DNA Repair Single Nucleotide Polymorphisms Research Articles

Thyroid Cancer: The Quest for Genetic Susceptibility Involving DNA Repair Genes

The incidence of thyroid cancer (TC), particularly well-differentiated forms (DTC), has been rising and remains the highest among endocrine malignancies. Although ionizing radiation (IR) is well established on DTC aetiology, other environmental and genetic factors may also be involved. DNA repair single nucleotide polymorphisms (SNPs) could be among the former, helping in explaining the high incidence. To further clarify the role of DNA repair SNPs in DTC susceptibility, we analyzed 36 SNPs in 27 DNA repair genes in a population of 106 DTCs and corresponding controls with the aim of interpreting joint data from previously studied isolated SNPs in DNA repair genes. Significant associations with DTC susceptibility were observed for XRCC3 rs861539, XPC rs2228001, CCNH rs2230641, MSH6 rs1042821 and ERCC5 rs2227869 and for a haplotype block on chromosome 5q. From 595 SNP-SNP combinations tested and 114 showing relevance, 15 significant SNP combinations (p < 0.01) were detected on paired SNP analysis, most of which involving CCNH rs2230641 and mismatch repair variants. Overall, a gene-dosage effect between the number of risk genotypes and DTC predisposition was observed. In spite of the volume of data presented, new studies are sought to provide an interpretability of the role of SNPs in DNA repair genes and their combinations in DTC susceptibility.

Polymorphisms of DNA repair genes are associated with colorectal cancer in patients with Lynch syndrome.

Background DNA repair genes are crucial for maintaining genomic stability by preventing mutagenesis and carcinogenesis. The present retrospective cohort study aimed at investigating whether MLH1,APEX1,MUTYH,OGG1,NUDT1,XRCC5, XPA, and ERCC2 single nucleotide polymorphisms (SNPs) are associated with colorectal cancer (CRC) in Chinese population with Lynch syndrome.MethodsFrom Amsterdam criteria family registry, we identified 270 patients with Lynch syndrome. Hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between DNA repair SNPs and CRC were calculated using a weighted Cox proportional hazard regression model.ResultsHeterozygous variants of rs1799832 in NUDT1 (HR = 2.97, 95% CI = 1.51–5.83) and rs13181 in ERCC2 (HR = 2.69, 95% CI = 1.10–6.55) were significantly associated with an increased risk of CRC compared with wild‐type homozygous CC and TT genotypes, respectively. However, the variant CG+GG genotype of MUTYH rs3219489 was associated with a decreased risk of CRC (HR = 0.49, 95% CI = 0.26–0.91) compared with the homozygous CC wild‐type counterparts.ConclusionOur findings revealed that polymorphisms of DNA repair genes that include NUDT1,ERCC2, and MUTYH are associated with CRC in patients with Lynch syndrome in Chinese population. Further studies with large sample size are needed to confirm our findings.

DNA repair variants and breast cancer risk

A functional DNA repair system has been identified as important in the prevention of tumour development. Previous studies have hypothesized that common polymorphisms in DNA repair genes could play a role in breast cancer risk and also identified the potential for interactions between these polymorphisms and established breast cancer risk factors such as physical activity. Associations with breast cancer risk for 99 single nucleotide polymorphisms (SNPs) from genes in ten DNA repair pathways were examined in a case-control study including both Europeans (644 cases, 809 controls) and East Asians (299 cases, 160 controls). Odds ratios in both additive and dominant genetic models were calculated separately for participants of European and East Asian ancestry using multivariate logistic regression. The impact of multiple comparisons was assessed by correcting for the false discovery rate within each DNA repair pathway. Interactions between several breast cancer risk factors and DNA repair SNPs were also evaluated. One SNP (rs3213282) in the gene XRCC1 was associated with an increased risk of breast cancer in the dominant model of inheritance following adjustment for the false discovery rate (P < 0.05), although no associations were observed for other DNA repair SNPs. Interactions of six SNPs in multiple DNA repair pathways with physical activity were evident prior to correction for FDR, following which there was support for only one of the interaction terms (P < 0.05). No consistent associations between variants in DNA repair genes and breast cancer risk or their modification by breast cancer risk factors were observed.

