Association between XRCC1 and XRCC3 polymorphisms with lung cancer risk: a meta-analysis from case-control studies

Impact of Interaction between Single Nucleotide Polymorphism of XRCC1, XRCC2, XRCC3 with Tumor Suppressor Tp53 Gene Increases Risk of Breast Cancer: A Hospital Based Case-Control Study

BACKGROUND

At present very little information is available on combined effects of DNA repair genes with tumor suppressor gene polymorphisms and their association with cancer susceptibility. No such association studies have been carried out with breast cancer or any other cancer from India. Present study was conducted to study the combined effects of SNPs of XRCC1, XRCC2, XRCC3 with Arg72Pro and Arg249Ser SNPs of TP53 gene in risk of BC in rural parts of India.

METHODS

The polymorphisms of Arg194Trp, Arg280His, Arg399Gln of XRCC1, Arg188His of XRCC2 and Thr241Met of  XRCC3 with Arg72Pro and Arg249Ser of TP53 gene polymorphisms was studied by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) method. The association among the polymorphisms with breast cancer risk was studied by Odds ratio within 95% confidence interval and SNP-SNP interaction were confirmed by logistic regression analysis.

RESULTS

The results of genotype frequency distribution of XRCC1, XRCC2, XRCC3 genotypes showed positive association between XRCC1 Arg280His polymorphism and BC risk (OR=4.54; 95% CI: 3.36- 6.15; p<0.0001).  Also the heterozygous genotypes Arg188His of XRCC2 (OR=1.58; 95% CI: 1.13- 2.21; p=0.007) and Thr241Met genotype of XRCC3 (OR=2.13; 95% CI: 1.44- 3.13; p=0.0001) were associated with BC risk. The combination of heterozygous Arg280His genotype of XRCC1 along with Arg72Pro genotype of TP53 increased the risk of BC (OR=4.53; 95% CI: 2.85-7.20); p<0.0001). Similarly,  the combined effect of heterozygous Arg/His genotype of XRCC1 with heterozygous Arg/Ser genotype of TP53 at codon 249 showed significant association with increased BC risk (OR=5.08; 95% CI: 2.86-9.04); p<0.0001).

CONCLUSION

The findings derived from our study concluded that the heterozygous variant Arg280His genotype of XRCC1 and Thr241Met polymorphism of XRCC3 in combination with heterozygous arginine72proline genotype and heterozygous Arg249Ser polymorphism of TP53 showed significant association with breast cancer risk in Maharashtrian women.

Association between XRCC3 rs861539 Polymorphism and the Risk of Ovarian Cancer: Meta-Analysis and Trial Sequential Analysis

Background

Current studies on the relationship between XRCC3 rs861539 polymorphism and ovarian cancer risk have been inconsistent. Therefore, we performed a meta-analysis to explore their association.

Methods

Six electronic databases (PubMed, Embase, Web of Science, Cochrane Library, China National Knowledge Infrastructure, and China Wanfang Database) were searched for relevant studies published before December 2021. Meta-analysis, subgroup analysis, sensitivity analysis, and publication bias analysis were performed using Stata software 16.0. Trial sequential analysis (TSA) was performed using TSA 0.9.5.10 Beta software.

Results

A total of 12 studies were included in 9 literatures, comprising 4,634 cases of ovarian cancer and 7,381 controls. After Bonferroni correction, the meta-analysis showed an association between XRCC3 rs861539 polymorphism and ovarian cancer risk in the heterozygote model and the dominant model (GA vs. GG: OR = 0.88, 95%CI = 0.81-0.96, P = 0.003; GG vs. GA+AA: OR = 0.89, 95%CI = 0.82-0.96, P = 0.004). In an ethnically stratified subgroup analysis, XRCC3 rs861539 was shown to reduce the risk of ovarian cancer in Caucasian in the heterozygote model and the dominant model (GA vs. GG: OR = 0.88, 95%CI = 0.81-0.96, P = 0.004; GG vs. GA+AA: OR = 0.88, 95%CI = 0.81-0.96, P = 0.004). In the control source and detection method stratified subgroup analysis, hospital-based studies and PCR-RFLP-based studies were found to increase ovarian cancer risk (GG vs. AA: OR = 1.30, 95%CI = 1.05-1.62, P = 0.016; GG vs. AA: OR = 1.31, 95%CI = 1.06-1.62, P = 0.013).

