核苷酸切除修复通路基因多态性与肺癌易感性研究

目的研究显示核苷酸切除修复通路在去除吸烟引起的DNA损伤中发挥着重要的作用,旨在探讨核苷酸切除修复通路单核苷酸多态性与吸烟相关性肺癌易感性的关系。方法选取1010例肺癌患者和1011例正常对照。采用基于通路的候选基因选点策略,从核苷酸切除修复通路相关的8个核心基因中筛选出40个标签SNPs进行检测和分析。结果单个位点分析发现6个SNPs（ERCC1 2个,DDB2 2个,ERCC4／XPF 1个,XPC 1个）与肺癌的易感性相关。进一步采用Logistic回归模型,调整年龄、性别、吸烟史和肿瘤家族史后,仍有3个SNPs（ERCC1 rs3212948,DDB2 rs830083,ERCC4 rs3136038）与肺癌易感性存在统计学关联。等位基因联合分析结果进一步表明肺癌的发病风险随着风险等位基因个数的增加而增加,尤其是ERCC1,ERCC2,ERCC3,ERCC5,XPA和XPC。结论本研究结果提示核苷酸切除修复通路基因多态性可能与中国汉族人群的肺癌个体易感性有关,值得进一步进行功能学探讨及大样本人群验证.     

Nucleotide excision repair genes and risk of lung cancer among San Francisco Bay Area Latinos and African Americans

Few studies on the association between nucleotide excision repair (NER) variants and lung cancer risk have included Latinos and African Americans. We examine variants in 6 NER genes (ERCC2, ERCC4, ERCC5, LIG1, RAD23B and XPC) in association with primary lung cancer risk among 113 Latino and 255 African American subjects newly diagnosed with primary lung cancer from 1998 to 2003 in the San Francisco Bay Area and 579 healthy controls (299 Latinos and 280 African Americans). Individual single nucleotide polymorphism and haplotype analyses, multifactor dimensionality reduction (MDR) and principal components analysis (PCA) were performed to assess the association between 6 genes in the NER pathway and lung cancer risk. Among Latinos, ERCC2 haplotype CGA (rs238406, rs11878644, rs6966) was associated with reduced lung cancer risk [odds ratio (OR) of 0.65 and 95% confidence interval (CI): 0.44-0.97], especially among nonsmokers (OR = 0.29; 95% CI: 0.12-0.67). From MDR analysis, in Latinos, smoking and 3 SNPs (ERCC2 rs171140, ERCC5 rs17655 and LIG1 rs20581) together had a prediction accuracy of 67.4% (p = 0.001) for lung cancer. Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increased lung cancer risk (OR = 1.78; 95% CI: 1.09-2.91), and LIG1 haplotype GGGAA (rs20581, rs156641, rs3730931, rs20579 and rs439132) was associated with reduced lung cancer risk (OR = 0.61; 95% CI: 0.42-0.88). Our study suggests different elements of the NER pathway may be important in the different ethnic groups resulting either from different linkage relationship, genetic backgrounds and/or exposure histories.     

Polymorphisms in DNA damage binding protein 2 (DDB2) and susceptibility of primary lung cancer in the Chinese: a case-control study

DNA damage binding protein 2 (DDB2) is one of the major DNA repair proteins involved in the nucleotide excision repair (NER) pathway. Mutations in the DDB2 gene can cause a repair-deficiency syndrome xeroderma pigmentosum group E. Because tobacco carcinogens can cause DNA damage that is repaired by NER and suboptimal NER capacity is reported to be associated with lung cancer risk, we hypothesized that common variants in the DDB2 gene are associated with lung cancer risk. To test this hypothesis, we conducted a case-control study of 1010 patients with incident lung cancer and 1011 cancer-free controls and genotyped two DDB2 single nucleotide polymorphisms (SNPs) (rs830083 and rs3781620) that are in linkage disequilibrium with other untyped SNPs. We found that compared with the rs830083CC, subjects carrying the heterozygous rs830083CG genotype had a significantly 1.31-fold increased risk of lung cancer [95% confidence interval (CI) 1.08-1.60] and those carrying the homozygous rs830083GG genotype had a non-significantly 1.22-fold elevated risk (95% CI 0.89-1.67). In addition, effects of the combined rs830083CG/GG variant genotypes were more evident in young subjects, heavy smokers and subjects with a positive family history of cancer. These findings indicate, for the first time, that the DDB2 rs830083 polymorphism may contribute to the etiology of lung cancer. Further functional studies on this SNP and/or related variants are warranted to elucidate the underlying molecular mechanisms of the association.     

