Lung Cancer Susceptibility Locus Research Articles

Abstract 2110: An attempt to replicate the results of genome-wide association studies on lung cancer susceptibility loci in a Korean population

Abstract Genome-wide association studies (GWASs) have identified three chromosomal regions at 5p15, 6p21, and 15q25 as being associated with lung cancer risk in European populations. This study was performed to confirm these associations in Korean patients with lung cancer. The genotypes of rs2736100, rs402710, rs401681, and rs31489 at 5p15, rs9295740 at 6p22, and rs2036534 and rs6495309 at 15q25 were determined in 1094 lung cancer patients and 1100 healthy controls frequency-matched for age and gender. The single nucleotide polymorphisms (SNPs) at 5p15 and 15q25 were significantly associated with lung cancer risk. The magnitude of effect was similar to that reported in previous studies and the association was in the same direction. The effect of SNPs at 5p15 region on the risk of lung cancer was significant only in adenocarcinoma. The two SNPs at 15q25 region were significantly associated with lung cancer risk in ever-smokers and squamous cell carcinoma. However, there was no association between the SNP at 6p22 and lung cancer risk. We confirmed the association between SNPs at the 5p15 and 15q25 regions and the risk of lung cancer in a Korean population. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2110. doi:1538-7445.AM2012-2110

Abstract 4210: Association of the 15q25 and 5p15 lung cancer susceptibility regions with gene expression in lung tumor tissue

Abstract Lung cancer is one of the most commonly diagnosed cancers worldwide, with 1.6 million new cases reported each year and ranks first in annual global cancer deaths. Genome-wide association studies have identified two independent lung cancer susceptibility loci at chromosome 15q25 and one locus at 5p15. We examined the association of genetic variants in these lung cancer susceptibility regions with gene expression in lung tumor tissue in an effort to elucidate carcinogenic mechanisms by which these variants influence lung cancer risk. We used data from two independent studies: the JBR.10 clinical trial (131 NSCLC patients) and a patient sample from the University Health Network (UHN) in Toronto (181 NSCLC patients). We genotyped seven 15q25 and five 5p15 variants and examined their association with the expression profiles of genes in the corresponding regions measured by Affymetrix HG-U133A. The minor allele (C) of a variant representing one of the two loci at 15q25 (rs2036534) was associated with increased expression of the IREB2 (iron-responsive element binding protein 2) gene in both studies (JBR.10 P=0.042; UHN P=0.002). An FDRα0.05 in the UHN sample increased our confidence in this association. The association appears to be more prominent among patients with lung adenocarcinoma. We did not detect an association between the genotype and expression profile for the other 15q25 locus (represented by rs16969968 and rs1051730). Previous studies suggest that 15q25 variants are associated with risk through an effect on smoking behaviour, indicating risk is modulated through activity of nicotinic acetylcholine receptor genes present in this region. Our results indicate there is a second mechanism through which variants at 15q25 influence risk, operating through modulation of IREB2 gene expression. This finding may have implications for future research on lung cancer chemoprevention strategies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4210. doi:1538-7445.AM2012-4210

New Lung Cancer Susceptibility Locus Identified: Significance and Implications for Other Genome-Wide Association Studies

Genome-wide association studies have identified more than 150 loci that influence the risk of cancer. In this issue of Cancer Discovery, Shi and colleagues report that a variant in RAD52 is a risk factor for squamous cell lung carcinoma. This work is important not only for its potential implications on control of this dreaded malignancy but also for its methodologic contributions that can advance the field of molecular-genetic epidemiology.

Association between C3orf21, TP63 polymorphisms and environment and NSCLC in never-smoking Chinese population

Recently, two genome-wide association studies in Asia identified gene polymorphisms known as rs4488809, rs9816619 in TP63 and rs2131877, rs952481 in C3orf21. It has been proposed that these polymorphisms are susceptibility loci for non-small cell lung cancer (NSCLC) development among Japanese and Korean populations. We ask whether susceptibility to NSCLC is limited to the Chinese population or whether the environment also affects genetic polymorphisms. We conducted a matched case–control study to explore this question. Results show that polymorphism of TP63 was not associated with NSCLC development, whereas variant genotypes of C3orf21 were nominally associated with a reduced risk of lung adenocarcinoma (OR=0.619, 95% CI=0.390–0.976). These results strongly suggest that environmental agents interact with human genetic polymorphism independent of ethnic background. In addition, the C3orf21 gene may be a potential susceptibility marker for lung adenocarcinoma independent of ethnic background and environmental agents.

