Lung Cancer Susceptibility Locus Research Articles

A locus on chromosome 8 controlling tumor regionality—a new type of tumor diversity in the mouse lung

Regional specificity of lung tumor formation has rarely been studied in mouse or human. By using crosses of strains semi-congenic for lung cancer susceptibility locus Sluc20, we have analyzed the genetic influences of Sluc20 and 5 other loci on tumor regionality in the mouse lung. We have mapped Sluc20 to a 27.92-MB proximal region of chromosome 8 and found that it controls the number and load of only those tumors that surround or are directly adjacent to the bronchi or bronchioli (peribronchial tumors). These tumors lie outside the bronchial basement membrane and tend to reach a larger size than the tumors at other locations in the lung. Similar to tumors of alveolar lineage at other locations, peribronchial tumors stain with SP-C but not CC10 antibody. The effects of Sluc20 alleles are additive because the number of peribronchial tumors in heterozygotes is intermediate. These findings show that tumor regionality in the mouse lung, which represents a novel level of lung tumor heterogeneity, is under specific genetic control. The identification of genes controlling lung tumor regionality will provide novel insights into the biology of lung tumors and potentially improve the possibilities of individualized prognosis and treatment in human lung cancer.

Mining the Epigenome for Methylated Genes in Lung Cancer

Lung cancer has become a global public health burden, further substantiating the need for early diagnosis and more effective targeted therapies. The key to accomplishing both these goals is a better understanding of the genes and pathways disrupted during the initiation and progression of this disease. Gene promoter hypermethylation is an epigenetic modification of DNA at promoter CpG islands that together with changes in histone structure culminates in loss of transcription. The fact that gene promoter hypermethylation is a major mechanism for silencing genes in lung cancer has stimulated the development of screening approaches to identify additional genes and pathways that are disrupted within the epigenome. Some of these approaches include restriction landmark scanning, methylation CpG island amplification coupled with representational difference analysis, and transcriptome-wide screening. Genes identified by these approaches, their function, and prevalence in lung cancer are described. Recently, we used global screening approaches to interrogate 43 genes in and around the candidate lung cancer susceptibility locus, 6q23-25. Five genes, TCF21, SYNE1, AKAP12, IL20RA, and ACAT2, were methylated at 14 to 81% prevalence, but methylation was not associated with age at diagnosis or stage of lung cancer. These candidate tumor suppressor genes likely play key roles in contributing to sporadic lung cancer. The realization that methylation is a dominant mechanism in lung cancer etiology and its reversibility by pharmacologic agents has led to the initiation of translational studies to develop biomarkers in sputum for early detection and the testing of demethylating and histone deacetylation inhibitors for treatment of lung cancer.

