Association between polymorphisms in COMT, PLCH1, and CYP17A1, and non-small-cell lung cancer risk in Chinese nonsmokers

Prognostic Implication of Energy Metabolism-Related Gene Signatures in Lung Adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is the major non-small-cell lung cancer pathological subtype with poor prognosis worldwide. Herein, we aimed to build an energy metabolism-associated prognostic gene signature to predict patient survival.

Methods

The gene expression profiles of patients with LUAD were downloaded from the TCGA and GEO databases, and energy metabolism (EM)-related genes were downloaded from the GeneCards database. Univariate Cox and LASSO analyses were performed to identify the prognostic EM-associated gene signatures. Kaplan–Meier and receiver operating characteristic (ROC) curves were plotted to validate the predictive effect of the prognostic signatures. A CIBERSORT analysis was used to evaluate the correlation between the risk model and immune cells. A nomogram was used to predict the survival probability of LUAD based on a risk model.

Results

We constructed a prognostic signature comprising 13 EM-related genes (AGER, AHSG, ALDH2, CIDEC, CYP17A1, FBP1, GNB3, GZMB, IGFBP1, SORD, SOX2, TRH and TYMS). The Kaplan–Meier curves validated the good predictive ability of the prognostic signature in TCGA AND two GEO datasets (p<0.0001, p=0.00021, and p=0.0034, respectively). The area under the curve (AUC) of the ROC curves also validated the predictive accuracy of the risk model. We built a nomogram to predict the survival probability of LUAD, and the calibration curves showed good predictive ability. Finally, a functional analysis also unveiled the different immune statuses between the two different risk groups.

Conclusion

Our study constructed and verified a novel EM-related prognostic gene signature that could improve the individualized prediction of survival probability in LUAD.

Residential PM2.5 exposure and the nasal methylome in children

RATIONALE

PM_2.5-induced adverse effects on respiratory health may be driven by epigenetic modifications in airway cells. The potential impact of exposure duration on epigenetic alterations in the airways is not yet known.

OBJECTIVES

We aimed to study associations of fine particulate matter PM_2.5 exposure with DNA methylation in nasal cells.

METHODS

We conducted nasal epigenome-wide association analyses within 503 children from Project Viva (mean age 12.9 y), and examined various exposure durations (1-day, 1-week, 1-month, 3-months and 1-year) prior to nasal sampling. We used residential addresses to estimate average daily PM_2.5 at 1 km resolution. We collected nasal swabs from the anterior nares and measured DNA methylation (DNAm) using the Illumina MethylationEPIC BeadChip. We tested 719,075 high quality autosomal CpGs using CpG-by-CpG and regional DNAm analyses controlling for multiple comparisons, and adjusted for maternal education, household smokers, child sex, race/ethnicity, BMI z-score, age, season at sample collection and cell-type heterogeneity. We further corrected for bias and genomic inflation. We tested for replication in a cohort from the Netherlands (PIAMA).

RESULTS

In adjusted analyses, we found 362 CpGs associated with 1-year PM_2.5 (FDR < 0.05), 20 CpGs passing Bonferroni correction (P < 7.0x10^-8) and 10 Differentially Methylated Regions (DMRs). In 445 PIAMA participants (mean age 16.3 years) 11 of 203 available CpGs replicated at P < 0.05. We observed differential DNAm at/near genes implicated in cell cycle, immune and inflammatory responses. There were no CpGs or regions associated with PM_2.5 levels at 1-day, 1-week, or 1-month prior to sample collection, although 2 CpGs were associated with past 3-month PM_2.5.

CONCLUSION

We observed wide-spread DNAm variability associated with average past year PM_2.5 exposure but we did not detect associations with shorter-term exposure. Our results suggest that nasal DNAm marks reflect chronic air pollution exposure.