The 18p11.22 locus is associated with never smoker non-small cell lung cancer susceptibility in Korean populations

The proportion of never smoker non-small cell lung cancer (NSCLC) in Asia is about 30-40%. Despite the striking demographics and high prevalence of never smoker NSCLC, the exact causes still remain undetermined. Although several genome wide association (GWA) studies were conducted to find susceptibility loci for lung cancer in never smokers, no regions were replicated except for 5p15.33, suggesting locus heterogeneity and different environmental toxic effects. To identify genetic loci associated with susceptibility of lung cancer in never smokers, we performed a GWA analysis using the Affymetrix 6.0 SNP array. For discovery GWA set, we recruited 446 never smoking Korean patients with NSCLC and 497 normal subjects. We tested association of SNPs with lung cancer susceptibility using the Cochran-Armitage trend test. For validation, 39 SNPs were selected from the top 50 SNPs and five additional SNPs were selected in the DAB1 gene region which showed significant associations in the GWA analysis. The validation SNPs were genotyped in an independent sample including 434 patients and 1,000 controls. Among the 44 validation SNPs, two SNPs (rs11080466 and rs11663246) near the APCDD1, NAPG and FAM38B genes in the 18p11.22 region were replicated. P value of rs11080466 was 1.08 × 10(-6) in the combined sets (2.68 × 10(-5) in the discovery set and 2.60 × 10(-3) in the validation set) and odds ratio was 0.68 (0.58-0.79). We observed similar association for rs11663246. Our result suggests the 18p11.22 region as a novel lung cancer susceptibility locus in never smokers.

Susceptibility Locus for Lung Cancer at 15q25.1 Is Not Associated With Risk of Pancreatic Cancer

Four genome-wide association (GWA) studies have found that variation in a region of strong linkage disequilibrium on the long arm of chromosome 15 (15q24-25.1) containing nicotinic acetylcholine receptor genes contributes to lung cancer risk. Because cigarette smoking is a major risk factor for developing both lung cancer and pancreatic cancer, we hypothesized that variation in this region may also modify individual susceptibility to pancreatic cancer. We conducted a case-control study of 523 patients with pathologically confirmed pancreatic adenocarcinoma and 1046 age-, sex-, ethnicity-, and smoking behavior-matched cancer-free controls. We found that 2 risk single nucleotide polymorphisms reported in the lung cancer GWA studies-rs8034191: A>G and rs1051730: G>A, located in this 15q24-25.1 region-were not associated with risk of pancreatic cancer. The results of our study suggest that the 2 single nucleotide polymorphisms at 15q25.1 do not modify pancreatic cancer risk.

A genome-wide association study identifies two new lung cancer susceptibility loci at 13q12.12 and 22q12.2 in Han Chinese

Lung cancer is the leading cause of cancer-related deaths worldwide. To identify genetic factors that modify the risk of lung cancer in individuals of Chinese ancestry, we performed a genome-wide association scan in 5,408 subjects (2,331 individuals with lung cancer (cases) and 3,077 controls) followed by a two-stage validation among 12,722 subjects (6,313 cases and 6,409 controls). The combined analyses identified six well-replicated SNPs with independent effects and significant lung cancer associations (P < 5.0 × 10(-8)) located in TP63 (rs4488809 at 3q28, P = 7.2 × 10(-26)), TERT-CLPTM1L (rs465498 and rs2736100 at 5p15.33, P = 1.2 × 10(-20) and P = 1.0 × 10(-27), respectively), MIPEP-TNFRSF19 (rs753955 at 13q12.12, P = 1.5 × 10(-12)) and MTMR3-HORMAD2-LIF (rs17728461 and rs36600 at 22q12.2, P = 1.1 × 10(-11) and P = 6.2 × 10(-13), respectively). Two of these loci (13q12.12 and 22q12.2) were newly identified in the Chinese population. These results suggest that genetic variants in 3q28, 5p15.33, 13q12.12 and 22q12.2 may contribute to the susceptibility of lung cancer in Han Chinese.

