The genotype distribution of the XRCC1gene indicates a role for base excision repair in the development of therapy-related acute myeloblastic leukemia

Acute myeloblastic leukemia (AML) is a clonal hemopoietic disorder that is frequently associated with genetic instability characterized by a diversity of chromosomal and molecular changes. Most cases of AML arise de novo, with no known exposure to leukemogenic substances. However, approximately 10% to 20% of all cases of AML arise after therapy, most often chemotherapy, used to treat other malignant diseases (therapy-related AML [t-AML]1).

Many genes encode proteins that function to protect cells against genetic instability by means of many mechanisms, including DNA repair pathways and protection against oxidative stress. DNA repair pathways play a vital role in maintaining genetic integrity, and it is becoming clear that defects in repair pathways are connected to many different types of diseases, including leukemia and cancer. It is now thought that an individual's DNA repair capacity is genetically determined and is the result of combinations of multiple genes that may display subtle differences in their activity (see Mohrenweiser and Jones2for review). Inactivating mutations in DNA repair genes are rare, resulting in embryonic death or serious genetic diseases and reflecting the importance of the gene products; however, polymorphisms have been identified in several DNA repair genes.3 Many of these polymorphisms result in amino acid substitutions and hence may alter wild-type (WT) protein function and affect cellular ability to repair endogenous and exogenous DNA damage, thereby contributing to disease susceptibility.

XRCC1, XRCC3, and XPD are polymorphic genes belonging to 3 of the major DNA repair pathways. XRCC1is involved in base excision repair (BER) and the repair of single-strand breaks. The XRCC1 gene product plays an important role in the pathway by acting as a scaffold for other DNA repair proteins, such as DNA polymerase β4 and DNA ligase III.5The protein also has a BRCA1 C-terminus (BRCT) domain, which is characteristic of proteins involved in the recognition of and response to DNA damage. XRCC1 interacts with poly (ADP-ribose) polymerase (PARP) by means of the BRCT domain to enable the recognition and subsequent repair of single-strand breaks.6,7 DNA damage caused by a variety of internal and external factors, including ionizing radiation, alkylating agents, and oxidation, requires repair by the BER pathway.

Several variants of XRCC1 have been described, including one affecting codon 399 in exon 10 that results in an arginine (Arg) to methionine (Met) substitution3 and one affecting codon 194 in exon 6 that results in an Arg to tryptophan (Trp) substitution. Both codon 194 and codon 399 are conserved across species. Codon 194 resides in a linker region connecting the domains that interact with PARP and DNA polymerase β, whereas codon 399 resides in the functionally important PARP-binding domain.8 Chinese hamster ovary cell lines with nonconservative amino acid substitutions in the PARP-binding domain were found to have a decreased ability to repair DNA damage.9 

The XRCC3 protein functions in the homologous DNA double-strand break (DSB) repair pathway and directly interacts with and stabilizes Rad51,10 one of the key components of the pathway. The homologous DNA DSB repair pathway uses the second, intact copy of a chromosome as a template to copy the information lost at the DSB site on the first chromosome, resulting in a high-fidelity process that has a vital role in preventing chromosomal aberrations. The threonine (Thr) to Met polymorphism at codon 241 of XRCC3 is a nonconservative change. Little is known about the functional consequence of this amino acid change, although positive associations between the variant allele and cancer have been observed in various investigations, including studies of bladder cancer11 and melanoma skin cancer.12 

The XPD protein, a 5′ to 3′ DNA helicase involved in the nucleotide excision repair pathway, functions to remove bulky damage adducts from DNA. The XPD lysine (Lys) 751–glutamine (Gln) polymorphism does not reside in a known functional domain of XPD and was initially thought to be unlikely to result in an altered DNA repair capacity.3,13 However, additional studies produced contrasting results, linking the XPD 751Gln variant allele to both reduced14 and elevated15 nucleotide excision repair capacity. Thus, more work is warranted to establish whether this polymorphism is clinically relevant.

