Strong association between two polymorphisms on 15q25.1 and lung cancer risk: a meta-analysis

Systematic druggable genome-wide Mendelian randomization identifies therapeutic targets for lung cancer

BACKGROUND

Drug repurposing provides a cost-effective approach to address the need for lung cancer prevention and therapeutics. We aimed to identify actionable druggable targets using Mendelian randomization (MR).

METHODS

Summary-level data of gene expression quantitative trait loci (eQTLs) were sourced from the eQTLGen resource. We procured genetic associations with lung cancer and its subtypes from the TRICL, ILCCO studies (discovery) and the FinnGen study (replication). We implemented Summary-data-based Mendelian Randomization analysis to identify potential therapeutic targets for lung cancer. Colocalization analysis was further conducted to assess whether the identified signal pairs shared a causal genetic variant.

FINDINGS

In the main analysis dataset, we identified 55 genes that demonstrate a causal relationship with lung cancer and its subtypes. However, in the replication cohort, only three genes were found to have such a causal association with lung cancer and its subtypes, and of these, HYKK (also known as AGPHD1) was consistently present in both the primary analysis dataset and the replication cohort. Following HEIDI tests and colocalization analyses, it was revealed that HYKK (AGPHD1) is associated with an increased risk of squamous cell carcinoma of the lung, with an odds ratio and confidence interval of OR = 1.28,95%CI = 1.24 to 1.33.

INTERPRETATION

We have found that the HYKK (AGPHD1) gene is associated with an increased risk of squamous cell carcinoma of the lung, suggesting that this gene may represent a potential therapeutic target for both the prevention and treatment of lung squamous cell carcinoma.

Rat Mammary carcinoma susceptibility 3 (Mcs3) pleiotropy, socioenvironmental interaction, and comparative genomics with orthologous human 15q25.1-25.2

Genome-wide association studies of breast cancer susceptibility have revealed risk-associated genetic variants and nominated candidate genes; however, the identification of causal variants and genes is often undetermined by genome-wide association studies. Comparative genomics, utilizing Rattus norvegicus strains differing in susceptibility to mammary tumor development, is a complimentary approach to identify breast cancer susceptibility genes. Mammary carcinoma susceptibility 3 (Mcs3) is a Copenhagen (COP/NHsd) allele that confers resistance to mammary carcinomas when introgressed into a mammary carcinoma susceptible Wistar Furth (WF/NHsd) genome. Here, Mcs3 was positionally mapped to a 7.2-Mb region of RNO1 spanning rs8149408 to rs107402736 (chr1:143700228-150929594, build 6.0/rn6) using WF.COP congenic strains and 7,12-dimethylbenz(a)anthracene-induced mammary carcinogenesis. Male and female WF.COP-Mcs3 rats had significantly lower body mass compared to the Wistar Furth strain. The effect on female body mass was observed only when females were raised in the absence of males indicating a socioenvironmental interaction. Furthermore, female WF.COP-Mcs3 rats, raised in the absence of males, did not develop enhanced lobuloalveolar morphologies compared to those observed in the Wistar Furth strain. Human 15q25.1-25.2 was determined to be orthologous to rat Mcs3 (chr15:80005820-82285404 and chr15:83134545-84130720, build GRCh38/hg38). A public database search of 15q25.1-25.2 revealed genome-wide significant and nominally significant associations for body mass traits and breast cancer risk. These results support the existence of a breast cancer risk-associated allele at human 15q25.1-25.2 and warrant ultrafine mapping of rat Mcs3 and human 15q25.1-25.2 to discover novel causal genes and variants.

The effect of CHRNA3 rs1051730 C>T and ABCB1 rs3842 A>G polymorphisms on non-small cell lung cancer and nicotine dependence in Iranian population

Aims

Lung cancer is still the leading cause of cancer mortality in all over the world. Nicotine and its derivatives are the most well-known carcinogens that participate in both etiology and progression of lung cancer. The objective of the current study was to investigate whether single nucleotide polymorphisms (SNPs) rs1051730C > T in CHRNA3 and rs3842A > G in ABCB1, two genes contributing in the mechanism of disposition and metabolism of nicotine and its derivatives, could modify the risk of developing lung cancer, as well as nicotine dependence in Iranian.

Main methods

The genotyping analysis for these two SNPs was conducted in a case-control study of 108 lung cancer cases and 120 healthy controls using ARMS-PCR and Tetra-primer ARMS-PCR techniques. The correlation between studied SNPs and lung cancer was assessed by the regression analysis.

Key findings

We observed a significant association between lung cancer and rs1051730C > T by using four genetic models: allele (OR:1.83; 95% CI:1.24-2.6; p = 0.002), dominant (OR: 2.19; 95% CI:1.27-3.78; p = 0.005), recessive (OR: 2.25; 95% CI: 1.02-4.95; p = 0.043) and additive (TT vs CC: OR:3.25; 95% CI:1.38-7.60; p = 0.007, CT vs CC: OR:1.96; 95% CI:1.10-3.48; p = 0.021). Furthermore, a significant association between this variant and nicotine dependence (OR: 2.27; 95% CI: 1.52-3.39; p = 0.00005) was reported. However, no association was found for rs3842A > G.

Significance

The results suggested that the CHRNA3 rs1051730C > T via a smoking-dependent manner could modify susceptibility to lung cancer among Iranian population.

Genetic analysis of colorectal carcinoma using high throughput single nucleotide polymorphism genotyping technique within the population of Jammu and Kashmir

BACKGROUND

SNP genotyping has become increasingly more common place to understand the genetic basis of complex diseases like cancer. SNP-genotyping through MassARRAY™ is a cost-effective method to quantitatively analyse the variation of gene expression in multiple samples, making it a potential tool to identify the underlying causes of colorectal carcinogenesis.

METHODS

In the present study, SNP genotyping was carried out using Agena MassARRAY™, which is a cost-effective, robust, and sensitive method to analyse multiple SNPs simultaneously. We analysed 7 genes in 492 samples (100 cases and 392 controls) associated with CRC within the population of Jammu and Kashmir. These SNPs were selected based on their association with multiple cancers in literature.