The TERT-CLPTM1L locus for lung cancer predisposes to bronchial obstruction and emphysema

Clinical studies suggest that bronchial obstruction and emphysema increase susceptibility to lung cancer. We assessed the possibility of a common genetic origin and investigated whether the lung cancer susceptibility locus on chromosome 5p15.33 increases the risk for bronchial obstruction and emphysema. Three variants in the 5p15.33 locus encompassing the TERT and CLPTM1L genes were genotyped in 777 heavy smokers and 212 lung cancer patients. Participants underwent pulmonary function tests and computed tomography of the chest, and completed questionnaires assessing smoking behaviour. The rs31489 C-allele correlated with reduced forced expiratory volume in 1 s (p=0.006). Homozygous carriers of the rs31489 C-allele exhibited increased susceptibility to bronchial obstruction (OR 1.82, 95% CI 1.24-2.69; p=0.002). A similar association was observed for diffusing capacity of the lung for carbon monoxide (p=0.004). Consistent with this, CC-carriers had an increased risk of emphysema (OR 2.04, 95% CI 1.41-2.94; p=1.73 × 10(-4)) and displayed greater alveolar destruction. Finally, CC-carriers also had an increased risk for lung cancer (OR 1.90, 95% CI 1.21-2.99; p=0.005), and were more susceptible to developing both lung cancer and bronchial obstruction than lung cancer alone (OR 2.11, 95% CI 1.04-4.26; p=0.038). The rs31489 variant on 5p15.33 is associated with bronchial obstruction, presence and severity of emphysema, and lung cancer.

Different Effects of &amp;lt;i&amp;gt;TERT&amp;lt;/i&amp;gt;, &amp;lt;i&amp;gt;TP&amp;lt;/i&amp;gt;63, and &amp;lt;i&amp;gt;CYP&amp;lt;/i&amp;gt;2&amp;lt;i&amp;gt;A&amp;lt;/i&amp;gt;6 Polymorphism on Individual Risk of Tobacco-Related Lung Cancer in Male Japanese Smokers

Recent genome-wide association studies have identified lung cancer susceptibility loci, such as chromosome 5p15 (telomerase reverse transcriptase, TERT and cleft lip and palate transmembrane protein 1-like, CLPTM1L), 15q25 (nicotinic cholinergic receptor α, CHRNA3-CHRNA5), and 3q28 (tumor protein p63, TP63). Replication study was performed to confirm the association of the recently-identified susceptible loci (i.e., TERT-CLPTM1L, CHRNA3-CHRNA5, and TP63) in a total of 1460 male Japanese smokers (885 lung cancer cases and 575 healthy control subjects), which were previously studied for a low odds ratio of impaired or deletion polymorphism in cytochrome P450 2A6 (CYP2A6) for lung cancer risk. The minor allele frequency (0.442) of rs2736100 on 5p15 (TERT) was significantly higher in lung cancer cases than that (0.395) of controls, with an odds ratio of 1.27 (95% CI of 1.07 - 1.50, p = 0.00504). A series of subgroup analyses revealed the significant associations of rs4488809 (TP63, odds ratio of 1.21, p = 0.0422) and rs2736100 (TERT, odds ratio of 1.47, p = 6.40 × 10–5) with the risk of lung adenocarcinoma. No significant association of CHRNA3-CHRNA5 and CLPTM1L was found in this population. The present results support replication of the association of TERT and TP63 loci with lung adenocarcinomas and suggest subtype-specific effects of these loci on higher risk of lung cancer in smokers. The CYP2A6 including copy number polymorphism, uninvestigated in large-scale genome-wide association studies, may influence lower risk to heavy tobacco use-related lung cancer.

Abstract B30: Susceptibility loci for lung cancer: Are COPD genes the missing link?