DNA repair and cancer in colon and rectum: Novel players in genetic susceptibility

Interindividual differences in DNA repair systems may play a role in modulating the individual risk of developing colorectal cancer. To better ascertain the role of DNA repair gene polymorphisms on colon and rectal cancer risk individually, we evaluated 15,419 single nucleotide polymorphisms (SNPs) within 185 DNA repair genes using GWAS data from the Colon Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), which included 8,178 colon cancer, 2,936 rectum cancer cases and 14,659 controls. Rs1800734 (in MLH1 gene) was associated with colon cancer risk (p-value = 3.5 × 10⁻⁶) and rs2189517 (in RAD51B) with rectal cancer risk (p-value = 5.7 × 10⁻⁶). The results had statistical significance close to the Bonferroni corrected p-value of 5.8 × 10⁻⁶. Ninety-four SNPs were significantly associated with colorectal cancer risk after Binomial Sequential Goodness of Fit (BSGoF) procedure and confirmed the relevance of DNA mismatch repair (MMR) and homologous recombination pathways for colon and rectum cancer, respectively. Defects in MMR genes are known to be crucial for familial form of colorectal cancer but our findings suggest that specific genetic variations in MLH1 are important also in the individual predisposition to sporadic colon cancer. Other SNPs associated with the risk of colon cancer (e.g., rs16906252 in MGMT) were found to affect mRNA expression levels in colon transverse and therefore working as possible cis-eQTL suggesting possible mechanisms of carcinogenesis.     

SNP-SNP interactions between DNA repair genes were associated with breast cancer risk in a Korean population

BACKGROUND:

Single nucleotide polymorphisms (SNPs) in nucleotide excision repair (NER) pathway genes may modulate DNA repair capacity and increase susceptibility to breast cancer (BC). A case‐control study was conducted by evaluating genes involved in DNA repair to identify polymorphisms associated with BC.

METHODS:

The 384 SNPs of 38 candidate genes were genotyped using the Illumina GoldenGate method. Genotypes were determined in a case‐control study that consisted of 346 BC patients and 361 controls. Odds ratios and 95% confidence intervals were computed using logistic regression models. Multiple logistic regression models adjusted for age, family history of BC, and body mass index were used.

RESULTS:

Gene–gene interaction analysis among the DNA repair pathway genes showed significant effects on BC risk. ERCC2 rs50872 (TC genotype) in combination with XPA rs2808668 (TC genotype) and rs1800975 (AG genotype) was strongly associated with an increased risk of BC (P = .0004 and .0002, P_Bonferroni = .023 and .014, respectively). Moreover, the T‐G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T allele in rs50872 carriers was also associated with additive risk effect of BC (odds ratios: 2.58, 2.62, and 3.49, respectively).

CONCLUSION:

Genetic variation in DNA repair genes involved in NER mechanisms increased the risk of BC development. These results suggested that a stronger combined effect of SNPs via gene–gene interaction may help to predict BC risk. Cancer 2012;. © 2011 American Cancer Society.     