Nicotinamide adenine dinucleotide phosphate:quinone oxidoreductase 1 (NQO1) functions to protect cells from oxidative stress by detoxifying several compounds. The enzyme reduces reactive quinones to the less reactive hydroquinones and so prevents accumulation of reactive oxygen species that may then go on to damage DNA. A polymorphism has been identified in NQO1 at codon 187.16 This polymorphism converts a proline (Pro) to a serine (Ser) residue and has been shown to result in inactivation of NQO1.17 The incidence of this polymorphism was found to be significantly increased both in patients with de novo AML18 and in those with t-AML, particularly those with chromosome 5/7 abnormalities.19 

In the current study, we investigated the genotype distributions of the XRCC1 Arg399Gln, XRCC3 Thr241Met, and NQO1 Pro187Ser polymorphisms in patients with AML, particularly those with t-AML, and in controls. We also studied the distribution of the XRCC1-194 and XPD-751 genotypes. In addition, because a malignant phenotype is likely to result from the accumulation of many minor genotypes, we assessed whether there was an association between DNA repair gene polymorphisms (XRCC1 andXRCC3) and a polymorphism in a protein involved with minimizing the effects of oxidative stress (NQO1).

Blood or bone marrow samples were obtained at the diagnosis of AML, after informed consent to participate was given according to the Declaration of Helsinki, from 168 white patients, including 34 with t-AML, presenting to the Haematology Department of Nottingham City Hospital. The diagnosis of AML was made by using the French-American-British criteria after conventional cytochemical and surface-marker analysis. The median age among patients with de novo AML was 63 years (range, 17-96 years); that among those with t-AML was 61.5 years (range, 37-88 years). Control peripheral blood samples were obtained from an equivalent number (n = 178; median age, 51.5 years; range, 15-97 years) of whites with no known malignant diseases who resided in the same geographic community. Samples were not matched for sex; however, previous investigations consistently found no significant difference between male and female subjects in the distribution of the genotypes investigated in this study.14,20 Genomic DNA was extracted from cells by using QIAamp blood DNA isolation kits (Qiagen, Crawley, United Kingdom) according to the manufacturer's protocol.

PCR followed by enzymatic digestion of the PCR products was used for genotyping the 3 polymorphisms. Approximately 50 ng genomic DNA was used as template in each of the PCR amplifications. The 50-μL reaction also consisted of 150 μM of each deoxynucleoside triphosphate (Amersham Biosciences, Little Chalfont, United Kingdom), 1 μM of each primer, 1.5 to 2.0 mM/L magnesium chloride (MgCl₂), and 2 U Amplitaq Gold (PE Applied Biosystems, Warrington, United Kingdom) in the manufacturer's buffer. After an initial heat-activation step at 95°C for 10 minutes, amplification was performed in a PTC-100 programmable thermal controller (MJ Research, Watertown, MA). For XRCC1 Arg399Gln, XRCC1 Arg194Gln, XPD Gln751Lys, and XRCC3 Thr241Met, we used denaturation at 95°C for 1 minute, annealing at 60°C for 1 minute, and extension at 72°C for 1 minute for a total of 30 cycles ending with a final extension at 72°C for 10 minutes. For NQO1 Pro187Ser, we used denaturation at 94°C for 50 seconds, 52°C for 50 seconds, and 72°C for 30 seconds for a total of 35 cycles, followed by a final extension step at 72°C for 10 minutes. PCR products were purified by using a QIAquick PCR purification kit (Qiagen) before digestion and/or sequencing.

The XRCC1 Arg399Gln polymorphism was amplified in a 616-bp fragment by using the following primers: xrcc1-399F 5′-TTGTGCTTTCTCTGTGTCCA-3′ and xrcc1-399R 5′-TCCTCCAGCCTTTACTGATA-3′21 with 2 mM/L MgCl₂. The PCR product was digested with 10 UMspI (Helena Biosciences, Sunderland, United Kingdom) in the manufacturer's buffer at 37°C overnight. The recognition site for the MspI restriction endonuclease is present only in the Arg (WT) allele; hence, digestion of the Arg allele results in products of 376 bp and 240 bp, whereas the Gln allele remains undigested.

