The TERT-CLPTM1L lung cancer susceptibility variant associates with higher DNA adduct formation in the lung

The updated relationship between the cleft‑lip and palate transmembrane protein‑1‑like rs401681 and lung cancer risk: A systematic review and meta‑analysis

Currently, the role of cleft-lip and palate transmembrane protein-1-like (CLPTM1L) rs401681 in various tumor types, particularly lung cancer, has garnered significant attention. However, the findings across studies have shown discrepancies. The aim of the present meta-analysis was to provide a more nuanced understanding of the involvement of CLPTM1L rs401681 in lung cancer development. Several electronic databases were systematically searched, including PubMed, Cochrane Library, Embase, Medline, Wanfang, Google Scholar and Chinese National Knowledge Infrastructure. Odds ratios (ORs) and 95% confidence intervals (CIs) were synthesized using random-effects models. Heterogeneity of included studies was assessed using the I2 statistic and Q test. Sensitivity analysis was conducted to evaluate the stability of overall estimates. Moreover, Egger's test was utilized to detect potential publication bias. The collective ORs indicated a significant association between the CLPTM1L rs401681 polymorphism and susceptibility to lung cancer across various genetic comparisons. These encompass allele T vs. allele C (OR=0.93, 95% CI=0.88-0.99, P<0.001), TT + CT vs. CC (OR=0.91, 95% CI=0.87-0.96, P<0.001), TT vs. CC + CT (OR=0.88, 95% CI=0.80-0.96, P<0.001), TT vs. CC (OR=0.84, 95% CI=0.75-0.94, P<0.001) and CT vs. CC (OR=0.84, 95% CI=0.75-0.94, P<0.001). Examination through statistical Q test and I2 statistic revealed pronounced heterogeneity across four genetic comparisons (allele T vs. allele C, TT + CT vs. CC, TT vs. CC and CT vs. CC). Ethnical distinctions emerged as the primary, if not exclusive, sources of the significant heterogeneity. Upon stratification by ethnicity, a notable reduction in heterogeneity was discernible within the Caucasian demographic. However, heterogeneity persisted within the Asian population. Furthermore, lung cancer risks were statistically significantly decreased for individuals possessing allele T through all genetic comparisons within Caucasians; whereas among Asians, significant reduction was observed solely in the TT vs. CC comparison. The present meta-analysis uncovers a significant association between the CLPTM1L rs401681 polymorphism and altered susceptibility to lung cancer.

Association of rs401681 (C > T) and rs402710 (C > T) polymorphisms in the CLPTM1L region with risk of lung cancer: a systematic review and meta-analysis

Although many genome-wide association studies (GWAS) have confirmed the negative associations between rs401681[T] / rs402710[T] in the Cleft lip and cleft palate transmembrane protein 1 (CLPTM1L) region and lung cancer (LC) susceptibility in Caucasian and Asian populations, some other studies haven't found these negative associations. The purpose of this study is to clarify the associations between them and LC, as well as the differences in these associations between patients of different ethnicities (Caucasians and Asians), LC subtypes and smoking status. Relevant literatures published before July 7, 2023 in PubMed, EMbase, Web of Science, MEDLINE were searched through the Internet. Statistical analysis of data was performed in Revman 5.3, including drawing forest plots, funnel plots and so on. Sensitivity and publication bias were performed in Stata 14.0. TSA software was performed for the trial sequential analysis (TSA) tests to assess the stability of the results. Registration number: CRD42023407890. A total of 41 literatures (containing 44 studies: 16 studies in Caucasians and 28 studies in Asians) were included in this meta-analysis, including 126476 LC patients and 191648 healthy controls. The results showed that the T allele variants of rs401681 and rs402710 were negatively associated with the risk of LC (rs401681[T]: [OR] = 0.87, 95% CI [0.86, 0.88]; rs402710[T]: [OR] = 0.88, 95% CI [0.86, 0.89]), and the negative associations were stronger in Caucasians than in Asians (Subgroup differences: I2 > 50%). In LC subtypes, the rs401681[T] was negatively associated with the risk of Non-small-cell lung carcinoma (NSCLC), Lung adenocarcinoma (LUAD) and Lung squamous cell carcinoma (LUSC) (P < 0.05), and these negative associations were stronger in Caucasians than in Asians (Subgroup differences: I2 > 50%). The rs402710[T] was negatively associated with the risk of NSCLC, LUAD and LUSC (P < 0.05), and these negative associations in Caucasians were the same as in Asians (Subgroup differences: I2 < 50%). The rs401681[T] was negatively associated with the risk of LC in both smokers and non-smokers (P < 0.05), and the negative association for smokers equals to that of non-smokers (Subgroup differences: P = 0.25, I2 = 24.2%). In LC subtypes, the rs401681[T] was negatively associated with the risks of NSCLC and LUAD in both Caucasian smokers and Asian non-smokers (P < 0.05). The rs402710[T] was negatively associated with the risk of LC in both smokers and non-smokers (P < 0.05), and there was no difference in the strength of this negative risk association between them in Caucasians (Subgroup differences: I2 = 0%). In Asians, this negative association was found to be predominantly among smokers ([OR] = 0.80, 95%CI [0.65, 0.99]). In LC subtypes, the rs402710[T]was negatively associated with the risk of NSCLC in non-smokers, and this negative association was found to be predominantly among non-smokers in Asians ([OR] = 0.75, 95%CI [0.60, 0.94]). The T allele variants of rs401681 and rs402710 are both negatively associated with the risk of developing LC, NSCLC (LUAD, LUSC) in the Caucasian and Asian populations, and the negative associations with the risk of LC are higher in Caucasians. Smoking is an important risk factor for inducing the rs401681 and rs402710 variants and causes LC development in both populations. Other factors like non-smoking are mainly responsible for inducing the development of NSCLC in Asians, and is concentrated in LUAD among Asian non-smoking women.

A Large-Scale Genome-Wide Gene-Gene Interaction Study of Lung Cancer Susceptibility in Europeans With a Trans-Ethnic Validation in Asians

INTRODUCTION

Although genome-wide association studies have been conducted to investigate genetic variation of lung tumorigenesis, little is known about gene-gene (G × G) interactions that may influence the risk of non-small cell lung cancer (NSCLC).

METHODS

Leveraging a total of 445,221 European-descent participants from the International Lung Cancer Consortium OncoArray project, Transdisciplinary Research in Cancer of the Lung and UK Biobank, we performed a large-scale genome-wide G × G interaction study on European NSCLC risk by a series of analyses. First, we used BiForce to evaluate and rank more than 58 billion G × G interactions from 340,958 single-nucleotide polymorphisms (SNPs). Then, the top interactions were further tested by demographically adjusted logistic regression models. Finally, we used the selected interactions to build lung cancer screening models of NSCLC, separately, for never and ever smokers.

RESULTS

With the Bonferroni correction, we identified eight statistically significant pairs of SNPs, which predominantly appeared in the 6p21.32 and 5p15.33 regions (e.g., rs521828C6orf10 and rs204999PRRT1, ORinteraction = 1.17, p = 6.57 × 10-13; rs3135369BTNL2 and rs2858859HLA-DQA1, ORinteraction = 1.17, p = 2.43 × 10-13; rs2858859HLA-DQA1 and rs9275572HLA-DQA2, ORinteraction = 1.15, p = 2.84 × 10-13; rs2853668TERT and rs62329694CLPTM1L, ORinteraction = 0.73, p = 2.70 × 10-13). Notably, even with much genetic heterogeneity across ethnicities, three pairs of SNPs in the 6p21.32 region identified from the European-ancestry population remained significant among an Asian population from the Nanjing Medical University Global Screening Array project (rs521828C6orf10 and rs204999PRRT1, ORinteraction = 1.13, p = 0.008; rs3135369BTNL2 and rs2858859HLA-DQA1, ORinteraction = 1.11, p = 5.23 × 10-4; rs3135369BTNL2 and rs9271300HLA-DQA1, ORinteraction = 0.89, p = 0.006). The interaction-empowered polygenetic risk score that integrated classical polygenetic risk score and G × G information score was remarkable in lung cancer risk stratification.