Conclusion

This meta-analysis showed a significant association between XRCC3 rs861539 polymorphism and ovarian cancer risk, especially in Caucasians. Large-scale multicenter case-control studies in more different regions will be needed in the future.

Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies

A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29^th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.

XRCC1 rs25487 genetic variant and TP53 mutation at codon 249 predict clinical outcomes of hepatitis B virus-related hepatocellular carcinoma after hepatectomy: A cohort study for 10 years' follow up

AIM

To investigate the effects of rs25487 (the DNA repair gene: x-ray repair complementing defective repair in Chinese hamster cells 1 [XRCC1]) and codon 249 mutation (TP53 gene) on clinical outcomes of post-hepatectomy hepatitis B virus (HBV)-related HCC.

METHODS

The XRCC1 rs25487 polymorphism and TP53 mutation at codon 249 of 485 hepatitis B surface antigen positive patients subjected to hepatectomy were genotyped via direct sequencing. SPSS software version 16.0 (SPSS, Chicago, IL, USA) was used to calculate survival of HCC patients according to primary end-points.

RESULTS

The presence of at least one A allele (AA/AG) of rs25487 was associated with unfavorable prognosis (P = 0.005). Moreover, A allele (AA/AG) carriers were significantly associated with high risk of vascular invasion (P = 0.025) and regional invasion (P = 0.005). Differences were not significant between mutant and wild-type TP53 cases with overall survival (adjusted P = 0.400). Among the 485 participants, patients (n = 73) carrying both the A allele (AA/AG) of rs25487 and 249Ser TP53 mutation displayed decreased overall survival, compared with patients (n = 184) with the GG genotype of rs25487 and wild-type codon 249 (adjusted P = 0.007).

CONCLUSION

Polymorphisms of rs25487 may play a potential role in survival of HBV-related hepatocellular carcinoma patients following hepatectomy. While mutation at codon 249 of TP53 is not associated with HBV-related HCC survival in this study.

Arg194–Arg399 haplotype of XRCC1 gene is susceptible to lung cancer in the Han population

Objective:

Lung cancer is still one of the most frequently diagnosed cancers all over the world, especially in developing countries. The aim of this study was to investigate the relationship between two well-characterized non-synonymous polymorphisms (Arg194Trp and Arg399Gln) in X-ray repair cross-complementing group 1 ( XRCC1) gene and the risk of lung carcinoma in the Han population.

Methods:

This study was hospital-based in design and included 159 participants (63 patients with lung carcinoma and 96 cancer-free controls) of Chinese Han descent. Genomic DNA from blood samples was extracted for PCR studies, followed by direct sequencing to determine the variants of the XRCC1 gene.

Results:

Carriers with Arg194–Arg399 haplotype of XRCC1 gene conferred a 189.3% increased risk compared to the non-carriers (95% confidence interval [CI], 1.195–2.998; P = 0.006). And single-locus analysis (both allele and genotype distributions of polymorphism Arg194Trp and Arg399Gln) identified neither association with cancer risk nor with clinico-pathological parameters of lung carcinoma in the Han population.

Conclusions:

Arg194–Arg399 haplotype of XRCC1 gene might increase lung cancer susceptibility and serve as a risk factor for lung cancer in the Han population.

Association of -77T>C and Arg194trp polymorphisms of XRCC1 with risk of coronary artery diseases in Iranian population

OBJECTIVES

Coronary artery disease (CAD) is the leading cause of death in both male and female worldwide. The main cause of CAD is the atherosclerosis of coronary arteries, which is, mostly caused by genetic alteration. 50% of such cases occur in mitotic cells where single-strand breaks occur spontaneously or due to ionizing radiation. X-ray repair cross-complementing protein 1 (XRCC1) as a key element, participate in the base excision repair (BER) and Single-strand Break Repair (SSBR) pathways. It has been suggested that XRCC1 functions as a scaffold protein able to coordinate and facilitate the various steps of DNA repair pathways. Two Single Nucleotide Polymorphisms (SNPs) (Arg194Trp and -77T>C) were reported to affect the function and expression of XRCC1, respectively.

MATERIALS AND METHODS

A case-control study was performed to investigate the relation between these polymorphisms and the CAD development. A population of 406 individuals was screened for SNPs by Restriction Fragment Length Polymorphisms (RFLP) method.

