Investigation of cyclin D1 rs9344 G>A polymorphism in colorectal cancer: a meta-analysis involving 13,642 subjects

The Investigation of Associations between TP53 rs1042522, BBC3 rs2032809, CCND1 rs9344, EGFR rs2227983 Polymorphisms and Breast Cancer Phenotype and Prognosis

Breast cancer is one of the most common oncological diseases among women worldwide. Cell cycle and apoptosis-related genes TP53, BBC3, CCND1 and EGFR play an important role in the pathogenesis of breast cancer. However, the roles of single nucleotide polymorphisms (SNPs) in these genes have not been fully defined. Therefore, this study aimed to analyze the association between TP53 rs1042522, BBC3 rs2032809, CCND1 rs9344 and EGFR rs2227983 polymorphisms and breast cancer phenotype and prognosis. For the purpose of the analysis, 171 Lithuanian women were enrolled. Genomic DNA was extracted from peripheral blood; PCR-RFLP was used for SNPs analysis. The results showed that BBC3 rs2032809 was associated with age at the time of diagnosis, disease progression, metastasis and death. CCND1 rs9344 was associated with tumor size, however an association resulted in loss of significance after Bonferroni correction. In survival analysis, significant associations were observed between BBC3 rs2032809 and OS, PFS and MFS. EGFR rs2227983 also showed some associations with OS and PFS (univariate Cox regression analysis). However, the results were in loss of significance (multivariate Cox regression analysis). In conclusion, BBC3 rs2032809 polymorphism was associated with breast cancer phenotype and prognosis. Therefore, it could be applied as potential markers for breast cancer prognosis.

Significant Association of Cyclin D1 Promoter Genotypes With Asthma Susceptibility in Taiwan

BACKGROUND/AIM

The molecular mechanisms underlying the association between cell cycle and asthma are poorly understood, and cyclin D1 (CCND1) is found to be upregulated in asthma airway smooth muscle. We investigated whether the most frequently examined functional variants in CCND1 determine asthma susceptibility.

MATERIALS AND METHODS

We genotyped 651 participants for single-nucleotide polymorphisms (SNPs) at rs9344 and rs678653 on CCND1 and assessed the association of these SNPs with asthma risk.

RESULTS

Significant differences were found in the distributions of genotypic (p=0.0064) and allelic (p=0.0021) frequencies of CCND1 rs9344. In addition, AG or GG carriers had 0.63- or 0.48-fold adjusted odds ratios for asthma risk (95%confidence intervals=0.48-0.92 and 0.22-0.78, respectively) than those who carried the AA wildtype.

CONCLUSION

Our results suggest that cell cycle regulation may play a role in asthma initiation and development, and the CCND1 rs9344 genotype may serve as an early detection marker for asthma.

Computational analysis of Cyclin D1 gene SNPs and association with breast cancer

CCND1 encodes for Cyclin D1 protein and single-nucleotide polymorphisms (SNPs) can modulate its activity. In the present study, the impact of CCND1 SNPs on structure and/or function of Cyclin D1 protein using in silico tools was investigated. Our analysis revealed only one splice site SNP (c.1988+5G<A) can effect CCND1 function. Subsequently, 78 out of 169 missense variants were predicted as pathogenic by Polyphen2, SIFT, PROVEAN, SNPs&GO, and PANTHER, and 4/78 missense SNPs were further evaluated because these four SNPs were found to be reside in highly conserved region of Cyclin D1. However, they did not show any major impact on tertiary structure and domain of Cyclin D1 but overall R15S and A190S has displayed a significant diseased phenotype and an altered molecular mechanism predicted by MutPred, FATHMM, SNPeffect, SNAP2, and PredictSNP. Consistently, A190S, R179L, and R15S may also cause a decrease in stability of Cyclin D1 anticipated by I-Mutant, HOPE and SNP effect. Furthermore, the Kaplan–Meier plotter has explained that high expression of CCND1 is associated with less survival rate of breast cancer patients. Altogether our study suggests that c.1988+5G<A, R15S, R179L, and A190S SNPs could directly or indirectly destabilize Cyclin D1.