RESULTS

This is the first study to explore these SNPs with colorectal cancer within the J&K population.7 SNPs with a call rate of 90% were selected for the study. Out of these, five SNPs rs2234593, rs1799966, rs2229080, rs8034191, rs1042522 were found to be significantly associated with the current study under the allelic model with an Odds Ratio OR = 2.981(1.731-5.136 at 95% CI); p value = 4.81E-05 for rs2234593,OR = 1.685(1.073-2.647 at 95% CI);; p value = 0.02292 for rs1799966, OR = 1.5 (1.1-2.3 at 95% CI), p value = 0.02 for rs2229080, OR = 1.699(1.035-2.791 at 95% CI); p value = 0.03521 for rs8034191, OR = 20.07 (11.26-35.75); p value = 1.84E-34 for rs1042522 respectively.

CONCLUSION

This is the first study to find the relation of Genetic variants with the colorectal cancer within the studied population using high throughput MassARRAY™ technology. It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

The relationship between CHRNA5/A3/B4 gene cluster polymorphisms and lung cancer risk: An updated meta-analysis and systematic review

BACKGROUND

Genetic polymorphisms in the 15q25 region have been associated with the risk of lung cancer (LC). However, studies have yielded conflicting results.

METHODS

Searches were conducted in databases, including PubMed, EMbase, Web of Science, CNKI, and Wanfang, for case-control studies up to August 1, 2019. After retrieving eligible studies and data extraction, we calculated pooled odds ratios with 95% confidence intervals. In the meta-analysis, we included 32 publications with a total of 52,795 patients with LC and 97,493 control cases to evaluate the polymorphisms in the CHRNA5/A3/B4 gene cluster in the 15q25 region.

RESULTS

Data of the meta-analysis showed a significantly increased risk of LC in the presence of genetic polymorphisms (rs1051730, rs16969968, rs8034191). In the smoking subgroup, the CHRNA3 rs1051730 polymorphism was found to contribute to LC risk using following 5 models: the allelic model, the homozygous model, the heterozygous model, the dominant model, and the recessive model. Thus, the rs1051730 polymorphism may modify LC susceptibility under the condition of smoking. Stratification studies for CHRNA5-rs8034191 showed that Caucasian groups with the wild-type genotype (C/C) may be susceptible to LC in all 5 models. No significant relationship between CHRNA3 rs6495309 or rs3743073 and LC susceptibility was found. However, Asians with the rs3743037 B-allele showed an obviously higher risk of LC susceptibility than the Caucasian population, observed via allelic, heterozygous, and dominant models.

CONCLUSIONS

The 3 polymorphisms of rs1051730, rs16969968 and rs8034191 in the CHRNA5/A3/B4 gene cluster in the 15q25 region were associated with LC risk, which might be influenced by ethnicity and smoking status.

Tobacco Smoking: Risk to Develop Addiction, Chronic Obstructive Pulmonary Disease, and Lung Cancer

BACKGROUND

The morbidity and mortality associated with tobacco smoking is well established. Nicotine is the addictive component of tobacco. Nicotine, through the non-neuronal α7nicotinic receptor, induces cell proliferation, neo-angiogenesis, epithelial to mesenchymal transition, and inhibits drug-induced apoptosis.

OBJECTIVE

To understand the genetic, molecular and cellular biology of addiction, chronic obstructive pulmonary disease and lung cancer.

METHODS

The search for papers to be included in the review was performed during the months of July- September 2018 in the following databases: PubMed (http://www.ncbi.nlm.nih.gov), Scopus (http://www.scopus.com), EMBASE (http://www.elsevier.com/online-tools/embase), and ISI Web of Knowledge (http://apps.webofknowledge.com/). The following searching terms: "nicotine", "nicotinic receptor", and "addiction" or "COPD" or "lung cancer" were used. Patents were retrieved in clinicaltrials.gov (https://clinicaltrials.gov/). All papers written in English were evaluated. The reference list of retrieved articles was also reviewed to identify other eligible studies that were not indexed by the above-mentioned databases. New experimental data on the ability of nicotine to promote transformation of human bronchial epithelial cells, exposed for one hour to Benzo[a]pyrene-7,8-diol-9-10-epoxide, are reported.

RESULTS

Nicotinic receptors variants and nicotinic receptors upregulation are involved in addiction, chronic obstructive pulmonary disease and/or lung cancer. Nicotine through α7nicotinic receptor upregulation induces complete bronchial epithelial cells transformation.

CONCLUSION

Genetic studies highlight the involvement of nicotinic receptors variants in addiction, chronic obstructive pulmonary disease and/or lung cancer. A future important step will be to translate these genetic findings to clinical practice. Interventions able to help smoking cessation in nicotine dependence subjects, under patent, are reported.

Gene-environment and gene-gene interactions between CHRNA3 rs1051730, XRCC1 rs25487, and ERCC1 rs735482 variants highly elevate the risk of lung cancer

Background

Gene-gene and gene-environment interactions play an important role in cancer susceptibility. In this work, we studied the association of XRCC1 rs25487, ERCC1 rs735482, and CHRNA3 rs1051730 variants with lung cancer and assessed the modulatory effect of potential interaction between these variants on disease risk.

Results

In this study, 86 primary lung cancer patients and 64 control subjects were genotyped for CHRNA3 rs1051730, XRCC1 rs25487, and ERCC1 rs735482 by real-time PCR. The frequency of the three studied variants was higher among lung cancer patients than in control subjects, but with no statistical significance. ERCC1 rs735482 variant was associated with 6.9-fold increased risk to develop lung cancer among smokers (p = 0.03). Concomitant presence of CHRNA3 and ERCC1 wild alleles was associated with 2.7-fold elevated risk of lung cancer (p < 0.0001), while concomitant presence of CHRNA3 rs1051730 variant allele with ERCC1 wild allele was associated with 20-fold elevated risk (p < 0.000). Concomitant presence of both variants, ERCC1 rs735482 and CHRNA3 rs1051730, was associated with 9.9-fold elevated risk (p < 0.0001). Meanwhile, the concomitant presence of XRCC1 rs25487 with either ERCC1 rs735482 or CHRNA3 rs1051730 or both was not associated with increased risk of the disease.

Conclusion

Our results emphasize the role of gene-gene interaction in the pathogenesis of lung cancer. Large-scale further studies to clarify the underlying mechanisms are needed.

CHRNA5 and CHRNA3 polymorphism and lung cancer susceptibility in Palestinian population

Objective

The genetic polymorphism (rs16969968 in CHRNA5, and rs1051730 in CHRNA3 genes) were recently shown to be associated with risk of LC. The aim of this study is to elucidate whether they predispose Palestinian individuals to lung cancer, and how is this related to smoking.