RESULTS

XRCC1 Arg194Trp polymorphism was associated with increased risk of CAD in examined population under a dominant model (Odds-ratio=2.604, P-value=0.001). Also the SNP of -77T>C revealed a protective role in the population under a dominant model (Odds-ratio=0.618, P-value=0.032).

CONCLUSION

Our findings demonstrated a contributory role of these two SNPs in CAD. Furthermore, our results support the role of DNA damages and the malfunctions of DNA repair system in cardiovascular disease development in Iranian patients.

XRCC3 Thr241Met Polymorphism is not Associated with Lung Cancer Risk in a Romanian Population

BACKGROUND AND AIMS

Deoxyribonucleic Acid (DNA) repair mechanisms play a critical role in protecting the cellular genome against carcinogens. X-ray cross-complementing gene 3 (XRCC3) is involved in DNA repair and therefore certain genetic polymorphisms that occur in DNA repair genes may affect the ability to repair DNA defects and may represent a risk factor in carcinogenesis. The purpose of our study was to investigate the association between XRCC3 gene substitution of Threonine with Methionine in codon 241 of XRCC3 gene (Thr241Met) polymorphism and the risk of lung cancer, in a Romanian population.

METHODS

We recruited 93 healthy controls and 85 patients with lung cancer, all smokers. Thr241Met, XRCC3 gene genotyping was determined by multiplex Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP).

RESULTS

Statistical analysis (OR, recessive model), did not revealed an increased risk for lung cancer, for the variant 241Met allele and Thr241Met genotypes (p=0.138, OR=0.634, CI=0.348-1.157; p=0.023, OR=0.257, CI=0.085-6.824). Also, there were no positive statistical associations between Thr241Met polymorphism of XRCC3 gene, gender, tobacco and various histopathological tumor type of lung cancer.

CONCLUSION

In conclusion, the results of the study suggest that the XRCC3 gene Thr241Met polymorphism is not associated with an increased risk for the development of lung cancer in this Romanian group.

Association Between X-Ray Cross-complementing Group 3 (XRCC3) Thr241Met Polymorphism and Risk of Thyroid Cancer: A Meta-Analysis

Background

The X-ray cross-complementing group 3 (XRCC3) gene encodes a protein that plays an important role in homologous recombination repair (HRR) of DNA double-strand break (DSB). Increasing attention has been drawn to the association of XRCC3 T241M polymorphism with various types of human cancers. In this study, a meta-analysis was performed to investigate whether there is an association between XRCC3 T241M polymorphism and thyroid cancer risk.

Material/Methods

A comprehensive search was conducted and a total of 8 studies that covered 963 thyroid cancer cases and 1942 controls were included in this analysis. The meta-analysis was performed on both overall database and 2 ethnic subgroups (Caucasian and Asian). The fixed-effects model was used to calculate odds ratio (OR) with 95% confidence intervals (CIs). The publication bias was evaluated using Begg’s funnel plots and Egger’s test.

Results

A positive association between XRCC3 T241M polymorphism and thyroid cancer risk was found by the analyses of the overall database using both recessive model (OR=1.40, 95% CI=1.08–1.81, P=0.012) and homozygote comparison (OR=1.41, 95% CI=1.07–1.86, P=0.015), but not by that using the dominant model (OR=1.12, 95% CI=0.95–1.33, P=0.18). However, no significant association of XRCC3 Thr241Met polymorphism with the risk of thyroid cancer was found in individual ethnic subgroups.

Conclusions

We conclude that the XRCC3 Thr241Met polymorphism is associated with an increased risk of thyroid cancer in the overall population, while no significant association was observed in individual ethnic subgroups due to limited population size.

Gene-gene and gene-environment interactions in meta-analysis of genetic association studies

Extensive genetic studies have identified a large number of causal genetic variations in many human phenotypes; however, these could not completely explain heritability in complex diseases. Some researchers have proposed that the “missing heritability” may be attributable to gene–gene and gene–environment interactions. Because there are billions of potential interaction combinations, the statistical power of a single study is often ineffective in detecting these interactions. Meta-analysis is a common method of increasing detection power; however, accessing individual data could be difficult. This study presents a simple method that employs aggregated summary values from a “case” group to detect these specific interactions that based on rare disease and independence assumptions. However, these assumptions, particularly the rare disease assumption, may be violated in real situations; therefore, this study further investigated the robustness of our proposed method when it violates the assumptions. In conclusion, we observed that the rare disease assumption is relatively nonessential, whereas the independence assumption is an essential component. Because single nucleotide polymorphisms (SNPs) are often unrelated to environmental factors and SNPs on other chromosomes, researchers should use this method to investigate gene–gene and gene–environment interactions when they are unable to obtain detailed individual patient data.

