Comprehensive genetic evaluation of common E-cadherin sequence variants and prostate cancer risk: strong confirmation of functional promoter SNP

A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers

Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.

The Associations of Genetic Variants in E-cadherin Gene With Clinical Outcome of Epithelial Ovarian Cancer

OBJECTIVE

The E-cadherin protein plays major roles in tumor progression, invasion, and metastasis. Polymorphisms located in the E-cadherin gene (CDH1) may contribute to increased risks of specific cancers. In this study, we evaluated the associations between genetic variants in CDH1 and the clinical outcomes of patients with epithelial ovarian cancer (EOC).

MATERIALS AND METHODS

We assessed the -160C/A and -347G/GA polymorphisms in the promoter region, as well as the 3'-UTR +54C/T polymorphism of E-cadherin, in 257 patients with EOC by ligase detection reaction-polymerase chain reaction.

RESULTS

Multivariate analysis showed that patients with EOC with the CDH1 -347GA/GA genotype had shorter progression-free survival and overall survival (hazard ratio [HR], 2.16; 95% confidence interval [CI], 1.06-4.40 and HR, 2.06; 95% CI, 1.01-4.19, respectively) compared to those carrying the G/G genotype. Likewise, the patients with the CDH1 -160A/A genotype had a shorter progression-free survival than those with the C/C genotype (HR, 4.12; 95% CI, 1.43-111.88). No significant association was detected between the CDH1 3'-UTR +54C/T polymorphism and survival of the patients with EOC.

CONCLUSIONS

The CDH1 -347GA/GA and -160A/A genotypes may be prognostic markers that can help to identify patients at increased risk of invasive/metastatic cancer in northern China.

The stromal genome heterogeneity between breast and prostate tumors revealed by a comparative transcriptomic analysis

Stromal microenvironment increases tumor cell survival, proliferation and migration, and promotes angiogenesis. In order to provide comprehensive information on the stromal heterogeneity of diverse tumors, here we employed the microarray datasets of human invasive breast and prostate cancer-associated stromals and applied Gene Set Enrichment Analysis (GSEA) to compare the gene expression profiles between them. As a result, 8 up-regulated pathways and 73 down-regulated pathways were identified in the breast tumor stroma, while 32 up-regulated pathways and 18 down-regulated pathways were identified in the prostate tumor stroma. Only 9 pathways such as tryptophan metabolism were commonly up or down regulated, but most of them (including ABC transporters) were specific for these two tumors. Several essential tumors stromal marker genes were also significantly identified. For example, CDH3 was significantly up-regulated in the stromals of both breast and prostate tumors, however EGFR was only significantly down-regulated in the stromal of breast tumor. Our study would be helpful for future therapeutic and predictive applications in breast and prostate cancers.

Regulatory Variants and Disease: The E-Cadherin -160C/A SNP as an Example

Single nucleotide polymorphisms (SNPs) occurring in noncoding sequences have largely been ignored in genome-wide association studies (GWAS). Yet, amounting evidence suggests that many noncoding SNPs especially those that are in the vicinity of protein coding genes play important roles in shaping chromatin structure and regulate gene expression and, as such, are implicated in a wide variety of diseases. One of such regulatory SNPs (rSNPs) is the E-cadherin (CDH1) promoter -160C/A SNP (rs16260) which is known to affect E-cadherin promoter transcription by displacing transcription factor binding and has been extensively scrutinized for its association with several diseases especially malignancies. Findings from studying this SNP highlight important clinical relevance of rSNPs and justify their inclusion in future GWAS to identify novel disease causing SNPs.