Abstract Epidemiological studies show COPD, characterized by reduced FEV1, is the most important independent risk factor for susceptibility to lung cancer. When spirometry is routinely measured, co-existing COPD is found in 50-80% of lung cancer cases compared to only 15-20% of randomly selected matched smokers. Recent GWA studies have identified a number of susceptibility loci for COPD, lung function and lung cancer. Several of these loci overlap suggesting that the gene conferring susceptibility to lung cancer might include COPD-related genes. In this case control study of Caucasian smokers matched for smoking exposure with COPD (n=458), lung cancer (N=454) and healthy smoker status (n=488) we compared the genotype frequencies of 12 loci on chromosomes 1q23, 4q22-24, 4q31, 5p15, 5q33, 6p21, 6q24 and 15q25. All subjects underwent spirometry, completed a modified ATS respiratory questionnaire and gave blood for DNA. Genotyping was done using Taqman real-time PCR (ABI 7900). We found (1) the AA genotype of CHRNA3/5 (previously associated with lung cancer) conferred susceptibility to lung cancer (OR=1.76, P=0.005) and COPD (OR-1.47, P=0.06), (2) the GG genotype of HHIP (previously associated with reduced risk of COPD) conferred protection from COPD (OR=0.59, P=0.006) and lung cancer (OR=0.70, P=0.05) and the CC genotype of FAM13A (previously associated with reduced risk of COPD) conferred protection from COPD (OR=0.71, P=0.02) and lung cancer (OR=0.64, P=0.003). These overlapping effects in lung cancer were independent of co-existing COPD. We conclude the genes conferring susceptibility to lung cancer overlap with those of COPD. Such an observation requires healthy smokers with normal lung function to be used as controls to best identify these COPD-related genes affecting the susceptibility of smokers to lung cancer. Citation Information: Cancer Prev Res 2010;3(12 Suppl):B30.

Ordered subset analysis identifies loci influencing lung cancer risk on chromosomes 6q and 12q.

Genetic susceptibility for cancer can differ substantially among families. We use trait-related covariates to identify a genetically homogeneous subset of families with the best evidence for linkage in the presence of heterogeneity. We performed a genome-wide linkage screen in 93 families. Samples and data were collected by the familial lung cancer recruitment sites of the Genetic Epidemiology of Lung Cancer Consortium. We estimated linkage scores for each family by the Markov chain Monte Carlo procedure using SimWalk2 software. We used ordered subset analysis (OSA) to identify genetically homogenous families by ordering families based on a disease-associated covariate. We performed permutation tests to determine the relationship between the trait-related covariate and the evidence for linkage. A genome-wide screen for lung cancer loci identified strong evidence for linkage to 6q23-25 and suggestive evidence for linkage to 12q24 using OSA, with peak logarithm of odds (LOD) scores of 4.19 and 2.79, respectively. We found other chromosomes also suggestive for linkages, including 5q31-q33, 14q11, and 16q24. Our OSA results support 6q as a lung cancer susceptibility locus and provide evidence for disease linkage on 12q24. This study further increased our understanding of the inheritability for lung cancer. Validation studies using larger sample size are needed to verify the presence of several other chromosomal regions suggestive of an increased risk for lung cancer and/or other cancers. OSA can reduce genetic heterogeneity in linkage study and may assist in revealing novel susceptibility loci.

Replication of Lung Cancer Susceptibility Loci at Chromosomes 15q25, 5p15, and 6p21: A Pooled Analysis From the International Lung Cancer Consortium

Genome-wide association studies have identified three chromosomal regions at 15q25, 5p15, and 6p21 as being associated with the risk of lung cancer. To confirm these associations in independent studies and investigate heterogeneity of these associations within specific subgroups, we conducted a coordinated genotyping study within the International Lung Cancer Consortium based on independent studies that were not included in previous genome-wide association studies. Genotype data for single-nucleotide polymorphisms at chromosomes 15q25 (rs16969968, rs8034191), 5p15 (rs2736100, rs402710), and 6p21 (rs2256543, rs4324798) from 21 case-control studies for 11 645 lung cancer case patients and 14 954 control subjects, of whom 85% were white and 15% were Asian, were pooled. Associations between the variants and the risk of lung cancer were estimated by logistic regression models. All statistical tests were two-sided. Associations between 15q25 and the risk of lung cancer were replicated in white ever-smokers (rs16969968: odds ratio [OR] = 1.26, 95% confidence interval [CI] = 1.21 to 1.32, P(trend) = 2 x 10(-26)), and this association was stronger for those diagnosed at younger ages. There was no association in never-smokers or in Asians between either of the 15q25 variants and the risk of lung cancer. For the chromosome 5p15 region, we confirmed statistically significant associations in whites for both rs2736100 (OR = 1.15, 95% CI = 1.10 to 1.20, P(trend) = 1 x 10(-10)) and rs402710 (OR = 1.14, 95% CI = 1.09 to 1.19, P(trend) = 5 x 10(-8)) and identified similar associations in Asians (rs2736100: OR = 1.23, 95% CI = 1.12 to 1.35, P(trend) = 2 x 10(-5); rs402710: OR = 1.15, 95% CI = 1.04 to 1.27, P(trend) = .007). The associations between the 5p15 variants and lung cancer differed by histology; odds ratios for rs2736100 were highest in adenocarcinoma and for rs402710 were highest in adenocarcinoma and squamous cell carcinomas. This pattern was observed in both ethnic groups. Neither of the two variants on chromosome 6p21 was associated with the risk of lung cancer. In this international genetic association study of lung cancer, previous associations found in white populations were replicated and new associations were identified in Asian populations. Future genetic studies of lung cancer should include detailed stratification by histology.