A genetic variant in microRNA target site of TGF-β signaling pathway increases the risk of colorectal cancer in a Chinese population

Evidence shows that single-nucleotide polymorphisms in microRNA (miRNA) target sites can create, destroy, or modify the miRNA/mRNA binding, therefore modulating gene expression and affecting cancer susceptibility. The transforming growth factor-β (TGF-β) signaling pathway plays a pivotal role in tumor initiation and progression. Intriguingly, recent advances of genome-wide association studies have identified multiple risk loci in this pathway to be associated with risk of colorectal cancer (CRC). To test the hypothesis that genetic variants in miRNA target sites in genes of the TGF-β signaling pathway may also be associated with CRC risk, we first systematically scanned the single-nucleotide polymorphisms (SNPs) in genes of TGF-β signaling pathway which potentially affect the miRNA/mRNA bindings. Through a series of filters, we narrowed down these candidates to four SNPs. Then, we conducted a case–control study with 600 CRC patients and 638 controls in Han Chinese population. We observed that compared with A carriers (AA?+?AG), the GG genotype of rs12997:ACVR1 is associated with a significantly higher risk of CRC (OR?=?1.52, 95 % confidence interval (95 % CI)?=?1.04–2.21, P?=?0.031), particularly in nonsmokers with a higher OR of 1.63 (95 % CI?=?1.04–2.55, P?=?0.032). Our study suggested that SNPs in miRNA target sites could contribute to the likelihood of CRC susceptibility and emphasized the important role of polymorphisms at miRNA-regulatory elements in carcinogenesis.     

Genotypes and haplotypes of ERCC1 and ERCC2/XPD genes predict levels of benzo[a]pyrene diol epoxide-induced DNA adducts in cultured primary lymphocytes from healthy individuals: a genotype-phenotype correlation analysis

Benzo[a]pyrene diol epoxide (BPDE)-induced DNA adducts are a risk factor for tobacco-related cancers. Excision repair cross-complementing complementation group 1 (ERCC1) and excision repair cross-complementing complementation group 2/xeroderma pigmentosum D (ERCC2/XPD) participate in the nucleotide excision repair (NER) pathway that removes BPDE-DNA adducts; however, few studies have provided population-based evidence for this association. Therefore, we assayed for levels of in vitro BPDE-induced DNA adducts and genotypes of single-nucleotide polymorphisms (SNPs) of the NER genes ERCC1 (rs3212986 and rs11615) and ERCC2/XPD (rs13181, rs1799793 and rs238406) in 707 healthy non-Hispanic whites. The linear trend test of increased adduct values in never to former to current smokers was statistically significant (P(trend) = 0.0107). The median DNA adduct levels for the ERCC2 rs1799793 GG, GA and AA genotypes were 23, 29 and 30, respectively (P(trend) = 0.057), but this trend was not observed for other SNPs. After adjustment for covariates, adduct values larger than the median value were significantly associated with the genotypes ERCC1 rs3212986TT [odds ratio (OR) = 1.89, 95% confidence interval (CI) = 1.03-3.48] and ERCC2/XPD rs238406AA (OR = 0.64, 95% CI = 0.41-0.99) and rs238406CA (OR = 0.63, 95% CI = 0.45-0.89) compared with their corresponding wild-type homozygous genotypes. The results of haplotype analysis further suggested that haplotypes CAC and CGA of ERCC2/XPD, TC of ERCC1 and CACTC of ERCC2/XPD and ERCC1 were significantly associated with high levels of DNA adducts compared with their most common haplotypes. Our findings suggest that the genotypes and haplotypes of ERCC1 and ERCC2/XPD may have an effect on in vitro BPDE-induced DNA adduct levels.     

miRNA相关SNPs与肺癌遗传易感性关系的研究进展

肺癌是世界最常见的癌症,已成为癌症死亡的主要原因。microRNAs（miRNAs）是一类高度保守、内源性非蛋白编码、长度约21~24核苷酸的小分子单链RNA,在基因调控中扮演着重要的角色。miRNA相关单核苷酸多态性（miRNA-related single nucleotide polymorphisms或miR-SNPs）主要包括miRNA基因SNPs、生物合成通路相关基因SNPs和miRNA靶基因中的SNPs,可通过影响miRNA的成熟过程、表达水平及与靶mRNA的识别结合等,使miRNA调控网络发生异常,从而参与肿瘤的发生发展。本文对miRNA相关SNPs与肺癌遗传易感性关系的研究进展进行综述,旨在为肺癌等恶性肿瘤的预防和控制提供参考。     