Promoter methylation and polymorphism of E-cadherin gene may confer a risk to prostate cancer: a meta-analysis based on 22 studies

Emerging evidence has suggested that -160C/A polymorphism and promoter methylation of E-cadherin gene may contribute to the risk of prostate cancer. However, the results are still conflicting. We aim to systematically evaluate the potential of promoter methylation and polymorphism in E-cadherin gene to confer a risk to prostate cancer through meta-analysis. PubMed, Embase, Web of Science, Cochrane Library, and Chinese National Knowledge Infrastructure (CNKI) databases were searched to identify eligible studies published before April 1, 2014. Pooled odds ratios (ORs) with their 95 % confidence intervals (95 % CIs) were calculated by using the random-effect model or the fixed-effect model, according to heterogeneity test. Subgroup analyses were also performed to explore the potential sources of heterogeneity. Sensitivity and publication bias analyses were used to test the robustness of our results. We performed a meta-analysis of 22 included studies, with 11 on -160C/A polymorphism and another 11 on promoter methylation of E-cadherin gene. Our meta-analysis results suggested that E-cadherin -160C/A polymorphism may be a potential risk factor for prostate cancer. Furthermore, we observed that the frequencies of promoter methylation of E-cadherin gene in the prostate cancer tissues were significantly higher than those of normal tissues, indicating that promoter methylation of E-cadherin gene may play an important role in prostate carcinogenesis. In conclusion, the present meta-analysis provides further evidence that promoter methylation and -160C/A polymorphism of E-cadherin gene may confer a risk to prostate cancer. Identifying these risk factors for prostate cancer will improve early detection, allow for selective chemoprevention, and provide further insights into its disease mechanisms.

Contribution of the -160C/A polymorphism in the E-cadherin promoter to cancer risk: a meta-analysis of 47 case-control studies

BACKGROUND

The -160C/A polymorphism (rs16260) of E-cadherin, a tumor repressor gene, has been shown to be a tumor susceptibility allele for various types of cancers. Because the significance of this polymorphism to cancer risk has been recognized, there are increasing studies investigating -160C/A in different types of cancers and ethnic populations. However, there is still uncertainty about the level of risk for a variety of cancers.

METHODS

To resolve the controversial question raised by these studies as of March 2012 and provide more statistical power for detecting the significance of -160C/A, we performed a meta-analysis of 47 case-control studies in 16 types of cancers (18,194 cases and 20,207 controls). A meta-regression model and subgroup analysis were employed to identify the source of heterogeneity. Publication bias was evaluated, and sensitivity analysis and cumulative evidence assessment were also performed.

RESULTS

Using fixed- and random-effects models, the -160AA homozygote was more susceptible to urothelial cancer compared with the -160CA heterozygote. Additionally, the -160A allele is an ethnicity-dependent risk factor for prostate and colorectal cancers. Carriers of the -160A allele in Asians and Europeans were more susceptible to prostate cancer, whereas their North American counterparts seemed tolerant. The -160AA homozygote plays a protective role for Europeans who develop colorectal cancer. The stability of these observations was confirmed by a one-way sensitivity analysis. However, the cumulative evidence for all cancer types was considered 'weak' using the Venice guidelines.

CONCLUSIONS

A meta-analysis indicated that the -160A allele of E-cadherin provides a higher risk for the development of prostate and urothelial cancers and a protective role for colorectal cancer in an ethnicity-dependent manner.

Possible involvement of the E-cadherin gene in genetic susceptibility to endometriosis

BACKGROUND

Endometriotic cells display invasive characteristics, despite their benign histological appearance. Recently, the epithelial-mesenchymal transition, in which epithelial cells acquire mesenchymal and migratory properties, has attracted attention as a mechanism of tumor invasion. We aimed to investigate the association between endometriosis and polymorphisms of the E-cadherin gene, a central player in the epithelial-mesenchymal transition, in Japanese women.

METHODS

Twelve single-nucleotide polymorphisms (SNPs) in the E-cadherin gene were identified by real-time polymerase chain reaction using a TaqMan assay in 511 women with endometriosis (the majority in Stages III and IV) and 498 healthy controls.

RESULTS

Allele frequency analysis indicated that there was a marginally higher frequency of the rs4783689 C allele in women with endometriosis compared with controls (corrected P = 0.007; odds ratio = 1.37; 95% confidence interval, 1.14-1.64). No significant associations with endometriosis were found for the other 11 SNPs.

CONCLUSIONS

Although this study was limited by sample size, the E-cadherin gene polymorphism rs4783689 was marginally associated with endometriosis in the Japanese population, suggesting that E-cadherin might be involved in genetic susceptibility to endometriosis.