Association between DNA repair gene polymorphisms and risk of glioma: A systematic review and meta-analysis

Association studies of germline DNA repair single nucleotide polymorphisms (SNPs) and glioma risk have yielded inconclusive results. We therefore performed a systematic review and meta-analysis of studies investigating this association. We identified 27 eligible studies investigating 105 SNPs in 42 DNA repair genes. Of these, 10 SNPs in 7 genes were analyzed in at least 4 studies and were therefore included in our meta-analysis. The meta-analysis was performed for homozygote comparison, heterozygote comparison, and dominant and recessive models by applying a fixed- or random-effects model. The funnel and forest plots were created using RevMan software. We found that SNPs rs3212986 (odds ratio [OR] = 1.35 (1.08-1.68), P = .008), rs13181 (OR = 1.18 (1.06-1.31), P = .002), and rs25487 (OR = 1.12 (1.03-1.22), P = .007) in DNA repair genes ERCC1, ERCC2 (XPD), and XRCC1 may increase the risk of glioma, while polymorphisms rs1136410 (OR = 0.78 (0.68-0.89), P = .0004) and rs12917 (OR = 0.84 (0.73-0.96), P = .01) in PARP1(ADPRT) and MGMT are associated with decreased susceptibility to glioma. No evidence of significant associations between ERCC2 rs1799793, OGG1 rs1052133, XRCC1 rs25489, XRCC1 rs1799782, or XRCC3 rs861539 and risk of glioma was observed. This study provides evidence that DNA repair genes ERCC1, ERCC2, and XRCC1 might be low-penetrance glioma-risk genes, while MGMT and PARP1 polymorphisms may confer protection against glioma.

Abstract 2636: Nonmelanoma skin cancer as a marker of a cancer-prone phenotype: Potential role of DNA repair gene variants

Abstract Purpose: For unknown reasons, nonmelanoma skin cancer (NMSC) is associated with increased risk of other malignancies. This study tested the hypothesis that DNA repair gene variants contribute to the increased cancer risk associated with a personal history of NMSC. Methods: From the parent CLUE II cohort study, established in 1989 in Washington County MD, the study consisted of a cancer-free control group (n=2,296) compared to three mutually exclusive groups of cancer cases ascertained through 2007: 1) Other (non-NMSC) cancer only (n=2,349); 2) NMSC only (n=694); and 3) NMSC plus other cancer (n=577). The frequency of minor alleles in 759 DNA repair single nucleotide polymorphisms (SNPs) was compared in these four groups. Results: Comparing those with both NMSC and other cancer versus those with no cancer, 10 SNPs had additive model p-values&amp;lt;0.01. The two top-ranked SNPs were both within the thymine DNA glycosylase gene (TDG). One was a nonsynonymous coding SNP (rs2888805) (per allele odds ratio (OR) 1.40, 95% confidence interval (CI) 1.16-1.70; p-value=0.0006) and the other was an intronic SNP in high linkage disequilibrium with rs2888805 (rs4135150). Conclusion: The results pinpoint DNA repair genes most likely to contribute to the NMSC cancer-prone phenotype. A promising lead is genetic variants in TDG, important not only in base excision repair but also in regulating the epigenome and gene expression, which may contribute to the NMSC-associated increase in overall cancer risk. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2636. doi:1538-7445.AM2012-2636

Abstract 2630: DNA repair single nucleotide polymorphisms interact with indoor tanning and melanoma

Abstract Development of melanoma has previously been associated with compromised DNA repair which can be analyzed by genotyping SNPs in DNA repair genes. The Minnesota Skin Health Study collected DNA samples to investigate the hypothesis that DNA repair SNPs are associated with increased risk for melanoma among tanning bed users. 92 SNPs, with minor allele frequencies greater than 0.05, were analyzed in 20 genes for 1659 samples_893 melanoma cases and 766 controls. The SNPs were genotyped on the Illumina BeadExpress GoldenGate platform. The SNPs were then analyzed for individual SNP associations with melanoma, haplotype associations with melanoma, individual SNP interactions with ever/never indoor tanning, and haplotype interactions with ever/never indoor tanning after adjustments for age, gender, and phenotypic index. There were several SNPs that had an association with melanoma including: six SNPs in three nucleotide excision repair genes ERCC4, ERCC6 (rs4253190, adjusted OR=1.19, 95%CI: 1.04-1.37; rs4838518, adjusted OR=0.86, 95%CI: 0.75-0.99; rs4253121, adjusted OR=0.84, 95%CI:0.71-0.99), and XPC, one SNP in base excision repair gene RFC1, one SNP in direct reversal DNA repair gene MGMT, and one SNP in a novel gene FBRSL1(rs4883571, adjusted OR=0.87, 95%CI: 0.75-1.00). There were four haplotype associations with melanoma including one ERCC6 block (rs10745261, rs6537537, rs4253121: GGA, adjusted OR: 0.84, 95%CI: 0.71-0.99), two MGMT blocks, and one XPC block. Additionally, there was one SNP in FBRSL1 (rs4883557, p=0.0056) and one SNP in ERCC6 (rs10745261, p=0.025) that had an interaction with indoor tanning along with two haplotypes including one block in ERCC6 (rs10745261, rs6537537, rs4253121: AAG, p=0.0355) and one block in MGMT. While the interaction analyses were suggestive, the study is limited because none of the SNPs or haplotypes were only significant (p&amp;lt;0.05) before Bonferroni correction. Further analyses of the function of these SNPs will be necessary, particularly for ERCC6, which had SNPs that were significant in every analysis, and FBRSL1, which is a novel gene whose function is unknown. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2630. doi:1538-7445.AM2012-2630