A Risky Business--Identifying Susceptibility Loci for Lung Cancer

The majority of lung cancers are attributable to tobacco usage and other behavioral and environmental risk factors. Tobacco-induced malignancies are fueled by multiple powerful carcinogens and nicotine, a potent addictive agent. Thus, lung cancer is often regarded as being primarily determined by behavioral and environmental factors. However, because only a minority of heavy smokers develops lung cancer, genetic differences in susceptibility to tobacco carcinogens must exist, and lung cancers must arise from complex a Risky Business—identifying Susceptibility loci for lung Cancer

Abstract 3921: Amplification of the TFAP2B gene and upregulation of its gene products promote human bronchial epithelial cell (HBEC) transformation and carcinogenesis

Abstract We previously showed that the transcription factor AP2B (TFAP2B) protein could specifically bind to the promoter of human telomerase reverse transcriptase (hTERT) and selectively activate hTERT in lung cancer cells but not in normal cells. The common 5p15.33 and 6p21.33 chromosomal variants that harbor the hTERT and TFAP2B genes, have been identified as susceptibility loci for lung cancer and show a significant autosomal copy number gain in lung adenocarcinoma. We tested the hypothesis that amplification of the TFAP2B gene and up-regulation of its gene products can transform lung cells and promote tumorigenesis. We first analyzed levels of TFAP2B gene expression in human lung cancer cell lines, small-airway epithelial cells (SAECs),primary normal HBEC and in immortalized or transformed HBECs by gene expression profiling on gene microarrays. Levels of TFAP2B gene expression varied significantly between different cell lines but on average were greater than those of primary normal HBECs and SAECs. A linkage distance cluster analysis of the TFAP2B pathway-associated genes showed a significant classification of lung cancer cell types, distinguishing tumor cells from normal ones. Differential expression of the TFAP2B gene in normal lung and cancer cells was confirmed by qRT-PCR. We analyzed copy number variations (CNVs) specifically linked to hTERT and TFAP2B loci by mining the published genome-wide SNP data set from 370 NSCLC tumor samples and confirmed a significant copy number gain for both hTERT and TFAP2B with average copy numbers of 4.5 and 3.5, respectively. We performed immunohistochemical (IHC) analysis of TFAP2B protein expression in 30 paired human lung tumors and normal lung tissues that are immediately (&amp;lt;1.0 cm) adjacent or distal (2-3 cm) to the tumor sites. Significantly up-regulated TFAP2B protein expression was detected in almost all the adenocarcinomas and squamous carcinomas and significantly reduced expression was observed in the immediately adjacent normal lung and HBECs and the distal normal lung and HBECs. The differential TGFAP2B protein expression patterns shown by the IHC analysis were confirmed by Western blot analysis. We performed immuno-fluorescence imaging analysis of the endogenous TFAP2B expression and detected distinctive subcellular and nuclear localization in normal HBECs compared to tumor cells. Ectopic activation of TFAP2B by wt-TFAP2B gene transfer significantly altered the cellular and nuclear compartmentalization and architecture. Activation of TFAP2B in stable clones of normal HBECs induced clonogenecity of these cells compared to the parent cells. Our results suggest an important role of TFAP2B in lung cancer carcinogenesis and potential translational applications using TFAP2B as a novel biomarker for lung cancer and as a therapeutic target. (Supported by NIH SPORE P50CA70907 and RO1CA116322 grants) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3921.

