Common gene polymorphisms, cancer progression and prognosis

Associations of the Expression Levels and Risk Variants of CDKN2B-AS1 Long Noncoding RNA With the Susceptibility and Progression of Prostate Cancer

Genetic variants of deregulated long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis, cancer progression and cancer recurrence. Single-nucleotide polymorphisms (SNPs) of the lncRNA cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) have been associated with the risk and progression of various cancers; however, their role in prostate cancer (PCa) remains underexplored. In this case-control study, we investigated the associations of CDKN2B-AS1 expression levels and variants with PCa risk and progression. For this, five SNPs of CDKN2B-AS1-rs564398, rs1333048, rs1537373, rs2151280 and rs8181047-were genotyped using a TaqMan allelic discrimination assay; data were collected from 695 patients with PCa and 695 healthy controls. Our findings revealed that, under a dominant model, patients with PCa carrying at least one minor C allele of rs1333048 exhibited an increased risk of developing tumours with high Gleason grades; this risk was particularly high in patients without biochemical recurrence. Data from the Genotype-Tissue Expression database indicated upregulated CDKN2B-AS1 expression in the prostates of individuals carrying the polymorphic C allele of rs1333048. Genotype screening of rs1333048 in PCa cell lines showed that cells with at least one minor C allele had higher CDKN2B-AS1 levels than those with the AA genotype. Furthermore, data from The Cancer Genome Atlas indicated that higher CDKN2B-AS1 levels in PCa tissues were correlated with larger tumour sizes (T3 + T4), more lymph node metastasis (N1), higher Gleason scores and shorter progression-free survival. In conclusion, the polymorphic variants of CDKN2B-AS1 at rs1333048 may modulate CDKN2B-AS1 expression, thus accelerating PCa progression.

Analysis of damaging non-synonymous SNPs in GPx1 gene associated with the progression of diverse cancers through a comprehensive in silico approach

Glutathione Peroxidase 1 (GPx1) gene has been reported for its role in cellular redox homeostasis, and the dysregulation of its expression is linked with the progression of diverse cancers. Non-synonymous single nucleotide polymorphism (nsSNPs) have been emerged as the crucial factors, playing their role in GPx1 overexpression. To understand the deleterious mutational effects on the structure and function of GPx1 enzyme, we delved deeper into the exploration of possibly damaging nsSNPs using in-silico based approaches. Eight widely utilized computational tools were employed to roughly shortlist the deleterious nsSNPs. Their damaging effects on structure and function of the genes were evaluated by using different bioinformatics tools. Subsequently, the three final proposed deleterious mutants including mutations rs373838463, rs2107818892, and rs763687242, were docked with their reported binder, TNF receptor-associated factor 2 (TRAF2). The lowest binding affinity and stability of the docked mutant complexes as compared to the wild type GPx1 were validated by molecular dynamic simulation. Finally, the comparison of RMSD, RMSF, RoG and hydrogen bond analyses between wild-type and mutant's complexes validated the deleterious effects of proposed nsSNPs. This study successfully identified and verified the possibly damaging nsSNPs in GPx1 enzyme, which may be linked the progression of various types of cancer. Our findings underscore the value of in-silico approaches in mutational analysis and encourage further preclinical and clinical trials.

Interplay between acute coronary syndromes and cancer: insights into pathophysiology, diagnostic challenges, and treatment options

Acute coronary syndromes (ACS) and cancer are among the leading causes of death worldwide. In recent years, increasing evidence has suggested an interplay between these 2 conditions. This article reviews the pathophysiology, diagnostic challenges, and treatment options for ACS and cancer. The interplay between these conditions may be due to environmental, genetic, and metabolic factors. For example, smoking, hypertension, and obesity are risk factors for both ACS and cancer. Diagnosis of ACS and cancer can be challenging because the symptoms of these conditions often overlap. For example, chest pain can be a symptom of both ACS and a neoplasms. Treatment options for ACS and cancer are varied and depend on the type of disease, stage of disease, and individual patient factors. Treatment for ACS may include angioplasty, stenting, or medication therapy. Treatment for cancer may include surgical removal of the tumour, radiation therapy, or chemotherapy.

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression

Lung adenocarcinoma (LUAD) is a deadly tumor with dynamic evolutionary process. Although much endeavors have been made in identifying the temporal patterns of cancer progression, it remains challenging to infer and interpret the molecular alterations associated with cancer development and progression. To this end, we developed a computational approach to infer the progression trajectory based on cross-sectional transcriptomic data. Analysis of the LUAD data using our approach revealed a linear trajectory with three different branches for malignant progression, and the results showed consistency in three independent cohorts. We used the progression model to elucidate the potential molecular events in LUAD progression. Further analysis showed that overexpression of BUB1B, BUB1 and BUB3 promoted tumor cell proliferation and metastases by disturbing the spindle assembly checkpoint (SAC) in the mitosis. Aberrant mitotic spindle checkpoint signaling appeared to be one of the key factors promoting LUAD progression. We found the inferred cancer trajectory allows to identify LUAD susceptibility genetic variations using genome-wide association analysis. This result shows the opportunity for combining analysis of candidate genetic factors with disease progression. Furthermore, the trajectory showed clear evident mutation accumulation and clonal expansion along with the LUAD progression. Understanding how tumors evolve and identifying mutated genes will help guide cancer management. We investigated the clonal architectures and identified distinct clones and subclones in different LUAD branches. Validation of the model in multiple independent data sets and correlation analysis with clinical results demonstrate that our method is effective and unbiased.

The presence of polymorphisms in genes controlling neurotransmitter metabolism and disease prognosis in patients with prostate cancer: a possible link with schizophrenia

Polymorphisms of neurotransmitter metabolism genes were studied in patients with prostate cancer (PC) characterized by either reduced or extended serum prostate-specific antigen doubling time (PSADT) corresponding to unfavorable and favorable disease prognosis respectively. The ‘unfavorable prognosis’ group (40 cases) was defined by PSADT ≤ 2 months, whereas patients in the ‘favorable prognosis’ group (67 cases) had PSADT ≥ 30 months. The following gene polymorphisms known to be associated with neuropsychiatric disorders were investigated: a) the STin2 VNTR in the serotonin transporter SLC6A4 gene; b) the 30-bp VNTR in the monoamine oxidase A MAOA gene; c) the Val158Met polymorphism in the catechol-ortho-methyltransferase COMT gene; d) the promoter region C-521T polymorphism and the 48 VNTR in the third exon of the dopamine receptor DRD4 gene.

The STin2 12R/10R variant of the SLC6A4 gene (OR = 2.278; 95% CI = 0.953–5.444) and the -521T/T homozygosity of the DRD4 gene (OR = 1.579; 95% CI = 0.663–3.761) tended to be overrepresented in PC patients with unfavorable disease prognosis. These gene variants are regarded as protective against schizophrenia, and the observed trend may be directly related to a reduced PC risk described for schizophrenia patients. These results warrant further investigation of the potential role of neurotransmitter metabolism gene polymorphisms in PC pathogenesis.