Results

Frequency of the rs16969968-A allele was significantly higher in the case group (36.7%) than in normal controls (17.5%; P = 0.022; OR = 6.83 for AA and 2.81 for AG genotypes). The frequency of rs1051730-T allele was also significantly higher in the case group (46.7%) than in the control group (22.5%; P = 0.001; OR = 2.20 for TC and 13.22 for TT genotypes). Frequency of rs16969968-A allele was higher in smokers (29.1%) than nonsmokers (15.7%) regardless of lung cancer; similarly, frequency of rs1051730-T allele was also higher in smokers than in smokers (46.7% vs 22.5%, respectively). The higher the proportion of the risk allele (rs16969968-A and rs1051730-T), the higher the mean number of daily consumed cigarettes (P = 0.006). Carrying rs16969968-A and/or rs1051730-T alleles results in an increased risk to lung cancer probably by increasing the individual’s tendency for heavy smoking. The allelic frequency of the rs16969968-A and rs1051730-T alleles among normal Palestinian controls is similar to different populations worldwide.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3310-0) contains supplementary material, which is available to authorized users.

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.

Novel Mutations of the CHRNA3 Gene in Non-Small Cell Lung Cancer in an Iranian Population

Background: Lung cancer, the leading cause of cancer-related worldwide deaths, largely results from the combined effects of smoking exposure and genetic susceptibility. CHRNA3, a nicotinic acetylcholine receptor gene, is associated with lung cancer risk. This study sought to identify variations in exon 3 of CHRNA3 in an Iranian population with non-small cell lung cancer (NSCLC). Materials and methods: A case-control study including 147 individuals with lung cancer and 145 healthy individuals was conducted. As mobility shift caused by nucleotide substitutions might be due to a conformational change of single-stranded DNAs, we designated these as single-strand conformation polymorphisms (SSCPs). PCR amplified products with SSCP were subjected to DNA sequencing. Results: The sequencing results showed 3 polymorphisms in exon 3 of CHRNA3, rs8040868, rs763384023 and rs2869547 , the latter two of which have not been reported in NSCLC, previously. Conclusion: It appears that the rs8040868 may be considered as a pathogenic mutation associated with the clinical phenotype. Polymorphisms are important factors for development of cancers and may provide additional insights into mechanisms underlying NSCLC.

Association between two CHRNA3 variants and susceptibility of lung cancer: a meta-analysis

Genome-wide association studies (GWAS) have identified two CHRNA3 polymorphisms (rs578776 and rs938682) associated with lung cancer risk. Furthermore, these polymorphisms were investigated and genotyped by PCR analysis. All eligible case-control studies published up to Mar 1st 2015 were identified by searching Pubmed and Embase database. Negative association between rs578776-T allele and risk of lung cancer was obtained without obvious heterogeneity (OR: 0.83, 95% CI: 0.79-0.86; p = 0.898 for Q test). Rs938682-C allele carriers had a 12% to 28% decreased risk. Genotype model analysis showed results of dominant model for rs578776 (OR with 95% CI: 0.839(0.718-0.981)), dominant model for rs938682 (OR with 95% CI: 0.778(0.663-0.912)) and homozygous model for rs938682 (OR with 95% CI: 0.767(0.708-0.831)) were statistically significant. Subgroup analysis indicated rs578776-T variant had protective effect in Smokers, Caucasians, two histology subgroups, and two match subgroups. Meanwhile, rs938682-C allele was associated with decreased risk in Smokers, Caucasians, Lung cancer, and two match subgroups. Meta-regression suggested ethnicity might be the major source of heterogeneity in allele model and homozygous model for rs938682. Moreover, smoking status might contribute to part of heterogeneity under allele model. In summary, this meta-analysis suggested both rs578776 and rs938682 were significantly associated with the susceptibility of lung cancer.

CHRNA5/CHRNA3 Locus Associates with Increased Mortality among Smokers

Polymorphisms in the nicotinic acetylcholine receptor gene (CHRNA5/CHRNA3 locus) have been associated with several smoking related traits such as nicotine dependence, cigarette consumption, smoking cessation, lung cancer, and COPD. The aim of this candidate gene study was to study the locus among the Finnish COPD patients and long-term smokers with regard to COPD risk, smoking behavior, cancer, and all-cause mortality. Genotyping of rs1051730, the locus tagging SNP was done in two longitudinal cohorts: Finnish COPD patients (N = 575, 74% men) and long-term smokers, all men (N = 1911). Finnish population sample (N = 1730) was used as controls. The analyses were done using logistic and Cox regression. The main findings were that the minor allele increased the risk of COPD when compared to the Finnish population at large (OR = 1.4, 95% CI 1.2-1.7, p = 3.2 × 10-5). Homozygosity for the risk allele was associated in both cohorts with all-cause mortality (crude HR 2.2, 95% CI 1.2-3.8 and 1.3, 95% CI 1.1-1.5, respectively), with any type of cancer (crude OR 2.3, 95% CI 1.0-5.1) among the COPD patients and with the number of pack-years (crude OR 1.4, 95% CI 1.1-1.9) among the male smokers. CHRNA5/CHRNA3 locus tagged by rs1051730, which has been previously associated with several smoking related diseases was now shown to be associated also with increased all-cause mortality among long-term smokers with or without clinical COPD further emphasizing the clinical importance of the finding.

A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry

BACKGROUND

Pulmonary function decline is a major contributor to morbidity and mortality among smokers. Post bronchodilator FEV1 and FEV1/FVC ratio are considered the standard assessment of airflow obstruction. We performed a genome-wide association study (GWAS) in 9919 current and former smokers in the COPDGene study (6659 non-Hispanic Whites [NHW] and 3260 African Americans [AA]) to identify associations with spirometric measures (post-bronchodilator FEV1 and FEV1/FVC). We also conducted meta-analysis of FEV1 and FEV1/FVC GWAS in the COPDGene, ECLIPSE, and GenKOLS cohorts (total n = 13,532).