Evaluation of COMT Gene rs4680 Polymorphism as a Risk Factor for Endometrial Cancer

Catechol-O-methyletransferase (COMT) enzyme is involved in the inactivation of catecholamine and catechol estrogens. Catechol estrogens have carcinogenic potential and DNA damaging ability. Several studies investigated COMT Val158Met polymorphism as risk factor for endometrial cancer but the results were inconclusive. Hence the objective of present study was to find out exact association between COMT gene Val158Met polymorphism and endometrial cancer by a meta-analysis. Pubmed, Google Scholar, Springer Link and Science Direct databases were searched for case-control articles which investigated COMT Val158Met polymorphism in endometrial cancer cases. All statistical analysis was performed using MetaAnalyst and Mix programs. The results of meta-analysis suggested that there were no association between COMT Val158Met polymorphism and endometrial cancer risk (allele contrast model-OR_{A vs. G} = 0.97, 95% CI = 0.86-1.10, p = 0.67; co-dominant model-OR_{AG vs. GG} = 0.91, 95% CI = 0.77-1.06, p = 0.23; homozygote model-OR_{AA vs. GG} = 1.01, 95% CI = 0.84-1.19, p = 0.29; dominant model-OR_{AA+AG vs. GG} = 0.93, 95% CI = 0.77-1.11, p = 0.43; recessive model-OR_{AA vs. AG+GG} = 1.02, 95% CI = 0.89-1.20, p = 0.62). Publication bias was absent. Subgroup analysis based on source of controls was also performed. In conclusion, results of present meta-analysis showed no association between COMT Val158Met polymorphism and susceptibility to endometrial cancer.

Integration of multi-omics data to mine cancer-related gene modules

The identification of cancer-related genes is a major research goal, with implications for determining the pathogenesis of cancer and identifying biomarkers for early diagnosis and treatment. In this study, by integrating multi-omics data, including gene expression, DNA copy number variation, DNA methylation, transcription factors, miRNA, and lncRNA data, we propose a method for mining cancer-related genes based on network models. First, using random forest-based feature selection method multi-omics data are integrated to identify key regulatory factors that affect gene expression, and then genome-wide regulatory networks are constructed. Next, by comparing the regulatory networks of key candidate genes in variant samples and non-variant samples, a differential expression regulatory network is generated. The differential network contains a collection of abnormal regulatory genes of key candidate genes. Then, by introducing the functional similarity as a distance metric for gene sets, a density-based clustering method is used to mine gene modules related to cancer. We applied this method to LUSC (lung squamous cell carcinoma) and mined cancer-related gene modules composed of 20 genes. GO function and KEGG pathway analyses indicated that the modules were closely related to cancer. A survival analysis was used to verify that the excavated gene modules can effectively distinguish between high- and low-risk groups. Overall, these results suggest that the proposed method can be used to identify cancer-related gene modules, providing a basis for the development of biomarkers for diagnosis and treatment.

Optimized monoclonal antibody treatment against ELTD1 for GBM in a G55 xenograft mouse model

Glioblastoma is an aggressive brain tumour found in adults, and the therapeutic approaches available have not significantly increased patient survival. Recently, we discovered that ELTD1, an angiogenic biomarker, is highly expressed in human gliomas. Polyclonal anti-ELTD1 treatments were effective in glioma pre-clinical models, however, pAb binding is potentially promiscuous. Therefore, the aim of this study was to determine the effects of an optimized monoclonal anti-ELTD1 treatment in G55 xenograft glioma models. MRI was used to assess the effects of the treatments on animal survival, tumour volumes, perfusion rates and binding specificity. Immunohistochemistry and histology were conducted to confirm and characterize microvessel density and Notch1 levels, and to locate the molecular probes. RNA-sequencing was used to analyse the effects of the mAb treatment. Our monoclonal anti-ELTD1 treatment significantly increased animal survival, reduced tumour volumes, normalized the vasculature and showed higher binding specificity within the tumour compared with both control- and polyclonal-treated mice. Notch1 positivity staining and RNA-seq results suggested that ELTD1 has the ability to interact with and interrupt Notch1 signalling. Although little is known about ELTD1, particularly about its ligand and pathways, our data suggest that our monoclonal anti-ELTD1 antibody is a promising anti-angiogenic therapeutic in glioblastomas.

Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma

Smoking is one of the most important factors associated with the development of lung cancer. However, the signaling pathways and driver genes in smoking-associated lung adenocarcinoma remain unknown. The present study analyzed 433 samples of smoking-associated lung adenocarcinoma and 75 samples of non-smoking lung adenocarcinoma from the Cancer Genome Atlas database. Gene Ontology (GO) analysis was performed using the Database for Annotation, Visualization and Integrated Discovery and the ggplot2 R/Bioconductor package. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed using the R packages RSQLite and org.Hs.eg.db. Multivariate Cox regression analysis was performed to screen factors associated with patient survival. Kaplan-Meier and receiver operating characteristic curves were used to analyze the potential clinical significance of the identified biomarkers as molecular prognostic markers for the five-year overall survival time. A total of 373 differentially expressed genes (DEGs; |log2-fold change|≥2.0 and P<0.01) were identified, of which 71 were downregulated and 302 were upregulated. These DEGs were associated with 28 significant GO functions and 11 significant KEGG pathways (false discovery rate <0.05). Two hundred thirty-eight proteins were associated with the 373 differentially expressed genes, and a protein-protein interaction network was constructed. Multivariate regression analysis revealed that 7 mRNAs, cytochrome P450 family 17 subfamily A member 1, PKHD1 like 1, retinoid isomerohydrolase RPE65, neurotensin receptor 1, fetuin B, insulin-like growth factor binding protein 1 and glucose-6-phosphatase catalytic subunit, significantly distinguished between non-smoking and smoking-associated adenocarcinomas. Kaplan-Meier analysis demonstrated that patients in the 7 mRNAs-high-risk group had a significantly worse prognosis than those of the low-risk group. The data obtained in the current study suggested that these genes may serve as potential novel prognostic biomarkers of smoking-associated lung adenocarcinoma.

COMT and Alpha-Tocopherol Effects in Cancer Prevention: Gene-Supplement Interactions in Two Randomized Clinical Trials

BACKGROUND

Vitamins are among the most frequently used supplements (48% of US adults). However, little is known about contributions of genetic variation to their efficacy and safety. Multiple pathways link catechol-O-methyltransferase (COMT) to the vitamin E supplement, alpha-tocopherol, and cancer.

METHODS

Here we determined if COMT exerted pharmacogenetic effects on cancer prevention in two randomized trials of alpha-tocopherol supplementation. Pharmacogenetic effects of common COMT rs4680 (val158met), which encodes a nonsynonymous valine-to-methionine substitution, were examined in the trial plus a 10-year post-trial follow-up (overall) period of The Women's Genome Health Study (WGHS, N = 23 294), a 10-year alpha-tocopherol and aspirin trial with 10 years post-trial follow-up. Results were validated in a case/control (N = 2396/2235) subset of the Alpha-Tocopherol Beta-Carotene Cancer Prevention Study (ATBC, N = 29 133). The primary outcome was total cancers. Rates of cancer types prevalent in women (colorectal, breast, lung, uterine, and lymphoma/leukemia) were also examined. All statistical tests were two-sided.

RESULTS

Random-effects meta-analysis of rs4680 genotype strata, in WGHS and ATBC overall periods, revealed differential alpha-tocopherol effects compared with placebo: met/met (hazard ratio [HR] = 0.88; 95% confidence interval [CI] = 0.80 to 0.97; P = .01), val/met (HR = 0.99; 95% CI = 0.92 to 1.06; P = .74), and val/val (HR = 1.18; 95% CI = 1.06 to 1.31; P = .002) with a statistically significant COMT by alpha-tocopherol interaction (Pinteraction <.001). Timing of effects differed, with stronger effects in WGHS trial and ATBC post-trial.

CONCLUSION

Pharmacogenetic analysis of COMT and cancer prevention in two large randomized trials revealed statistically significant COMT by alpha-tocopherol interaction, such that alpha-tocopherol was beneficial among rs4680 met-allele (28.0%), but not val-allele (22.8%) homozygotes. These effects indicate the need for additional studies of genetic variation as a determinant of the benefits and possible harms of over-the-counter supplements, like alpha-tocopherol, used for health promotion.