Association between methylenetetrahydrofolate reductase tagging polymorphisms and susceptibility of hepatocellular carcinoma: a case-control study

Polymorphisms in one-carbon metabolism genes may influence the susceptibility to hepatocellular carcinoma (HCC). In the present study, we studied methylenetetrahydrofolate reductase (MTHFR) tagging polymorphisms in 584 HCC cases and 923 controls. Polymerase chain reaction was harnessed to detect MTHFR genotype. Overall, our results showed that genotype distribution of MTHFR rs4846048 and rs4845882 polymorphisms was not different between HCC patients and controls. MTHFR rs9651118 and rs1801133 loci were protective factors for HCC (rs9651118: CT vs. TT: adjusted odds ratio (OR) = 0.67, 95% confidence interval (CI): 0.49–0.90, P=0.008 and TC/CC vs. TT: adjusted OR = 0.70, 95% CI: 0.53–0.93, P=0.015; rs1801133: GA vs. GG: adjusted OR = 0.72, 95% CI: 0.54–0.97, P=0.031, AA/GA vs. GG: adjusted OR = 0.76, 95% CI: 0.57–0.99, P=0.045). However, MTHFR rs3753584 locus was a candidate for susceptibility to HCC (CT vs. TT: adjusted OR = 1.67, 95% CI: 1.20–2.32, P=0.003 and TC/CC vs. TT: adjusted OR = 1.59, 95% CI: 1.15–2.20, P=0.005). Results of haplotype analysis suggested that MTHFR G_rs1801133T_rs3753584G_rs4845882A_rs4846048T_rs9651118 was associated with the risk of HCC (OR = 1.55, 95% CI: 1.16–2.07, P=0.003). The power of our study also confirmed these associations (the value of power >0.80). In summary, our findings suggested that MTHFR rs3753584, rs9651118 and rs1801133 polymorphisms may affect the risk of HCC in Chinese Han population. In future, our findings should be further validated in additional case–control studies.

Investigation of Leptin and its receptor (LEPR) for single nucleotide polymorphisms in colorectal cancer: a case-control study involving 2,306 subjects

Single nucleotide polymorphisms (SNPs) in the genes coding for leptin (LEP) and its receptor (LEPR) might regulate energy balance and be implicated in the development of colorectal cancer (CRC). In the present investigation, 1,003 CRC cases and 1,303 matched controls was compared. Five functional SNPs in LEP and LEPR genes were chosen to evaluate the correlation of these chosen SNPs with CRC susceptibility. We used the SNPscan^TM genotyping assay to genotype LEP and LEPR SNPs. A significantly decreased risk of CRC was found to be associated with the LEPR rs6588147 polymorphism (GA vs. GG: crude P=0.007 and GA/AA vs. GG: crude P=0.018). With adjustments for risk factors (e.g. age, gender, drinking, BMI and smoking), these associations were not changed. In subgroup analyses, the association of LEP rs2167270 with a decreased risk of CRC was found in the ≥61 years old subgroup. For LEPR rs1137100, the association of this SNP with an increased susceptibility of CRC was found in the BMI <24 kg/m² subgroup. In subgroup analyses for LEPR rs6588147, we identified that this locus also decreased the susceptibility of CRC in the male subgroup, <61 years old subgroup, never smoking subgroup and never drinking subgroup. For LEPR rs1137101, the relationship of this polymorphism with a decreased susceptibility to CRC was found in the never drinking subgroup. In summary, the present study highlights that LEPR rs6588147, rs1137101 and LEP rs2167270 may decrease the risk of CRC. However, LEPR rs1137100 is associated with susceptibility to CRC. Further case-control studies with larger sample sizes should be conducted to validate our findings.