A segment of the XRCC1 gene containing the Arg194Trp polymorphism was amplified by using the primer pairs xrcc1-194F 5′-GGTAAGCTGTACCTGTCACTC-3′ and xrcc1-194R 5′-GACCCAGGAATCTGAGCC-3′ with 1.5 mM/L MgCl₂. The PCR products were digested at 37°C overnight with 10 U MspI. The PCR product contains an internal MspI site, and products with the 194Arg genotype contain an additional MspI site, resulting in 20-, 117-, and 167-bp products. The 194Trp allele is digested only at the internal MspI site, resulting in 137- and 167-bp products.

XRCC3 Thr241Met was amplified in a 415-bp product by using the primers xrcc3-241F 5′-GGTCGAGTGACAGTCCAAAC-3′ and xrcc3-241R 5′-CTACCCGCAGGAGCCGGAGG-3′3 with 2 mM/L MgCl₂. The PCR products were digested at 37°C overnight with 10 UNlaIII (New England Biolabs, Hitchin, United Kingdom) in 1 ×  buffer supplied with the enzyme and supplemented with 100 ng/μL bovine serum albumin. All XRCC3 PCR products contain an internal NlaIII site, and the presence of the Met polymorphism also generates an additional NlaIII site, resulting in 104-, 141-, and 170-bp products for the polymorphic allele and 141- and 274-bp products for the WT Thr allele.

The XPD Lys751Gln polymorphism was amplified in a 344-bp fragment by using the following primers: xpd-751F 5′-TCAAACATCCTGTCCCTACT-3′ and xpd-751R 5′-CTGCCGATTAAAGGCTGTGGA-3′3 with 2 mM/L MgCl₂. The PCR product was digested with 10 UPstI (Helena Biosciences) at 37°C overnight. All PCR products contain an internal PstI site, resulting in 110- and 234-bp products in the 751Lys allele. In addition, an extraPstI site is present in the Gln allele, resulting in 63-, 110-, and 171-bp products.

The NQO1 Pro187Ser polymorphism was amplified in a 304-bp fragment by using the primers nqo1F 5′-AAGCCCAGACCAACTTCT-3′ and nqo1R 5′-TCTCCTCATCCTGTACCTCT-3′15 with 1.5 mM/L MgCl₂. The PCR products were digested overnight at 37°C with 10 U HinfI (New England Biolabs) in the manufacturer's buffer. All PCR products contain an internal HinfI site, and the Ser polymorphism also introduces an additional HinfI site, resulting in 33-, 120-, and 151-bp digested fragments, whereas the WT allele results in 33- and 271-bp products.

The digested products were resolved on 3% agarose gels (Helena Biosciences), stained with ethidium bromide and analyzed under UV light. Two reviewers independently scored all genotypes, and samples that could not be scored were sequenced. Sequencing was also carried out on a 10% random sample population of control and AML PCR products.

Sequencing reactions were set up with approximately 200 ng purified PCR product and 10 mM primer by using a Thermo Sequenase II dye terminator cycle sequencing premix kit according to the manufacturer's instructions (Amersham Biosciences). The primers used for sequencing were the same as those used for the PCR amplifications. The reactions were electrophoresed by using an ABI 377 automated DNA sequencer (PE Applied Biosystems, Foster City, CA) as recommended by the manufacturer.

The observed genotype frequencies of the 3 polymorphisms in the control cohorts were compared with those calculated by using the Hardy-Weinberg equilibrium (p2 + q2 + 2pq = 1; where p is the variant allele frequency). The distribution of genotypes in AML populations compared with the control population was assessed for significance by χ² testing, and odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression analysis and adjusted for the effect of age. P values of less than or equal to .05 were considered to represent significance. All analyses used the statistical package SPSS for Windows (version 9; SPSS, Chicago, IL).