Aberrant DNA Methylation Links Cancer Susceptibility Locus 15q25.1 to Apoptotic Regulation and Lung Cancer

Nicotinic acetylcholine receptor (nAChR) genes form a highly conserved gene cluster at the lung cancer susceptibility locus 15q25.1. In this study, we show that the CHRNalpha3 gene encoding the nAChRalpha3 subunit is a frequent target of aberrant DNA hypermethylation and silencing in lung cancer, whereas the adjacent CHRNbeta4 and CHRNalpha5 genes exhibit moderate and no methylation, respectively. Treatment of cancer cells exhibiting CHRNalpha3 hypermethylation with DNA methylation inhibitors caused demethylation of the CHRNalpha3 promoter and gene reactivation. Restoring CHRNalpha3 levels through ectopic expression induced apoptotic cell death. Small hairpin RNA-mediated depletion of nAChRalpha3 in CHRNalpha3-expressing lung cancer cells elicited a dramatic Ca(2+) influx response in the presence of nicotine, followed by activation of the Akt survival pathway. CHRNalpha3-depleted cells were resistant to apoptosis-inducing agents, underscoring the importance of epigenetic silencing of the CHRNalpha3 gene in human cancer. In defining a mechanism of epigenetic control of nAChR expression in nonneuronal tissues, our findings offer a functional link between susceptibility locus 15q25.1 and lung cancer, and suggest nAChRs to be theranostic targets for cancer detection and chemoprevention.

ASCL1 Regulates the Expression of the CHRNA5/A3/B4 Lung Cancer Susceptibility Locus

Tobacco contains a variety of carcinogens as well as the addictive compound nicotine. Nicotine addiction begins with the binding of nicotine to its cognate receptor, the nicotinic acetylcholine receptor (nAChR). Genome-wide association studies have implicated the nAChR gene cluster, CHRNA5/A3/B4, in nicotine addiction and lung cancer susceptibility. To further delineate the role of this gene cluster in lung cancer, we examined the expression levels of these three genes as well as other members of the nAChR gene family in lung cancer cell lines and patient samples using quantitative reverse transcription-PCR. Overexpression of the clustered nAChR genes was observed in small-cell lung carcinoma (SCLC), an aggressive form of lung cancer highly associated with cigarette smoking. The overexpression of the genomically clustered genes in SCLC suggests their coordinate regulation. In silico analysis of the promoter regions of these genes revealed putative binding sites in all three promoters for achaete-scute complex homolog 1 (ASCL1), a transcription factor implicated in the pathogenesis of SCLC, raising the possibility that this factor may regulate the expression of the clustered nAChR genes. Consistent with this idea, knockdown of ASCL1 in SCLC, but not in non-SCLC, led to a significant decrease in expression of the alpha 3 and beta 4 genes without having an effect on any other highly expressed nAChR gene. Our data indicate a specific role for ASCL1 in regulating the expression of the CHRNA5/A3/B4 lung cancer susceptibility locus. This regulation may contribute to the predicted role that ASCL1 plays in SCLC tumorigenesis.

Individuals susceptible to lung adenocarcinoma defined by combined HLA-DQA1 and TERT genotypes

Adenocarcinoma (ADC) is the commonest histological type of lung cancer, and its weak association with smoking indicates the necessity to identify high-risk individuals for targeted screening and/or prevention. By a genome-wide association study (GWAS), we identified an association of polymorphisms in the 6p21.31 locus containing four human leukocyte antigen (HLA) class II genes with lung ADC risk. DQA1*03 of the HLA-DQA1 gene was defined as a risk allele with odds ratio (OR) of 1.36 [95% confidence interval (CI) = 1.21-1.54, P = 5.3 x 10(-7)] by analysis of 1656 ADC cases and 1173 controls. DQA1*03 and the minor allele for a polymorphism, rs2736100, in TERT, another lung cancer susceptibility locus identified in recent GWASs on Europeans and Americans, were indicated to independently contribute to ADC risk with per allele OR of 1.43 (95% CI = 1.31-1.56, P = 7.8 x 10(-16)). Individuals homozygous both for the DQA1*03 and minor TERT alleles were defined as high-risk individuals with an OR of 4.76 (95% CI = 2.53-9.47, P = 4.2 x 10(-7)). The present results indicated that individuals susceptible to lung ADC can be defined by combined genotypes of HLA-DQA1 and TERT.