Relationship between the Monocyte Chemo-attractant Protein-1 gene rs1024611 A>G Polymorphism and Cancer Susceptibility: A Meta-analysis Involving 14,617 Subjects

BACKGROUND

Inflammatory and inducible chemokines are the hallmarks of malignancy. Monocyte chemo-attractant protein-1 (MCP-1) is a crucial chemokine implicated in infection and inflammation. Methods: We performed an updated meta-analysis of thirty independent case-control studies with 6,777 cancer cases and 7,840 controls to determine if the MCP-1 gene rs1024611 A > G variant is associated with the risk of cancer. Results: The G allele carriers of rs1024611 in the MCP-1 gene might have a null association with cancer risk in overall comparison. In a subgroup analysis by ethnicity, we identified a marked association between the MCP-1 G allele rs1024611 polymorphism and cancer risk in the Caucasian populations (GG vs. AA: OR = 1.72, 95% CI, 1.12-2.64, P = .013, and GG vs. AG/AA: OR = 1.82, 95% CI, 1.19-2.78, P = .006). The potential bias in literature selection was witnessed in this meta-analysis (G vs. A: P _Begg's =  0.187, P_Egger's =  0.049; and GG/GA vs. AA: P _Begg's =  0.069, P_Egger's =  0.024). The adjusted ORs and CIs of the nonparametric "trim-and-fill" method demonstrated the reliability of these findings. The outcome of heterogeneity analysis indicated that heterogeneity might be due to small sample sizes (<1000 subjects), cancer types (bladder cancer, other cancers), ethnicity (Asians), and population-based studies. However, the sensitivity analysis validated the reliability of the findings. Conclusion: In conclusion, this updated meta-analysis showed that the G carrier of the MCP-1 gene rs1024611 is associated with susceptibility to cancer in Caucasian.

Associations Between microRNA Polymorphisms and Development of Coronary Artery Disease: A Case-Control Study

Coronary artery disease (CAD), a common cardiovascular disease, has become a vital cause of mortality worldwide. Genetic microRNA (miR) polymorphisms might contribute to CAD susceptibility. In this study, we selected miR-146a, miR-196a2, and miR-499 single nucleotide polymorphisms and conducted a case-control study. In total, 505 CAD cases and 1109 controls were recruited. We used SNPscan™ genotyping assay to obtain genotyping of miR rs2910164, rs11614913, and rs3746444 variants. We found that miR-196a2 rs11614913 T > C decreased the susceptibility of myocardial infarction (MI) (TC vs. TT: adjusted p = 0.007 and CC/TC vs. TT: adjusted p = 0.012). In female subgroup, our results indicated that miR-196a2 rs11614913 T > C variants might also decrease the susceptibility of CAD (TC vs. TT: adjusted p = 0.017 and TC/CC vs. TT: adjusted p = 0.015). In summary, these results suggest that miR-196a2 rs11614913 T > C locus decreases the susceptibility of CAD in female and MI subgroups. However, further studies are needed to validate the potential associations of miR-196a2 rs11614913 locus with CAD.

Relationship between IGF2BP2 and IGFBP3 polymorphisms and susceptibility to non-small-cell lung cancer: a case-control study in Eastern Chinese Han population

Background

IGF2BP2 and IGFBP3 polymorphisms may be associated with cancer risk.

Methods

With an aim to determine the association of variations in IGF2BP2 and IGFBP3 genes with risk of non-small-cell lung cancer (NSCLC), IGF2BP2 rs1470579 A>C, rs4402960 G>T and IGFBP3 rs2270628 C>T, rs3110697 G>A, and rs6953668 G>A polymorphisms were selected and genotyped in 521 NSCLC patients and 1,030 controls.