We examined the frequency of 3 polymorphisms in 134 patients with de novo AML (median age, 63 years) and 178 controls (median age, 51.5 years). We also analyzed a subgroup of 34 patients with t-AML (median age, 61.5 years). Because of an inadequate amount of DNA in some cases, several samples did not generate complete information for all 3 polymorphisms. Among the controls, the variant allele frequencies were 0.48 for XRCC1 399Gln, 0.30 for XRCC3 241Met, and 0.22 for NQO1 187Ser. All genotype frequencies in the control population were consistent with those expected from the Hardy-Weinberg equilibrium (XRCC1 Arg399Gln, χ² = 1.93 and P = .38; XRCC3 Thr241Met, χ² = 1.22 and P = .54; and NQO1 Pro187Ser, χ² = 0.94 and P = .63). The distributions of the frequencies of the polymorphisms in AML cases and controls are shown in Table 1. The results for the XRCC1 Arg399Gln polymorphism showed that the proportion of AML and t-AML patients homozygous for the WT Arg allele was higher than in the control group, with the difference in the distribution of genotypes reaching statistical significance in the t-AML group (P = .03 on χ² testing). Neither the XRCC3-241 nor the NQO1 genotype distributions showed any differences in either the de novo AML or t-AML group compared with the control group. The adjusted ORs for the individual genotypes are shown in Table2. The XRCC1 399 homozygous variant genotype is a protective factor in both the de novo AML and t-AML patient groups. When the presence of at least one Gln allele is considered, it becomes apparent that the variant allele is significantly protective against the development of t-AML (OR, 0.46; 95% CI, 0.20-0.93).

We also studied 2 additional polymorphisms, XRCC1 Arg194Trp and XPD Lys751Gln, in a smaller cohort of patients and controls. Among the controls, the variant allele frequencies were 0.07 for XRCC1 194Trp and 0.38 for XPD 751Gln. The genotype distributions among the control population were consistent with those expected from the Hardy-Weinberg equilibrium (XRCC1 Arg194Trp, χ² = 2.49 andP = .29; and XPD Lys751Gln, χ² = 0.25 andP = .88). The distributions of the frequencies of the polymorphisms in AML patients and controls are shown in Table 1; adjusted ORs are shown in Table 2. No significant differences were observed between the AML patient cohort and the controls.

Table 3 shows the combined analysis for either the XRCC1 Arg399Gln or XRCC3 Thr241Met genotypes with the NQO1 Pro187Ser genotype. Because of the small numbers of t-AML samples available, these were grouped with the samples from the de novo AML cases for this analysis. The DNA repair gene polymorphisms did not show an interaction with the detoxification NQO1 Pro187Ser polymorphism.

Although it has been established that mismatch repair is important in a subset of patients with AML,22-24 little is known about the role of the other DNA repair pathways in this disease. In this study, we found that a polymorphism in a DNA repair gene belonging to the BER pathway, XRCC1 Arg399Gln, is associated with a protective effect against the development of AML, particularly t-AML. Hence, patients in whom AML develops as a result of therapy for a primary malignant disease are more likely to have the WT XRCC1 399 Arg allele.

It is possible that differences between the cases and controls may have contributed to the observed association, but we believe that this is unlikely. Both populations were from the same small geographical area in the United Kingdom and had the same age range. Sex has been shown not to have any influence on the XRCC1 Arg399Gln genotype,20 and although race was previously found to be an important factor in the distribution of the XRCC1 Arg399Gln genotype,25,26 all our patients and controls were white.

We did not find any differences between the distributions of the XRCC3 Thr241Met and NQO1 Pro187Ser genotypes. Others have observed a significant increase in the incidence of the variant NQO1 allele in patients with AML, particularly those with chromosome 5/7 abnormalities.19 This association was not evident in our AML groups, although the number of patients with chromosome 5/7 abnormalities in our cohort was small and that may have accounted for the difference from previous studies. We were able to obtain cytogenetic information for approximately 100 of our patients, and only 10 of them had chromosome 5/7 abnormalities. We combined the de novo AML and t-AML groups to examine possible associations between either the XRCC1 Arg399Gln or XRCC3 Thr241Met genotypes and the NQO1 Pro187Ser genotypes. No significant association was observed, suggesting that the phenotypes resulting from these proteins do not interact to increase the risk of AML. However, our number of t-AML samples was too small to allow us to conduct combined logistic regression analysis of this group alone.

We also performed PCR-RFLP analysis of a smaller number of patients and controls to study the distribution of genotypes of an additional polymorphism in XRCC1 (XRCC1 Arg194Trp) and a polymorphism in XPD (XPD Lys751Gln), a gene involved in the nucleotide excision repair pathway. No significant differences were found between controls and patients with AML.