CONCLUSIONS

Important G × G interactions were identified and enriched in the 5p15.33 and 6p21.32 regions, which may enhance lung cancer screening models.

CLPTM1L Is a Novel Putative Oncogene Promoting Tumorigenesis in Oral Squamous Cell Carcinoma

This study aimed to explore the function of CLPTM1L in oral squamous cell carcinoma and mechanism of tumorigenesis. The expression of CLPTM1L was detected by immunohistochemistry. The localization in cells was detected by immunofluorescence. Cell invasion, proliferation, and migration were detected by transwell, CCK-8 and scratch-wound test. The possible characteristics of CLPTM1L were analysed in TCGA, GO, KEGG and String databases. IHC revealed that the expression of CLPTM1L in 92 cases of OSCC tissues was significantly higher (P < 0.01) than 29 cases of normal oral epithelium tissues. The expression of CLPTM1L was significantly higher in oral squamous cell carcinoma in TCGA database. CLPTM1L expression was not significantly correlated with the patients’ clinical parameters. High expression of CLPTM1L was associated with worse prognosis. Cox regression analysis demonstrated that the CLPTM1L expression was the significant risk factor. CLPTM1L was mainly localized in the perinuclear cytoplasm. The vitro studies revealed that the knockdown of CLPTM1L suppressed invasion, proliferation and migration. CLPTM1L related genes were enriched in protein processing in the endoplasmic reticulum, protein folding, endoplasmic reticulum formation, N-glycan biosynthesis, and protein hydroxylation. Highly expressed CLPTM1L may contribute to a poor prognosis and increase invasion, proliferation and migration of oral squamous cell carcinoma. CLPTM1L may play an important role in tumorgenesis and would be a valuable target gene for the treatment of oral squamous cell carcinoma.

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.

Association of strong risk of hTERT gene polymorphic variants to malignant glioma and its prognostic implications with respect to different histological types and survival of glioma cases

BACKGROUND

Germline genetic variants of human telomerase reverse transcriptase (hTERT) are known to predispose for various malignancies, including glioma. The present study investigated genetic variation of hTERT T/G (rs2736100) and hTERT G/A (rs2736098) with respect to glioma risk.

METHODS

Confirmed cases (n = 106) were tested against 210 cancer-free healthy controls by the polymerase chain reaction-restriction fragment length polymorphism technique for genotyping.

RESULTS

Homozygous variant 'GG' genotype of rs2736100 frequency was > 4-fold significantly different in cases versus controls (39.6% 17.2%; p < 0.0001). Furthermore, variant 'G' allele was found to be significantly associated with cases (0.5 versus 0.2 in controls; p < 0.0001). Homozygous variant rs2736098 'AA' genotype (35.8% versus 23.8%) and allele 'A' (0.49 versus 0.34) showed a marked significant difference in cases and controls, respectively (p < 0.05). In hTERT rs2736100, the GG genotype significantly presented more in higher grades and GBM (p < 0.0001). Furthermore, the GG variant of hTERT rs2736100 had a poor probability with respect to the overall survival of patients compared to TG and TT genotypes (log rank p = 0.03). Interestingly, two haplotypes of hTERT rs2736100/rs2736098 were identified as GG and GA that conferred a > 3- and 5-fold risk to glioma patients respectively, where variant G/A haplotype was observed to have the highest impact with respect to glioma risk (p < 0.0001).

CONCLUSIONS

The results of the present study indicate that hTERT rs2736098 and rs2736100 variants play an important role in conferring a strong risk of developing glioma. Furthermore, hTERT rs2736100 GG variant appears to play a role in the bad prognosis of glioma patients. Haplotypes GG and GA could prove to be vital tools for monitoring risk in glioma patients.

A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck

To identify genetic variants for risk of squamous cell carcinoma of the head and neck (SCCHN), we conducted a two-phase genome-wide association study consisting of 7,858,089 SNPs in 2,171 cases and 4,493 controls of non-Hispanic white, of which, 434,839 typed and 7,423,250 imputed SNPs were used as the discovery. SNPs with P < 1 × 10-3 were further validated in the OncoArray study of oral and pharynx cancer (5,205 cases and 3,232 controls of European ancestry) from databases of Genotypes and Phenotypes. Meta-analysis of the discovery and replication studies identified one novel locus 6p22.1 (P = 2.96 × 10-9 for the leading rs259919) and two cancer susceptibility loci 6p21.32 (rs3135001, HLA-DQB1) and 6p21.33 (rs1265081, CCHCR1) associated with SCCHN risk. Further stratification by tumor site revealed four known cancer loci (5p15.33, 6p21.32, 6p21.33, and 2p23.1) associated with oral cavity cancer risk and oropharyngeal cancer risk, respectively. In addition, one novel locus 18q22.2 (P = 2.54 × 10-9 for the leading SNP rs142021700) was identified for hypopharynx and larynx cancer risk. For SNPs in those reported or novel loci, we also performed functional annotations by bioinformatics prediction and expression quantitative trait loci analysis. Collectively, our identification of four reported loci (2p23.1, 5p15.33, 6p21.32, and 6p21.33) and two novel loci (6p22.1 and 18q22.2) for SCCHN risk highlight the importance of human leukocyte antigen loci for oropharyngeal cancer risk, suggesting that immunologic mechanisms are implicated in the etiology of this subset of SCCHN. SIGNIFICANCE: Two novel risk loci for SCCHN in non-Hispanic white individuals highlight the importance of immunologic mechanism in the disease etiology.

CHRNA5 rs16969968 polymorphism is associated with lung cancer risk: A meta-analysis

OBJECTIVE

To evaluate the genetic association between rs16969968 and lung cancer risk by meta-analysis.

DATA SOURCE

We searched eligible studies from MEDLINE, Web of Science and EMBASE up to Dec, 2017.

STUDY SELECTION

Association studies concerning rs16969968 and lung cancer risk were included. We assessed the association strength between this polymorphism and risk of lung cancer by calculating odds ratios (OR) and 95% confidence interval (95%CI).

RESULTS

A total of 26 data sets comprising 30 772 lung cancers and 90 954 controls were included. rs16969968 was found to be associated with lung cancer risk in population of European ancestry in all models (A vs. G: OR = 1.30, 95%CI 1.27-1.33, P < 0.001; AA + GA vs. GG: OR = 1.38, 95%CI 1.33-1.43, P < 0.001; AA vs. GG + GA: OR = 1.45, 95%CI 1.38-1.53, P < 0.001), consistent with previous genome-wide association study (GWAS). However, no association was observed in Asians (A vs. G: OR = 1.19. 95%CI 0.95-1.49, P = 0.131). The minor allele A may increase the risk of lung cancer in both smokers (OR = 1.33, 95%CI 1.29-1.39, P < 0.001) and nonsmokers (OR = 1.25, 95%CI 1.12-1.39, P < 0.001). There was no obvious publication bias in all analyses.

CONCLUSIONS

Our analysis provided more evidence that rs16969968 is a susceptibility locus of lung cancer in the Caucasians and that it may be not associated with the risk in the Asians.