Results

We found that there was no difference in IGF2BP2 and IGFBP3 genotype distribution among the NSCLC patients and controls. The stratified analyses suggested that IGF2BP2 rs1470579 A>C polymorphism decreased the risk of NSCLC in some subgroups (female subgroup: CC vs AA: adjusted P=0.032 and CC vs AC/AA: adjusted P=0.028; <60 years subgroup: CC vs AA: adjusted P=0.012 and CC vs AC/AA: adjusted P=0.013; and never drinking subgroup: CC vs AA: adjusted P=0.046 and CC vs AC/AA: adjusted P=0.031). The stratified analyses also found that IGF2BP2 rs4402960 G>T polymorphism decreased the risk of NSCLC in some subgroups (female subgroup: TT vs GG: adjusted P=0.031 and TT vs GT/GG: adjusted P=0.026; <60 subgroup: TT vs GG: adjusted P=0.037 and TT vs GT/GG: adjusted P=0.038; and never drinking subgroup: TT vs GT/GG: adjusted P=0.046). Haplotype analysis indicated A_rs1470579C_rs2270628G_rs3110697G_rs4402960A_rs6953668 haplotype decreased susceptibility of NSCLC (P=0.007).

Conclusion

Our study suggests that IGF2BP2 rs1470579 A>C, rs4402960 G>T single-nucleotide polymorphisms are candidates for decreased susceptibility to NSCLC among female, <60 years, and never drinking subgroups. In the future, more case–control studies with functional analysis are needed to confirm these preliminary findings.

Relationship of PPARG, PPARGC1A, and PPARGC1B polymorphisms with susceptibility to hepatocellular carcinoma in an eastern Chinese Han population

Background

PPARG, PPARGC1A, and PPARGC1B polymorphisms may be implicated in the development of cancer.

Participants and methods

In this study, we selected PPARG rs1801282 C>G and rs3856806 C>T, PPARGC1A rs2970847 C>T, and PPARGC1B rs7732671 G>C and rs17572019 G>A single-nucleotide polymorphisms to explore the relationship between these polymorphisms and hepatocellular carcinoma (HCC) risk. A total of 584 HCC patients and 923 controls were enrolled.

Results

We found that PPARG rs1801282 C>G polymorphism was correlated with a decreased susceptibility of HCC (CG vs CC, adjusted OR 0.47, 95% CI 0.27-0.82, P=0.007; CG/GG vs CC, adjusted OR 0.52, 95% CI 0.31-0.88, P=0.015). However, PPARG rs3856806 C>T polymorphism was a risk factor for HCC (TT vs CC, adjusted OR 2.33, 95% CI 1.25-4.36, P=0.008; TT vs CT/CC, adjusted OR 2.26, 95% CI 1.22-4.17, P=0.010). In a subgroup analysis by chronic hepatitis B virus (HBV)-infection status, age, sex, alcohol use, and smoking status, a significant association between PPARG rs1801282 C>G polymorphism and a decreased risk of HCC in male, ≥53 years, never-smoking, never-drinking, and nonchronic HBV-infection-status subgroups was found. However, we found PPARG rs3856806 C>T polymorphism increased the risk of HCC in never-smoking, never-drinking, and nonchronic HBV-infection-status subgroups. Haplotype-comparison analysis indicated that C_rs1801282T_rs3856806C_rs2970847G_rs7732671G_rs17572019, C_rs1801282T_rs3856806T_rs2970847G_rs7732671G_rs17572019, and C_rs1801282C_rs3856806C_rs2970847C_rs7732671A_rs17572019 haplotypes increased the risk of HCC. PPARG C_rs1801282T_rs3856806 and G_rs1801282C_rs3856806 haplotypes also influenced the risk of HCC.

Conclusion

In conclusion, our findings suggest PPARG polymorphisms may influence the susceptibility of HCC. The PPARG, PPARGC1A, and PPARGC1B haplotypes might be associated with HCC risk.

Investigation of LEP and LEPR polymorphisms with the risk of hepatocellular carcinoma: a case-control study in Eastern Chinese Han population

Background

Leptin (LEP) and LEP receptor (LEPR) polymorphisms may be associated with the development of cancer.

Methods

In this study, we selected five functional LEP and LEPR single-nucleotide polymorphisms (SNPs) and conducted a case–control study to determine the relationship of LEP and LEPR polymorphisms with hepatocellular carcinoma (HCC) risk in Eastern Chinese Han population. There were 584 HCC cases and 923 cancer-free controls included in our study. HCC patients and controls were fully matched by age and sex. SNPscan™ genotyping method was used to analyze the genotyping of LEP rs2167270 G>A, rs7799039 A>G, LEPR rs6588147 G>A, rs1137100 G>A, and rs1137101 G>A SNPs.