A case-control study examining associations of germ-line oxidative DNA repair single-nucleotide polymorphisms (SNPs) with lethal prostate cancer (PCa) risk.

4645 Background: PCa risk is multi-factorial with both genetic and environmental influences. Candidate SNPs identifying risk of lethal PCa have been poorly characterized. This case control study wa...

Impact on response and survival of DNA repair single nucleotide polymorphisms in relapsed or refractory multiple myeloma patients treated with thalidomide

Single nucleotide polymorphisms (SNPs) in 12 genes involving multidrug resistance, drug metabolic pathways, DNA repair systems and cytokines were examined in 28 patients with relapsed/refractory multiple myeloma (MM) treated with single agent thalidomide and the results were correlated with response, toxicity and overall survival (OS). The response rate was higher in patients with SNPs in ERCC1 (rs735482) ( p = 0.006), ERCC5 (rs17655) ( p = 0.04) or XRCC5 (rs1051685) ( p = 0.013). Longer OS was associated with the SNP in ERCC1 (rs735482) ( p = 0.005) and XRCC5 (rs1051685) ( p = 0.02). Finally, polymorphism in GSTT1 (rs4630) was associated with a lower frequency of thalidomide-induced peripheral neuropathy ( p = 0.04).

Impact on Response and Survival of DNA Repair Single Nucleotide Polymorphisms In Relapsed or Refractory Multiple Myeloma Patients Treated with Thalidomide

AbstractAbstract 4041 Background:Thalidomide was the first of the so-called new drugs incorporated in the treatment of multiple myeloma (MM). In this era of emerging novel agents, there is a real need for increased knowledge of the pre-treatment genetic profile of patients who will potentially benefit from each drug. The analysis of polymorphisms in drug metabolism pathways and in immune system genes can help to identify patients with possible different treatment response and outcome. Single nucleotide polymorphisms (SNPs) are the most frequent type of genomic polymorphisms and are involved in chemotherapy response in different tumors, including MM. We examined SNPs in 12 genes and correlated our findings with response, toxicity and overall survival (OS) to thalidomide in patients with relapsed MM. Methods:Twenty-eight patients (13M/15F; median age 59 years, range 40 to 82 years) with relapsed or refractory MM from November 1999 to December 2003 were treated with single agent thalidomide at a single institution. The median duration of thalidomide treatment was 4 months and the median dose was 400 mg/day. Median follow-up for alive patients was 103 months (range 86 to 112). Genomic DNA was isolated from bone marrow slides using a commercial assay (Qiagen). SNPs were analyzed by TaqMan assay in an ABI Prism 7500 Sequence Detection system (Applied Biosystems). The genes explored were those related to multidrug resistance (ABCB1 [rs3842, rs1045642]), drug metabolic pathways (NR1I2 [rs1523130, rs1523127], GSTT1 [rs4630], SULT1C2 [rs1402467]), DNA repair systems (XPA [rs1800975], ERCC1 [rs735482], ERCC2 [rs13181], ERCC5 [rs17655, rs1047768], XRCC1 [rs25487], XRCC5 [rs1051677, rs1051685], TOP2A [rs13695]) and cytokines (VEGFA [rs10434, rs2010963]). Results:Partial response (PR) was attained in 17.9% (5/28) and minimal response (MR) in 28.6% (8/28), while 3 (10.7%) and 12 (42.9%) patients showed no response (NR) or progressive disease (PD), respectively. The response rate (PR+MR vs. NR+PD) to thalidomide was higher (66.7%) in patients with hetero- (AC) or homozygous (CC) SNPs in ERCC1 (rs735482) than in those with wild type (AA) (33.3%) (p=0.006). Patients with the ERCC5 heterozygous SNP rs17655 (CG) had a higher response rate (77.8%) than those with the homozygous SNP (GG) or wild type (CC) (31.6%) (p=0.04). Patients with heterozygous XRCC5 (AG) polymorphism rs1051685 showed a higher response rate (100%) than those with wild type (AA) (34.8%) (p=0.013). Longer OS was associated with the homo- and the heterozygous SNP in ERCC1 (AC + CC vs. AA; p=0.005) and with the heterozygous SNP in XRCC5 (rs1051685) (AG vs. AA; p=0.02) (Figures 1 and 2). A trend to longer OS was also observed in patients with polymorphisms in XRCC1 (p=0.06). The heterozygous polymorphism in GSTT1 (CT vs. TT) was associated with a lower frequency of thalidomide-induced peripheral neuropathy (p=0.04). Conclusion:SNPs in ERCC1 and XRCC5 were strongly associated with higher response rate and longer OS to thalidomide in patients with relapsed/refractory MM. SNPs in ERCC5 were also associated with greater response rate. Since the polymorphism in XRCC1 was not related to a better response to thalidomide, it can be speculated that the trend to prolonged OS could be related to other molecular mechanisms. Our findings could be useful to identify patients with MM who are more likely to benefit from thalidomide-based therapies. [Display omitted] [Display omitted] Disclosures:Cibeira:Janssen-Cilag: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees. Rosiñol:Janssen-Cilag: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees. Blade:Janssen-Cilag: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.