The E-cadherin (CDH1)--160 C/A polymorphism and prostate cancer risk: a meta-analysis

Published data on the association between E-cadherin (CDH1) -160 C/A polymorphism and prostate cancer (PCA) risk are inconclusive. To derive a more precise estimation of the relationship, a meta-analysis was performed. A logistic regression approach proposed for molecular association studies was used to estimate a biological model of the gene effect. A total of 11 studies including 2637 cases and 2673 controls were involved in this meta-analysis. Logistic regression analysis indicated that the CDH1 -160 C/A genotypes were associated with PCA risk. The genetic model test indicated that the genetic model was most likely to be dominant (CA+AA vs CC). Overall, meta-analysis indicated that the -160A allele carriers (CA+AA) had a 21% elevated risk of PCA, when compared with the homozygotes (CC) (odds ratio (OR)=1.21; 95% confidence interval (CI): 0.97-1.51; P=0.090, P(heterogeneity)=0.001). In the subgroup analyses by ethnicity, significantly elevated risks were associated with -160 variant genotypes (CA+AA) in both European and Asian populations (OR=1.24; 95% CI: 1.08-1.43; P=0.003, P(heterogeneity)=0.220 and OR=1.54; 95% CI: 1.23-1.93; P<0.001, P(heterogeneity)=0.200). However, no significant associations were found in Africans (OR=0.59; 95% CI: 0.32-1.09; P=0.090, P(heterogeneity)=0.070). Although some modest bias could not be eliminated, this meta-analysis suggests that the CDH1 -160A allele is a low-penetrant risk factor for developing PCA, especially in Europeans and Asians.

Clinical characteristics and primary treatment of prostate cancer in Sweden between 1996 and 2005

OBJECTIVE

The incidence of prostate cancer is rising rapidly in Sweden and there is a need to better understand the pattern of diagnosis, tumor characteristics and treatment.

MATERIAL AND METHODS

Between 1996 and 2005, all new cases of adenocarcinoma of the prostate gland were intended to be registered in the National Prostate Cancer Register (NPCR). This register contains information on diagnosing unit, date of diagnosis, cause of diagnosis, tumor grade, tumor stage according to the TNM classification in force, serum prostate-specific antigen (PSA) levels at diagnosis and primary treatment given within the first 6 months after diagnosis.

RESULTS

In total, 72,028 patients were registered, comprising >97% of all pertinent incident cases of prostate cancer in the Swedish Cancer Register (SCR). During the study period there was a considerable decrease in median age at the time of diagnosis, a stage migration towards smaller tumors, a decrease in median serum PSA values at diagnosis, a decrease in the age-standardized incidence rate of men diagnosed with distant metastases or with a PSA level of > 100 ng/ml at diagnosis and an increase in the proportion of tumors with Gleason score <6. Relatively large geographical differences in the median age at diagnosis and the age-standardized incidence of cases with category T1c tumors were observed. Treatment with curative intent increased dramatically and treatment patterns varied according to geographical region. In men with localized tumors and a PSA level of <20 ng/ml at diagnosis, expectant treatment was more commonly used in those aged > or =75 years than in those aged <75 years. Also, the pattern of endocrine treatment varied in different parts of Sweden.

CONCLUSIONS

All changes in the register seen over time are consistent with increased diagnostic activity, especially PSA testing, resulting in an increased number of cases with early disease, predominantly tumors in category T1c. The patterns of diagnosis and treatment of prostate cancer vary considerably in different parts of Sweden. The NPCR continues to be an important source for research, epidemiological surveillance of the incidence, diagnosis and treatment of prostate cancer.

A novel diffuse gastric cancer susceptibility variant in E-cadherin (CDH1) intron 2: a case control study in an Italian population

BACKGROUND

Inherited genetic factors such as E-cadherin (CDH1) promoter variants are believed to influence the risk towards sporadic diffuse gastric cancer (DGC). Recently, a new regulatory region essential for CDH1 transcription has been identified in CDH1 intron 2.

METHODS

We genotyped all known polymorphisms located within conserved sequences of CDH1 intron 2 (rs10673765, rs9932686, rs1125557, rs9282650, rs9931853) in an Italian population consisting of 134 DGC cases and 100 healthy controls (55 patient relatives and 45 unrelated, matched individuals). The influence of individual variants on DGC risk was assessed using chi2-tests and logistic regression. The relative contribution of alleles was estimated by haplotype analysis.