Association of TERT-CLPTM1L and 8q24 Common Genetic Variants with Gallbladder Cancer Susceptibility and Prognosis in North Indian Population

Gallbladder carcinoma (GBC) is one of the common malignancy of the biliary tract. Several genome wide and candidate gene studies have reported associations between multiple cancer types and single-nucleotide polymorphisms on 5p15.33 and 8q24.21 loci. However, predisposition potential of these genetic variants has not been assessed in GBC. We performed the present study to assess the potential of five polymorphisms on 5p15.33 and one on 8q24.21 locus in GBC risk and treatment response in patients undergoing chemoradiotherapy. We extracted genomic DNA from peripheral blood and genotyped selected SNPs using TaqMan allelic discrimination assays in 523 GBC cases and 274 controls from the north-Indian population. Statistical tests were performed to assess the association of selected common genetic variants with gallbladder cancer susceptibility and prognosis. Binary logistic regression analysis showed significant association of TERT rs2736100C > A [OR(CI) = 0.690(0.515-0.924), p value = 0.013], CLPTM1L rs401681C > T [OR(CI) = 0.586(0.405-0.847), p value = 0.004], and CASC8 rs6983267G > T [OR(CI) = 1.629(1.215-2.186), p value = 0.001] with GBC risk. Further, using multivariate logistic regression, we observed that haplotype CLPTM1L Crs401681Crs31489 TERT Trs2853676Ars2736100 MIR4457 Grs4635969 [OR(CI) = 7.52 (1.79-31.52), p value = 0.0064] is significantly associated with poor treatment response. In survival analysis, Kaplan-Meier survival curves showed significantly poor survival and COX regression suggested significantly higher hazard ratio in TT genotype carriers of CASC8 rs6983267 [OR(CI) = 4.28(1. 07-17.10), p value = 0.040] as compared to major allele and heterozygous (GG+GT) genotypes in metastatic GBC cases. The study revealed that 5p15.33 and 8q24.21 genetic variants significantly influence GBC risk and treatment response in north-Indian population.

Evaluating the effect of nicotinic cholinergic receptor genes on the risk of nonsyndromic cleft lip with or without cleft palate

OBJECTIVE

Multiple studies have suggested nonsyndromic cleft lip with or without cleft palate (NSCL/P), and lung cancer may have common genetic etiology. Previous studies have showed genetic variants in nicotinic cholinergic receptor genes (CHRNs) may influence risk of lung cancer. We aimed to explore the effect of CHRNs on risk of NSCL/P considering gene-gene (GxG) interaction for these genes.

SUBJECTS AND METHODS

We selected 120 markers in 14 CHRNs to test for GxG interaction using 806 Chinese case-parent trios recruited from an international consortium established for a GWAS of oral clefts.

RESULTS

Totally, two pairs of SNPs yielded significant GxG interactions after Bonferroni correction (rs935865 and rs2337980 with p = 4.04 × 10^-5 , rs2741335 and rs3743077 with p = 4.80 × 10^-4 ), and these pairwise interactions were confirmed in permutation tests. In addition, the relative risk (RR) of the putative interaction between rs935865 and rs2337980 was 1.10 (95% CI: 0.92~1.31).

CONCLUSIONS

While the single SNP association and the gene-environment interaction analysis of 14 CHRN genes yielded no signal, this study did demonstrate the importance of considering potential GxG interaction for exploring etiology of NSCL/P. This study suggests an important role for particular combinations of SNPs in CHRN genes in influencing risk to NSCL/P, which needs further study.

A Decade of GWAS Results in Lung Cancer

Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."

CLPTM1L gene rs402710 (C > T) and rs401681 (C > T) polymorphisms associate with decreased cancer risk: a meta-analysis

Cleft lip and palate transmembrane 1-like (CLPTM1L) gene rs402710 (C > T) and rs401681 (C > T) polymorphisms have been widely studied for their potential relation to cancer risk, but studies have produced conflicting results. To systematically evaluate the association between these two polymorphisms and overall cancer risk, we conducted a comprehensive meta-analysis on all relevant articles found in the PubMed and EMBASE databases published prior to May 1, 2017. There were 26 articles with 28 studies, including 30,770 cases and 34,089 controls, for the rs402710 polymorphism and 38 articles with 48 studies, including 67,849 cases and 328,226 controls, for the rs401681 polymorphism. The pooled results indicated that both rs402710 and rs401681 polymorphisms are significantly associated with decreased overall cancer risk. In our stratification analysis, a significant association of the rs402710 polymorphism with lung and bladder cancers was identified among Asian and Caucasian populations in both hospital-based and population-based studies. The rs401681 polymorphism was significantly associated with a decreased risk of lung cancer, bladder cancer, and basal cell carcinoma in Asians and in hospital-based studies. CLPTM1L gene rs402710 and rs401681 polymorphisms thus have a protective association with various types of cancer, especially lung cancer among Asians.

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.

Lung adenocarcinoma: from molecular basis to genome-guided therapy and immunotherapy

Although adenocarcinoma (ADC) is the most frequent lung cancer, its diagnosis is often late, when the local invasion is important and/or the metastases have already appeared. Therefore, the mortality at 5 years is still very high, ranging from 51% to 99%, depending on the stage. The implementation of different molecular techniques has allowed genomic studies even in relatively small histological samples such as obtained with non-invasive or minimally invasive techniques, facilitating a better phenotyping of lung ADC. Thus, current classification differentiates between preinvasive lesions (atypical adenomatous hyperplasia and in situ ADC), minimally invasive ADC (MIA) and invasive ADC. 'Field cancerization' is a concept that refers to progressive loco-regional changes occurring in tissues exposed to carcinogens, due to the interaction of the latter with a predisposing genetic background and an appropriate tissue microenvironment. Somatic genetic alterations, including mutations but also other changes, are necessary for oncogenesis, being especially frequent in lung ADC. Changes in the epidermal growth factor receptor (EGFR) gene, Kirsten rat sarcoma viral oncogene (KRAS), v-Raf murine sarcoma viral oncogene homolog B (BRAF), gene encoding neurofibromin (NF1), anaplastic lymphoma kinase (ALK) and ROS1 are the main genes that suffer alterations in the tumors of patients with ADC. Molecular profiling of these tumors allows more targeted treatments through two distinct strategies, genome-guided therapy and immunotherapy. The former, targets the aberrant pathways secondary to the genomic alteration, whereas the latter may be based on the administration of antibodies [such as those against cytotoxic T-lymphocyte antigen 4 (CTLA-4) or the programmed cell death ligand 1/protein 1 pathway (PD-L1/PD-1)] or the stimulation of the patient's own immune system to produce a specific response. These strategies are obtaining better results in selected ADC patients.

Fine mapping of chromosome 5p15.33 identifies novel lung cancer susceptibility loci in Han Chinese

Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer Genome wide association studies (GWASs) with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations. These were rs10054203 in TERT (resequencing: OR = 1.69, p = 2.70 × 10^-4 ; validation: OR = 1.34, p = 2.10 × 10^-23 for Asian, and OR = 1.09, p = 6.00 × 10^-3 for European), and rs397640 in CLPTM1L (resequencing: OR = 0.37, p = 1.19 × 10^-4 ; validation: OR = 0.75, p = 5.89 × 10^-8 for Asian, and OR = 0.90, p = 2.40 × 10^-2 for European). Expression quantitative trait loci analysis showed the risk allele (C) of rs10054203 was significantly associated with lower mRNA expression of CTD-2245Ef15.3 (p = 0.019) and Tubulin Polymerization-Promoting Protein (TPPP, p = 0.031) in 167 lung tissues. In conclusion, in this largest and first resequencing-based fine-mapping analysis of 5p15.33 region in Han Chinese, we identified two novel variants associated with lung cancer susceptibility. Further validation studies and functional work is required to confirm the roles of the newly discovered variants.