Association between CBR1 polymorphisms and NSCLC in the Chinese population

Carbonyl reductase 1 (CBR1) is theorized to participate in various cellular processes, such as signal transduction, apoptosis, carcinogenesis and drug resistance, and is highly expressed in certain malignancies, including lung tumors. Several studies have provided evidence that gene polymorphisms may affect susceptibility to non-small cell lung cancer (NSCLC). The present study aimed to investigate the association between the CBR1 single-nucleotide polymorphisms (SNPs) rs3787728 and rs2835267, and NSCLC in a Chinese population. The data indicated that the allele frequency in CBR1 rs3787728 was significantly different between patients with NSCLC and the controls [odds ratio (OR)=1.209; 95% confidence interval (CI)=1.013-1.442; P=0.0349], and was significantly different between male patients with NSCLC and the corresponding controls (OR=1.278; 95% CI=1.016-1.607; P=0.0358). The CBR1 rs3787728 thymine (T)/T allele homozygote was associated with an increased risk of NSCLC in all patients (OR=1.382; 95% CI=1.019-1.875; P=0.037), and patients possessing the rs3787728 T/T major allele homozygote exhibited a 1.537-fold greater risk with respect to developing lung squamous-cell carcinoma (SCC) in all patients (95% CI=1.019-2.318; P=0.0395). The CBR1 rs3787728 cytosine (C)/C allele homozygote was associated with a decreased risk of adenocarcinoma (ADC) in male patients (OR=0.633; 95% CI=0.413-0.969; P=0.0348); however, no significant association was observed in CBR1 rs2835267 between SNPs and SCC or ADC-type NSCLC. In conclusion, the results revealed that genetic polymorphisms of CBR1 rs3787728 were associated with susceptibility to NSCLC. Additional studies are required to identify the functional impact of CBR1 expression and activity in NSCLC.

The Val158Met polymorphism in COMT gene and cancer risk: role of endogenous and exogenous catechols

Catechol-O-methyltransferase, COMT, is an important phase II enzyme catalyzing the transfer of a methyl-group from S-adenosylmethionine to a catechol-containing substrate molecule. A genetic variant Val158Met in the COMT gene leads to a several-fold decrease in the enzymatic activity giving rise to the accumulation of potentially carcinogenic endogenous catechol estrogens and their reactive intermediates and increasing thus the risk of tumorigenesis. However, numerous association studies between the COMT genotype and susceptibility to various malignancies have shown inconsistent and controversial findings indicating that additional gene-gene and gene-environment interactions might be crucial in modulating the physiological role of the COMT. In this review article, the important contribution of dietary catechol-containing flavonoids to modification of the relationships between the COMT genotype and cancer risk is discussed. Whereas, the diverse anticancer activities of common phytochemicals, such as green tea polyphenols, quercetin, fisetin or luteolin, can be markedly changed (both decreased or increased) by the COMT-mediated O-methylation of these exogenous substrates, flavonoids can also behave as potent inhibitors of the COMT enzyme slowing detoxification of endogenous catechol estrogens. Such a many-featured functioning of the COMT and its complex regulation by several different genetic and environmental factors, including plant-based food ingredients, emphasizes the necessity to further stratify the association studies between the COMT genotype and tumor risk by consumption of catechol-containing dietary flavonoids. Currently, it can be only speculated that some of the possible associations might be masked by the regular intake of specific food polyphenols, taking effect in certain communities or populations.

Two novel susceptibility loci for non-small cell lung cancer map to low-density lipoprotein receptor-related protein 5