RESULTS

We observed a significant (p < 0.0004) association of the CDH1 163+37235G>A variant (rs1125557) with DGC risk. Odds ratios were 4.55 (95%CI = 2.09-9.93) and 1.38 (95%CI = 0.75-2.55) for AA and GA carriers, respectively. When adjusted for age, sex, smoking status, alcohol intake and H. pylori infection, the risk estimates remained largely significant for AA carriers. Haplotype analysis suggested the 163+37235A-allele contributes to disease risk independently of the other variants studied.

CONCLUSION

The CDH1 163+37235G>A polymorphism may represent a novel susceptibility variant for sporadic DGC if confirmed in other populations. Considering the broad expression of E-cadherin in epithelia, this exploratory study encourages further evaluation of the 163+37235A-allele as a susceptibility variant in other carcinomas.

Combinational polymorphisms of four DNA repair genes XRCC1, XRCC2, XRCC3, and XRCC4 and their association with oral cancer in Taiwan

BACKGROUND

Many single nucleotide polymorphisms (SNPs) have been found to be associated with oral cancer but the biological interactions through SNPs are seldom addressed. In this study, we focused on the joint effect for SNP combinations of four DNA repair genes, X-ray repair cross-complementing groups (XRCCs) 1-4, involved in major cancer-related pathways.

METHODS

Single nucleotide polymorphism genotyping was determined using by polymerase chain reaction-restriction fragment length polymorphism in this study (case = 103, control = 98). Different numbers of combinational SNPs with genotypes called the pseudo-haplotypes from these chromosome-wide genes were used to evaluate their joint effect on oral cancer risk.

RESULTS

Except for XRCC2 rs2040639-AG, none of these SNPs was found to individually contribute to oral cancer risk. However, for two combined SNPs, the proportion of subjects with oral cancer was significantly higher in the pseudo-haplotype with AG-CC genotypes in rs2040639-rs861539 (XRCC2-XRCC3) compared with those with non-AG-CC genotypes. Similarly, the pseudo-haplotype of rs2040639-rs861539-rs2075685 (XRCC2-XRCC3-XRCC4) and rs2040639-rs861539-rs2075685-rs1799782 (XRCCs 1-4) with specific genotype pattern (AG-CC-TG and CT-AG-CC-TG) among three and four combinational SNPs were significantly associated with oral cancer. After controlling for age, gender, smoking, drinking, and betel nut chewing, the estimated odds ratio of oral cancer were 2.45, 5.03, and 10.10 for two, three and four specific SNP combinations, respectively, comparing these specific pseudo-haplotypes to their corresponding non-pseudo-haplotypes.

CONCLUSION

We have identified the potential combined XRCCs 1-4 SNPs with genotypes that were associated with oral cancer risk and may have an impact on identification of a high-risk population.

Constitutional polymorphisms of prostate cancer: prognostic and diagnostic implications

Prostate cancer is the most common cancer diagnosis in men. While often perceived as a slow, indolent malignancy, prostate cancer trails only lung cancer among cancer-related mortality in men. Current diagnosis and treatment algorithms are plagued by overdiagnosis of non-lethal indolent prostate cancer with no proven means to predict, detect, and prevent aggressive lethal prostate cancer in men most at risk. These challenges are particularly concerning for African-American men who demonstrate increased rates of prostate cancer incidence and mortality when compared to other ethnic groups. With the completion of the human genome project, technology and techniques now exist to differentiate cancer from normal tissues based on the expression patterns of thousands of genes assessed simultaneously on a single microarray gene 'chip'. This platform has greatly improved our understanding of genes that regulate tumor behavior once cancer is established. Microarrays can also be utilized in patients without cancer to determine which patients are at high risk for tumor development and in need of rational prevention strategies. Constitutional single nucleotide polymorphisms (SNPs) are one source of genetic variation and may serve as a means to identify these high-risk individuals. SNPs are single nucleotide base pair changes within a gene which occur in one percent or more of the population. SNPs can contribute to a disease state by altering the function of a protein encoded by a gene without affecting gene expression. This review will examine the current understanding of constitutional SNPs associated with prostate cancer carcinogenesis, highlight two current diagnostic array platforms and discuss implications for future prevention and screening programs.