Evaluation of microRNA Gene Polymorphisms in Liver Transplant Patients with Hepatocellular Carcinoma

Background: Genetic polymorphism in the miRNA sequence might alter miRNA expression and/or maturation, which is associated with the development and progression of hepatocellular carcinoma (HCC) in liver transplant patients. Objectives: Therefore, the prevalence of miRNA-146a G > C (rs2910164), miRNA-499A > G (rs3746444), miRNA-149C > T (rs2292832), and miRNA-196a-2 C > T (rs11614913) gene polymorphisms was evaluated in liver recipients with HCC with or without experiencing graft rejection. Methods: In a cross-sectional study, tissue samples were collected from 60 HCC patients who underwent liver transplant surgery at Namazi Hospital, Shiraz, Iran, in 2013 - 2015. A control group consisting of 120 individuals was randomly selected, as well. The genomic DNA was extracted from collected tissues and blood samples. The miRNA-146a (rs2910164), miRNA-499 (rs3746444), miRNA-149 (rs2292832), and miRNA-196a-2 (rs11614913) gene polymorphisms were evaluated in patients with HCC using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: The CC genotype and C allele of the miRNA-146a (rs2910164) polymorphism were significantly associated with the increased risk of transplant rejection in patients with HCC (P = 0.05 and P = 0.05, respectively). The CC genotype and C allele of the miRNA-146a (rs2910164) were also significantly more frequent in male liver transplant patients who experienced acute rejection than in non-rejected ones (P = 0.05 and P = 0.03, respectively). However, no significant association was found between the genotypes and alleles of miRNA-499 (rs3746444), miRNA-149 (rs2292832), and miRNA-196a-2 (rs11614913) polymorphisms and HCC outcomes in liver transplant recipients. Conclusions: The importance of the CC genotype and C allele of the miRNA-146a (rs2910164) polymorphism in increasing the risk of transplant rejection was confirmed, but it needs further studies in larger populations.

Polymorphisms of TNF-α -308 G/A and IL-8 -251 T/A Genes Associated with Urothelial Carcinoma: A Case-Control Study

Cigarette smoking and exposure to environmental tobacco smoke are well-known risk factors for urothelial carcinoma (UC). We conducted a hospital-based case-control study involving 287 UC cases and 574 cancer-free controls to investigate the joint effects of cigarette smoking and polymorphisms of inflammatory genes on UC risk. Tumor necrosis factor alpha (TNF-α) -308 G/A and interleukin-8 (IL-8) -251 T/A polymorphisms were determined using a polymerase chain reaction-restriction fragment length polymorphism method. People who had ever smoked and those who were exposed to environmental tobacco smoke had significantly increased UC odds ratios (ORs) of 1.65 and 1.68, respectively. Participants who had smoked more than 18 pack-years had a significantly increased UC OR of 2.64. People who had ever smoked and who carried the A/A genotype of the TNF-α -308 G/A polymorphism had a significantly higher UC OR (10.25) compared to people who had never smoked and who carried the G/G or G/A genotype. In addition, people who had ever smoked and who carried the IL-8 -251 T/T genotype had a significantly increased UC OR (3.08) compared to people who had never smoked and who carried the T/A or A/A genotype. In a combined analysis of three major risk factors (cumulative cigarette smoking, the TNF-α -308 A/A genotype, and the IL-8 -251 T/T genotype), subjects with any one, any two, and all three risk factors experienced significantly increased UC ORs of 1.55, 2.89, and 3.77, respectively, compared to individuals with none of the risk factors. Conclusions. Our results indicate that the combined effects of cumulative cigarette exposure and the TNF-α -308 A/A genotype and/or the IL-8 -251 T/T genotype on UC OR showed a significant dose-response relationship.

A meta-analytic review of the association between two common SNPs in miRNAs and lung cancer susceptibility

Background

MicroRNAs (miRNAs) are involved in many biological processes, including tumor suppression. Multiple studies have shown an association between the miRNA-196a2 rs11614913 and miRNA-146a rs2910164 polymorphisms and cancer risk. However, the implications of the reported data are debatable and inconclusive.

Materials and methods

Relevant articles were retrieved from the PubMed, EMBASE, China National Knowledge Infrastructure, and WanFang databases from January 1, 2007, to April 30, 2017. Studies were assessed based on designated inclusion and exclusion criteria, and data were manually extracted from relevant studies by two investigators. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to explore the association between two single-nucleotide polymorphisms (SNPs) in miRNAs and lung cancer susceptibility.

Results

Nine eligible articles were included, consisting of 3,101 cancer cases and 3,234 controls for miRNA-196a2 rs11614913, and 3,483 cases and 3,578 controls for miRNA-146a rs2910164. For studies evaluating miRNA-196a2 rs11614913, significant associations with lung cancer risk were discovered. Overall, the pooled analysis showed that miRNA-196a2 rs11614913 was associated with a decreased cancer risk (CC vs TT: OR = 1.25, 95% CI: 1.09–1.44; CT vs TT: OR = 1.26, 95% CI: 1.03–1.53). For miRNA-146a rs2910164, only the CC genotype was found to be associated with high lung cancer risk (OR = 1.30, 95% CI: 1.13–1.49). Subgroup analyses based on ethnicity, source of control group, and country indicated that there were strong associations between miRNA-146a rs2910164 and cancer risk.

Conclusion

The results indicated that lung cancer risk was significantly associated with miRNA-196a2 rs11614913 and miRNA-146a rs2910164. These two common SNPs in miRNAs may be potential biomarkers of lung cancer.

Association of two FOXP3 polymorphisms with breast cancer susceptibility in Chinese Han women

BACKGROUND

Forkhead box P3 (FOXP3) is a key gene in the immune system which also plays a role in tumor development. This study aims to explore the association of two FOXP3 polymorphisms (rs3761548 and rs3761549) with susceptibility to breast cancer (BC).

METHOD

A case-control study was conducted, involving 560 patients and 583 healthy individuals from the Chinese Han population. The genotypes of FOXP3 polymorphisms were detected using the Sequenom MassARRAY method. The association between FOXP3 polymorphisms and BC risk was evaluated using a χ2 test with an odds ratio (OR) and 95% confidence intervals (95% CIs) under six genetic models. False-positive report probability was utilized to examine whether the significant findings were noteworthy.

RESULTS

We observed that rs3761548 was associated with a higher BC risk in heterozygous, dominant, overdominant, and allele genetic models (CA vs CC: OR =1.32, P=0.031; CA/AA vs CC: OR =1.32, P=0.023; CA vs CC/AA: OR =1.29, P=0.042; A vs C: OR =1.26, P=0.029), whereas no significant association was found between rs3761549 and BC risk. In addition, CA, CA/AA genotype, and A allele of rs3761548 were related to larger tumor size, and the A allele was also correlated with a positive status of Her-2 in BC patients.

CONCLUSION

Our study suggests that FOXP3 polymorphism rs3761548 is associated with BC susceptibility in the Chinese and may be involved in tumor progression. Future studies are needed to confirm the results in a larger population with more races.

MicroRNA-34a functions as a tumor suppressor by directly targeting oncogenic PLCE1 in Kazakh esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the frequent malignant tumors with poor prognosis worldwide. Identifying the prognostic biomarkers and potential mechanisms of such tumors has attracted increasing interest in esophageal cancer biology. Our previous study showed that phospholipase C elipson 1 (PLCE1) expression is up-regulated and associated with disease progression in esophageal carcinoma. MicroRNAs (miRNAs) play vital roles in regulating its target gene expression. However, studies on miRNA-regulated PLCE1 expression and its cellular function are still very few. We found that miR-34a is significantly expressed lower in ESCC tissues. We further showed that PLCE1 is a direct functional target gene of miR-34a, and the functional roles of miR-34a in ESCC cell lines in vitro were also determined through gain- and loss-of-function analyses. Results revealed that miR-34a functions as a tumor suppressor by inhibiting the proliferation, migration, and EMT phenotype, as well as promoting apoptosis of ESCC cell lines. Moreover, PLCE1 is overexpressed in ESCC tumors and promotes tumorigenicity in vivo and vitro. PLCE1 expression is negatively correlated with miR-34a profiles in ESCC tissues. Our data suggest that miR-34a exerts its anti-cancer function by suppressing PLCE1. The newly identified miR-34a/PLCE1 axis partially illustrates the molecular mechanism of ESCC metastasis and represents a new candidate therapeutic target for ESCC treatment.