Several previous studies assessed the functional relevance of polymorphisms in DNA repair genes. Lunn et al21 measured genotoxic end points of DNA damage and showed that the XRCC1 399Gln allele was associated with increased placental aflatoxin DNA adducts and increased glycophorin A mutations in erythrocytes. They suggested that the Arg to Gln change at codon 399 may alter the phenotype of the XRCC1 protein, resulting in deficient DNA repair. In addition, Duell et al27 measured DNA damage by using a sister chromatid exchange assay and also detected polyphenol DNA adducts. They found more damage in current smokers homozygous for the XRCC1 399Gln allele than in current smokers with the homozygous WT allele. A sister chromatid assay was also used by Abdel-Rahman and El-Zein,28 who found that a higher level of DNA damage after treatment with a tobacco-specific nitrosamine occurred in XRCC1 399Gln homozygotes.

Several polymorphism studies have observed a positive association of the XRCC1 399 Gln allele with various malignant diseases, including cancer of the head and neck,20 breast,25lung,26 and colon and rectum.29 The researchers suggested that these results correlated with the in vitro functional data and illustrated the adverse effects of deficient DNA repair systems. However, other studies, including ours, had conflicting results. We found that the presence of the XRCC1 399Gln allele is protective against the development of t-AML. The same protective effect has been observed in studies of bladder cancer30 and nonmelanoma skin cancer.31 This may indicate the presence of a strong gene-environment interaction that is tumor specific. There is a fine balance between deficient and functional DNA repair systems. Although it is important for damaged DNA to be recognized and repaired, it is also vital for the cell to be able to recognize when the damage is too extensive to be repaired and to allow the apoptotic pathway to be stimulated; this prevents cells from potentially misrepairing damage and surviving with mutations. This process may be particularly important in the development of t-AML. Chemotherapy and radiotherapy both induce immense amounts of DNA damage and have the aim of achieving cell death. Even subtle changes in DNA repair capacity are likely to be important when large external influences such as chemotherapy or radiotherapy are present. We hypothesize that when hematopoietic progenitor cells in the bone marrow are damaged by therapy, the cells with the XRCC1 399 Gln allele and resulting reduced DNA repair capacity are more likely to be driven toward apoptosis. This is contrary to what happens to cells with the WT genotype, which are more likely to repair their damage, possibly harbor mutations, and initiate clonal disease resulting in t-AML. Hence, we suggest the XRCC1 399 Gln allele is protective against the development of t-AML. A similar proposal was made by Nelson et al31 in their large study of nonmelanoma skin cancer.

Our hypothesis can be extended to the opposite situation observed in many primary malignant diseases in which the XRCC1 399Gln allele has been shown to be a risk factor. Although DNA damage caused by “low-dose” exogenous sources (for example, smoking and diet) is considered to be an important contributory factor in many malignant diseases, the resulting oxidative burden on the cells is significantly smaller than that following chemotherapy or radiotherapy, which can be considered to cause “high-dose” damage. Hence, a BER pathway with a fully functional XRCC1 gene (XRCC1 399Arg) would be expected to repair the damage caused by low-dose damaging agents (smoking and diet), whereas a deficiency in the DNA repair pathway, such as an XRCC1 399Gln allele, would reduce the effectiveness of the pathway in repairing damage from low-dose sources and thus increase the risk of a primary malignant disease.

Additional work is now required to determine whether polymorphisms do indeed lead to a reduced DNA repair capacity in vivo and to identify the consequences of these phenotypes in different environmental conditions. The identification of polymorphisms or mutations in many genes and the determination of their functional importance in AML will allow susceptibility-risk models to be designed for de novo and therapy-related disease. Intervention strategies and early detection approaches could then be targeted at those individuals genetically identified to be at higher risk of AML or t-AML.

We thank Tricia McKeever for assistance with the statistical analysis; Stephen Langabeer and the Kay Kendall Leukaemia Fund for t-AML DNA samples from the DNA/RNA banking facilities at University College Hospital, London; and the Medical Research Council (MRC) Acute Leukaemia Working Party for access to samples from patients with AML entered into MRC trials.