Prognostic significance of CLPTM1L expression and its effects on migration and invasion of human lung cancer cells

BACKGROUND

CLPTM1L (Cleft lip and palate transmembrane protein 1-like) has been previously shown to be overexpressed in lung cancer and is involved in regulating cisplatin sensitivity. In this study, we assessed the relationship between CLPTM1L expression and prognosis of lung cancer in patients and explored its role in regulating cell migration and invasion.

METHODS

Immunohistochemistry was used to examine CLPTM1L expression levels on a tissue microarray containing 73 sets of human lung cancer specimens with adjacent normal tissue. The correlation between CLPTM1L expression and patient survival was analysed by the Kaplan-Meier method. In addition, CLPTM1L-knockdown lung cells were used to investigate the effect of CLPTM1L on cell migration and invasion in vitro.

RESULTS

The results of immunohistochemical analysis showed that CLPTM1L was overexpressed in lung cancer tissues compared with adjacent normal tissues. Kaplan-Meier analyses revealed that patients with high CLPTM1L expression showed poorer survival than those with low CLPTM1L expression. In addition, in vitro studies revealed that the knockdown of CLPTM1L expression in 95-D lung cancer cells suppressed cell migration and invasion. Further, the loss of CLPTM1L resulted in decreased matrix metalloproteinase-2 (MMP-2) expression in these cells.

CONCLUSION

Our data demonstrate that CLPTM1L overexpression can predict poor prognosis in patients with lung cancer and suggest that CLPTM1L might be associated with the regulation of cell migration and invasion.

CLPTM1L polymorphism as a protective factor for lung cancer: a case-control study in southern Chinese population

Variants of the cleft lip and palate trans-membrane 1 like (CLPTM1L) gene, located on chromosome 5p15.33, were previously determined to influence lung cancer susceptibility. Here, we performed a case-control study to examine the potential association of CLPTM1L single nucleotide polymorphisms (SNPs) with lung cancer in a Chinese Han population. We selected four SNPs in the CLPTM1L gene that were previously reported to be associated with lung cancer. Odds ratios (ORs) and 95 % confidence intervals (CIs) were calculated to estimate the strength of the relationship between each CLPTM1L SNP and lung cancer risk. Allelic model analysis revealed that the minor alleles of all four SNPs were significantly associated with decreased lung cancer risk. Similar significant results were detected using genetic model analysis. In addition, we observed a protective effect of haplotype "TT" in the CLPTM1L gene. Our results verified that certain CLPTM1L polymorphisms are protective factors against lung cancer in a southern Chinese Han population and may be potential diagnostic and molecular markers for lung cancer patients.

Mutations in TP53 increase the risk of SOX2 copy number alterations and silencing of TP53 reduces SOX2 expression in non-small cell lung cancer

Background

Amplifications of the transcription factor, SRY (sex determining region Y)-box 2 (SOX2), are common in non-small cell lung cancer (NSCLC). SOX2 signaling is important in maintaining the stem cell-like phenotype of cancer cells and contributes to the pathogenesis of lung cancer. TP53 is known to inhibit gene amplifications and to repress many stem cell-associated genes following DNA damage. The aim of this study was to investigate if TP53 mutational status affected SOX2 copy number variation and gene expression in early-stage NSCLC patients; moreover, to assess if TP53 regulates SOX2 expression in human lung cancer cells.

Methods

258 early-stage lung cancer patients were included in the study. Exons 4–9 in the TP53 gene were sequenced for mutations in tumor tissues. SOX2 copy number as well as TP53 and SOX2 gene expression were analyzed in tumor and in adjacent non-tumorous tissues by qPCR. TP53 and SOX2 were silenced using gene-specific siRNAs in human lung adenocarcinoma A427 cells, and the expression of TP53, SOX2 and subset of selected miRNAs was analyzed by qPCR. The odds ratios (ORs) for associations between copy number variation and lung cancer were estimated by conditional logistic regression, and the correlation between gene status and clinicopathological characteristics was assessed by Chi-square or Fisher’s exact test. Gene expression data was analyzed using nonparametric Mann–Whitney test.

Results

TP53 mutations were associated with an increased risk of acquiring a SOX2 copy number alteration (OR = 2.08, 95 % CI: 1.14–3.79, p = 0.017), which was more frequently occurring in tumor tissues (34 %) than in adjacent non-tumorous tissues (3 %). Moreover, SOX2 and TP53 expression levels were strongly correlated in tumor tissues. In vitro studies showed that a reduction in TP53 was associated with decreased SOX2 expression in A427 cells. Furthermore, TP53 knockdown reduced the miRNA hsa-miR-145, which has previously been shown to regulate SOX2 expression.

Conclusions

TP53 signaling may be important in the regulation of SOX2 copy number and expression in NSCLC tumors, and the miRNA hsa-miR-145-5p may be one potential driver. This prompts for further studies on the mechanisms behind the TP53-induced regulation of SOX2 expression and the possible importance of hsa-miR-145 in lung cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-016-2061-3) contains supplementary material, which is available to authorized users.

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.

Increased risk of developing lung cancer in Asian patients carrying the TERT rs2736098 G>A polymorphism: evidence from 3,354 cases and 3,518 controls

BACKGROUND

The association between telomerase reverse transcriptase (TERT) rs2736098 G>A and risk of lung cancer (LC) remains inconclusive. To explore the association more precisely, we performed a comprehensive search and conducted a meta-analysis on all eligible case-control studies involving 3,354 cases and 3,518 controls.

METHODS

The 95% confidence interval (95% CI) and the pooled odds ratio (OR) were calculated using a random or fixed effect model. Publication bias, heterogeneity, and sensitivity analysis were also explored.

RESULTS

All studies were case-control studies on LC in patients of Asian descent, consisting of one Korean study and five Chinese studies. Overall, the variant A allele of TERT rs2736098 G>A was found to significantly increase the risk of LC in all genetic models (GA vs GG: OR =1.13, 95% CI =1.02-1.25, P=0.017; AA vs GG: OR =1.78, 95% CI =1.53-2.07, P<0.001; GA/AA vs GG: OR =1.25, 95% CI =1.14-1.38, P<0.001; AA vs

GA/GG

OR =1.66, 95% CI =1.45-1.92, P<0.001). In the subgroup analysis, significant associations were found in Chinese group and hospital-based studies. Different genotype test methods showed no influence on the final results.

CONCLUSION

Our study identified that TERT rs2736098 G>A polymorphism significantly increased the risk of LC in Asian populations.

Genetic Polymorphism, Telomere Biology and Non-Small Lung Cancer Risk

Recent genome-wide association studies (GWAS) have identified a number of chromosomal regions associated with the risk of lung cancer. Of these regions, single-nucleotide polymorphisms (SNPs), especially rs2736100 located in the telomerase reverse transcriptase (TERT) gene show unique and significant association with non-small cell lung cancer (NSCLC) in a few subpopulations including women, nonsmokers, East Asians and those with adenocarcinoma. Recent studies have also linked rs2736100 with a longer telomere length and lung cancer risk. In this review, we seek to summarize the relationship between these factors and to further link the underlying telomere biology to lung cancer etiology. We conclude that genetic alleles combined with environmental (e.g., less-smoking) and physiological factors (gender and age) that confer longer telomere length are strong risk factors for NSCLC. This linkage may be particularly relevant in lung adenocarcinoma driven by epidermal growth factor receptor (EGFR) mutations, as these mutations have also been strongly linked to female gender, less-smoking history, adenocarcinoma histology and East Asian ethnicity. By establishing this connection, a strong argument is made for further investigating of the involvement of these entities during the tumorigenesis of NSCLC.