RESULTS

Among NHW in the COPDGene cohort, both measures of pulmonary function were significantly associated with SNPs at the 15q25 locus [containing CHRNA3/5, AGPHD1, IREB2, CHRNB4] (lowest p-value = 2.17 × 10(-11)), and FEV1/FVC was associated with a genomic region on chromosome 4 [upstream of HHIP] (lowest p-value = 5.94 × 10(-10)); both regions have been previously associated with COPD. For the meta-analysis, in addition to confirming associations to the regions near CHRNA3/5 and HHIP, genome-wide significant associations were identified for FEV1 on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 9 [DBH] (p-value = 9.69 × 10(-9)) and 19 [CYP2A6/7] (p-value = 3.49 × 10(-8)) and for FEV1/FVC on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 4 [FAM13A] (p-value = 3.88 × 10(-12)), 11 [MMP3/12] (p-value = 3.29 × 10(-10)) and 14 [RIN3] (p-value = 5.64 × 10(-9)).

CONCLUSIONS

In a large genome-wide association study of lung function in smokers, we found genome-wide significant associations at several previously described loci with lung function or COPD. We additionally identified a novel genome-wide significant locus with FEV1 on chromosome 9 [DBH] in a meta-analysis of three study populations.

Analyzing large-scale samples confirms the association between the rs1051730 polymorphism and lung cancer susceptibility

The early genome-wide association studies (GWAS) found a significant association between lung cancer and rs1051730 (15q25) polymorphism. However, the subsequent studies reported consistent and inconsistent results in different populations. Three meta-analysis studies were thus performed to reevaluate the association. But their results remain inconsistent. After that, some new GWAS studies reported conflicting results again. We think that the divergence of these results may be due to small-scale samples or heterogeneity among different populations. Therefore, we reevaluated the association by collecting more samples (N = 33,617 cases and 116,639 controls) from 31 studies, which incorporate 8 new studies and 23 previous studies used by one or more of the three meta-analysis studies. We observed a significant association between lung cancer and rs1051730 in pooled population by using allele (OR = 1.30, 95% CI = 1.27–1.34, P  <  0.0001), dominant (OR = 1.41, 95% CI = 1.29–1.55, P < 0.0001), recessive (OR = 1.53, 95% CI = 1.42–1.65, P < 0.0001) and additive (OR = 1.75, 95% CI = 1.61–1.90, P < 0.0001) models. Through the subgroup analysis, we observed a significant heterogeneity only in East Asian population (P = 0.006, I² = 66.9%), and the association is significant in all subgroups (OR = 1.2976, 95% CI = 1.2622–1.3339 (European ancestry), OR = 1.5025, 95% CI = 1.2465–1.8110 (African), OR = 1.7818, 95% CI = 1.3915–2.2815 (East Asian), P < 0.0001). We believe that these results will contribute to understanding the genetic mechanism of lung cancer.

Association of APE1 Gene Asp148Glu Variant with Digestive Cancer: A Meta-Analysis

Background

Apurinic/apyrimidinic endonuclease-1 (APE1) is a rate-limiting enzyme in DNA base excision repair and has been implicated in carcinogenesis. In this study, we summarize available data to examine the susceptibility of APE1 gene Asp148Glu variant to digestive cancer via a meta-analysis.

Material/Methods

Study selection and data abstraction were conducted independently by 2 authors. Random-effects model was utilized to pool effect estimates. Heterogeneity and publication bias were addressed.

Results

Sixteen articles involving 4916 digestive cancer patients and 7748 controls were qualified for this meta-analysis. Overall association showed an indicative association between Asp148Glu variant and digestive cancer under allelic (odds ratio or OR=1.11; 95% confidence interval or CI: 0.99–1.25; P=0.074) and dominant (OR=1.18; 95% CI: 1.00–1.40; P=0.056) models, with strong evidence of heterogeneity. Deviation from Hardy-Weinberg equilibrium was an obvious source of heterogeneity. In subgroup analyses by cancer sites, this variant was significantly associated with the increased risk for hepatocellular cancer under allelic (OR=1.50; 95% CI: 1.25–1.80; P<0.001) and homozygous genotypic (OR=1.55; 95% CI: 1.02–2.29; P=0.028) models. There were low probabilities of publication bias for the above comparisons.

Conclusions

The results of this meta-analysis collectively suggest that APE1 gene Asp148Glu variant is not a risk-conferring factor for digestive cancer. Further large and well-designed studies are required.

Dependence and independence: Structure and inference

Evaluations of relationships between pairs of variables, including testing for independence, are increasingly important. Erich Leo Lehmann noted that "the study of the power and efficiency of tests of independence is complicated by the difficulty of defining natural classes of alternatives to the hypothesis of independence." This paper presents a general review, discussion and comparison of classical and novel tests of independence. We investigate a broad spectrum of dependence structures with/without random effects, including those that are well addressed in both the applied and the theoretical scientific literatures as well as scenarios when the classical tests of independence may break down completely. Motivated by practical considerations, the impact of random effects in dependence structures are studied in the additive and multiplicative forms. A novel index of dependence is proposed based on the area under the Kendall plot. In conjunction with the scatterplot and the Kendall plot, the proposed method provides a comprehensive presentation of the data in terms of graphing and conceptualizing the dependence. We also present a graphical methodology based on heat maps to effectively compare the powers of various tests. Practical examples illustrate the use of various tests of independence and the graphical representations of dependence structures.

Genetic association between AGPHD1 variant and lung cancer risk

The knowledge of molecular mechanism that underlies the genetic predisposition to lung cancer is yet limited. Results from previous studies addressing the association of AGPHD1 variant rs8034191 with lung carcinogenesis remain inconclusive. Herein, we combined these data and re-examined the association. We performed a meta-analysis of Asian studies identified through various ways. Using the data collected from each eligible study, we combined the effect estimates (ORs and its 95 % CIs) with the fixed effects model (Mantel-Haenszel method). Statistical analyses were done using STATA software. Data from nine studies (29,290 subjects) carried out in Asian populations were analyzed in this work. There was no overall association between variant rs8034191 and lung cancer risk under the allele frequency model (OR = 1.03, 95 % CI = 0.93-1.13, P heterogeneity = 0.522). We observed the same associations under other genetic models and in the subgroup analyses by ethnicity and smoking status. Our results indicate that variant rs8034191 in the AGPHD1 gene may not modify the genetic risk of lung cancer in Asian populations.

The SNP rs931794 in 15q25.1 Is Associated with Lung Cancer Risk: A Hospital-Based Case-Control Study and Meta-Analysis

Background

Lung cancer is one of the most common human malignant diseases and the leading cause of cancer death worldwide. The rs931794, a SNP located in 15q25.1, has been suggested to be associated with lung cancer risk. Nevertheless, several genetic association studies yielded controversial results.