Abstract 1869: Genetic variants of DNA repair genes and lung cancer among nonsmokers: A pooled analysis in the International Lung Cancer Consortium

Abstract Background Lung cancer among nonsmokers has been considered as a different disease from that among smokers. Involuntary smoking has been suggested to be a risk factor for lung cancer among nonsmokers with a modest effect. Few studies have examined the role of single nucleotide polymorphisms (SNPs) of the DNA repair genes and their potential interactions with involuntary smoking on the development of lung cancer among nonsmokers. Methods We evaluated the associations between SNPs of the DNA repair genes and lung cancer based on a pooled data of the International Lung Cancer Consortium. The individual-level epidemiological data and genotyping data on eight SNPs from six participating studies were pooled, including 845 nonsmoker cases and 4,262 nonsmoker controls. Logistic regression models with adjustment by age, sex, ethnicity, study, and ever involuntary smoking status were used to obtain odds ratios (OR) and 95% confidence intervals (CI). Results Among nonsmokers, the associations with the polymorphisms in OGG1 S326C and XPD D312N were observed among those with involuntary smoking (for OGG1 S326C: OR=1.61, 95% CI 1.18-2.20 for CG, OR=1.74, 0.99-3.06 for GG, compared to CC; for XPD D312N: OR=1.06, 0.76-1.47 for AG, OR=1.60, 1.06-2.42 for AA, compared to GG), but not for those without involuntary smoking (for OGG1 S326C: OR=0.78, 0.39-1.54 for CG, OR=0.88, 0.25-3.06 for GG, compared to CC; for XPD D312N: OR=1.13, 0.57-2.21 for AG, OR=0.81, 0.27-2.43 for AA, compared to GG). The association with XRCC3 T241M variant was detected for adenocarcinoma and non-small cell lung cancer among those without exposure to involuntary smoking (adenocarcinoma: OR=3.52, 1.21-10.20 for AA, OR=0.94, 0.38-2.38 for GA, compared to GG; and non-small cell lung cancer: OR=2.75, 1.05-7.21 for AA, OR=1.10, 0.51-2.38 for GA, compared to GG, respectively). Due to limited power, no apparent interaction between DNA repair SNPs and involuntary smoking was detected. Conclusion This is the first large-scale collaborative study on the relationship between DNA repair genetic variants and lung cancer among nonsmokers, accounting for involuntary smoking. Our results show that SNPs of the DNA repair genes may play an important role for lung cancer among nonsmokers, and the associations may vary by involuntary smoking status and histological subtype. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1869.

Polyunsaturated Fatty Acids, DNA Repair Single Nucleotide Polymorphisms and Colorectal Cancer in the Singapore Chinese Health Study