Meta-analysis of the association between the rs8034191 polymorphism in AGPHD1 and lung cancer risk

BACKGROUND

Possible associations between the single nucleotide polymorphism (SNP) rs8034191 in the aminoglycosidephosphotransferase domain containing 1 (AGPHD1) gene and lung cancer risk have been studied by many researchers but the results have been contradictory.

MATERIALS AND METHODS

A computerized search for publications on rs8034191 and lung cancer risk was performed. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association between rs8034191 and lung cancer risk with 13 selected case-control studies. Sensitivity analysis, test of heterogeneity, cumulative meta-analysis, and assessment of bias were also performed.

RESULTS

A significant association between rs8034191 and lung cancer susceptibility was found using the dominant genetic model (OR=1.344, 95% CI: 1.285-1.406), the additive genetic model (OR=1.613, 95% CI: 1.503-1.730), and the recessive genetic model (OR=1.408, 95% CI: 1.319-1.503). Moreover, an increased lung cancer risk was found with all genetic models after stratification of ethnicity.

CONCLUSIONS

The association between rs8034191 and lung cancer risk was significant using multiple genetic models, suggesting that rs8034191 is a risk factor for lung cancer. Further functional studies of this polymorphism and lung cancer risk are warranted.

Systematical analyses of variants in CTCF-binding sites identified a novel lung cancer susceptibility locus among Chinese population

Genome-wide association studies identified genetic susceptibility variants mostly lie outside of protein-coding regions. It suggested variants located at transcriptional regulatory region should play an important role in cancer carcinogenesis including lung cancer. In the present study, we systematically investigated the associations between the variants in the binding sites of an extensive transcription factor CTCF and lung cancer risk in Chinese population. A two-stage case-control design was conducted to evaluate the variants located at the uniform CTCF ChIP-seq peaks in a Chinese population (2,331 vs 3,077; 1,115 vs 1,346). The ChIP-seq data for CTCF, specified on lung cancer cell line A549, were downloaded from ENCODE database. Imputation was performed to increase the genome coverage in the CTCF binding regions. Three variants in CTCF binding sites were found to associate with lung cancer risk in the first stage. Further replication revealed a novel single nucleotide polymorphism rs60507107 was significantly associated with increased risk of lung cancer in two stages (Additive model: OR = 1.19, 95%CI = 1.11–1.27, P = 6.98 × 10⁻⁷). Our results indicate that rs60507107 in the binding site of CTCF is associated with an increased risk of lung cancer. This may further advance our understanding of regulatory DNA sequences in cancer development.

Genetic variations in TERT-CLPTM1L genes and risk of lung cancer in a Chinese population

BACKGROUND

This study was conducted to investigate the association between single nucleotide polymorphisms (SNPs) in telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane1-like (CLPTM1L) and lung cancer risk in a Chinese population.

METHODS

We performed a hospital-based case-control study, including 980 lung cancer cases and 1000 cancer-free controls matched for age and sex. Each case and control was interviewed to collect information by well-trained interviewers. A total of 5 ml of venous blood was collected for genotype testing of TERT rs2736098 and CLPTM1L rs401681 using TaqMan methodology.

RESULTS

The results revealed that the variant homozygote TERT rs2736098TT was associated with an increased risk of lung cancer (OR=2.017, 95%CI=1.518-2.681), especially lung adenocarcinoma (OR=2.117, 95%CI=1.557-3.043) and small cell carcinoma (OR=1.979, 95%CI: 1.174-3.334), compared with the TERT rs2736098CC genotype. Similar results were observed in non-smokers.

CONCLUSION

The TERT rs2736098 polymorphism might affect the susceptibility to lung cancer in Chinese populations. The associations need to be verified in larger and different populations.

CLPTM1L genetic polymorphisms and interaction with smoking and alcohol drinking in lung cancer risk: a case-control study in the Han population from northwest China

Genetic variants of cleft lip and palate trans-membrane 1-like (CLPTM1L) genes in the p15.33 region of chromosome 5 were previously identified to influence susceptibility to lung cancer. We examined the association of single nucleotide polymorphisms (SNPs) in CLPTM1L genes with lung cancer and explored their potential effects on the relationship between environmental risk factors (smoking, drinking) and lung cancer in a Chinese Han population. We genotyped 9 single nucleotide polymorphisms (SNPs) of CLPTM1L in a case-control study with 228 lung cancer cases and 301 controls from northwest China. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by unconditional logistic regression. We identified that the minor alleles of rs451360, rs402710, and rs31484 in CLPTM1L were associated with a 0.52-fold, 0.76-fold, and 0.70-fold decreased risk of lung cancer in allelic model analysis, respectively. In the genetic model analysis, we found rs402710 and rs401681 were associated with decreased lung cancer risk. Further stratification analysis showed that rs380286 displayed a significantly decreased lung cancer risk (OR=0.65, P=0.041) in the non-drinkers. In addition, Haplotype "GTTATCTGT" was found to be associated with decreased lung cancer risk (OR=0.50, P=0.033). Our results verified that genetic variants of CLPTM1L contribute to lung cancer susceptibility in the northwest Chinese Han population. Additionally, we found that consumption of alcohol may interact with CLPTM1L polymorphisms to contribute to overall lung cancer susceptibility.

Correlation of CLPTM1L polymorphisms with lung cancer susceptibility and response to cisplatin-based chemotherapy in a Chinese Han population

The implication of genetic factors in predisposition to cancer is a recognized fact. The Cleft lip and palate transmembrane 1-like (CLPTM1L) gene resides in a locus in the chromosome 5p15.33 region that is associated with lung cancer susceptibility and has a role in carcinogenesis. We conducted a case-control study in a Chinese population of 309 pathologically confirmed lung cancer patients and 310 controls to investigate the effect of variant genotypes within the CLPTM1L locus on susceptibility to lung cancer and sensitivity to cisplatin-based chemotherapy. We genotyped nine single nucleotide polymorphisms (SNPs) within the CLPTM1L locus and examined their correlation with lung cancer risk and treatment response using χ (2) and unconditional logistic regression analysis. We identified rs451360 as a novel SNP associated with lung cancer risk in the Chinese Han population. The "T" allele of rs451360 was associated with decreased risk of lung cancer (p = 0.007, odd ratio (OR) = 0.59, 95 % confidence interval (CI): 0.40-0.87). Significant multiplicative interactions were observed between gender and polymorphisms of rs402710, the "T/T" genotype of which was associated with decreased lung cancer risk in male patients (p = 0.016, OR = 0.35, 95 % CI: 0.17-0.73). CLPTM1L polymorphisms did not affect the tumor sensitivity to cisplatin combination chemotherapy in our study patients. The results of the present study suggest a potential association between CLPTM1L variants and lung cancer risk in the Chinese Han populations.

Analytic P-value calculation for the higher criticism test in finite d problems

The higher criticism is effective for testing a joint null hypothesis against a sparse alternative, e.g., for testing the effect of a gene or a genetic pathway that consists of d genetic markers. Accurate p-value calculations for the higher criticism based on the asymptotic distribution require a very large d, which is not the case for the number of genetic variants in a gene or a pathway. In this paper we propose an analytic method that accurately computes the p-value of the higher criticism test for finite d problems. Unlike previous treatments, this method does not rely on asymptotics in d or simulation, and is exact for arbitrary d when the test statistics are normally distributed. The method is particularly computationally advantageous when d is not large. We illustrate the proposed method with a case-control genome-wide association study of lung cancer and compare its power to competing methods through simulations.