Smoking Out the Cholinergic Component in Lung Cancer

Smoking remains an important risk factor for lung cancer, and a clear association among single nucleotide polymorphisms in the chromosome 15q24/15q25.1 region and lung cancer susceptibility has been recently shown in three comprehensive wide genome association studies (1–3). In brief, although Hung et al. (1) reports that a strong susceptibility locus for lung cancer maps to nicotine acetylcholine receptor (nAChR) subunit genes, Thorgeirsson et al. (2), interestingly, identifies a common variant in the same nAChR cluster with an effect on (a) smoking quantity, (b) nicotine dependence, and (c) risk of lung cancer and peripheral arterial disease.Simultaneously, Amos et al. (3) concludes that a variation in the region containing nAChR genes contributes to the risk of developing lung cancer. In the analysis made by Burton (4), and recently reported in Lancet Oncology, the central role of smoking in lung cancer risk is matched with, and again underlined in light of the three reported wide genome association studies (1–3), focusing on similar candidate polymorphisms in the same genomic region.Although additional evidence is needed, the message that genes in this chromosomal region could interact directly with tobacco to cause lung cancer or to determine an increase in tobacco smoking dependency is very clear.More information on this relevant topic is available in the results reported by Lam et al. (5); in fact, they have identified differential gene expressions in non–small cell lung cancers with class-predictive significance: whereas nicotine exposure was significantly present at elevated levels of expression for the nicotinic subunit genes (CHRNA1, CHRNA5, and CHRNA7) shown. These data led researchers to the conclusion that nicotine receptor subunit genes could play an important role in the pathogenesis of bronchogenic carcinoma and may mediate the effects of nicotine addiction in lung cancer patients of different gender.Furthermore, up-regulation of the α7 nicotinic subunit gene was found in normal human bronchial epithelial cells upon exposure to nicotine (6) and in small cell lung cancer cell lines leading to increased proliferation (7). nAChRs were first implicated in the growth regulation of lung cancer when nicotine was found to stimulate DNA synthesis in human lung cancer cell lines and this was supported by subsequent identification that the receptor involved was nAChR α7 (8, 9).We have a longstanding interest in this topic, and in our previous studies, we have shown that nicotine exposure of non–small cell lung cancer cells induces an overexpression of the α7 nicotinic receptorial subunit and that the expression of α7-nAChR in human non–small cell lung cancer tissues was higher in smokers who developed squamous cell carcinoma compared to those with adenocarcinoma, as well as in smokers who were males compared with females (10).All these findings of functional acetylcholine receptors on lung epithelial cells and lung tumors raise the extremely important question of whether chronic exposure to nicotine could also participate in lung cancer pathogenesis. The matter is particularly relevant for current smokers who might feel protected by annual CT screening and abandon any attempt of quitting tobacco.If it is true that nicotine dependence induces nAChR's clustering into categories and influences lung cancer predisposition, nicotine very easily could act on lung tissue at a posttranscriptional and posttranslational level inducing differences in nAChR's expression and biological responses that might influence cancerogenesis downstream as well.All these findings strongly implicate the participation of the nonneuronal cholinergic system in lung cancer biology, and suggest screening for new therapy targeted at α7-nAChR.No potential conflicts of interest were disclosed.

Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1.

To identify risk variants for lung cancer, we conducted a multistage genome-wide association study. In the discovery phase, we analyzed 315,450 tagging SNPs in 1,154 current and former (ever) smoking cases of European ancestry and 1,137 frequency-matched, ever-smoking controls from Houston, Texas. For replication, we evaluated the ten SNPs most significantly associated with lung cancer in an additional 711 cases and 632 controls from Texas and 2,013 cases and 3,062 controls from the UK. Two SNPs, rs1051730 and rs8034191, mapping to a region of strong linkage disequilibrium within 15q25.1 containing PSMA4 and the nicotinic acetylcholine receptor subunit genes CHRNA3 and CHRNA5, were significantly associated with risk in both replication sets. Combined analysis yielded odds ratios of 1.32 (P < 1 x 10(-17)) for both SNPs. Haplotype analysis was consistent with there being a single risk variant in this region. We conclude that variation in a region of 15q25.1 containing nicotinic acetylcholine receptors genes contributes to lung cancer risk.

Promoter Methylation of Genes in and around the Candidate Lung Cancer Susceptibility Locus 6q23-25

Chromosomal aberrations associated with lung cancer are frequently observed in the long arm of chromosome 6. A candidate susceptibility locus at 6q23-25 for lung cancer was recently identified; however, no tumor suppressor genes inactivated by mutation have been identified in this locus. Genetic, epigenetic, gene expression, and in silico screening approaches were used to select 43 genes located in 6q12-27 for characterization of methylation status. Twelve (28%) genes were methylated in at least one lung cancer cell line, and methylation of 8 genes was specific to lung cancer cell lines. Five of the 8 genes with the highest prevalence for methylation in cell lines (TCF21, SYNE1, AKAP12, IL20RA, and ACAT2) were examined in primary lung adenocarcinoma samples from smokers (n = 100) and never smokers (n = 75). The prevalence for methylation of these genes was 81%, 50%, 39%, 26%, and 14%, respectively, and did not differ by smoking status or age at diagnosis. Transcription of SYNE1, AKAP12, and IL20RA was completely silenced by hypermethylation and could be restored after treatment with 5-aza-2-deoxycytidine. Significant associations were found between methylation of SYNE1 and TCF21, SYNE1 and AKAP12, and AKAP12 and IL20RA, indicating a coordinated inactivation of these genes in tumors. A higher prevalence for methylation of these genes was not associated with early-onset lung cancer cases, most likely precluding their involvement in familial susceptibility to this disease. Together, our results indicate that frequent inactivation of multiple candidate tumor suppressor genes within chromosome 6q likely contributes to development of sporadic lung cancer.