Results

We found that LEP rs7799039 A>G and rs2167270 G>A polymorphisms were associated with the susceptibility of HCC in this population (LEP rs7799039 A>G: GG vs AA: adjusted odds ratio [OR]=2.03, 95% CI, 1.22–3.38, P=0.006 and GG vs AA/AG: adjusted OR=1.97, 95% CI, 1.20–3.22, P=0.007; rs2167270 G>A: AA vs GG: adjusted OR=2.03, 95% CI, 1.10–3.75, P=0.024 and AA vs GG/GA: adjusted OR=2.01, 95% CI, 1.10–3.68, P=0.023). However, LEPR rs6588147 G>A polymorphism decreased the risk of HCC (GA vs GG: adjusted OR=0.62, 95% CI, 0.45–0.86, P=0.005 and AA/GA vs GG: adjusted OR=0.64, 95% CI, 0.47–0.88, P=0.007).

Conclusion

This case–control study highlights that LEP rs7799039 A>G and rs2167270 G>A polymorphisms increase the susceptibility to HCC; however, LEPR rs6588147 G>A polymorphism may be a protective factor for HCC in Eastern Chinese Han population.

Low penetrance genetic polymorphisms as potential biomarkers for colorectal cancer predisposition

Colorectal cancer is a leading form of cancer in both males and females. Early detection of individuals at risk of colorectal cancer allows proper treatment and management of the disease to be implemented, which can potentially reduce the burden of colorectal cancer incidence, morbidity and mortality. In recent years, the role of genetic susceptibility factors in mediating predisposition to colorectal cancer has become more and more apparent. Identification of high-frequency, low-penetrance genetic polymorphisms associated with the cancer has therefore emerged as an important approach which can potentially aid prediction of colorectal cancer risk. However, the overwhelming amount of genetic epidemiology data generated over the past decades has made it difficult for one to assimilate the information and determine the exact genetic polymorphisms that can potentially be used as biomarkers for colorectal cancer. This review comprehensively consolidates, based primarily on results from meta-analyses, the recent progresses in the search of colorectal cancer-associated genetic polymorphisms, and discusses the possible mechanisms involved.

Methylenetetrahydrofolate reductase tagging polymorphisms are associated with risk of non-small cell lung cancer in eastern Chinese Han population

Previous reports implicated 5,10-ethylenetetrahydrofolate reductase (MTHFR) polymorphisms acted as a potential risk factor for several cancers. In order to explore the effect of MTHFR SNPs on non-small cell lung cancer (NSCLC), we selected MTHFR tagging single nucleotide polymorphisms (SNPs) and carried out a case-control study to determine the potential relationship of MTHFR SNPs with NSCLC risk. Our study consisted of 521 NSCLC patients and 1,030 non-cancer controls. MTHFR SNPs were genotyped by SNPscan^TM genotyping assay. Using four genetic models (additive, Homozygote, dominant, recessive), the genotype frequencies were compared using the chi-squared (χ²) test. Crude/adjusted odds ratios (ORs) with their 95% confidence intervals (CIs) were used to assess the difference for the genotype distribution. We found that MTHFR rs1801133 G>A polymorphism decreased the risk of overall NSCLC. In a subgroup analysis, MTHFR rs1801133 G>A polymorphism also decreased NSCLC risk in female, < 60 years and never smoking subgroups. However, we identified that MTHFR rs4845882 G>A polymorphism was associated with the development of NSCLC in female subgroup. In addition, MTHFR rs9651118 T>C polymorphism increased the risk of NSCLC in < 60 years, never smoking and BMI < 24 kg/m² subgroups. In conclusion, the current study highlights MTHFR rs1801133 G>A variants decreases the risk of NSCLC. Nevertheless, MTHFR rs4845882 G>A and rs9651118 T > C polymorphisms may be associated with NSCLC susceptibility. Well-designed large-scale studies are needed to confirm these findings and explore the interactions of gene-gene and gene-environment involved in MTHFR SNPs and NSCLC.