TERT-CLPTM1L Rs401681 C>T polymorphism was associated with a decreased risk of esophageal cancer in a Chinese population

Background

Esophageal cancer was the fifth most commonly diagnosed cancer and the fourth leading cause of cancer-related death in China in 2009. Esophageal squamous cell carcinoma (ESCC) accounts for more than 90 percent of esophageal cancers. Genetic factors probably play an important role in the ESCC carcinogenesis.

Methods

We conducted a hospital based case-control study to evaluate functional hTERT rs2736098 G>A and TERT-CLPTM1L rs401681 C>T single nucleotide polymorphisms (SNPs) on the risk of ESCC. Six hundred and twenty-nine ESCC cases and 686 controls were recruited. Their genotypes were determined using the ligation detection reaction (LDR) method.

Results

When the TERT-CLPTM1L rs401681 CC homozygote genotype was used as the reference group, the CT genotype was associated with a significantly decreased risk of ESCC (adjusted OR  = 0.74, 95% CI  = 0.58–0.94, p = 0.012); the CT/TT variants were associated with a 26% decreased risk of ESCC (adjusted OR  = 0.74, 95% CI  = 0.59–0.93, P = 0.009). The significantly decreased risk of ESCC associated with the TERT-CLPTM1L rs401681 C>T polymorphism was associated with male sex, young age (<63 years in our study) and alcohol consumption. No association between the hTERT rs2736098 G>A polymorphism and ESCC risk was observed.

Conclusion

TERT-CLPTM1L rs401681 CT and CT/TT genotypes were associated with decreased risk of ESCC, particularly among men, young patients and those reported to be drinkers. However, our results are preliminary conclusions. Larger studies with more rigorous study designs are required to confirm the current findings.

CRR9p polymorphism as a protective factor for lung cancer

A number of studies have investigated the association between CRR9p polymorphism and risk of lung cancer (LC), yet the role in LC pathogenesis remains unclear owing to inconsistencies across studies. We searched PubMed, Embase, and Web of Science for all medical literature published until January 2014. Pooled odds ratios (ORs) and 95 % confidence intervals (CIs) were obtained by means of the fixed effects model. Data from eight studies satisfying the predesigned inclusion criteria were selected for this meta-analysis. We found a statistically significant evidence for a protective effect on the overall LC risk (TT vs. CC: OR = 0.78, 95 % CI = 0.70-0.87, P het = 0.299; TT vs. CT + CC: OR = 0.81, 95 % CI = 0.73-0.90, P het = 0.113; T vs. C: OR = 0.90, 95 % CI = 0.86-0.95, P het = 0.758; TT + CT vs. CC: OR = 0.92, 95 % CI = 0.87-0.98, P het = 0.892). Both Caucasian and Asian populations were suggested to have a reduced risk of developing such cancer. In the analysis of the association between rs401681 and non-small cell lung cancer (NSCLC) risks, all of the contrast models showed similar results except the CT vs. CC genetic model (OR = 0.93, 95 % CI = 0.84-1.02, P het = 0.568). Our meta-analysis provides supportive evidence that CRR9p polymorphism may influence a risk of LC and NSCLC in a protective model.

Genetic polymorphisms of TERT and CLPTM1L and risk of lung cancer: a case-control study in northeast Chinese male population

Recently, some genome-wide association studies have implicated telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane 1-like gene (CLPTM1L) in lung cancer development. Here, we present a case-control study that evaluates the genetic effects of TERT-rs2736098 and CLPTM1L-rs401681 variants on the risk of lung cancer development in a Chinese male population. We found that the homozygous variant genetic model of the TERT gene was associated with a significantly increased risk of lung cancer with an adjusted odds ratio (OR) of 1.988. The TERT-rs2736098 T allele was also associated with increased lung cancer risk both in adenocarcinoma and squamous cell carcinoma. No association was found between CLPTM1L-rs401681 and lung cancer risk. However, the joint effect of TERT and CLPTM1L variants increased the risk of lung cancer, especially squamous cell carcinoma, with an adjusted OR of 3.274. However, the exact functional effect of these two variant genes remains unclear, and further investigation is needed in the future.

A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms

We describe a method for pooling and sequencing DNA from a large number of individual samples while preserving information regarding sample identity. DNA from 576 individuals was arranged into four 12 row by 12 column matrices and then pooled by row and by column resulting in 96 total pools with 12 individuals in each pool. Pooling of DNA was carried out in a two-dimensional fashion, such that DNA from each individual is present in exactly one row pool and exactly one column pool. By considering the variants observed in the rows and columns of a matrix we are able to trace rare variants back to the specific individuals that carry them. The pooled DNA samples were enriched over a 250 kb region previously identified by GWAS to significantly predispose individuals to lung cancer. All 96 pools (12 row and 12 column pools from 4 matrices) were barcoded and sequenced on an Illumina HiSeq 2000 instrument with an average depth of coverage greater than 4,000×. Verification based on Ion PGM sequencing confirmed the presence of 91.4% of confidently classified SNVs assayed. In this way, each individual sample is sequenced in multiple pools providing more accurate variant calling than a single pool or a multiplexed approach. This provides a powerful method for rare variant detection in regions of interest at a reduced cost to the researcher.

A genetic sequence variant (GSV) at susceptibility loci of 5p15.33 (TERT-CLPTM1L) is associated with survival outcome in locally advanced and metastatic non-small-cell lung cancer (NSCLC)

INTRODUCTION

Lung cancer is a leading cause of cancer-related mortality in North America. In addition to tobacco smoking, inherited genetic factors can also influence the development of lung cancer. These genetic factors may lead to biologically distinct subsets of cancers that have different outcomes. We evaluated whether genetic sequence variants (GSVs) associated with lung cancer risk are associated with overall survival (OS) and progression-free survival (PFS) in stage-III-IV non-small-cell lung cancer (NSCLC) patients.

METHODS

A total of 20 candidate GSVs in 12 genes previously reported to be associated with lung cancer risk were genotyped in 564 patients with stage-III or IV NSCLC. Multivariate Cox proportional hazard models adjusted for potential clinical prognostic factors were generated for OS and PFS.

RESULTS

After taking into account multiple comparisons, one GSV remained significant: rs4975616 on chromosome 5p15.33, located near the TERT-CLPTM1L gene. The adjusted hazard ratio (aHR) for OS was 0.75 (0.69-0.91), p = 0.002; for PFS aHR was 0.74 (0.62-0.89), p < 0.001 for each protective variant allele. Results were similar in both Stage III (OS: aHR = 0.70; PFS: aHR = 0.71) and Stage IV patients (OS: aHR = 0.81; PFS: aHR = 0.77).

CONCLUSION

A GSV on 5p15.33 is not only a risk factor for lung cancer but may also be associated with survival in patients with late stage NSCLC. If validated, GSVs may define subsets of patients with different risk and prognosis of NSCLC.

Quantitative assessment of common genetic variants on chromosome 5p15 and lung cancer risk

Several genome-wide association studies on lung cancer (LC) have reported similar findings of a new susceptibility locus, 5p15. After that, a number of studies reported that the rs2736100, rs401681, rs402710, and rs31489 polymorphisms at chromosome 5p15 have been implicated in LC risk. However, the studies have yielded contradictory results. To derive a more precise estimation of the relationship, we performed this meta-analysis. Databases including MEDLINE, PubMed, EMBASE, ISI Web of Science, and China National Knowledge Infrastructure (CNKI) were searched to find relevant studies. Odds ratios (ORs) with 95 % confidence intervals (CIs) were used to assess the strength of association. The random effect model was applied, addressing heterogeneity and publication bias. A total of 31 articles involving 72,401 cases and 141,258 controls were included. Overall, significantly elevated LC risk was associated with rs2736100, rs401681, rs402710, and rs31489 polymorphisms when all studies were pooled into the meta-analysis. In the subgroup analysis by ethnicity, sample size, histology, sex, and smoking behavior, significantly increased risks were also detected for these polymorphisms. Our findings demonstrated that these common variations at 5p15 are a risk factor associated with increased LC susceptibility. However, these associations vary between different ethnicity.