Homologous Recombination Repair Polymorphisms and the Risk for Osteosarcoma

Background

DNA repair mechanisms are essential for maintaining genome stability, and genetic variability in DNA repair genes may contribute to cancer susceptibility. Our aim was to evaluate the influence of polymorphisms in the homologous recombination repair genes XRCC3, RAD51, and NBN on the risk for osteosarcoma.

Methods

In total, 79 osteosarcoma cases and 373 controls were genotyped for eight single nucleotide polymorphisms (SNPs) in XRCC3, RAD51, and NBN. Logistic regression was used to determine the association of these SNPs with risk for osteosarcoma.

Results

None of the investigated SNPs was associated with risk for osteosarcoma in the whole cohort of patients, however, in patients diagnosed before the age of thirty years XRCC3 rs861539 C>T and NBN rs1805794 G>C were associated with significantly decreased risk for osteosarcoma (P=0.047, OR=0.54, 95% CI=0.30–0.99 and P=0.036, OR=0.42, 95% CI=0.19–0.94, respectively). Moreover, in the carriers of a combination of polymorphic alleles in both SNPs risk for osteosarcoma was decreased even more significantly (P_trend=0.007). The risk for developing osteosarcoma was the lowest in patients with no wild-type alleles for both SNPs (P=0.039, OR=0.31, 95% CI=0.10–0.94).

Conclusions

Our results suggest that polymorphisms in homologous recombination repair genes might contribute to risk for osteosarcoma in patients diagnosed below the age of thirty years.

The influence of XRCC1 genetic variants on lung cancer susceptibility in Chinese Han population

Growing evidence suggests that genetic variants of X-ray repair cross-complementing group 1 proteins (XRCC1) contribute to genetic effects on the development of lung cancer. This case-control study aims to evaluate the genetic effects of XRCC1 c.482C>T and c.1686C>G single nucleotide polymorphisms (SNPs) on lung cancer susceptibility. 391 lung cancer patients and 398 cancer-free controls were enrolled in this study. The genotypes of c.482C>T and c.1686C>G genetic variants were detected by the created restriction site-polymerase chain reaction (CRS-PCR), PCR-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing methods. The genetic effects on lung cancer susceptibility were evaluated using association analyses by the unconditional logistic regression model. Our data indicated that there were significant differences in the distribution of allelic and genotypic frequencies between lung cancer patients and cancer-free controls. The XRCC1 c.482C>T and c.1686C>G genetic variants were significantly associated with the susceptibility to lung cancer (for c.482C>T, TT versus (vs.) CC: OR=2.14, 95% CI 1.31-3.48, P=0.002; T vs. C: OR=1.37, 95% CI 1.10-1.69, P=0.004; for c.1686C>G, GG vs. CC: OR=2.53, 95% CI 1.46-4.38, P=0.001; G vs. C: OR=1.33, 95% CI 1.06-1.65, P=0.012). These preliminary results suggested that the XRCC1 c.482C>T and c.1686C>G genetic variants might play genetic effects on the susceptibility to lung cancer in the studied population.

Putative functional variants of XRCC1 identified by RegulomeDB were not associated with lung cancer risk in a Korean population