Pre-micro RNA-499 Gene Polymorphism rs3746444 T/C is Associated with Susceptibility to Rheumatoid Arthritis in Egyptian Population

Pre-miRNA-499 gene is associated with autoimmune disease. Mir-449 rs3746444 polymorphism is inconsistent for rheumatoid arthritis (RA). This study aimed to investigate association of mir-499 rs3746444 polymorphism with RA activity and severity in Egyptian population. The study population was conducted as case control study in 100 RA patients diagnosed according to the American College of Rheumatology classification criteria for RA, and the control group included 100 healthy subjects who were age-and sex-matched to the RA group. Different genotypes were assessed using polymerase chain reaction-restriction fragment length polymorphism. 95% Confidence interval and odds ratio were defined to assess the strength of association. Regarding patients, thirty-three patients carried TT genotype, fifty-three patients carried TC genotype and fourteen patients carried CC genotype. So the frequency of the minor C allele in RA patients was significantly higher than the control subjects (P = 0.037). TC, CC genotypes and C allele frequencies were significantly associated with disease severity as they had high rheumatoid factor (55.78 µIU/ml) and anti-cyclic citrullinated peptide (Anti-CCP) antibody (297.32 µIU/ml). Moreover, the heterozygote TC had more severe and more active form of the disease compared with homozygote CC or TT as they had high Anti-CCP antibody, and disease activity score 28 (score 5). Our work suggests that C allele of Pre-miRNA rs3746444 polymorphism contributes to heritability of susceptibility to RA compared to T allele. This polymorphism was associated with the activity and severity of the disease.

Genetic variations in the PI3K-PTEN-AKT-mTOR pathway are associated with distant metastasis in nasopharyngeal carcinoma patients treated with intensity-modulated radiation therapy

Distant metastasis is the primary failure pattern of nasopharyngeal carcinoma(NPC) in intensity-modulated radiation therapy(IMRT) era. This study was conducted to find the impact of genetic variations in the phosphatidylinositol 3-kinase(PI3K)/phosphatase and tensin homologue(PTEN)/v-akt murine thymoma viral oncogene homologue(AKT)/mammalian target of rapamycin(mTOR) pathway on the risk of distant metastasis in NPC. We genotyped 16 single-nucleotide polymorphisms(SNPs) in five core genes in this pathway from 496 patients treated by IMRT with or without chemotherapy. The relationships between genetic polymorphisms and distant progression were evaluated. We observed that two loci in the AKT1 gene(rs3803300 and rs2494738 alone or combined) were associated with prognosis, with patients carrying at least one variant allele had significantly reduced risk of distant failure, especially in N2-3 group. In addition, we found that genetic variation may had some joint effect with N classification in recursive-partitioning analysis(RPA) analysis, with which patients were stratified into four different risk subgroups (RPA model): RPA1(low risk), RPA2(moderate risk), RPA3(high risk) and RPA4(highest risk). Our findings suggested that genetic variations within the PI3K signaling pathway modulate the development and invasion of NPC patients. Further research is needed to replicate the study in other centers and races, and to unravel the functional significance of these polymorphisms.

Association of microRNA polymorphisms with the risk of head and neck squamous cell carcinoma in a Chinese population: a case-control study

BACKGROUND

MicroRNA (miRNA) polymorphisms may alter miRNA-related processes, and they likely contribute to cancer susceptibility. Various studies have investigated the associations between genetic variants in several key miRNAs and the risk of human cancers; however, few studies have focused on head and neck squamous cell carcinoma (HNSCC) risk. This study aimed to evaluate the associations between several key miRNA polymorphisms and HNSCC risk in a Chinese population.

METHODS

In this study, we genotyped five common single-nucleotide polymorphisms (SNPs) in several key miRNAs (miR-149 rs2292832, miR-146a rs2910164, miR-605 rs2043556, miR-608 rs4919510, and miR-196a2 rs11614913) and evaluated the associations between these SNPs and HNSCC risk according to cancer site with a case-control study including 576 cases and 1552 controls, which were matched by age and sex in a Chinese population.

RESULTS

The results revealed that miR-605 rs2043556 [dominant model: adjusted odds ratio (OR) 0.71, 95% confidence interval (CI) 0.58-0.88; additive model: adjusted OR 0.74, 95% CI 0.62-0.89] and miR-196a2 rs11614913 (dominant model: adjusted OR 1.36, 95% CI 1.08-1.72; additive model: adjusted OR 1.28, 95% CI 1.10-1.48) were significantly associated with the risk of oral squamous cell carcinoma (OSCC). Furthermore, when these two loci were evaluated together based on the number of putative risk alleles (rs2043556 A and rs11614913 G), a significant locus-dosage effect was noted on the risk of OSCC (P trend < 0.001). However, no significant association was detected between the other three SNPs (miR-149 rs2292832, miR-146a rs2910164, and miR-608 rs4919510) and HNSCC risk.

CONCLUSION

Our study provided the evidence that miR-605 rs2043556 and miR-196a2 rs11614913 may have an impact on genetic susceptibility to OSCC in Chinese population.

Rare SNPs in receptor tyrosine kinases are negative outcome predictors in multiple myeloma

Multiple myeloma (MM) is a plasma cell disorder that is characterized by a great genetic heterogeneity. Recent next generation sequencing studies revealed an accumulation of tumor-associated mutations in receptor tyrosine kinases (RTKs) which may also contribute to the activation of survival pathways in MM. To investigate the clinical role of RTK-mutations in MM, we deep-sequenced the coding DNA-sequence of EGFR, EPHA2, ERBB3, IGF1R, NTRK1 and NTRK2 which were previously found to be mutated in MM, in 75 uniformly treated MM patients of the "Deutsche Studiengruppe Multiples Myelom". Subsequently, we correlated the detected mutations with common cytogenetic alterations and clinical parameters. We identified 11 novel non-synonymous SNVs or rare patient-specific SNPs, not listed in the SNP databases 1000 genomes and dbSNP, in 10 primary MM cases. The mutations predominantly affected the tyrosine-kinase and ligand-binding domains and no correlation with cytogenetic parameters was found. Interestingly, however, patients with RTK-mutations, specifically those with rare patient-specific SNPs, showed a significantly lower overall, event-free and progression-free survival. This indicates that RTK SNVs and rare patient-specific RTK SNPs are of prognostic relevance and suggests that MM patients with RTK-mutations could potentially profit from treatment with RTK-inhibitors.

Association between single nucleotide polymorphism in miR-499, miR-196a2, miR-146a and miR-149 and prostate cancer risk in a sample of Iranian population

MicroRNAs (miRNAs) play an important role in regulating gene expression at the post-transcriptional level and are involved in numerous physiological processes. Accumulating evidence suggests that single-nucleotide polymorphisms (SNPs) in human miRNA genes may affect miRNA biogenesis pathway and influence the susceptibility to several diseases such as cancer. The present study aimed to evaluate the impact of miR-499 rs3746444, miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms on prostate cancer (PCa) risk in a sample of Iranian population. This case-control study was done on 169 patients with pathologically confirmed PCa and 182 benign prostatic hyperplasia (BPH). The genotyping assays were done using T-ARMS-PCR or PCR-RFLP methods. The findings indicated that CC genotype of miR-499 rs3746444 polymorphism increased the risk of PCa (OR = 1.76, 95% CI = 1.12-2.79, P = 0.019) compared to TT genotype. No statistically significant association was found between miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms and PCa risk. In summary, the findings indicated that miR-499 rs3746444 polymorphism increased the risk of PCa in an Iranian population. Further studies with larger sample sizes and different ethnicities are necessary to verify the findings of the present study.