Genetic variant rs401681 at 5p15.33 modifies susceptibility to lung cancer but not esophageal squamous cell carcinoma

BACKGROUND

The human 5p15.33 locus contains two well-known genes, the telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane 1-like (CLPTM1L) genes, which have been implicated in carcinogenesis. A common sequence variant, rs401681, located in an intronic region of CLPTM1L, has been reported to be associated with lung cancer risk based on genome-wide association study. However, subsequent replication studies in diverse populations have yielded inconsistent results. In addition, genetic variants at 5p15.33, including rs401681, have been shown to be involved in the susceptibility to multiple malignancies. Nevertheless, the role of these TERT-CLPTM1L variants in the etiology of esophageal squamous cell carcinoma (ESCC) remains unknown.

METHODS

We genotyped the rs401681 polymorphism using TaqMan methodology and analyzed its association with the risk of lung cancer and ESCC in a case-control study of 1,479 cancer patients (726 with lung cancer and 753 with ESCC) and 860 healthy individuals.

RESULTS

Logistic regression analyses revealed that rs401681 T genotypes were associated with a significantly decreased risk of lung cancer (CT vs. CC: adjusted OR=0.782, 95% CI=0.625-0.978, P=0.031; CT/TT vs. CC: adjusted OR=0.786; 95% CI=0.635-0.972, P=0.026). Stratification analysis by histology type indicated that rs401681 T genotypes were associated with a significantly reduced risk of both adenocarcinoma and squamous cell carcinoma. Furthermore, no significant association was observed between rs401681 and the risk of ESCC (CT vs. CC: adjusted OR=0.910, 95% CI=0.734-1.129, P=0.392; TT vs. CC: adjusted OR=0.897, 95%CI=0.624-1.290, P=0.558; CT/TT vs. CC: adjusted OR=0.908, 95% CI=0.740-1.114, P=0.355).

CONCLUSIONS

Our findings provide further evidence supporting rs401681 as a genetic variant associated with the risk of lung cancer. In addition, we investigated the correlation between the rs401681 variant and the risk of ESCC in a Han Chinese population, and our results suggest that this genetic variant may not be involved in ESCC risk.

CRR9/CLPTM1L regulates cell survival signaling and is required for Ras transformation and lung tumorigenesis

The transmembrane protein CLPTM1L is overexpressed in non-small cell lung cancer, where it protects tumor cells from genotoxic apoptosis. Here, we show that RNA interference-mediated blockade of CLPTM1L inhibits K-Ras-induced lung tumorigenesis. CLPTM1L expression was required in vitro for morphologic transformation by H-RasV12 or K-RasV12, anchorage-independent growth, and survival of anoikis of lung tumor cells. Mechanistic investigations indicated that CLPTM1L interacts with phosphoinositide 3-kinase and is essential for Ras-induced AKT phosphorylation. Furthermore that the anti-apoptotic protein Bcl-xL is regulated by CLPTM1L independently of AKT activation. Constitutive activation of AKT or Bcl-xL rescued the transformed phenotype in CLPTM1L-depleted cells. The CLPTM1L gene lies within a cancer susceptibility locus at chromosome 5p15.33 defined by genome-wide association studies. The risk genotype at the CLPTM1L locus was associated with high expression of CLPTM1L in normal lung tissue, suggesting that cis-regulation of CLPTM1L may contribute to lung cancer risk. Taken together, our results establish a protumorigenic role for CLPTM1L that is critical for Ras-driven lung cancers, with potential implications for therapy and chemosensitization.

Quantitative assessment of the influence of common variations (rs8034191 and rs1051730) at 15q25 and lung cancer risk

Several genome-wide association studies on lung cancer (LC) have reported similar findings of a new susceptibility locus, 15q25. After that, a number of studies reported that rs8034191 and rs1051730 polymorphisms at chromosome 15q25 have been implicated in LC risk. However, studies have yielded contradictory results. To derive a more precise estimation of the relationship, a meta-analysis of 43,742 LC cases and 58,967 controls from 17 published case-control studies was performed. Overall, significantly elevated LC risk was associated with rs8034191-C (OR = 1.26, 95% CI 1.22-1.31, P < 10(-5)) and rs105173-A variant (OR = 1.28, 95% CI 1.20-1.36, P < 10(-5)) when all studies were pooled into the meta-analysis. In the subgroup analysis by ethnicity, significantly increased risks were found for rs8034191 and rs105173 polymorphisms among Caucasians and African American, while no significant associations were observed for the two polymorphisms in East Asians. In addition, we found that rs8034191 and rs105173 confer risk, for both adenocarcinoma and squamous cell carcinoma when stratified by histological types of LC. Furthermore, our results on stratified analysis according to smoking status showed an increased LC risk in ever-smokers, while no associations were detected among never-smokers for the two polymorphisms. In conclusion, this meta-analysis demonstrated that the two common variations (rs8034191 and rs1051730) at 15q25 are a risk factor associated with increased LC susceptibility, but these associations vary in different ethnic populations.

CTCF mediates the TERT enhancer-promoter interactions in lung cancer cells: identification of a novel enhancer region involved in the regulation of TERT gene

Telomerase activation is a hallmark of cancer. Although the regulation of the telomerase reverse transcriptase catalytic subunit (TERT), the rate-limiting factor for telomerase activity, has been studied intensively it remains incompletely understood. In cells devoid of telomerase activity, TERT is embedded in a region of condensed chromatin and the chromatin remodeling protein CCCTC-binding factor (CTCF) has been implicated in the inhibition of TERT expression. The importance of TERT activation for cellular immortalization and carcinogenesis is attested by the fact that the gene is expressed in more than 90% of immortal cell lines and tumors and that gain of TERT is the most frequent amplification event in early stage lung cancer. This study was designed to study the mechanisms of regulation of the TERT gene expression by the CTCF transcription factor in three human lung cancer cell lines, A427, A549 and H838. Depletion of CTCF by siRNA resulted in reduced TERT mRNA levels in two (A427 and A549) of the three cell lines. A novel enhancer element was identified approximately 4.5 kb upstream of the TERT transcription start site. Chromatin immunoprecipitation experiments revealed recruitment of CTCF to this enhancer element. Chromosome conformation capture experiments demonstrated the presence of CTCF-dependent chromatin loops between this enhancer element and the TERT proximal promoter in A427 and A549 cell lines. In summary, the results show that CTCF plays an important role in maintaining TERT expression in a subset of human lung cancer cell lines. This role may be due to CTCF-dependent enhancer-promoter interactions.

EGFR and KRAS mutations, and ALK fusions: current developments and personalized therapies for patients with advanced non-small-cell lung cancer

Personalized therapy has significantly developed in lung cancer treatment over recent years. VEGF and EGF play a major role in non-small-cell lung cancer (NSCLC) tumor angiogenesis and aggressiveness. EGFR mutation as well as KRAS and ALK rearrangements are important biomarkers in the field owing to potential targeted therapies involved in clinical practice: erlotinib, geftinib, cetuximab and crizotinib. More recently, regulation of tumor immunity through CTLA4 and PD1/L1 has emerged as a promising field in NSCLC management. This review will focus on the current and future biomarkers in the advanced NSCLC field and also address potential related targeted therapies for these patients.