The Encyclopedia of DNA elements (ENCODE) project revealed that nearby or distantly located non-coding DNA regulates the expression of coding genes. RegulomeDB (http://regulome.stanford.edu) is a new database that can be used to predict whether a variant affects transcription factor binding and gene expression. We investigated the association between lung cancer risk and potentially functional polymorphisms of XRCC1 that were selected using RegulomeDB in a Korean population. A total of 185 polymorphisms of XRCC1 were evaluated using RegulomeDB. Strong evidence suggested that 10 polymorphisms, from among the 185, affected XRCC1 expression with scores of 1a-1f that were based on the RegulomeDB scoring system. The rs2854510 polymorphism was rare in Asians (minor allele frequency < 0.05). Eight polymorphisms were in strong linkage disequilibrium (LD). The rs2854509 polymorphism, which was one of the 8 polymorphisms in LD, and rs7248167, which was not in the LD block, were genotyped in 610 lung cancer patients and 607 age- and sex-matched controls. Additionally, four polymorphisms of XRCC1 (rs25487, rs25489, rs1799782, and rs3213245), which were investigated with regard to their association with lung cancer risk in previous studies, were also genotyped. Two polymorphisms (rs2854509 and rs7248167) that were predicted to affect XRCC1 expression based on their RegulomeDB scores were not associated with lung cancer risk (P = 0.31 and 0.93, respectively). When stratified according to age, gender, smoking status, and tumor histology, the two polymorphisms of XRCC1 were not associated with lung cancer risk. Among the four polymorphisms that were previously studied, only rs25489 of XRCC1 was significantly associated with lung cancer risk (dominant model, adjusted odds ratio = 0.61, 95% confidence interval = 0.46-0.83, P = 0.002). Although RegulomeDB is an attractive tool for predicting the regulatory potential of variants, the two polymorphisms that were selected using RegulomeDB were not associated with lung cancer risk.

Association between TNF-α gene 308G>A polymorphism and lung cancer risk: a meta-analysis

Many studies have investigated the association between tumor necrosis factor alpha (TNF-α) gene 308G/A polymorphism and lung cancer risk, but the results were inconsistent. We thus comprehensively searched the PubMed, EMBASE, and BIOSIS Previews databases and extracted data from all eligible articles to estimate the association between TNF-α gene 308G/A polymorphism and lung cancer risk. The pooled odds ratio (OR) with 95 % confidence intervals (CIs) were calculated. Twelve case-control studies in 11 articles involving 2,436 cases and 2,573 controls were included in the meta-analysis to assess the association between TNF-α gene 308G>A polymorphism and susceptibility to lung cancer. Overall, TNF-α gene 308G>A polymorphism was significantly associated with an increased risk of lung cancer for A vs. G (OR = 1.13, 95 % CI 1.00 ~ 1.27, P = 0.04). Subgroup analysis by ethnicity showed that there was a significant association between TNF-α gene 308G>A polymorphism and increased risk of lung cancer in Asians, but not in Caucasians. In subgroup analysis by tumor type, there were significant associations between TNF-α gene 308G>A polymorphism and increased risk of lung cancer in small cell lung cancer (SCLC) for AA+AG vs. GG, in non-small cell lung cancer (NSCLC) for A vs. G, AA vs. GG, and AA+AG vs. GG. No association between the genotypes and different stages of lung cancer was detected. The meta-analysis suggests that TNF-α gene 308G>A polymorphism is associated with an increased risk of lung cancer, particularly among Asians, both for SCLC and NSCLC, considering tumor type.

XRCC1 Arg399Gln polymorphism confers risk of breast cancer in American population: a meta-analysis of 10846 cases and 11723 controls

Background

In the X-ray repair cross-complementing group 1 (XRCC1) gene, a polymorphism, Arg399Gln (rs25487), has been shown to change neoconservative amino acid and thus result in alternation of DNA repair capacity. Numerous studies have investigated the association between Arg399Gln and breast cancer risk in the American population, but yielding inconsistent results. This study aimed to clarify the role of this polymorphism in susceptibility to breast cancer.

Methods

Literatures were searched in multiple databases including PubMed, Springer Link, Ovid, EBSCO and ScienceDirect databases up to April 2013. A comprehensive meta-analysis was conducted to estimate the overall odds ratio (OR), by integrating data from 18 case control studies of 10846 cases and 11723 controls in the American population.

Results

Overall, significant association was observed between the Arg399Gln polymorphism and breast cancer risk under the random-effects model (OR for dominant model = 1.12, 95% CI: 1.02–1.24, P_{heterogeneity} = 0.003; OR for additive model = 1.07, 95% CI: 1.01–1.14, P_{heterogeneity} = 0.017). Further sensitivity analysis supported the robust stability of this current result by showing similar ORs before and after removal of a single study.

Conclusions

This meta-analysis suggests that the XRCC1 Arg399Gln polymorphism may significantly contribute to susceptibility of breast cancer in the American population.