Evaluation of genetic variation in the double-strand break repair pathway and bladder cancer risk

The double-strand break DNA repair (DSBR) pathway is implicated in maintaining genomic stability and therefore could affect bladder cancer risk. Here we present data evaluating 39 single-nucleotide polymorphisms (SNPs) in seven candidate genes whose products are involved in DNA break sensing (NBS1, BRCA1 interacting genes BRIP1 and ZNF350), non-homologous end-joining (NHEJ) DNA repair (XRCC4) and homologous recombination (HR) repair (RAD51, XRCC2 and XRCC3). SNPs for RAD51 and XRCC2 covered most of the common variation. Associations with bladder cancer risk were evaluated in 1,150 newly diagnosed cases of urinary bladder transitional cell carcinomas and 1,149 controls conducted in Spain during 1997-2001. We found that the genetic variants evaluated significantly contributed to bladder cancer risk (global likelihood ratio test P = 0.01). Subjects with the ZNF350 R501S (rs2,278,415) variant allele showed significantly reduced risk compared with common homozygote variants, odds ratio (OR) [95% confidence interval (95% CI)]: 0.76 (0.62-0.93) per variant allele. Carriers of a putative functional SNP in intron 7 of XRCC4 (rs1,805,377) had significantly increased bladder cancer risk compared with common homozygotes: 1.33 (1.08-1.64) per variant allele. Lastly, XRCC2 homozygote variants for three promoter SNPs (rs10,234,749, rs6,464,268, rs3,218,373) and one non-synonymous SNP (rs3,218,536, R188H) were associated with reduced bladder cancer risk (ORs ranging from 0.36 to 0.50 compared with common homozygotes). Meta-analysis for XRCC3 T241M (rs861,539) had a significant small increase in risk among homozygote variants: OR (95% CI) = 1.17 (1.00-1.36). Results from this study provide evidence for associations between variants in genes in the DSBR pathway and bladder cancers risk that warrant replication in other study populations.     

Comprehensive analyses of DNA repair pathways,smoking and bladder cancer risk in Los Angeles and Shanghai

Tobacco smoking is a bladder cancer risk factor and a source of carcinogens that induce DNA damage to urothelial cells. Using data and samples from 988 cases and 1,004 controls enrolled in the Los Angeles County Bladder Cancer Study and the Shanghai Bladder Cancer Study, we investigated associations between bladder cancer risk and 632 tagSNPs that comprehensively capture genetic variation in 28 DNA repair genes from four DNA repair pathways: base excision repair (BER), nucleotide excision repair (NER), non‐homologous end‐joining (NHEJ) and homologous recombination repair (HHR). Odds ratios (ORs) and 95% confidence intervals (CIs) for each tagSNP were corrected for multiple testing for all SNPs within each gene using pACT and for genes within each pathway and across pathways with Bonferroni. Gene and pathway summary estimates were obtained using ARTP. We observed an association between bladder cancer and POLB rs7832529 (BER) (p_ACT = 0.003; p_pathway = 0.021) among all, and SNPs in XPC (NER) and OGG1 (BER) among Chinese men and women, respectively. The NER pathway showed an overall association with risk among Chinese males (ARTP NER p = 0.034). The XRCC6 SNP rs2284082 (NHEJ), also in LD with SREBF2, showed an interaction with smoking (smoking status interaction p_gene = 0.001, p_pathway = 0.008, p_overall = 0.034). Our findings support a role in bladder carcinogenesis for regions that map close to or within BER (POLB, OGG1) and NER genes (XPC). A SNP that tags both the XRCC6 and SREBF2 genes strongly modifies the association between bladder cancer risk and smoking.     