PTEN polymorphisms contribute to clinical outcomes of advanced lung adenocarcinoma patients treated with platinum-based chemotherapy

This study aimed to elucidate the impact of PTEN single nucleotide polymorphism (SNP) on clinical outcomes for advanced lung adenocarcinoma (LAC) patients treated with platinum-based chemotherapy. Three functional SNPs (rs11202607 G>A, rs701848 A>G, and rs11202592 G>C) of PTEN gene were genotyped by using DNA from blood samples of 618 advanced LAC patients, and their relationships with clinical outcomes were analyzed. The carriers of homozygous mutant of rs701848 and rs11202592 polymorphisms revealed significantly worse overall survival (OS) than those with heterozygote or wild-type homozygote (18.83 vs. 21.47 vs. 24.37 months, P = 0.034 and 13.40 vs. 19.03 vs. 21.90 months, P = 0.025, respectively). Subgroup analysis revealed that this association was particularly significant in tumor-lymph-node metastasis (TNM) stage III patients. The objective response rates (ORR) and disease control rates (DCR) of patients with genotype AA, AG, and GG in PTEN rs701848 polymorphism were statistically different (24.1 vs 16.6 vs 12.2 %, P = 0.017 and 82.7 vs 76.0 vs 70.2 %, P = 0.029, respectively). Haplotype analysis revealed a protective effect of the haplotype G-A-A (in the order of rs11202592, rs701848, and rs11202607) on chemotherapy efficacy and survival. Taken together, PTEN polymorphisms may contribute to survival and chemotherapy efficacy of advanced LAC patients treated with platinum-based agents.

An insertion/deletion polymorphism at miRNA-122 binding site in the IL1A is associated with a reduced risk of cervical squamous cell carcinoma

OBJECTIVE

Previous studies have shown that miRNA plays a key role in cervical carcinogenesis. Interleukin (IL)-1α can promote tumor growth, invasion, migration, and angiogenesis. An insertion/deletion polymorphism (rs3783553) in the IL1A 3' untranslated region may disrupt a binding site for miR-122 and miR-378 and thus change the transcription of IL-1α. The purpose of this study was to evaluate the association between the rs3783553 polymorphism and the risk of cervical squamous cell carcinoma (CSCC).

METHODS

Polymerase chain reaction was used to genotype the IL1A rs3783553 polymorphism in 235 patients with CSCC and 326 controls.

RESULTS

We found that the ins/ins genotype had a decreased risk to develop CSCC (odds ratio [OR]=0.48, 95% confidence interval [CI], 0.25-0.95). However, no significant association was observed between the IL1A rs3783553 genotype and clinical features.

CONCLUSION

These findings indicate that the IL1A rs3783553 polymorphism may be associated with the etiology of CSCC.

Genetic Variation in miR-146a Is Not Associated with Susceptibility to IgA Nephropathy in Adults from a Chinese Han Population

BACKGROUND

MicroRNA 146a (miR-146a) is a 19 to 23 nucleotide long, small non-coding RNA with gene regulatory functions that has influence on the pathogenesis of many diseases. A single nucleotide polymorphism (rs2910164 C>G) in pre-miR-146a is correlated with the expression of miR-146a. The aim of this study was to perform an association analysis of rs2910164 with IgA nephropathy in adult patients from a Chinese Han population.

METHODS

A total of 145 patients with renal biopsy-proved IgA nephropathy (IgAN) and 179 healthy controls were recruited to the current study. rs2910164 was genotyped by the polymerase chain reaction (PCR) and high-resolution melting methods (HRM). Clinical characteristics and pathology grading of patients with IgAN were recorded at the time of kidney biopsy.

RESULT

There were significant differences among the population of patients grouped by different age of onset in a co-dominant model (CG vs. CC vs. GG) (p = 0.033) and a recessive model (CG+CC vs. GG) (p = 0.001). However, no significant difference was observed in the distribution of genotypes between cases and controls (p = 0.144). There was also no significant difference between rs2910164 and patient quantitative traits (all p > 0.003) or different pathology grading (Lee's grading system and tubular atrophy/interstitial fibrosis in the Oxford classification) (all p > 0.05).

CONCLUSIONS

There was no association of rs2910164 with susceptibility to IgAN in adults from a Chinese Han population. However, rs2910164 was correlated with the age of onset of IgAN in adult patients.

MicroRNA-146a rs2910164 polymorphism and the risk of diffuse large B cell lymphoma in the Chinese Han population

The aim of this study was to determine the association of the microRNA-146a (miR-146a) polymorphism with the risk of diffuse large B cell lymphoma (DLBCL). The genotyping of miR-146a rs2910164 polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that CC genotype and C alleles distribution in the DLBCL patient was significantly higher than that of the controls (p = 0.01 and p = 0.01, respectively). No significant differences were found between the two subgroups when stratified by clinical characteristics including sexual, age at admission, performance status, pathological type, Ann Arbor stage, LDH and β2-MG value. The miR-146a expression was detected by the Taqman real-time PCR. The result showed that the miR-146a expression was notably upregulated in DLBCL patients when compared with controls (p = 0.02). In addition, the miR-146a expression of CC genotypes subgroup was drastically downregulated than that of GC/GG genotype subgroup in DLBCL patients (p = 0.0003), suggesting that this polymorphism can functionally affect the expression of miR-146a. In conclusion, it was shown that the miR-146a rs2910164 polymorphism is associated with the risk of DLBCL in the Chinese Han population.

Matrix metalloproteinases and genetic mouse models in cancer research: a mini-review

Carcinogenesis is a multistep and also a multifactorial process that involves agents like genetic and environmental factors. Matrix metalloproteinases (MMPs) are major proteolytic enzymes which are involved in cancer cell migration, invasion, and metastasis. Genetic variations in genes encoding the MMPs were shown in human studies to influence cancer risk and phenotypic features of a tumor. The complex role of MMPs seems to be important in the mechanism of carcinogenesis, but it is not well recognized. Rodent studies concentrated particularly on the better understanding of the biological functions of the MMPs and their impact on the pathological process, also through the modification of Mmp genes. This review presents current knowledge and the existing evidence on the importance of selected MMPs in genetic mouse models of cancer and human genetic association studies. Further, this work can be useful for scientists studying the role of the genetic impact of MMPs in carcinogenesis.

MicroRNA-146a rs2910164 polymorphism is associated with susceptibility to non-small cell lung cancer in the Chinese population

The aim of the present study was to investigate the association of single nucleotide polymorphisms (SNP) of the microRNA-146a (miR-146a) genes with the risk of nonsmall cell lung cancer (NSCLC). The genotyping of miR-146a rs2910164 polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that CC genotype and C allele distribution in the NSCLC patient were significantly higher than that of the controls (P=0.03 and 0.03, respectively). No significant differences were found between the two subgroups when stratified by clinical characteristics including age, sexual, smoke status, histological type, lymph node metastasis and clinical stage. In addition, the expression of miR-146a was detected by the Taqman real-time PCR. It demonstrated that the miR-146a expression was significantly decreased in NSCLC patients compared with that of nonmalignant lung tissues (P=0.01). In addition, the miR-146a expression of CC genotypes subgroup was significantly decreased than of GC/GG genotype subgroup in tumor tissues (P=0.0022). It confirmed that the SNP rs2910164 could functionally affect the miR-146a expression levels. In conclusion, it showed that the rs2910164 polymorphism of miR-146a is associated with the risk of NSCLC in the Chinese population.