The relationship between IGF2BP2 and PPARG polymorphisms and susceptibility to esophageal squamous-cell carcinomas in the eastern Chinese Han population

The aim of this case–control study was to assess whether PPARG and IGF2BP2 polymorphisms confer susceptibility to esophageal squamous-cell carcinoma (ESCC). A total of 507 patients pathologically confirmed for ESCC and 1,496 age-, sex-, and residence-matched healthy individuals were enrolled. The PPARG rs1801282 C>G and rs3856806 C>T and IGF2BP2 rs1470579 A>C and rs4402960 G>T polymorphisms were selected and genotyped by SNPscan genotyping assays. Multivariable logistic analysis suggested that the PPARG rs3856806 C>T polymorphism might increase the risk of ESCC. In different stratified analyses, there were significant associations between PPARG rs3856806 C>T and risk of ESCC in female, never-smoking, drinking, and never-drinking subgroups. In addition, we also found that PPARG rs1801282 C>G increased ESCC risk in the never-smoking subgroup. There was significant difference in C_rs1470579G_rs4402960C_rs1801282C_rs3856806-haplotype distribution among ESCC cases and control subjects. In conclusion, our findings highlight that PPARG rs1801282 C>G and rs3856806 C>T polymorphisms are candidates for susceptibility to ESCC in the eastern Chinese Han population. The C_rs1470579G_rs4402960C_rs1801282C_rs3856806 haplotype is associated with susceptibility to ESCC.

Investigation of TCF7L2, LEP and LEPR polymorphisms with esophageal squamous cell carcinomas

Single nucleotide polymorphisms (SNPs) in energy metabolism related gene may be key agents in the development of human malignancies. In this study, we aimed to examine the association of transcription factor 7-like 2, Leptin (LEP) and LEP receptor (LEPR) polymorphisms with esophageal squamous cell carcinoma (ESCC). A total of 507 ESCC cases and 1,496 controls were enrolled. We found that LEPR rs6588147 AA genotype was associated with ESCC risk (AA vs. GG/GA: adjusted OR=1.90, 95%CI=1.00-3.61, P=0.049). In the stratified analyses, LEPR rs6588147 G>A polymorphism increased the risk of ESCC (<63 years subgroup: AA vs. GG: adjusted OR=2.58, 95%CI=1.00-6.62, P=0.049 and AA vs. GA/GG: adjusted OR=2.71, 95%CI=1.06-6.91, P=0.038; male subgroup: AA vs. GG: adjusted OR=2.19, 95%CI=1.02-4.67, P=0.044 and AA vs. GA/GG: adjusted OR=2.26, 95%CI=1.06-4.80, P=0.035). However, LEP rs7799039 A>G decreased the risk of ESCC (≥63 years subgroup: GG vs. AA: adjusted OR=0.47, 95%CI=0.23-0.95, P=0.035 and GG vs. AA/AG: adjusted OR=0.48, 95%CI=0.24-0.96, P=0.038; BMI≥24 kg/m² subgroup: AG vs. AA: adjusted OR=0.66, 95%CI=0.45-0.99, P=0.044). In addition, LEPR rs1137101 G>A polymorphism decreased ESCC risk in some subgroups (ever smoking subgroup: GA vs. GG: adjusted OR=0.66, 95%CI=0.44-1.00, P=0.049; ever drinking subgroup: GA vs. GG: adjusted OR=0.54, 95%CI=0.31-0.95, P=0.031 and GA/AA vs. GG: adjusted OR=0.54, 95%CI=0.31-0.93, P=0.027). Our findings suggest that LEPR rs6588147 G>A polymorphism is associated with the increased risk of ESCC; however, LEP rs7799039 A>G and LEPR rs1137101 G>A polymorphisms may be protective factors for ESCC.