Identification of a Novel Tumor Suppressor Gene p34 on Human Chromosome 6q25.1

In this study, we observed loss of heterozygosity (LOH) in human chromosomal fragment 6q25.1 in sporadic lung cancer patients. LOH was observed in 65% of the 26 lung tumors examined and was narrowed down to a 2.2-Mb region. Single-nucleotide polymorphism (SNP) analysis of genes located within this region identified a candidate gene, termed p34. This gene, also designated as ZC3H12D, C6orf95, FLJ46041, or dJ281H8.1, carries an A/G nonsynonymous SNP at codon 106, which alters the amino acid from lysine to arginine. Nearly 73% of heterozygous lung cancer tissues with LOH and the A/G SNP also exhibited loss of the A allele. In vitro clonogenic and in vivo nude mouse studies showed that overexpression of the A allele exerts tumor suppressor function compared with the G allele. p34 is located within a recently mapped human lung cancer susceptibility locus, and association of the p34 A/G SNP was tested among these families. No significant association between the less frequent G allele and lung cancer susceptibility was found. Our results suggest that p34 may be a novel tumor suppressor gene involved in sporadic lung cancer but it seems not to be the candidate familial lung cancer susceptibility gene linked to chromosomal region 6q23-25.

Context-dependent cancer risk

A new study in mice shows that genetic variants underlying a previously mapped lung cancer susceptibility locus can have opposing effects on cancer risk depending on whether an oncogenic somatic mutation at the same locus subsequently arises in cis or in trans. These findings illustrate the complex interplay between genetic background and somatic events in contributing to cancer risk.

A functional switch from lung cancer resistance to susceptibility at the Pas1 locus in Kras2LA2 mice

Pulmonary adenoma susceptibility 1 (Pas1) is the major mouse lung cancer susceptibility locus on chromosome 6 (ref. 1). Kras2 is a common target of somatic mutation in chemically induced mouse lung tumors and is a candidate Pas1 gene. M. spretus mice (SPRET/Ei) carry a Pas1 resistance haplotype for chemically induced lung tumors. We demonstrate that the SPRET/Ei Pas1 allele is switched from resistance to susceptibility by fixation of the parental origin of the mutant Kras2 allele. This switch correlates with low expression of endogenous Kras2 in SPRET/Ei. We propose that the Pas1 modifier effect is due to Kras2, and that a sensitive balance between the expression levels of wild-type and mutant alleles determines lung tumor susceptibility. These data demonstrate that cancer predisposition should also be considered in the context of somatic events and could have major implications for the design of human association studies to identify cancer susceptibility genes.

Genetic Susceptibility to Lung Cancer

Lung cancer is the most common cause of cancer death in the world. Environmental factors, particularly cigarette smoking, are of paramount importance in determining lung cancer risk. Lung cancer and chronic obstructive lung disease are likely to share some common susceptibility genes, but these have not yet been identified. Evidence from various sources, including twin studies, segregation analyses, and case-control studies, support a heritable component to lung cancer risk in humans. As with many common diseases, susceptibility genes for lung cancer appear to be of low penetrance. Family studies of lung cancer susceptibility using linkage analysis and positional cloning have not been reported; however, a consortium is currently carrying out such studies, and results may soon be available. Association studies support lung cancer risk being partly determined by genes that control the metabolism of carcinogens found in tobacco smoke, with the heritable effects being most prominent in smokers with shorter smoking histories. Of these, the CYP1A1 and GSTM1 polymorphisms have been most consistently implicated. In the mouse, an oligonucleotide repeat polymorphism within an intron of the Ki-ras oncogene is the major lung cancer susceptibility locus; however this locus is not clearly involved in susceptibility to lung cancer in the human. Further understanding of the genetic basis of lung cancer susceptibility has many important implications, ranging from targeting prevention and screening efforts to the most highly susceptible population to developing novel chemopreventive therapies.