The prostaglandin synthase 2/cyclooxygenase 2 (PTGS2/ COX2) rs5277 polymorphism does not influence risk of colorectal cancer in an Iranian population

BACKGROUND

The prostaglandin-endoperoxide synthase 2 [PTGS2, commonly known as cyclooxygenase-2 (COX-2)] is an enzyme induced by proinflammatory stimuli that is often overexpressed in malignant tissue and involved in the synthesis of prostaglandins and thromboxanes, regulators of processes such as inflammation, cell proliferation, and angiogenesis, all relevant for cancer development. We investigated whether a functional genetic polymorphism, rs5277, in COX-2 may have a risk-modifying effect on sporadic colorectal cancer in an Iranian population.

MATERIALS AND METHODS

We conducted a case-control study on 167 patients with colorectal cancer and 197 cancer-free controls in Taleghani Hospital in Tehran, Iran, between 2007 and 2011. Peripheral blood samples of both groups were processed for DNA extraction and genotyping of the COX-2 gene polymorphism (rs5277) using PCR-RFLP. RFLP results were confirmed by direct sequencing. Logistic regression analysis was performed to calculate the adjusted odds ratio (OR) and 95% confidence interval (95% CI).

RESULTS

There was no significant difference in the distribution of COX-2 gene rs5277 polymorphism genotype and the allelic form, among CRC patients compared with the healthy control group (p: 0.867).

CONCLUSIONS

Our results suggest that rs5277 polymorphism in COX2 could not be a good prognostic indicator for patients with CRC.

Influence of methylenetetrahydrofolate reductase C677T polymorphism on the risk of lung cancer and the clinical response to platinum-based chemotherapy for advanced non-small cell lung cancer: an updated meta-analysis

PURPOSE

Methylenetetrahydrofolate reductase (MTHFR) has been implicated in lung cancer risk and response to platinum-based chemotherapy in advanced non-small cell lung cancer (NSCLC). However, the results are controversial. We performed meta-analysis to investigate the effect of MTHFR C677T polymorphism on lung cancer risk and response to platinum-based chemotherapy in advanced NSCLC.

MATERIALS AND METHODS

The databases of PubMed, Ovid, Wanfang and Chinese Biomedicine were searched for eligible studies. Nineteen studies on MTHFR C677T polymorphism and lung cancer risk and three articles on C677T polymorphism and response to platinum-based chemotherapy in advanced NSCLC, were identified.

RESULTS

The results indicated that the allelic contrast, homozygous contrast and recessive model of the MTHFR C677T polymorphism were associated significantly with increased lung cancer risk. In the subgroup analysis, the C677T polymorphism was significantly correlated with an increased risk of NSCLC, with the exception of the recessive model. The dominant model and the variant T allele showed a significant association with lung cancer susceptibility of ever smokers. Male TT homozygote carriers had a higher susceptibility, but the allelic contrast and homozygote model had a protective effect in females. No relationship was observed for SCLC in any comparison model. In addition, MTHFR 677TT homozygote carriers had a better response to platinum-based chemotherapy in advanced NSCLC in the recessive model.

CONCLUSION

The MTHFR C677T polymorphism might be a genetic marker for lung cancer risk or response to platinum- based chemotherapy in advanced NSCLC. However, our results require further verification.

Polymorphisms in DNA repair and apoptosis-related genes and clinical outcomes of patients with non-small cell lung cancer treated with first-line paclitaxel-cisplatin chemotherapy

This study was conducted to analyze a comprehensive panel of single nucleotide polymorphisms (SNPs) in genes in DNA repair and apoptosis pathways and determine the relationship between polymorphisms and treatment outcomes of patients with non-small cell lung cancer (NSCLC) treated with first-line paclitaxel-cisplatin chemotherapy. Three hundred eighty two patients with NSCLC were enrolled. Seventy-four SNPs in 48 genes (42 SNPs in 27 DNA repair pathway genes and 32 SNPs in 21 apoptotic pathway genes) were genotyped and their associations with chemotherapy response and overall survival (OS) were analyzed. Among SNPs in DNA repair genes, BRCA1 rs799917 was significantly associated with both chemotherapy response and OS. XRCC1 rs25487 exhibited a significant association with chemotherapy response and ERCC2 rs1052555 with OS. Four SNPs in apoptotic genes (TNFRSF1B rs1061624, BCL2 rs2279115, BIRC5 rs9904341, and CASP8 rs3769818) were significantly associated with OS, but not with response to chemotherapy. When the six SNPs which were associated with OS in individual analysis were combined, OS decreased as the number of bad genotypes increased (P(trend) = 2 × 10(-6)). Patients with 3, and 4-6 bad genotypes had significantly worse OS compared with those carrying 0-2 bad genotypes (adjusted hazard ratio [aHR] = 1.54, 95% CI = 1.14-2.08, P = 0.005; aHR = 2.10, 95% CI = 1.55-2.85, P = 2 × 10(-6), respectively). In conclusion, these findings suggest that the six SNPs identified, particularly their combined genotypes, could be used as biomarkers predicting chemotherapy response and survival of NSCLC patients treated with first-line paclitaxel-cisplatin chemotherapy.

A functional polymorphism rs11614913 in microRNA-196a2 is associated with an increased risk of colorectal cancer although not with tumor stage and grade

A C/T polymorphism (rs11614913) was identified in the microRNA (miRNA) 196a2 (miR-196a2) gene and was implicated in the susceptibility to cancer. Numerous studies have investigated its association with the risk of colorectal cancer (CRC). However, the results were inconsistent and inconclusive. The present meta-analysis was conducted based on the results of six published case-control studies comprising 1,754 cases and 2,430 controls (up to November, 2012). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for the allelic and genotypic comparisons following the co-dominant, dominant and recessive genetic models. The Chi-square-based Q-test was used to assess heterogeneity. Egger's test and inverted funnel plots were used to investigate publication bias. Subgroup analysis was also performed. The results demonstrated that almost all the genetic models (except the model of CT vs. TT) indicated a significant association between rs11614913 polymorphism and CRC risk. The subgroup analysis in an Asian population also demonstrated similar results. However, there was no significant association of miR-196a2 rs11614913 polymorphism with the clinical characteristics of CRC patients. Our results confirmed the association of the polymorphism rs11614913 with the risk of CRC, but not with tumor stage and grade.