Impact of Polymorphism in Base Excision Repair and Nucleotide Excision Repair Genes and Risk of Cervical Cancer: A Case-Control Study

Background: Last few years, several studies all over the world revealed the association of DNA repair genes with risk of developing different type of cancers, but were ambiguous to support the evidences in case of cervical cancer risk. These differences in earlier studies directed us to study the association of polymorphisms of BER genes (XRCC1, hOGG1, XPC) and NER genes (XPC, XPD) with cervical cancer susceptibility in the women of rural population of Maharashtra. Materials and Methods: The genetic polymorphism in BER and NER pathway genes was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method using DNA isolated from intravenous blood samples of patients and normal controls. The study included 400 clinically confirmed cervical cancer patients and 400 healthy women from a tertiary care hospital (Krishna Hospital and Medical Research Centre) of south-western Maharashtra. The association of polymorphisms was confirmed by Odds ratio (OR) with 95% confidence interval. Results: The single nucleotide polymorphism (SNP) of BER genes including XRCC1, hOGG1 and APE1 were analyzed and the results were noted that 27466AA (OR=4.88; 95% CI: 3.61- 6.60; p<0.0001) and 28152AA (OR=2.89; 95% CI: 1.57- 5.31; p=0.0005) genotypes of XRCC1 (rs25489, rs25487) were significantly associated with cervical cancer risk. The 1245GG genotype of hOGG1 (rs1052133) (OR=45.30; 95% CI: 3.76- 7.46; p=0.001) also showed significant correlation, whereas 2197GG genotype of APE1 (rs1130409) gene showed negative association with cervical carcinogenesis (OR=0.59; 95% CI: 0.35- 0.97; p=0.005). Similarly when we studied SNPs of NER genes including XPC and XPD genes, 21151TT genotype of XPC (rs 2228000) was positively associated with cervical cancer development and 23591AA genotype of XPD (rs1799793) showed negative association (OR=0.34; 95% CI: 0.17- 0.64; p=0.001). Conclusion: The findings from this study supported that rs25489, rs25487SNPs of XRCC1, rs1052133 of hOGG1 and rs2228000 of XPC may increase cervical cancer risk, whereas rs1130409 SNP of APE1 and rs1799793 SNP of XPD gene lower the risk of cervical cancer in the studied population.     

Genetic variation in an miRNA-1827 binding site in MYCL1 alters susceptibility to small-cell lung cancer

Genetic variations in microRNAs (miRNA) that affect control of their target genes may alter individual susceptibilities to cancer. In this study, we took an in silico approach to identify single-nucleotide polymorphisms (SNP) within the 3'-untranslated region (UTR) of miRNA genes deregulated in human small-cell lung cancer (SCLC), and then investigated their associations with SCLC susceptibility in 666 SCLC patients and 758 controls. Odds ratios (OR) were estimated by multivariate logistic regression, and biochemical assays were conducted to investigate SNP functions. We identified 2 SNPs, rs3134615 and rs2291854, which were located in the 3'-UTR of the L-MYC gene MYCL1 and the neuronal development Achaete-Scute Complex homolog ASCL1. Case-control analyses showed that the rs3134615T allele was associated with a significantly increased risk of SCLC, with the OR for carrying the GT or TT genotype being 2.08 (95% confidence interval, 1.39-3.21; P = 0.0004) compared with the GG genotype. In support of the likelihood that these 3'-UTR SNPs may directly affect miRNA-binding sites, reporter gene assays indicated MYCL1 as the target of hsa-miR-1827 and the rs3134615 G>T change resulted in altered regulation of MYCL1 expression. Our findings define a 3'-UTR SNP in the human L-MYC oncogene that may increase susceptibility to SCLC, possibly resulting from attenuated interaction with the miRNA hsa-miR-1827.     