This study investigated the effect of single-nucleotide polymorphisms (SNPs) of low-density lipoprotein receptor-related protein 5 (LRP5) on the risk of developing non-small cell lung cancer (NSCLC). A total of 500 NSCLC patients and 500 healthy controls were recruited for genotyping of 11 SNPs of LRP5. The association between genotype and NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) from multivariate unconditional logistic regression analyses. Eleven Tag SNPs were detected. The frequency of the LRP5 rs3736228 T allele (18.9% in male NSCLC cases and 23.9% in male controls) was statistically different between male NSCLCs and male controls (P=0.03), and the T allele was associated with a lower risk of NSCLC (OR=0.74; 95% CI, 0.56–0.67), whereas the C/C homozygous genotype and the LRP5 rs64843 T/T genotype were associated with an increased risk of NSCLC and squamous cell carcinoma (SCC), respectively (OR=1.43 and 1.77, respectively). Using Haploview software, the frequency of the haplotypes of rs312009/rs3120015/rs3120014 CCC was was significantly higher in female SCC cases compared with female controls (0.064 vs. 0.009, P=0.04). LRP5 rs3736228 and rs64843 SNPs were significantly associated with an increased risk of NSCLC and SCC, respectively. Further studies are required to investigate the functional changes in LRP5 expression and activity in NSCLC in vitro.

Association between the COMT Val158Met polymorphism and risk of cancer: evidence from 99 case-control studies

Catechol-O-methyltransferase (COMT) plays a central role in DNA repair and estrogen-induced carcinogenesis. Many recent epidemiologic studies have investigated the association between the COMT Val158Met polymorphism and cancer risk, but the results are inconclusive. In this study, we performed a meta-analysis to investigate the association between cancer susceptibility and COMT Val158Met in different genetic models. Overall, no significant associations were found between COMT Val158Met polymorphism and cancer risk (homozygote model: odds ratio [OR] =1.05, 95% confidence interval [CI] = [0.98, 1.13]; heterozygote model: OR =1.01, 95% CI = [0.98, 1.04]; dominant model: OR =1.02, 95% CI [0.97, 1.06], and recessive model: OR =1.03, 95% CI [0.97, 1.09]). In the subgroup analysis of cancer type, COMT Val158Met was significantly associated with increased risks of bladder cancer in recessive model, and esophageal cancer in homozygote model, heterozygote model, and dominant model. Subgroup analyses based on ethnicities, COMT Val158Met was significantly associated with increased risk of cancer in homozygote and recessive model among Asians. In addition, homozygote, recessive, and dominant models were significantly associated with increased cancer risk in the subgroup of allele-specific polymerase chain reaction genotyping. Significant associations were not observed when data were stratified by the source of the controls. In summary, this meta-analysis suggested that COMT Val158Met polymorphism might not be a risk factor for overall cancer risk, but it might be involved in cancer development at least in some ethnic groups (Asian) or some specific cancer types (bladder and esophageal cell cancer). Further evaluations of more preclinical and epidemiological studies are required.

Tankyrase 2 (TNKS2) polymorphism associated with risk in developing non-small cell lung cancer in a Chinese population

OBJECTIVES

We investigated the association between poly(ADP-ribose) polymerase Tankyrase 2 (TNKS2) single-nucleotide polymorphisms (SNPs) and the risk of developing non-small cell lung cancer (NSCLC) in a Han Chinese population.

METHODS

Five-hundred NSCLC cases and 500 healthy controls were genotyped for four TNKS2 tagging SNPs (rs1538833, rs1538833, rs1340420, and rs1340420). The association between genotype and NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) using multivariate unconditional logistic regression analyses.

RESULTS

Individual alleles of the four TNKS2 SNPs were not associated with NSCLC risk in the studied Chinese population. However, patients carrying TNKS2 rs1340420 G/G and A/G genotypes were associated with a lower risk of developing NSCLC and adenocarcinoma (OR=0.14; 95% CI=0.02-1.15 and OR=0.11; 95% CI=0.03-0.91, respectively), whereas females patients homozygous for the TNKS2 rs1770474 T allele, a rare type, were associated with a higher risk of developing squamous-cell carcinoma (SCC) (OR=4.67; 95% CI=0.87-25.01).

CONCLUSION

TNKS2 rs1340420 SNP was associated with lower NSCLC risk, whereas rs1770474 SNP was associated with higher SCC risk, suggesting that these two SNPs may be useful predictors of risk of developing NSCLC and SCC in this Chinese population.

Glutathione-S-transferase (GSTM1, GSTT1) null phenotypes and risk of lung cancer in a Korean population

PURPOSE

The aim of this study was to evaluate any association of GSTM1 and GSTT1 null genotypes with the risk of lung cancer in a South Korean population.