Association of the microRNA-499 variants with susceptibility to hepatocellular carcinoma in a Chinese population

microRNAs (miRNAs) are a new class of small non-coding RNAs that function as tumor suppressors or oncogenes. Single nucleotide polymorphisms (SNPs) in miRNA may contribute to cancer development. We hypothesized that genetic variations of the miRNA could be associated with the risk of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). A total of 100 patients with HCC, 100 cases of chronic hepatitis B and 100 health adults were enrolled in this present study. Two common polymorphisms in pre-miRNAs: Homo sapiens miRNA-146a (hsa-mir-146a) (rs291016, guanine to cytosine [G-C]) and hsa-mir-499 (rs3746444; adenine to guanine [C-T]) were genotyped by PCR-Restriction Fragment Length Polymorphism and confirmed by bidirectional DNA sequencing. Significant differences were found in frequency and distribution of the genotypes of miRNA-499 between the HCC and the control group. Compared with miRNA-499 T/T, the odds ratio (OR) of patients with miRNA-499 C/C for developing HCC was 3.630 (95% CI: 1.545-8.532), and OR for developing HBV-related HCC was 3.133 (95% CI: 1.248-7.861). There was no significant association between miRNA-146a polymorphism and the risk of HCC in all subjects. Our results suggested that hsa-mir-499 polymorphism was associated with susceptibility to HBV-related HCC in Chinese population. Further characterization of miRNA SNPs may open new avenue for the study of cancer and therapeutic interventions.

Evidence that polymorphisms in detoxification genes modulate the susceptibility for sporadic medullary thyroid carcinoma

AIM

Polymorphic low-penetrance genes have been consistently associated with the susceptibility to a series of human tumors, including differentiated thyroid cancer.

METHODS

To determine their role in medullary thyroid cancer (MTC), we used TaqMan SNP method to genotype 47 sporadic MTC (s-MTC) and a control group of 578 healthy individuals for CYP1A2*F, CYP1A1m1, GSTP1, NAT2 and 72TP53. A logistic regression analysis showed that NAT2C/C (OR=3.87; 95% CI=2.11-7.10; P=2.2×10(-5)) and TP53C/C genotypes (OR=3.87; 95% CI=1.78-6.10; P=2.8×10(-4)) inheritance increased the risk of s-MTC. A stepwise regression analysis indicated that TP53C/C genotype contributes with 8.07% of the s-MTC risk.

RESULTS

We were unable to identify any relationship between NAT2 and TP53 polymorphisms suggesting they are independent factors of risk to s-MTC. In addition, there was no association between the investigated genes and clinical or pathological features of aggressiveness of the tumors or the outcome of MTC patients.

CONCLUSION

In conclusion, we demonstrated that detoxification genes and apoptotic and cell cycle control genes are involved in the susceptibility of s-MTC and may modulate the susceptibility to the disease.

Lysyl oxidase G473A polymorphism is closely associated with susceptibility to gastric cancer in a South Korean population

The aim of this study was to determine whether a single nucleotide polymorphism at G473A (rs1800449) within the LOX-propeptide is associated with susceptibility to gastric cancer. We investigated the genotype and allele frequencies of this gene in tissue specimens from 458 gastric cancer patients and 282 healthy individuals. Polymorphism analysis was performed by amplifying the propeptide region of LOX and digestion with NotI followed by sequencing of the products. The frequencies of the LOX G473A G/G, G/A, and A/A genotypes were 54.4% (249/458), 34.3% (157/458), and 11.3% (52/458), respectively, in gastric cancer patients and 58.9% (166/300), 35.5% (100/282), and 5.7% (16/282), respectively, in the healthy controls. Statistically significant differences in the genotype and allele frequency of LOX rs1800449 were observed between the healthy controls and gastric cancer patients (p = 0.0294 and p = 0.0339). When the data were stratified according to gastric cancer histologic subtype, the risk of diffuse-type gastric cancer in carriers with an A allele (G/A or A/A genotypes) was statistically higher compared to that of carriers with the G/G genotype (p = 0.0001). Our findings suggest that G473A polymorphism of the LOX gene may be closely associated with susceptibility to the development and differentiation of gastric cancer in South Korean patients.

Association of polymorphisms in pre-miRNA with inflammatory biomarkers in rheumatoid arthritis in the Chinese Han population

The aim of this study was to detect the association between 2 single nucleotide polymorphisms (SNPs), rs2910164 G>C and rs3746444 T>C, in pre-miRNA (hsa-mir-146a and hsa-mir-499) and the chronic inflammation in the Chinese Han population with rheumatoid arthritis (RA). Two hundred sixty-two Han Chinese patients with RA were recruited in this study. The SNPs were genotyped by polymerase chain reaction restriction fragment length polymorphism. C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), and the plasma concentrations of interleukin (IL)-6, tumor necrosis factor α (TNF-α), and transforming growth factor β1 (TGF-β1) were measured. There was a significant difference in the levels of CRP and ESR among different genotypes in rs3746444 (p = 0.031 and p = 0.047, respectively). The heterozygote CT had significantly higher levels of CRP and ESR compared with homozygotes CC and TT. No significant association was observed between the SNP rs2910164 and the levels of CRP, ESR, IL-6, TNF-α, and TGF-β1 (all p > 0.05). The results of this study provided the first evidence that the SNP rs3746444 in pre-miR-499 could affect the inflammatory reaction in patients with RA. The findings were significant and might contribute to the clinical assessment of inflammatory activity, which in turn may influence therapeutic decision making.

AKT1 polymorphisms and survival of early stage non-small cell lung cancer

BACKGROUND AND OBJECTIVES

This study was conducted to investigate the impact of polymorphisms in the AKT1 gene on the survival of early stage non-small cell lung cancer (NSCLC) patients.

METHODS

Three hundred and ten patients with surgically resected NSCLC were enrolled. The rs3803300, rs1130214, rs3730358, rs1130233, and rs2494732 single nucleotide polymorphisms (SNPs) in the AKT1 gene were investigated. The genotype and haplotype associations with overall survival (OS) and disease free survival (DFS) were analyzed.

RESULTS

The three SNPs (rs3803300, rs1130214, and rs2494732) were significantly associated with survival outcomes on multivariate analysis. When the three SNPs were combined, OS and DFS were decreased in a dose-dependent manner as the number of bad genotypes increased (P(trend)  = <1.0 × 10(-4) and 0.001, respectively). Patients with 2 bad genotypes had a significantly worse OS and DFS compared with those with 0 bad genotypes (adjusted hazard ratio (HR) = 3.08, 95% confidence interval (CI) = 1.61-5.89, P = 0.001; and adjusted HR = 2.04, 95% CI = 1.22-3.43, P = 0.01).

CONCLUSIONS

These results suggest that the AKT1 polymorphisms could be used as prognostic markers for the patients with early-stage NSCLC.

APEX microarray panel for genotyping polymorphisms in cancer chemotherapy and estimation frequencies in a Slovak population

Aim: Many studies focus on monitoring response to chemotherapy, adverse effects and prediction of therapeutic effects, which depend on individual gene variability. The amount of various polymorphisms in genes involved in the folate cycle, and other metabolic pathways involved in the metabolism of chemotherapeutic drugs, are an essential topic of such studies. This work focuses on the design and establishment of a pharmacogenetically relevant panel, which could be applied to the rapid genotyping of patients treated with thiopurines, 5-fluorouracil, methotrexate, irinotecan and glucocorticoids. Materials & methods: A total of 97 variations in 36 genes associated with side effects of chemotherapeutic treatment were selected. Of these, 94 SNPs were genotyped by the arrayed primer extension (APEX; Asper Biotech Ltd) microarray method or direct sequencing. Variations of tandem repeats or gene deletions were genotyped by capillary electrophoresis and PCR detection. A total of 300 DNA samples from healthy volunteers were tested to estimate genotype frequencies for a Slovak population. All data were checked for Hardy–Weinberg equilibrium and genetic linkage between variations. Results: We designed an APEX microarray for genotyping pharmacologically relevant polymorphisms in patients undergoing chemotherapy. We estimated genotype frequencies for all 97 polymorphisms testing 300 individuals from the Slovak population, which may also serve as an estimate of central European frequencies. These data also allowed for the testing of genetic linkage between loci. Many of the determined genotype frequencies in this study were in similar ranges found in other European populations but four SNPs, rs11760837 (p = 0.018), rs1801265 (p = 0.0375), rs1801394 (p = 0.0066) and rs182455 (p = 0.0083), demonstrated stronger deviation. Conclusion: Genetic variability in genes involved in metabolic pathways of chemotherapeutic drugs, such as methotrexate, 5-fluorouracil, thiopurines or irinotecan, is responsible for individual therapy response and development of side effects. A comprehensive approach in genotyping of numerous variants is aimed to improve individual access to patients and the selection of appropriate drugs for treatment. The APEX microarray method is a valuable tool for fast, reliable and cost-effective genotyping of variants which can be used for the typing of known variants in patients prior to treatment as well as in studies searching for new genotype–phenotype associations. The opportunity of adding additional variants during the study makes the APEX microarray technology flexible and suitable for such trials.