ERCC6/CSB gene polymorphisms and lung cancer risk

Nucleotide excision repair (NER) enzymes are critical for the removal of bulky DNA adducts caused by environmental carcinogens such as smoking. Of them, Cockayne syndrome complementation group B (CSB), coded by ERCC6, recruits NER repair factors to the DNA damage site and plays an important role in the repair process. Genetic variants of ERCC6 may alter the regulation of DNA repair and therefore were hypothesized to be associated with altered risk of smoking-related lung cancer. To test this hypothesis, we genotyped eight tagging single nucleotide polymorphisms (tSNPs) and three potentially functional SNPs of ERCC6 in 500 incident lung cancer cases and 517 controls in a Chinese population. Single locus analyses showed that none of the single SNP alone had the significant main affect on the risk of lung cancer. However, the combined variant genotypes of the four loci with P(trend) approaching to 0.10 (rs2228526, rs4253160, rs12571445 and rs3793784) were associated with a significantly increased lung cancer risk (adjusted OR 1.35, 95% CI, 1.04-1.75 among subjects carrying three or more variant alleles), indicating that multiple loci in ERCC6 may jointly contribute to the susceptibility of lung cancer. These findings, if validated, may contribute to identify at-risk subjects in the general population for smoking-related lung cancer.     

Association of genetic polymorphisms in DNA repair pathway genes with non-small cell lung cancer risk

DNA repair function is believed to play an important role in cancer development and to be affected by genetic polymorphisms. Numerous epidemiological studies have examined the associations between single nucleotide polymorphisms (SNPs) in the DNA repair genes and lung cancer risk, but the results are inconsistent. The aim of this study was to investigate the associations of several SNPs in the DNA repair pathways and risk of non-small cell lung cancer (NSCLC) in a Chinese population. The study included 581 NSCLC cases and 603 healthy controls. The polymorphisms studied include XRCC1 (rs25487), hOGG1 (rs1052133), MUTYH (rs3219489) in the base excision repair (BER) pathway, XPA (rs1800975), ERCC2 (rs1799793 and rs13181) in the nucleotide excision repair (NER) pathway and XRCC3 (rs861539) in the double strand break repair (DSB) pathway. The associations between lung cancer risk and genetic polymorphisms were evaluated using the logistic regression models and subgroup analyses. Meta-analyses were conducted for the SNPs shown to be significantly associated with lung cancer risk in our study. Our findings showed that XPA −4G>A (rs1800975) had a significant association with lung cancer (OR = 1.64; 95% CI: 1.03-2.60), and the association was more evident in squamous cell carcinoma (OR = 1.69; 95% CI: 1.00-2.84). Three BER polymorphisms showed no independent effects on the risk of lung cancer. The stratified analysis showed higher lung cancer risk among the smokers carrying the variant XPA allele (OR = 1.75; 95% CI: 1.15-2.65) and among the non-smokers carrying the variant ERCC2 allele of 312Asn (OR = 2.10; 95% CI: 1.22-3.64). Meta-analysis showed that individuals with the variant AA genotype of XPA (−4G>A) had higher risk of lung cancer compared to those with the ‘G’ wild allele (OR = 1.28; 95% CI: 1.12-1.47); and those with variant alleles of ERCC2 312Asn had higher risk compared to those with wild 312Asp alleles among nonsmokers (OR = 1.58; 95% CI: 1.20-2.08). Although smoking is the dominant risk factor of lung cancer, XPA −4G>A (rs1800975) is also associated with the risk of NSCLC, especially for squamous cell carcinoma, among Asian young smokers. ERCC2 Asp/Asn (rs1799793) polymorphism may also affect lung cancer risk among nonsmokers. The NER pathway seems to have more strong influences on lung cancer than the BER pathway.     

Polymorphisms in the DNA nucleotide excision repair genes and lung cancer risk in Xuan Wei, China