Animal and in vitrostudies support a role for polyunsaturated fatty acids (PUFAs) in colon carcinogenesis; however, the epidemiological evidence is inconclusive. Recently, we investigated their role within the Singapore Chinese Health Study, a population-based cohort of Singapore Chinese men and women. We reported that a high intake of marine n–3 PUFAs was associated with an increased risk of colorectal cancer (CRC). Oxidation of PUFAs incorporated into cell membranes generates lipid hydroperoxides, which can be mutagenic. In this report, we investigated whether single nucleotide polymorphisms (SNPs) in DNA repair genes modified the effect of PUFAs on CRC risk using a nested case-control study within the Singapore Chinese Health Study. We genotyped 1,181 controls and 311 cases (180 colon and 131 rectal cancer) for SNPs in the XRCC1 (Arg194Trp, Arg399Gln), OGG1 (Ser326Cys), PARP (Val762Ala, Lys940Arg), and XPD (Asp312Asn, Lys751Gln) genes. We observed that the PARP Val762Ala SNP modified the association between marine n–3 PUFA and rectal cancer risk, with no evidence of interaction among colon cancer (heterogeneity test p = 0.003). Our results suggest a positive association between high intake of marine n–3 PUFA and rectal cancer risk among carriers of at least one PARP codon 762 Ala allele (odds ratio = 1.7, 95% confidence interval = 1.1–2.7).

DNA Repair Single-Nucleotide Polymorphisms in Colorectal Cancer and their Role as Modifiers of the Effect of Cigarette Smoking and Alcohol in the Singapore Chinese Health Study

Recently, we reported that among Singapore Chinese, cigarette smoking and alcohol drinking were independent risk factors for colorectal cancer. Both tobacco smoking and alcohol use are plausible colorectal cancer risk factors, partly due to their ability to induce mutations in the colorectal lumen. In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphisms in five DNA repair genes: XRCC1 (Arg(194)Trp and Arg(399)Gln), PARP (Val(762)Ala, Lys(940)Arg), XPD (Asp(312)Asn, Lys(751)Gln), OGG1 (Ser(326)Cys), and MGMT (Leu(84)Phe). We conducted this study within the Singapore Chinese Health Study, a population-based cohort of 63,257 middle-aged and older Singapore Chinese men and women enrolled between 1993 and 1998. Our study included 1,176 controls and 310 cases (180 colon and 130 rectum cancer). We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colorectal cancer risk [odds ratio (OR), 1.8; 95% confidence interval (95% CI), 1.1-3.1], and an inverse association between the MGMT codon 84 Leu/Phe or Phe/Phe genotypes and colon cancer risk (OR, 0.6; 95% CI, 0.3-0.9), but not rectal cancer (test of heterogeneity by tumor site, P=0.027). We observed evidence that XRCC1 may modify the effects of smoking (interaction P=0.012). The effect of smoking among carriers of the Arg(194)-Gln(399) haplotype was OR=0.7 (95% CI, 0.4-1.1), whereas, among carriers of the Trp(194)-Arg(399) haplotype, it was OR=1.6 (95% CI, 1.1-2.5). We also observed a nonstatistically significant modification of XRCC1 on the effects of alcohol (P=0.245). Whereas alcohol had no effect among carriers of the codon 194 Arg/Arg (OR, 1.0; 95% CI, 0.6-1.7) or Arg/Trp genotypes (OR, 1.1; 95% CI, 0.6-1.9), there was a positive association among carriers of the Trp/Trp genotype (OR, 2.8; 95% CI, 1.0-8.1). Our results support a role for reactive oxygen species as relevant genotoxins that may account for the effects of both smoking and alcohol on colorectal cancer risk.

DNA repair gene polymorphisms and probability of p53 mutation in bladder cancer

We investigated if the presence of single nucleotide polymorphisms (SNPs) in the XRCC1, XRCC3, and XPD genes were associated with the type and frequency of p53 mutations in bladder cancer. Using a hospital-based case-control study we have previously reported risks for the XRCC1 codon 194, XRCC1 codon 399, XRCC3 codon 241, and XPD codon 751 SNPs 1-3. We have also previously reported mutation data for 149 cases from this study who were screened for mutations in exons 4 through 9 of the p53 gene 4. Here we investigate possible associations between the DNA repair SNPs mentioned above and the presence of p53 mutations by comparing the frequency of each genotype between p53 mutation positive and negative cases. We also considered different classes of p53 mutations, including any mutation (nonsense, missense or silent), transversions and transitions and estimated odds ratios (ORs) and 95% confidence intervals (CI) for these associations. Cases with the XRCC1 codon 399 Gln/Gln genotype were positively associated with the presence of p53 transversions (OR = 4.8; 94% CI = 0.8-30). Cases with the XPD codon 751 Gln/Gln genotype were positively associated with the presence of p53 transitions (OR = 2.8; 95% CI = 0.8-9.3), in particular G:C-A:T transitions (OR = 3.7; 95% CI = 1.1-13). Our data provide some limited support for the hypothesis that mutations in the p53 gene in bladder cancer may differ according to the presence or absence of certain DNA repair gene variants.