The SNP rs402710 in 5p15.33 is associated with lung cancer risk: a replication study in Chinese population and a meta-analysis

Background

Lung cancer is the most commonly diagnosed cancer and leading cause of cancer mortality in the world. A single nucleotide polymorphism (SNP), rs402710, located in 5p15.33, was firstly identified to be associated with the lung cancer risk in a genome-wide association study. However, some following replication studies yielded inconsistent results.

Methodology and Findings

A case-control study of 611 cases and 1062 controls in a Chinese population was conducted, and then a meta-analysis integrating the current and previously published studies with a total 31811 cases and 36333 controls was performed to explore the real effect of rs402710 on lung cancer susceptibility. Significant associations between the SNP rs402710 and lung cancer risk were observed in both case-control study and meta-analysis, with ORs equal to 0.77 (95%CI = 0.63–0.95) and 0.83 (95%CI = 0.81–0.86) in dominant model, respectively. By stratified analysis of our case-control study, the associations were also observed in never smoker group and non-small cell lung cancer(NSCLC) group with ORs equal to 0.71 (95%CI = 0.53–0.95) and 0.69 (95%CI = 0.55–0.87), which was remarkable that larger effect of the minor allele T was seen in the two groups than that in overall lung cancer. Besides, the sensitive and cumulative analysis indicated the robust stability of the current results of meta-analysis.

Conclusion

The results from our replication study and the meta-analysis provided firm evidence that rs402710 T allele significantly contributed to decreased lung cancer risk, and the case-control study implied that the variant may yield stronger effect on NSCLC and never smokers. However, the mechanism underlying the polymorphism conferring susceptibility to lung cancer is warranted to clarify in the follow-up studies.

Weighted SNP set analysis in genome-wide association study

Genome-wide association studies (GWAS) are popular for identifying genetic variants which are associated with disease risk. Many approaches have been proposed to test multiple single nucleotide polymorphisms (SNPs) in a region simultaneously which considering disadvantages of methods in single locus association analysis. Kernel machine based SNP set analysis is more powerful than single locus analysis, which borrows information from SNPs correlated with causal or tag SNPs. Four types of kernel machine functions and principal component based approach (PCA) were also compared. However, given the loss of power caused by low minor allele frequencies (MAF), we conducted an extension work on PCA and used a new method called weighted PCA (wPCA). Comparative analysis was performed for weighted principal component analysis (wPCA), logistic kernel machine based test (LKM) and principal component analysis (PCA) based on SNP set in the case of different minor allele frequencies (MAF) and linkage disequilibrium (LD) structures. We also applied the three methods to analyze two SNP sets extracted from a real GWAS dataset of non-small cell lung cancer in Han Chinese population. Simulation results show that when the MAF of the causal SNP is low, weighted principal component and weighted IBS are more powerful than PCA and other kernel machine functions at different LD structures and different numbers of causal SNPs. Application of the three methods to a real GWAS dataset indicates that wPCA and wIBS have better performance than the linear kernel, IBS kernel and PCA.

Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population

Recent genome-wide association studies (GWAS) have reported multiple genetic variations at 5p15.33 (TERT-CLPTM1L) associated with risk of lung cancer. However, most of the associated variations identified by GWAS thus far are unlikely to be the actual causal variants, but may be mostly marker-single nucleotide polymorphisms tagging functional variations that influence gene expression. This study aimed to explore the function-validated and potentially functional variations in TERT-CLPTM1L locus conferring susceptibility to lung cancer. A case-control study including 502 cases and 502 controls in Chinese Han population was firstly conducted. Bioinformatic approaches are applied to prioritize genetic variations based on their potential functionality. In the logistic regression analysis, TERT-rs2853669, rs2736108, and CLPTM1L-rs31490 were significant associated with increased risk of lung cancer (OR = 1.46, 95% CI = 1.22-1.75; OR = 1.22, 95% CI = 1.00-1.49 and OR = 1.74, 95% CI = 1.35-2.23 under additive model, respectively). The significant associations were observed in non-small-cell lung cancer but not-in-small-cell lung cancer, and more prominent in adenocarcinoma. Haplotype analysis presented a significant allele-dose effect of haplotypes in increasing risk of lung cancer (P for trend = 1.894 × 10(-6)). Moreover, significant multiplicative interactions were observed between smoking and these three polymorphisms of TERT-rs2853669, rs2736108, and CLPTM1L-rs31490, even after bonferroni correction for multiple comparisons (Pinteraction = 1.316 × 10(-9), 3.912 × 10(-4), and 2.483 × 10(-5), respectively). These findings indicated that the function-validated and potentially functional variations in TERT-CLPTM1L locus, modified by smoking, may play a substantial role in the susceptibility to lung cancer.

Urinary bladder cancer susceptibility markers. What do we know about functional mechanisms?

Genome-wide association studies (GWAS) have been successful in the identification of the several urinary bladder cancer (UBC) susceptibility loci, pointing towards novel genes involved in tumor development. Despite that, functional characterization of the identified variants remains challenging, as they mostly map to poorly understood, non-coding regions. Recently, two of the UBC risk variants (PSCA and UGT1A) were confirmed to have functional consequences. They were shown to modify bladder cancer risk by influencing gene expression in an allele-specific manner. Although the role of the other UBC risk variants is unknown, it can be hypothesized-based on studies from different cancer types-that they influence cancer susceptibility by alterations in regulatory networks. The insight into UBC heritability gained through GWAS and further functional studies can impact on cancer prevention and screening, as well as on the development of new biomarkers and future personalized therapies.

Genetic variations in TERT-CLPTM1L genes and risk of lung cancer in Chinese women nonsmokers

Background

The TERT gene is the reverse transcriptase component of telomerase and is essential for the maintenance of telomere DNA length, chromosomal stability and cellular immortality. CLPTM1L gene encodes a protein linked to cisplatin resistance, and it is well conserved and express in various normal or malignant tissues, including lung.

Methods

To test this hypothesis, we genotyped for two significant SNPs TERT-rs2736098 and CLPTM1L-rs4016981 in a case-control study with 501 cancer cases and 576 cancer-free controls in Chinese nonsmoking population. Information concerning demographic and risk factors was obtained for each case and control by a trained interviewer. Gene polymorphisms were determined by TaqMan methodology.

Results

We found that the homozygous variant genetic model of TERT gene was associated with a significantly increased risk of lung cancer with adjusted OR of 1.72(95%CI = 1.19–2.51, P = 0.004 for heterogeneity). The joint effect of TERT and CLPTM1L increased risk for lung cancer with adjusted OR is 1.31(95%CI = 1.00–1.74, P = 0.052 for heterogeneity).

Conclusion

Genetic variants in TERT and CLPTM1L may affect the susceptibility of lung cancer, especially adenocarcinoma in Chinese women nonsmokers.

SNP set association analysis for genome-wide association studies

Genome-wide association study (GWAS) is a promising approach for identifying common genetic variants of the diseases on the basis of millions of single nucleotide polymorphisms (SNPs). In order to avoid low power caused by overmuch correction for multiple comparisons in single locus association study, some methods have been proposed by grouping SNPs together into a SNP set based on genomic features, then testing the joint effect of the SNP set. We compare the performances of principal component analysis (PCA), supervised principal component analysis (SPCA), kernel principal component analysis (KPCA), and sliced inverse regression (SIR). Simulated SNP sets are generated under scenarios of 0, 1 and ≥2 causal SNPs model. Our simulation results show that all of these methods can control the type I error at the nominal significance level. SPCA is always more powerful than the other methods at different settings of linkage disequilibrium structures and minor allele frequency of the simulated datasets. We also apply these four methods to a real GWAS of non-small cell lung cancer (NSCLC) in Han Chinese population