The lung cancer mortality rate in Xuan Wei County is among the highest in China and has been attributed to exposure to indoor smoky coal emissions that contain very high levels of polycyclic aromatic hydrocarbons (PAHs). Nucleotide excision repair (NER) plays a key role in reversing DNA damage from exposure to environmental carcinogens, such as PAHs, that form bulky DNA adducts. We studied single nucleotide polymorphisms (SNPs) and their corresponding haplotypes in 6 genes (ERCC1, ERCC2/XPD, ERCC4/XPF, ERCC5/XPG, RAD23B and XPC) involved in NER in a population-based case-control study of lung cancer in Xuan Wei. A total of 122 incident primary lung cancer cases and 122 individually matched controls were enrolled. Three linked SNPs in ERCC2 were associated with lung cancer with similar ORs; e.g., persons with the Gln allele at codon 751 had a 60% reduction of lung cancer (OR = 0.40, 95% CI 0.18-0.89). Moreover, one haplotype in ERCC2 was associated with a decreased risk of lung cancer (OR = 0.40, 95% CI 0.19-0.85) compared to the most common haplotype. In addition, subjects with one or 2 copies of the Val allele at codon 249 of RAD23B had a 2-fold increased risk of lung cancer (OR = 1.91, 95% CI 1.12-3.24). In summary, our results suggest that genetic variants in genes involved in the NER pathway may play a role in lung cancer susceptibility in Xuan Wei. However, due to the small sample size, additional studies are needed to evaluate these associations within Xuan Wei and in other populations with substantial environmental exposure to PAHs.     

Evaluation of genetic variants in microRNA biosynthesis genes and risk of breast cancer in Chinese women

MicroRNAs (miRNA) are a class of small, noncoding RNA molecules involved in a diversity of cellular functions. Single nucleotide polymorphisms (SNPs) in miRNA biosynthesis genes may affect the biogenesis of miRNAs and consequently affect the miRNAs regulation. In this study, we systematically selected 24 functional SNPs located in eight key biosynthesis genes of miRNA (DROSHA, DGCR8, RAN, DICER, AGO2, GEMIN3, GEMIN4 and HIWI) and investigated the association between these SNPs and the risk of breast cancer in a Chinese population. All 24 SNPs were firstly genotyped in stage 1 (878 cases and 900 controls) and three promising SNPs (DROSHA rs2291109, RAN rs7301722 and DGCR8 rs417309) were selected for further validation in stage 2 (914 cases and 967 controls). We found that only one SNP (rs417309) located in the 3′‐UTR of DGCR8 was consistently associated with an increased breast cancer risk in two stages with a combined odds ratio (OR) of 1.50 [95% confidence interval (CI) = 1.16–1.93]. Based on the bioinformatics prediction, rs417309 is located at the binding sites of miR‐106b and miR‐579 in the 3′‐UTR of DGCR8. To evaluate whether rs417309 variant affects the binding capacity of miRNAs, we cotransfected luciferase reporter plasmids of DGCR8 3′‐UTR and miR‐106b/miR‐579 in three cell lines. Luciferase activity assay showed a higher expression level with rs417309 A allele compared with G allele in MCF‐7 cell lines (p = 3.31 × 10^–7, 9.29 × 10^–7 for miR‐106b and miR‐579, respectively). Our findings suggested that DGCR8 rs417309 G > A might affect breast cancer risk through the interruption of miRNA binding.     

Identification of candidate genes carrying polymorphisms associated with the risk of colorectal cancer by analyzing the colorectal mutome and microRNAome

BACKGROUND:

The presence of single‐nucleotide polymorphisms (SNPs) within the 3′‐untranslated regions of genes could affect the binding between a microRNA (miRNA) and its target, with consequences on gene expression regulation. Considering the important role of miRNAs in carcinogenesis, it is hypothesized here that these SNPs could also affect the individual risk of colorectal cancer (CRC).

METHODS:

To test this hypothesis, a list was developed of 140 somatically mutated genes deduced from previous works on the mutome of the CRC. A further selection was conducted of SNPs within target sites for miRNAs that are expressed only in the colorectum (the colorectal microRNAome) and having adequate population frequencies. This yielded 12 SNPs that were genotyped in a case‐control association study on 717 colorectal cases and 1171 controls from the Czech Republic.

RESULTS:

Statistically significant associations were found between the risk of CRC and the variant alleles of KIAA0182 (rs709805) (odds ratio = 1.57; 95% confidence interval = 1.06‐2.78, for the variant homozygotes) and NUP210 genes (rs354476) (odds ratio = 1.36; 95% confidence interval = 1.02‐1.82, for the variant homozygotes).