Methods and Findings

A hospital-based case-control study involving 611 cases and 1062 controls revealed the variant of rs931794 was related to increased lung cancer risk. Stratified analyses revealed the G allele was significantly associated with lung cancer risk among smokers. Following meta-analysis including 6616 cases and 7697 controls confirmed the relevance of rs931794 variant with increased lung cancer risk once again. Heterogeneity should be taken into account when interpreting the consequences. Stratified analysis found ethnicity, histological type and genotyping method were not the sources of between-study heterogeneity. Further sensitivity analysis revealed that the study “Hsiung et al (2010)” might be the major contributor to heterogeneity. Cumulative meta-analysis showed the trend was increasingly obvious with adding studies, confirming the significant association.

Conclusions

Results from our current case-control study and meta-analysis offered insight of association between rs931794 and lung cancer risk, suggesting the variant of rs931794 might be related with increased lung cancer risk.

Unbalanced acetylcholinesterase activity in larynx squamous cell carcinoma

Previous reports have demonstrated that a non-neuronal cholinergic system is expressed aberrantly in airways. A proliferative effect is exerted directly by cholinergic agonists through the activation of nicotinic and muscarinic receptors. In cancer, particularly those related with smoking, the mechanism through which tumour cells respond to aberrantly activated cholinergic signalling is a key question. Fifty paired pieces of larynx squamous cell carcinoma and adjacent non-cancerous tissue were compared in terms of their acetylcholinesterase activity (AChE). The AChE activity in non-cancerous tissues (0.248 ± 0.030 milliunits per milligram of wet tissue; mU/mg) demonstrates that upper respiratory tissues express sufficient AChE activity for controlling the level of acetylcholine (ACh). In larynx carcinomas, the AChE activity decreased to 0.157 ± 0.024 mU/mg (p=0.009). Larynx cancer patients exhibiting low ACh-degrading enzymatic activity had a significantly shorter overall survival (p=0.031). Differences in the mRNA levels of alternatively spliced AChE isoforms and molecular compositions were noted between glottic and supraglottic cancers. Our results suggest that the low AChE activity observed in larynx squamous cell carcinoma may be useful for predicting the outcome of patients.

Dysregulated cholinergic network as a novel biomarker of poor prognostic in patients with head and neck squamous cell carcinoma

BACKGROUND

In airways, a proliferative effect is played directly by cholinergic agonists through nicotinic and muscarinic receptors activation. How tumors respond to aberrantly activated cholinergic signalling is a key question in smoking-related cancer. This research was addressed to explore a possible link of cholinergic signalling changes with cancer biology.

METHODS

Fifty-seven paired pieces of head and neck squamous cell carcinoma (HNSCC) and adjacent non-cancerous tissue (ANCT) were compared for their mRNA levels for ACh-related proteins and ACh-hydrolyzing activity.

RESULTS

The measurement in ANCT of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activities (5.416 ± 0.501 mU/mg protein and 6.350 ± 0.599 mU/mg protein, respectively) demonstrated that upper respiratory tract is capable of controlling the availability of ACh. In HNSCC, AChE and BChE activities dropped to 3.584 ± 0.599 mU/mg protein (p = 0.002) and 3.965 ± 0.423 mU/mg protein (p < 0.001). Moreover, tumours with low AChE activity and high BChE activity were associated with shorter patient overall survival. ANCT and HNSCC differed in mRNA levels for AChE-T, α3, α5, α9 and β2 for nAChR subunits. Tobacco exposure had a great impact on the expression of both AChE-H and AChE-T mRNAs. Unaffected and cancerous pieces contained principal AChE dimers and BChE tetramers. The lack of nerve-born PRiMA-linked AChE agreed with pathological findings on nerve terminal remodelling and loss in HNSCC.

CONCLUSIONS

Our results suggest that the low AChE activity in HNSCC can be used to predict survival in patients with head and neck cancer. So, the ChE activity level can be used as a reliable prognostic marker.

Polymorphisms in C-reactive protein and Glypican-5 are associated with lung cancer risk and Gartrokine-1 influences Cisplatin-based chemotherapy response in a Chinese Han population

The role of genetics in progression of cancer is an established fact, and susceptibility risk and difference in outcome to chemotherapy may be caused by the variation in low-penetrance alleles of risk genes. We selected seven genes (CRP, GPC5, ACTA2, AGPHD1, SEC14L5, RBMS3, and GKN1) that previously reported link to lung cancer (LC) and genotyped single nucleotide polymorphisms (SNPs) of these genes in a case-control study. A protective allele "C" was found in rs2808630 of the C-reactive protein (CRP). Model association analysis found genotypes "T/C" and "C/C" in the dominant model and genotype "T/C" in the overdominant model of rs2808630 associated with reduced LC risk. Gender-specific analysis in each model showed that genotypes "T/T" and "C/C" in rs2352028 of the Glypican 5 (GPC5) were associated with increased LC risk in males. Logistic regression analysis showed "C/T" genotype carriers of rs4254535 in the Gastrokine 1 (GKN1) had less likelihood to have chemotherapy response. Our results suggest a potential association between CRP and GPC5 variants with LC risk; variation in GKN1 is associated with chemotherapy response in the Chinese Han population.

Do genetic defects of DNA repair relevant proteins alter susceptibility to hypertension? A case-control study in northeastern Han Chinese

The aim of this study was to examine the individual and interactive associations of five non-synonymous variants of four DNA repair relevant genes (XRCC1, XRCC3, hOGG1, NQO1) with hypertension in a large northeastern Han Chinese population. This was a hospital-based study involving 1009 hypertensive patients and 756 normotensive controls. All five variants satisfied the Hardy-Weinberg equilibrium. With a Bonferroni corrected alpha of 0.05/5, significance was only attained in the genotype (P=0.007) and allele (P=0.006) distributions of rs25487 in XRCC1 gene between patients and controls, with its mutant allele conferring 29% (95% CI: 1.09-1.53; P=0.003), 31% (95% CI: 1.05-1.62; P=0.015) and 66% (95%CI: 1.10-2.52; P=0.016) increased risks of hypertension under the additive, dominant and recessive models, respectively after adjusting for confounders. The frequency of allele combination C-A-C-G-C (alleles in order of rs1799782, rs25487, rs861539, rs1052133 and rs1800566) was significantly higher in patients than in controls (P=0.003), while that of C-G-C-C-C was significantly lower (P=0.001). Interaction analysis failed to identify any suggestive evidence of synergism across five examined variants. Our findings provide evidence for a contributory role of XRCC1 gene rs25487 variant in the development of hypertension, and this variant possibly acted in a recessive pattern.