A strong candidate gene for the Papg1 locus on mouse chromosome 4 affecting lung tumor progression.

Lung cancer is the leading cause of cancer death among both men and women, accounting for more than 28% of all cancer deaths. In fact, more people die of lung cancer than of colon, breast, and prostate cancers combined. Although lung cancer is largely induced by smoking, there is strong evidence for genetic susceptibility and gene-environment interactions in the development of lung cancer. Inbred mouse models offer an effective means of identifying candidate lung cancer susceptibility loci since genetic heterogeneity and enormous variation in exposure levels to environmental agents make it difficult to identify lung cancer susceptibility loci in humans. Papg-1 (pulmonary adenoma progression 1) was previously mapped to a region on mouse chromosome 4. This locus contains a candidate gene, Cdkn2a also referred to as Ink4a/Arf, which dually encodes two established tumor suppressors p16(INK4a) and ARF. Cdkn2a became a primary candidate for Papg-1 for two reasons: (1) two haplotypes of mouse Cdkn2a were found to segregate with differential genetic susceptibility to lung tumor progression in mice; and (2) in vitro studies showed that the p16(INK4a) allele from the BALB/cJ mouse had a significantly decreased ability to bind and inhibit CDK6 and to suppress cell growth when compared with the p16(INK4a) allele from the A/J mouse. Here, we report that mice with a heterozygous deficiency for the A/J Cdkn2a allele were significantly more susceptible to lung tumor progression than mice with a heterozygous deficiency for a BALB/cJ Cdkn2a allele, when compared to their respective wild type mice. These results offer strong evidence that naturally occurring variation of p16(INK4a) influences susceptibility to enhance lung tumor progression making it a strong candidate for the lung tumor progression locus, Papg-1.

Evidence for age-specific genetic relative risks in lung cancer.

Recent studies of familial aggregation suggest that family history of lung cancer among first-degree relatives is associated with increased risk for early-onset, but not late-onset, lung cancer. To assess whether this could be explained by variability in genetic relative risk across age, segregation analysis was performed on the Louisiana Lung Cancer Dataset. This data set consisted of 337 probands who died of lung cancer between 1976 and 1979 and their first-degree relatives. A variation of the Cox proportional hazards model was used that allowed estimation of age- and genotype-specific incidence rates, from which the authors obtained estimates of age-specific genetic relative risks. The best-fitting model included an autosomal dominant locus (allele frequency, 0.043), with carrier-to-noncarrier relative risks that exceeded 100 for ages less than 60 years and declined monotonically to 1.6 by age 80. The hypothesis of proportional genetic relative risk across age was rejected (p = 0.009). The estimated proportion of persons with lung cancer who carry the high-risk allele exceeds 90% for cases with onset at age 60 years or less and decreases to approximately 10% for cases with onset at age 80 years or older. These findings support previous evidence of a major susceptibility locus for lung cancer and suggest that linkage studies should preferentially recruit young lung cancer cases and their relatives.

Pas1 is a common lung cancer susceptibility locus in three mouse strains.

Inherited predisposition to lung cancer is a phenotypic trait shared by different mouse inbred strains that show either a high or an intermediate predisposition. Other strains are instead genetically resistant. The Pas1 locus is the major determinant of lung cancer predisposition in the A/J strain (Gariboldi et al. 1993). To define the determinants of susceptibility to lung tumorigenesis in the highly susceptible SWR/J and in the intermediately susceptible BALB/c mice, we analyzed (BALB/c x SWR/J)F2 and (BALB/c x C3H/He)F2 crosses by genetic linkage experiments. The present results provide unequivocal evidence that the same Pas1/+ allele that leads to lung cancer predisposition is shared by A/J, SWR/J, and BALB/c strains. The intermediate susceptibility of the BALB/c strain would result by interaction of Pas1 locus with lung cancer resistance loci.