CONCLUSIONS:

The results support the study hypothesis and highlight the importance of SNPs within miRNA‐dependent regulatory regions. Further studies on the role exerted by NUP210 and KIAA0182 in colorectal carcinogenesis are warranted. Cancer 2012. © 2012 American Cancer Society.     

Polymorphisms within micro-RNA-binding sites and risk of sporadic colorectal cancer

Recent evidence indicate that small non-coding RNA molecules,called micro-RNAs (miRNAs), can bind to the 3' untranslatedregions (UTRs) of messenger RNAs and interfere with their translation,thereby regulating cell growth, differentiation, apoptosis andtumorigenesis. Genetic polymorphisms can reside on miRNA-bindingsites. Thus, it is conceivable that the miRNA regulation maybe affected by polymorphisms on the 3' UTRs. Since gene deregulationis one of the key mechanisms by which cells can progress tocancer, we hypothesize that common polymorphisms within miRNA-targetbinding sites could play a role in the individual risk of cancer.In the present study, we selected the 3' UTRs of 104 genes candidatefor colorectal cancer (CRC) and we identified putative miRNA-bindingsites by specialized algorithms (PicTar, DianaMicroT, miRBase,miRanda, TargetScan and microInspector). Fifty-seven single-nucleotidepolymorphisms (SNPs) were identified in miRNA-binding sites.We evaluated the SNPs for their ability to affect the bindingof the miRNA with its target, by assessing the variation ofGibbs free energy between the two alleles of each SNP. We foundeight common polymorphisms that were further investigated bya case–control association studies. The study was carriedout on a series of cases and controls from Czech Republic, apopulation with the highest worldwide incidence of CRC. We foundstatistically significant associations between risk of CRC andvariant alleles of CD86 [odds ratio (OR) = 2.74; 95% confidenceinterval (CI) = 1.24–6.04, for the variant homozygotes]and INSR genes (OR = 1.94; 95% CI = 1.03–3.66, for thevariant homozygotes). These results are the first reportingpositive association between miRNA-binding SNPs sequences andcancer risk. Abbreviations: CRC, colorectal cancer; CI, confidence interval; mRNA, messenger RNA; miRNA, micro-RNA; MAF, minor allele frequency; nt, nucleotide; OR, odds ratio; SNP, single-nucleotide polymorphism; UTR, untranslated region Received October 24, 2007; revised December 6, 2007; accepted December 22, 2007.     

Genetic variation in the nucleotide excision repair pathway and colorectal cancer risk.

Nucleotide excision repair (NER) enzymes are critical for the removal of bulky DNA adducts caused by environmental carcinogens, such as heterocyclic amines and polycyclic aromatic hydrocarbons, which are found in two putative risk factors for colorectal cancer, tobacco smoke and meat cooked at high temperature. To examine the association between common genetic variants in NER genes and the risk of colorectal cancer, we conducted a case-cohort study within the CLUE II cohort. Twenty-two single nucleotide polymorphisms in 11 NER genes were genotyped in 250 colorectal cancer cases and a subcohort of 2,224 participants. Incidence rate ratios (RR) and 95% confidence intervals (95% CI) were estimated using a modified Cox regression model and robust variance estimate. The ERCC6 1213G variant, which is thought to reduce NER capacity, was associated with an increased risk of colorectal cancer compared with the homozygous wild type (RR, 1.36; 95% CI, 1.00-1.86 and RR, 2.64; 95% CI, 1.53-4.58 for the RG and GG genotypes respectively with P(trend) = 0.0006). Having at least one XPC 492H allele was also associated with an increased risk of colorectal cancer (RR, 1.75; 95% CI, 1.20-2.57). When the combined effects of ERCC6 R1213G and XPC R492H were examined, the risk of colorectal cancer significantly increased with increasing number of variant alleles (P(trend) = 0.00003). Our study suggests that genetic polymorphisms in the NER genes, ERCC6 and XPC, may be associated with an increased risk of colorectal cancer.