A Simple Density-Based Empirical Likelihood Ratio Test for Independence

We develop a novel nonparametric likelihood ratio test for independence between two random variables using a technique that is free of the common constraints of defining a given set of specific dependence structures. Our methodology revolves around an exact density-based empirical likelihood ratio test statistic that approximates in a distribution-free fashion the corresponding most powerful parametric likelihood ratio test. We demonstrate that the proposed test is very powerful in detecting general structures of dependence between two random variables, including non-linear and/or random-effect dependence structures. An extensive Monte Carlo study confirms that the proposed test is superior to the classical nonparametric procedures across a variety of settings. The real-world applicability of the proposed test is illustrated using data from a study of biomarkers associated with myocardial infarction.

Acetylcholine receptor pathway in lung cancer: New twists to an old story

Genome-wide association studies revealed that allelic variation in the α5-α3-β4 nicotine acetylcholine receptor (nAChR) cluster on chromosome 15q24-15q25.1 was associated with lung cancer risk. nAChRs are membrane ligand-gated cation channels whose activation is triggered by the binding of the endogenous neurotransmitter acetylcholine (ACh) or other biologic compounds including nicotine. nAChRs have been found on lung cancer cells, underscoring the idea that the non-neuronal nAChR pathway has important implications for lung cancer. Several studies focusing on the treatment with nAChR antagonists with improved selectivity might trigger novel strategies for the intervention and prevention of lung cancer. Here we review the genetic risk factors for lung cancer in the nAChR gene cluster, the roles of nicotine receptors, and the molecular mechanisms of acetylcholine receptor pathways to lead to more opportunities for intervention and prevention of lung cancer.

The association between the rs6495309 polymorphism in CHRNA3 gene and lung cancer risk in Chinese: a meta-analysis

The association between the rs6495309 polymorphism in CHRNA3 gene and lung cancer risk has been studied in Chinese by several number case-control control studies with small number of cases and controls, and these studies might be underpowered to reveal the true association. Thus we sought to investigate the association with the risk of lung cancer by performing a comprehensive meta-analysis on the polymorphism. Five case-control studies were extracted from 3 articles on the polymorphism involving 4608 lung cancer cases and 4617 controls. The results of meta-analysis showed that significant increased risk were found for the polymorphism with the risk of lung cancer in Chinese: OR = 1.47, 95%CI = 1.33-1.63, P < 0.00001 for CC + TC vs. TT; OR = 1.24, 95%CI = 1.07-1.44, P = 0.005 for CC vs. TT + TC; OR = 1.62, 95%CI = 1.32-2.00, P < 0.00001 for CC vs. TT; OR = 1.42, 95%CI = 1.26-1.61, P < 0.00001 for CT vs. TT; OR = 1.42, 95%CI = 1.26-1.61, P < 0.00001. No significant publication bias was found for the five genetic models. Our findings demonstrated that CHRNA3 gene rs6495309 polymorphism might be a risk factor for the development of lung cancer in Chinese.

Interactive contribution of serine/threonine kinase 39 gene multiple polymorphisms to hypertension among northeastern Han Chinese

Serine/threonine kinase 39 (STK39) gene has been reported to be a hypertension-susceptibility gene by a recent genome-wide association study in Western populations. To validate this finding in Chinese, we focused on five well-characterized common polymorphisms in STK39 gene to examine their potential association with hypertension in a large northeastern Han population. This is a hospital-based case-control study involving 1009 hypertensive patients and 756 normotensive controls. Data were analyzed by the Haplo.Stats and multifactor dimensionality reduction (MDR) softwares. The genotype and allele distributions of rs6749447, rs3754777 and rs6433027 differed significantly between patients and controls (P < 0.001) even after the Bonferroni correction. The majority of derived haplotypes also showed remarkable differences between the two groups (P ≤ 0.001). As indicated by MDR analysis, a three-locus model including rs6749447, rs35929607 and rs3754777 was selected as the overall best with a larger testing accuracy of 0.7309 and a maximum cross-validation consistency of 10 (P < 0.001). The utility of this model was reinforced by a Logistic regression analysis. Taken together, our findings suggest the potential interactive role of STK39 gene multiple polymorphisms in the development of hypertension among northeastern Han Chinese.

Genetic variants of the matrix metalloproteinase family genes and risk for hypertension: a case-control study among northeastern Han Chinese

In this study, we sought to examine the association between 10 genetic variants in the matrix metalloproteinase (MMP) family genes and the risk of hypertension among northeastern Han Chinese. This was a hospital-based case-control study involving 1009 sporadic hypertensive patients and 756 age-, gender- and ethnicity-matched normotensive controls. The genotypes of the 10 examined variants were determined by PCR-ligase detection reaction method. The genotype/allele distributions of rs3025058 and rs679620 differed significantly between patients and controls, with a Bonferroni corrected α of 0.05/10. The probability of having hypertension was significant for rs3025058 under the additive (odds ratio; 95% confidence interval; P: 1.33; 1.16-1.53; <0.001) and dominant (1.43; 1.18-1.73; <0.001) models and was significant for rs679620 under the additive (1.27; 1.1-1.46; <0.001) model after adjusting for confounders. In a combined analysis, when compared with the reference group (score<3.5 for unfavorable genotypes), participants in the medium- and high-risk groups had odds ratios that increased to 1.61 (95% CI: 1.25-2.51; P<0.001) and 1.92 (95% CI: 1.54-2.39; P<0.001) after adjustment, respectively. Interaction analysis showed that a three-locus model including rs3025058, rs679620 and rs243865 was the best, with a maximum testing accuracy of 0.6605 and a cross-validation consistency of 10 (P=0.0022). Taken together, our findings suggest that the true association between individual variants and the risk of hypertension may not be revealed until combined analyses of multiple variants from genes involving a specific physiological or cellular function are performed. Moreover, we propose a three-locus model that can best characterize the genetic interactions of the MMP multiple gene family.