Tobacco, Genetic Susceptibility and Lung cancer

Exposure to tobacco smoke is an established risk factor for lung cancer, although a possible role for genetic susceptibility in the development of lung cancer has been inferred from familial clustering of the disease and segregation analysis. Findings of familial aggregation and statistical evidence for a major susceptibility gene have led to the search for high penetrant, rare, single genes and low penetrant, high frequency susceptibility genes for lung cancer. The relatively small number of linkage studies conducted to date, have identified potential lung cancer susceptibility loci on chromosomes 6q, 12p, and 19q. A variety of studies have examined single nucleotide polymorphisms of several low penetrant, high frequency genes encoding for enzymes involved in the metabolism of carcinogens and DNA damage repair, as likely candidate susceptibility genes. These studies have produced somewhat conflicting findings and, when significant, only modest associations have been reported. Relatively few studies have looked for potential gene-environment interactions, explored associations between two or more genetic polymorphisms or evaluated interactions between genetic polymorphisms and endogenous risk factors. Few large scale genome wide association studies conducted recently have provided evidence that common variation on chromosome 15q25.1, 5p15.33 and 6p21.33 influences lung cancer risk and cancer types with strong environmental risk factors. It is hoped that newer research strategies, selecting candidate genes within pathways and genotype at multiple markers within a gene, employing new technologies, may allow complete coverage of the variation within candidate genes in multiple pathways and to unravel the genetic susceptibility to lung cancer. This knowledge could, in turn, be used to identify persons at risk, to individualize treatments such as chemoprevention, to personalize harms of smoking and to motivate cessation.

Genetic Variants on Chromosome 15q25 Associated with Lung Cancer Risk in Chinese Populations

Recent three genome-wide association studies have mapped a lung cancer susceptibility locus to chromosome 15q25 in Caucasians. However, the reported risk single nucleotide polymorphisms (SNPs) are extremely rare in Asians, arguing against any of these being causative variants. This study sought to identify other variants on 15q25 associated with lung cancer susceptibility in Chinese. Two-stage case-control studies were conducted in subjects derived from both Northern and Southern China. The first-stage, consisting of 576 cases and 576 controls, was to discover novel risk variants using a haplotype-tagging SNP approach, and these variants were then replicated in the second-stage, consisting of 2,989 cases and 2,880 controls. Associations were estimated by logistic regression models, and function of the variants was examined by biochemical assays. We found that the three risk SNPs reported in Caucasians were not associated with lung cancer risk in Chinese. However, we identified four novel SNPs (rs2036534C>T, rs667282C>T, rs12910984G>A, and rs6495309T>C) that were associated with significantly increased lung cancer risk and smoking behavior, which were all confirmed in the replication analyses [odds ratios (95% confidence intervals) in the dominant model: 1.39 (1.23-1.57; P = 2.3 x 10(-7)), 1.52 (1.35-1.71; P = 2.0 x 10(-12)), 1.44 (1.28-1.63; P = 2.7 x 10(-9)), and 1.43 (1.27-1.61; P = 2.6 x 10(-9)), respectively]. We characterized the rs6495309T>C change in the CHRNA3 promoter as a functional variant because it affected the Oct-1 binding ability, resulting in increased CHRNA3 expression. These results support 15q25 as a susceptibility region for lung cancer in Chinese but underscore the difference in genetic markers among different ethnic populations.

Fine mapping of chromosome 6q23-25 region in familial lung cancer families reveals RGS17 as a likely candidate gene.

We have previously mapped a major susceptibility locus influencing familial lung cancer risk to chromosome 6q23-25. However, the causal gene at this locus remains undetermined. In this study, we further refined this locus to identify a single candidate gene, by fine mapping using microsatellite markers and association studies using high-density single nucleotide polymorphisms (SNP). Six multigenerational families with five or more affected members were chosen for fine-mapping the 6q linkage region using microsatellite markers. For association mapping, we genotyped 24 6q-linked cases and 72 unrelated noncancer controls from the Genetic Epidemiology of Lung Cancer Consortium resources using the Affymetrix 500K chipset. Significant associations were validated in two independent familial lung cancer populations: 226 familial lung cases and 313 controls from the Genetic Epidemiology of Lung Cancer Consortium, and 154 familial cases and 325 controls from Mayo Clinic. Each familial case was chosen from one high-risk lung cancer family that has three or more affected members. A region-wide scan across 6q23-25 found significant association between lung cancer susceptibility and three single nucleotide polymorphisms in the first intron of the RGS17 gene. This association was further confirmed in two independent familial lung cancer populations. By quantitative real-time PCR analysis of matched tumor and normal human tissues, we found that RGS17 transcript accumulation is highly and consistently increased in sporadic lung cancers. Human lung tumor cell proliferation and tumorigenesis in nude mice are inhibited upon knockdown of RGS17 levels. RGS17 is a major candidate for the familial lung cancer susceptibility locus on chromosome 6q23-25.