Original submitted 4 October 2010; Revision submitted 23 November 2010.

Hodgkin disease risk: role of genetic polymorphisms and gene-gene interactions in inflammation pathway genes

Inflammation is a critical component of cancer development. The clinical and pathological features of Hodgkin disease (HD) reflect an abnormal immunity that results from cytokines secreted by Reed-Sternberg cells and the surrounding tumor. Numerous studies have reported the association between genetic polymorphisms in cytokine genes and the susceptibility to different hematologic cancers. However, the effects of such SNPs on modulating HD risk have not yet been investigated. We hypothesized that gene-gene interactions between candidate genes in the anti- and pro-inflammatory pathways carrying suspicious polymorphisms may contribute to susceptibility to HD. To test this hypothesis, we conducted a study on 200 HD cases and 220 controls to assess associations between HD risk and 38 functional SNPs in inflammatory genes. We evaluated potential gene-gene interactions using a multi-analytic strategy combining logistic regression, multi-factor dimensionality reduction, and classification and regression tree (CART) approaches. We observed that, in combination, allelic variants in the COX2, IL18, ILR4, and IL10 genes modify the risk for developing HD. Moreover, the cumulative genetic risk score (CGRS) revealed a significant trend where the risk for developing HD increases as the number of adverse alleles in the cytokine genes increase. These findings support the notion that epigenetic-interactions between these cytokines may influence pathogenesis of HD modulating the proliferation of regulatory T cells. In this way, the innate and adaptative immune responses may be altered and defy their usual functions in the host anti-tumor response. Our study is the first to report the association between polymorphisms in inflammation genes and HD susceptibility risk.

Association study of single nucleotide polymorphisms in pre-miRNA and rheumatoid arthritis in a Han Chinese population

The aim of this study was to perform an association study between two single nucleotide polymorphisms (SNPs) rs2910164 G>C and rs3746444 T>C in pre-miRNA (hsa-mir-146a and hsa-mir-499) and rheumatoid arthritis (RA) in the Han Chinese population. 208 Han Chinese patients with RA and 240 healthy controls were recruited in this study. The SNPs was genotyped by polymerase chain reaction-restriction fragment length polymorphism. Anti-cyclic citrullinated peptide (anti-CCP) antibody was measured by enzyme linked immunosorbent assay and rheumatoid factor (RF) was measured by rate nephelometry. The genotype frequencies between cases and controls were compared by χ(2) analysis. No significant association between the SNPs (rs2910164 and rs3746444) and RA was observed (P = 0.631 and 0.775, respectively), and the SNPs did not show any association with the RF-positive (P = 0.631 and 0.775, respectively). However, there was a significant difference on the level of anti-CCP antibody between different genotypes in rs3746444 (P = 0.007). The heterozygote CT had significantly higher level of anti-CCP antibody compared with homozygote CC and TT (P = 0.054 and 0.003, respectively). We first investigated the association between the SNPs (rs2910164 G>C and rs3746444 T>C) in the pre-miRNA (hsa-mir-146a and hsa-mir-499) and RA in a Han Chinese population. We did not find a significant association between the SNPs and the susceptibility to RA, while the SNP rs3746444 may affect anti-CCP antibody production.

Comprehensive analysis of DNA repair gene polymorphisms and survival in patients with early stage non-small-cell lung cancer

This study was conducted to analyze a comprehensive panel of single nucleotide polymorphisms (SNP) in DNA repair genes to determine the relationship between polymorphisms and the survival outcome of patients with early stage non-small-cell lung cancer (NSCLC). Three hundred and ten consecutive patients with surgically resected NSCLC were enrolled. Forty-eight SNP in 27 DNA repair genes were genotyped and their associations with overall survival (OS) and disease-free survival (DFS) were analyzed. Individually, six SNP exhibited significant associations with survival outcome. When the six SNP were combined, OS and DFS decreased as the number of bad genotypes increased (P(trend) <0.0001 for both). Patients with three, and four or five bad genotypes had a significantly worse OS and DFS compared with those carrying zero or one bad genotypes (adjusted hazard ratio [aHR] for OS=3.53, 95% confidence interval [CI]=1.25-9.97, P=0.02, and aHR for DFS=3.31, 95% CI=1.41-7.76, P=0.006; and aHR for OS=5.47, 95% CI=1.87-16.00, P=0.002, and aHR for DFS=4.42, 95% CI=1.82-10.74, P=0.001, respectively). These findings suggest that the six SNP identified can be used as prognostic markers for patients with surgically resected early stage NSCLC.

Association of pre-microRNAs genetic variants with susceptibility in systemic lupus erythematosus

MicroRNAs (miRNAs) may play important roles in SLE, but genetic polymorphisms of miRNAs and their relationships with various autoantibodies present in SLE patients remain unclear. Here, we report that 213 SLE patients and 209 healthy individuals of Chinese had been taken into this case-control studies, which had been performed by selecting two miRNAs (hsa-mir-146a rs2910164 G>C, and hsa-mir-499 rs3746444 T>C) to analyze the genetic polymorphisms. The single nucleotide polymorphism (SNP) variants had been analyzed by PCR-RFLP and serum anti-ribonucleoprotein (anti-RNP), anti-Sm nuclear antigen (anti-Sm) antibodies had been determined by an anti-ENA kit and serum anti-double-stranded DNA (anti-dsDNA) antibodies had been assessed by indirect immunofluorescence. We found that hsa-mir-146a rs2910164 and hsa-mir-499 rs3746444 polymorphisms had no significant relationship with SLE susceptibility. The genotype frequencies of rs2910164 (GG, CC, and GC) were 16, 37, and 47% in SLE patients, but 11, 39, and 50% in healthy group (P = 0.397), respectively; The genotype frequencies of rs3746444 (CC, TT, and TC) were 3, 74, and 23% in SLE patients, but 3, 76, and 22% in healthy group (P = 0.892), respectively. The G and C allele frequencies of rs2910164 were 39 and 61% in SLE patients, but 36 and 64% in healthy group (P = 0.990), respectively. The C and T allele frequencies of rs3746444 were 15 and 85% in SLE patients, but 14 and 86% in healthy group (P = 0.702), respectively. In addition, we also showed no significant difference in the distribution of rs2910164 and rs3746444 genotypes in each of the three antibodies (anti-RNP, anti-Sm, and anti-dsDNA).