The relationship between seven common polymorphisms from five DNA repair genes and the risk for breast cancer in northern Chinese women

BACKGROUND

Converging evidence supports the central role of DNA damage in progression to breast cancer. We therefore in this study aimed to assess the potential interactions of seven common polymorphisms from five DNA repair genes (XRCC1, XRCC2, XRCC3, XPA and APEX1) in association with breast cancer among Han Chinese women.

METHODOLOGY/PRINCIPAL FINDINGS

This was a case-control study involving 606 patients diagnosed with sporadic breast cancer and 633 age- and ethnicity-matched cancer-free controls. The polymerase chain reaction-ligase detection reaction method was used to determine genotypes. All seven polymorphisms were in accordance with Hardy-Weinberg equilibrium in controls. Differences in the genotypes and alleles of XRCC1 gene rs25487 and XPA gene rs1800975 were statistically significant between patients and controls, even after the Bonferroni correction (P<0.05/7). Accordingly, the risk for breast cancer was remarkably increased for rs25487 (OR = 1.28; 95% CI: 1.07-1.51; P = 0.006), but decreased for rs1800975 (OR = 0.77; 95% CI: 0.67-0.90; P = 0.001) under an additive model at a Bonferroni corrected alpha of 0.05/7. Allele combination analysis showed higher frequencies of the most common combination C-G-G-C-G-G-G (alleles in order of rs1799782, rs25487, rs3218536, rs861539, rs1800975, rs1760944 and rs1130409) in controls than in patients (PSim = 0.002). In further interaction analysis, two-locus model including rs1800975 and rs25487 was deemed as the overall best model with the maximal testing accuracy of 0.654 and the cross-validation consistency of 10 out of 10 (P = 0.001).

CONCLUSION

Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both independent and interactive effects on the development of breast cancer among northern Chinese women.

The relationship between RAGE gene four common polymorphisms and breast cancer risk in northeastern Han Chinese

We aimed to evaluate the association of four common polymorphisms (rs1800625, rs1800624, rs2070600, and rs184003) in receptor for advanced glycation end products (RAGE) gene to evaluate their epistatic influence on breast cancer risk in northeastern Han Chinese. This is a hospital-based case-control study involving 509 histologically-proven breast cancer patients and 504 cancer-free controls. The genotype and allele distributions of rs184003 differed significantly between patients and controls, even after the Bonferroni correction. Individuals carrying the rs184003 T allele exhibited 1.62-fold increased risk of breast cancer (odds ratio (OR) = 1.62; 95% confidence interval (95% CI): 1.26–2.08; P < 0.001) after adjusting for confounders. The frequency of haplotype T-T-G-T (alleles in order of rs1800625, rs1800624, rs2070600, and rs184003) was remarkably higher in patients than in controls (Simulated P = 0.001), and this haplotype was significantly associated with a 1.43-fold (95% CI: 1.01–2.01; P = 0.041) increase in adjusted risk of breast cancer. Further analysis indicated that there was synergistic interaction between rs184003 and rs2070600, whereas their joint information gain value was relatively small (0.27%). Taken together, although there was no suggestive evidence for the presence of epistasis in RAGE gene, our findings clearly demonstrate that rs184003 might play a predominant role in the development of breast cancer.

The contributory role of angiotensin receptor-like 1 gene multiple polymorphisms in hypertension among northeastern Han Chinese

Background and Objective

Via direct sequencing, we have recently identified six common polymorphisms in angiotensin receptor-like 1 (AGTRL1) gene, and found only two polymorphisms were significantly associated with hypertension in a family-based analysis on 1,015 southern Han Chinese. Extending our previous work and considering the ubiquity of epistasis in determining disease susceptibility, we, in this study, sought to explore the potential interaction of AGTRL1 gene six polymorphisms with hypertension in a large northeastern Han Chinese population.

Methods and Results

This was a case-control study involving 1,009 sporadic hypertensive patients and 756 normotensive controls. Data were analyzed by Haplo.Stats and multifactor dimensionality reduction (MDR) softwares. There were no deviations from Hardy-Weinberg equilibrium for all polymorphisms. The genotypes and alleles of rs7119675 and rs11544374 differed significantly between the two groups (P<0.0005), even after the Bonferroni correction. Under three genetic models, significant association was consistently observed for rs7119675 and rs11544374, and this association was independent of confounding factors. Taking rs7119375 as an example, the odds of having hypertension was 2.46 (95% confidence interval (95% CI): 2.06–2.94), 2.82 (95% CI: 2.29–3.46) and 3.97 (95% CI: 2.37–6.64) under additive, dominant and recessive models (P<0.001), respectively, whereas the adjusted risk estimates were slightly attenuated but still significant. The frequencies of most derived haplotypes differed significantly between patients and controls. Haplotype-phenotype analyses indicated marginal association for triglyceride (P_Sim = 0.011) and total cholesterol (P_Sim = 0.025) in patients and for triglyceride in controls (P_Sim = 0.023). The overall best MDR model included rs11544374, rs7119375 and rs948847 with the maximal testing accuracy of 0.737 and cross-validation consistency of 10 out of 10 (P<0.0001). Further interaction entropy graph suggested that the interaction of rs7119375 with rs11544374 and rs948847 was strongly antagonized.

Conclusions

Our findings demonstrate that AGTRL1 genetic polymorphisms might contribute to the development of hypertension independently and/or through complex interaction.

Association between CHRNA3 rs1051730 genotype and lung cancer risk in Chinese Han population: a case-control study

Recent population-based genome wide association studies have revealed potential susceptibility loci of lung cancer at the region of chromosome 15q25.1 containing nicotinic acetylcholine receptor genes. The loci increasing lung cancer risk has been widely identified in Caucasians, but whether this association also exists in Asians and whether this association is a direct role or mediated via tobacco smoking indirectly has not been fully established. We conducted a case-control study comprising of 210 histologically confirmed lung cancer cases and 200 healthy controls to examine rs1051730 genotyping, a single nucleotide polymorphism receiving much attention recently, and its influence on lung cancer risk as well as nicotine dependence in a Chinese Han population. Our results showed that the heterozygous C/T genotype and minor allele T conferred a significant higher risk of lung cancer than the CC homozygotes and allele C (adjusted OR=2.25, 95% CI=1.04-4.89, P=0.040 and OR=2.18, 95% CI=1.02-4.67, P=0.045 respectively). However, no association between the smoking habit and the CHRNA3 rs1051730 polymorphism was observed in this study. The results suggested that the rs1051730 polymorphism may modify susceptibility to lung cancer via a smoking-independent manner among Chinese Han population. Additional studies in vitro and in vivo are warranted to further elucidate the impact of rs1051730 on lung cancer susceptibility.