METHODS

We conducted a large-scale, population-based case-control study including 3,933 lung cancer cases and 1,699 controls. Genotypes of GSTM1 and GSTT1 were determined using real-time polymerase chain reaction.

RESULTS

In logistic regression analysis adjusted for age and smoking, we did not find any association between GSTM1 or GSTT1 and LC risk in women. However, in men, the GSTM1 and GSTTI null genotypes were borderline associated with risk (OR=1.18, 95% CI=0.99-1.41 for GSTM1, OR=1.18, 95% CI=0.99-1.41 for GSTT1), and combined GSTM1 and GSTT1 null genotypes conferred an increased risk for LC in men (OR=1.39, 95% CI=1.08-1.78). The OR for the GSTT1 null genotype was greater in subjects aged 55 years old or younger (OR=1.45, 95% CI=1.09-1.92 for men; OR=1.36, 95% CI=0.97-1.90 for women), than in those over age 55 (OR=1.03, 95% CI=0.83-1.27 for men; OR=0.86, 95% CI=0.66-1.12 for women) in both genders (p for interaction <0.05).

CONCLUSIONS

In the Korean population, the GSTM1 and GSTT1 null genotypes are risk factors for LC in men; the GSTT1 null genotype has a more prominent effect on LC risk in younger people (age 55 years and under) than in older individuals.

Association between Catechol-O-methyltransferase rs4680 (G>A) polymorphism and lung cancer risk

Background

The association between the Val158Met polymorphism in the catechol-O-methyltransferase (COMT) gene and lung cancer risk remains controversial and inconclusive. Therefore, the meta-analysis was performed to provide a quality reevaluation of the association between the COMT Val158Met polymorphism and the risk of lung cancer.

Methods

Two major public databases (Pubmed and Embase) and several Chinese databases were searched for eligible studies. Pooled odds ratios (OR) and 95% confidence intervals (CI) were calculated to estimate the strength of the association.

Results

Five publications, including six individual studies with a total of 4,043 subjects (1,796 cases and 2,247 controls) regarding the association of COMT Val158Met polymorphism with lung cancer susceptibility were included in this meta-analysis. Overall, pooled analysis indicated that there was no significant association between COMT Val158Met polymorphism and lung cancer susceptibility under all genetic models. Likewise, no association was observed in the stratified analysis by ethnicity and control source, either. However, Val158Met polymorphism was shown to increase lung cancer risk among women (AG vs. GG, OR = 1.190, 95% CI = 1.001–1.422, p = 0.049).

Conclusion

These findings suggested that the COMT l58Val/Met polymorphism confer genetic susceptibility to lung cancer among women. However, no evidence was found for the association with lung cancer risk in ethnicity and smoking status.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_192

The Val158Met polymorphism in the COMT gene is associated with increased cancer risks in Chinese population

The Val158Met polymorphism in the COMT gene may affect the DNA repair pathways and be associated with the risk of cancer in Chinese population. However, the results of previous studies are inconsistent. The objective of this study was to investigate the association between the Val158Met polymorphism in the COMT gene and the risk of cancer for Chinese population by meta-analysis. We searched PubMed, Embase, CNKI, Weipu, and Wanfang databases, and the last search was updated on Sep. 26, 2013. Statistical analysis was performed using the Revman4.2 and Stata10.0 software. A total of 18 case-control studies concerning 5034 case and 6234 controls were included. In the total analysis, the results suggested a significant association between the Val158Met polymorphism in the COMT gene and the cancer risk in Chinese population: OR = 1.34, 95%CI = 1.04-1.73, and P = 0.03 for AA vs. AG + GG; OR = 1.39, 95%CI = 1.06-1.82, and P = 0.02; OR = 1.13, 95%CI = 1.01-1.27, and P = 0.04. In the subgroup analysis by cancer types, significant association was found in the breast cancer and esophageal squamous cell carcinoma. The current meta-analysis confirmed that the Val158Met polymorphism in the COMT gene may be a risk factor for cancer in Chinese population. In the future, more case-control studies are needed to validate our results.