K-RAS mutation in the screening, prognosis and treatment of cancer

The potential use of K-RAS mutation as a cancer screening biomarker has been investigated for many years. Numerous associations between K-RAS mutation and various cancers have been established, but these associations have not been translated into effective, cost-efficient cancer screening strategies. This lack of progress may be due to the existence of K-RAS mutation in nontumor tissues and/or using detection, rather than quantitation, of K-RAS mutation as the endpoint for cancer risk categorization. K-RAS mutation appears to be a useful prognostic biomarker for colon cancer. Recent progress toward sensitive and quantitative mutation characterization and the successful use of K-RAS mutation in a personalized medicine approach to targeted biological therapy selection are likely to re-direct and expand the use of K-RAS mutation as a cancer biomarker in the near future.

Gender-specific association of methylenetetrahydrofolate reductase genotype and haplotype with the aggressiveness and prognosis of clear cell renal cell carcinoma in Japanese patients

OBJECTIVE

To determine if the two common polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene, C677T and A1298C, affect tumour aggressiveness or prognosis of clear cell renal cell carcinoma (CCRCC) in Japanese patients.

PATIENTS AND METHODS

MTHFR C677T and A1298C polymorphisms have been reported to cause decreased enzyme activity, which reduces the quantity of methyl groups available for DNA methylation and leads to mis-incorporation of uracil into DNA, resulting in single-strand DNA breaks. These effects might induce the accumulation of several genetic changes, leading to the development and progression of CCRCC. Therefore, we investigated the associations between MTHFR genotypes and haplotypes and the clinicopathological characteristics and survival rates in 240 Japanese patients with histopathologically confirmed CCRCC. MTHFR C677T and A1298C were genotyped and haplotypes were analysed using appropriate software.

RESULTS

The variant genotypes of MTHFR A1298C were significantly associated with some advanced characteristics of CCRCC in all patients, and these associations were stronger among men. However, among women, the variant genotypes of MTHFR C677T were associated with some advanced characteristics of CCRCC and the C677T variant genotypes or the 677T-1298A haplotype was significantly associated with decreased overall survival (P = 0.007 and P = 0.009, respectively).

CONCLUSION

To our knowledge, this is the first report on the association between MTHFR polymorphisms and CCRCC aggressiveness or prognosis. These results suggest that the MTHFR genotypes and haplotype might be useful, in a gender-specific manner, as predictive factors for the clinical course of CCRCC. Furthermore, these findings will contribute to the understanding of the mechanisms underlying CCRCC progression.

The Int7G24A variant of transforming growth factor-beta receptor type I is a risk factor for colorectal cancer in the male Spanish population: a case-control study

BACKGROUND

The Int7G24A variant of transforming growth factor-beta receptor type I (TGFBR1) has been shown to increase the risk for kidney, ovarian, bladder, lung and breast cancers. Its role in colorectal cancer (CRC) has not been established. The aims of this study were to assess the association of TGFBR1*Int7G24A variant with CRC occurrence, patient age, gender, tumour location and stage.

METHODS

We performed a case-control study with 504 cases of sporadic CRC; and 504 non-cancerous age, gender and ethnically matched controls. Genotyping analysis was performed using allelic discrimination assay by real time PCR.

RESULTS

The Int7G24A variant was associated with increased CRC incidence in an additive model of inheritance (P for trend = 0.005). No significant differences were found between Int7G24A genotypes and tumour location or stage. Interestingly, the association of the Int7G24A variant with CRC risk was significant in men (odds ratio 4.10 with 95% confidence intervals 1.41-11.85 for homozygous individuals; P for trend = 0.00023), but not in women. We also observed an increase in susceptibility to CRC for individuals aged less than 70 years.

CONCLUSION

Our data suggest that the Int7G24A variant represents a risk factor for CRC in the male Spanish population.

Cell proliferation-related genetic polymorphisms and gastric cancer risk: systematic review and meta-analysis

Apart from Helicobacter pylori infection and lifestyle factors, host genetic susceptibility has been suggested to contribute to individual variation in gastric cancer risk as well. Aiming to evaluate the associations between host cell proliferation-related genetic polymorphisms and gastric cancer susceptibility, we reviewed the related studies published until 15 September 2008 and quantitatively summarized the associations of the most widely studied polymorphisms (TP53 Arg72Pro, L-myc EcoRI) using meta-analysis. Fifty-five eligible studies were included in this review. Twenty-three polymorphisms significantly related to gastric cancer risk in at least one study were identified. Polymorphisms determining higher levels of growth factors, which are important for tissue repair, were recently observed to be associated with reduced risk of gastric cancer. In the meta-analysis, TP53 72Pro was associated with increased risk of diffuse gastric cancer among Asians (OR, 1.44; 95% CI, 1.04-1.99), but decreased risk of intestinal gastric cancer among Caucasians (OR, 0.56; 95% CI, 0.36-0.89). This review suggests that cell proliferation-related genetic polymorphisms could be candidate biomarkers of gastric cancer risk, but current evidence for the use for risk stratification is still very limited. Modestly significant associations in meta-analyses stratified by population or type of gastric cancer may be observed by chance because of the limited number of studies and small sample size. Larger studies are warranted to clarify the effect of cell proliferation-related genetic polymorphisms on gastric carcinogenesis.

Brain tumor epidemiology: consensus from the Brain Tumor Epidemiology Consortium

Epidemiologists in the Brain Tumor Epidemiology Consortium (BTEC) have prioritized areas for further research. Although many risk factors have been examined over the past several decades, there are few consistent findings, possibly because of small sample sizes in individual studies and differences between studies in patients, tumor types, and methods of classification. Individual studies generally have lacked samples of sufficient size to examine interactions. A major priority based on available evidence and technologies includes expanding research in genetics and molecular epidemiology of brain tumors. BTEC has taken an active role in promoting understudied groups, such as pediatric brain tumors; the etiology of rare glioma subtypes, such as oligodendroglioma; and meningioma, which, although it is not uncommon, has only recently been registered systematically in the United States. There also is a pressing need for more researchers, especially junior investigators, to study brain tumor epidemiology. However, relatively poor funding for brain tumor research has made it difficult to encourage careers in this area. In this report, BTEC epidemiologists reviewed the group's consensus on the current state of scientific findings, and they present a consensus on research priorities to identify which important areas the science should move to address.

A functional polymorphism in the miR-146a gene is associated with the risk for hepatocellular carcinoma

A G > C polymorphism (rs2910164) is located in the stem region opposite to the mature miR-146a sequence, which results in a change from G:U pair to C:U mismatch in the stem structure of miR-146a precursor. Here, we elucidated the biological significance of this polymorphism, based on cancer association study and cell model system. The cancer association study included 479 hepatocellular carcinoma (HCC) and 504 control subjects. We found that the genotype distribution of this polymorphism in HCC cases was significantly different from that in control subjects (P = 0.026). The association between the genotype and the risk of HCC was further analyzed using multivariate unconditional logistic regression, with adjustment for sex, age and hepatitis B virus status. The results revealed that male individuals with GG genotype were 2-fold more susceptible to HCC (odds ratio = 2.016, 95% confidence interval = 1.056-3.848, P = 0.034) compared with those with CC genotype. We next examined the influence of this polymorphism on the production of mature miR-146a and found that G-allelic miR-146a precursor displayed increased production of mature miR-146a compared with C-allelic one. Further investigations disclosed that miR-146a could obviously promote cell proliferation and colony formation in NIH/3T3, an immortalized but non-transformed cell line. These data suggest that the G > C polymorphism in miR-146a precursor may result in important phenotypic traits that have biomedical implications. Our findings warrant further investigations on the relation between microRNA polymorphism and human diseases.