimental Design

311 bladder-cancer patients from a population-based cohort and 337 population controls were genotyped using the PCR-restriction fragment length polymorphism (RFLP) technique.

Results

We found complete linkage between the K939Q (A > C) and PAT (−/+) polymorphisms and therefore only the K939Q (A > C) polymorphism was included in analyses. The over all estimated odds ratio was 1.7 (95% CI 1.3–2.4) for A499V (C > T) and 1.4 (95% CI 1.0–2.0) for K939Q (A > C). The associated odds ratio increase with the variant allele homozygotes was six-fold for the A499V (C > T) and three-fold for the K939Q (A > C) polymorphism (OR = 5.7, 95% CI 3.4–9.5 and OR = 2.6, 95% CI 1.3–5.6, respectively). The variant allele haplotype of the two polymorphisms (T499C939) was associated with a nearly four fold increased odds ratio compared to the common allele haplotype (C499A939) (OR = 3.6, 95% CI:1.9–6.9). Combined genotype analysis showed an increased disease association with increasing number of variant alleles (p < 0.0001), with a dominant effect of the A499V polymorphism. In addition we observed association of the disease with increasing number of variant alleles for the A499V polymorphism and an early age at diagnosis (p = 0.004).

Conclusions

Our results suggest an association between the XPC genotypes of the A499V, K939Q and PAT polymorphisms and urinary-bladder cancer. We propose a poly-allelic effect of these polymorphisms where the cumulative effect on disease becomes higher than the individual allelic effects.

Introduction

The occurrence of urinary bladder cancer, one of the ten most common cancers in the western world, can be influenced by dietary intake and environmental factors e.g. polycyclic aromatic hydrocarbons and polychlorinated biphenyls [1], [2], [3]. Many chemical carcinogens form bulky DNA adducts after activation by various metabolic enzymes [4], [5]. These bulky adducts are in general removed by a multi-step nucleotide excision repair (NER) pathway [6]. Un-repaired DNA damage, due to defective NER, can lead to mis-incorporation of bases at the damaged sites, fixation of mutations and ultimately cancer [7]. Molecular epidemiological studies have shown considerable inter-individual variations in the DNA repair capacity in the general population which could partially stem from the genetic polymorphisms in genes involved in the repair processes. Therefore, it has been postulated that inherited polymorphisms in NER genes can modulate the susceptibility to cancer in the general population.

The xeroderma pigmentosum group C (XPC) protein has a vital function in the repair process of potential carcinogenic lesions. The protein binds to RAD23B (also known as HR23B) and plays a key role in damage detection and initiating NER [8]. The XPC gene spans 33 kb on chromosome 3 and contains 16 exons and 15 introns, encoding a 940 amino acid protein [9]. Germ line mutations in the XPC gene result in defective NER, and are associated with the Xeroderma pigmentosum syndrome, complementation group C. Beside mutations, several polymorphisms in this gene have been reported (listed in e.g. http://snp500cancer.nci.nih.gov/home.cfm) [10], [11]. Although the functional effects of these polymorphisms have not yet been fully elucidated, it is plausible that genotypes, haplotypes and diplotypes of some of these polymorphisms may have an effect on NER capacity, thereby modulating the risk of cancer.

In two previous studies we reported an association of bladder cancer with the variant allele of the A499V (C > T, rs2228000) and the K939Q (A > C, rs2228001) polymorphisms in the XPC gene [12], [13]. In the present study we extended these analysis and also investigated the poly AT polymorphism (PAT −/+) of XPC [11]. In addition we studied linkage disequilibrium (LD) between the A499V (C > T), K939Q (A > C) and PAT (−/+) polymorphic loci and investigated the association of the three polymorphisms in XPC with urinary-bladder cancer with regards to allele frequencies, genotypes, haplotypes and diplotypes.

Section snippets

Subjects

Our study group was drawn from a population-based patient material consisting of 78% (563/721) of all newly diagnosed bladder-cancer patients 1995–1996 in the Stockholm County, Sweden [14]. Venous blood was collected at a later time point and was available for 311 patients of Caucasian origin (201 men, 94 women and 16 unknown), which were included in the present study. DNA was extracted from blood as described previously [15]. Tumor stage was assessed according to a modified TNM system by Hall

Association of genotype and allele frequencies of XPC polymorphisms and bladder cancer

The frequencies of the variant allele genotypes (CT and TT) and variant allele (T) of the A499V (C > T) polymorphism were significantly higher in the cases than controls (Table 1). We found a six-fold increased odds ratio for the variant allele homozygotes (p < 0.0001) when compared to common allele homozygotes (Table 1). The frequency of the K939Q (A > C) variant allele homozygous CC genotype was also significantly higher in the urinary-bladder cancer cases than in population controls. This study

Discussion

DNA damages induced by occupational exposure to chemicals and smoking are well known risk factors for bladder cancer. The XPC protein is crucial in the recognition and initiation of the nucleotide excision pathway (NER), which eliminates a wide variety of DNA damages induced by chemical and environmental exposures such as aromatic amines and UV light. Polymorphisms in the XPC gene have been shown to influence an individual's DNA repair capacity, and hence it is plausible that genetic variation

Conflict of interest

None.

Acknowledgement

Grants were obtained from the Swedish Cancer Association (Cancerfonden CAN2007/649), the regional agreement on medical training and clinical research between Stockholm County Council and Karolinska Institutet (ALF), Magnus Bergvall's Foundation and the Foundation in Memory of Johanna Hagstrand and Sigfrid Linnér.

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