Replication of the top 10 most significant polymorphisms from a large blood pressure genome-wide association study of northeastern Han Chinese East Asians

The replication of genome-wide significant association signals in independent populations is a practical approach for characterizing gene-disease relationships. Therefore, we sought to explore the top 10 polymorphisms from a large blood pressure genome-wide association study of northeastern Han Chinese East Asians. This was a hospital-based study involving 1009 patients with essential hypertension and 756 normotensive controls from Qiqihar city, China. Genotyping was conducted with a polymerase chain reaction-ligase detection reaction method. All polymorphisms except for rs6825911 satisfied Hardy-Weinberg equilibrium. Overall, the genotype differences between the patients and controls were significant for rs35444 (P<0.001), rs11191548 (P=0.017) and rs17249754 (P=0.017). The per-minor-allele odds ratios of rs35444, rs11191548 and rs17249754 were 0.54 (95% confidence interval (95% CI): 0.46-0.62; P<0.01), 1.23 (95% CI: 1.07-1.43; P=0.005) and 1.23 (95% CI: 1.07-1.41; P=0.004), respectively. Similarly, the carriers of minor homozygotes had a significant reduction in adjusted systolic and diastolic blood pressure for rs35444 (P<0.01) but an increase for both rs11191548 (P<0.01) and rs17249754 (P<0.04). Further application of the genetic risk score method indicated that subjects with risk scores of 8, 10 and 12-16 had 1.66-fold (95% CI: 1.01-2.72), 1.72-fold (95% CI: 1.03-2.86) and 1.97-fold (95% CI: 1.12-3.46) increases, respectively, in the odds of developing hypertension, and similar increases were also observed for blood pressure. Taken together, our findings demonstrate that although only three of the top 10 polymorphisms were successfully validated in the northeastern Han Chinese population, the genetic risk score analyses led us to more profound insights into the possible joint effects of multiple polymorphisms on hypertension risk and blood pressure variation.

An interactive association of advanced glycation end-product receptor gene four common polymorphisms with coronary artery disease in northeastern Han Chinese

Background

Growing evidence indicates that advanced glycation end-product receptor (RAGE) might play a contributory role in the pathogenesis of coronary artery disease (CAD). To shed some light from a genetic perspective, we sought to investigate the interactive association of RAGE gene four common polymorphisms (rs1800625 or T-429C, rs1800624 or T-374A, rs2070600 or Gly82Ser, and rs184003 or G1704A) with the risk of developing CAD in a large northeastern Han Chinese population.

Methodology/Principal Findings

This was a hospital-based case-control study incorporating 1142 patients diagnosed with CAD and 1106 age- and gender-matched controls. All individuals were angiographically confirmed. Risk estimates were expressed as odds ratio (OR) and 95% confidence interval (CI). Overall there were significant differences in the genotype and allele distributions of rs1800625 and rs184003, even after the Bonferroni correction. Logistic regression analyses indicated that rs1800625 and rs184003 were associated with significant risk of CAD under both additive (OR = 1.20 and 1.23; 95% CI: 1.06–1.37 and 1.06–1.42; P = 0.006 and 0.008) and recessive (OR = 1.75 and 2.39; 95% CI: 1.28–2.40 and 1.47–3.87; P<0.001 and <0.001) models after adjusting for confounders. In haplotype analyses, haplotypes C-T-G-G and T-A-G-T (alleles in order of rs1800625, rs1800624, rs2070600 and rs184003), overrepresented in patients, were associated with 52% (95% CI: 1.19–1.87; P = 0.0052) and 63% (95% CI: 1.14–2.34; P = 0.0075) significant increases in adjusted risk for CAD. Further interactive analyses identified an overall best multifactor dimensionality reduction (MDR) model including rs1800625 and rs184003. This model had a maximal testing accuracy of 0.6856 and a cross-validation consistency of 10 out of 10 (P = 0.0016). The validity of this model was substantiated by classical Logistic regression analysis.

Conclusions

Our findings provided strong evidence for the potentially contributory roles of RAGE multiple genetic polymorphisms, especially in the context of locus-to-locus interaction, in the pathogenesis of CAD among northeastern Han Chinese.

Contributory role of five common polymorphisms of RAGE and APE1 genes in lung cancer among Han Chinese

BACKGROUND

Lung cancer is the leading cause of cancer mortality in China. Given the ubiquitous nature of gene-to-gene interaction in lung carcinogenesis, we sought to evaluate five common polymorphisms from advanced glycosylation end product-specific receptor (RAGE) and apurinic/apyrimidinic endonuclease 1 (APE1) genes in association with lung cancer among Han Chinese.

METHODS AND RESULTS

819 patients with lung cancer and 803 cancer-free controls were recruited from Qiqihar city. Genotypes of five examined polymorphisms (RAGE gene: rs1800625, rs1800624, rs2070600; APE1 gene: rs1760944, rs1130409) were determined by ligase detection reaction method. Data were analyzed by R software and multifactor dimensionality reduction (MDR). Hardy-Weinberg equilibrium was satisfied for all five polymorphisms. Overall differences in the genotype and allele distributions were significant for rs1800625 (Pgenotype<0.0005; Pallele<0.0005), rs2070600 (Pgenotype = 0.005; Pallele = 0.004) and rs1130409 (Pgenotype = 0.009; Pallele = 0.004) polymorphisms. Haplotype C-A-A (alleles in order of rs1800625, rs1800624 and rs2070600) of RAGE gene was overrepresented in patients, and conferred a 2.1-fold increased risk of lung cancer (95% confidence interval: 1.52-2.91), independent of confounding factors. Further application of MDR method to five examined polymorphisms identified the overall best interaction model including rs2070600 and rs1130409 polymorphisms. This model had a maximal testing accuracy of 64.63% and a maximal cross-validation consistency of 9 out of 10 at the significant level of 0.006.

CONCLUSIONS

Our findings demonstrated a potential interactive contribution of RAGE and APE1 genes to the pathogenesis of lung cancer among Han Chinese. Further studies are warranted to confirm or refute these findings.