A short guide to hereditary diffuse gastric cancer

Hereditary diffuse gastric cancer (HDGC) is the only known predisposition syndrome dominated by carcinoma of the stomach and with a recognised genetic cause. Germline mutations in the E-cadherin gene (CDH1) co-segregate with the disease in about half of the families with multiple diffuse gastric cancer. In these families, identification of the CDH1 mutation allows for clinical measures to be taken. Importantly, clinical intervention is likely to be therapeutic and associated with tolerable morbidity. This review is thus aimed at providing a current overview of the clinical management and the underlying biology of HDGC.

DNA variation in MSR1, RNASEL and E-cadherin genes and prostate cancer in Poland

INTRODUCTION

We investigated whether or not inherited variation in MSR1, RNASEL and E-cadherin contribute to prostate cancer risk in Poland.

MATERIAL AND METHODS

We sequenced the coding region of these three genes in individuals from Poland and identified five common DNA variants (R462Q and D541E in RNASEL, R293X and P275A in MSR1, and 2076C>T (A692A) in E-cadherin). These five variants and the -160C>A promoter change in E-cadherin were genotyped in 737 prostate cancer cases and 511 controls.

RESULTS

The frequencies of genotyped variants in MSR1, RNASEL and E-cadherin genes in cases and controls were similar. We did not see any association for the studied variants when cases were stratified by age of diagnosis, by family history, by prostate-specific antigen level at the time of diagnosis, by Gleason sore or by tumor stage.

CONCLUSIONS

Inherited variation in RNASEL, MSR1 and E-cadherin genes do not seem to contribute to prostate cancer development in Poland.

SNP genotyping: technologies and biomedical applications

Single nucleotide polymorphisms (SNPs) are the most frequently occurring genetic variation in the human genome, with the total number of SNPs reported in public SNP databases currently exceeding 9 million. SNPs are important markers in many studies that link sequence variations to phenotypic changes; such studies are expected to advance the understanding of human physiology and elucidate the molecular bases of diseases. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis, yielding a large number of distinct approaches. This article presents a review of SNP genotyping techniques and examines their principles of genotype determination in terms of allele differentiation strategies and detection methods. Further, several current biomedical applications of SNP genotyping are discussed.

Significance of an E-cadherin gene promoter polymorphism for risk and disease severity of prostate cancer in a Japanese population

OBJECTIVES

To explore the significance of an E-cadherin gene promoter polymorphism for risk and disease severity of prostate cancer in a Japanese population.

METHODS

We enrolled 200 patients with sporadic prostate cancer and 159 control patients with benign prostatic hyperplasia in this case-control study. The -160C/A polymorphism in the E-cadherin gene promoter was genotyped by polymerase chain reaction-restriction fragment length analysis.

RESULTS

The C/C, C/A, and A/A genotypes were observed in 58%, 39%, and 3% of patients, respectively, whereas the C/C, C/A, and A/A genotypes were observed in 75%, 25%, and 0.63% of control subjects, respectively. Japanese men carrying the A allele and A/A genotype had 1.88-fold (95% confidence interval [CI], 1.25 to 2.84) and 9.03-fold (95% CI, 1.50 to 172.36) higher risks, respectively, for prostate cancer than did carriers of the C allele and C/C genotype. There was no significant association between the polymorphism and clinical stage or pathologic grade.

CONCLUSIONS

The presence of the A allele of the -160C/A polymorphism in the E-cadherin gene may be a risk factor for prostate cancer in the Japanese population.

Genetic variation in p53 and ATM haplotypes and risk of glioma and meningioma

BACKGROUND

P53 and ATM are central checkpoint genes involved in the repair of DNA damage after ionising irradiation, which has been associated with risk of brain tumours. Therefore, we tested the hypothesis that polymorphisms and haplotypes in p53 and ATM could be associated with glioma and meningioma risk.

MATERIAL AND METHODS

Six hundred and eighty glioma cases (298 glioblastoma (GBM)), 503 meningioma cases, and 1555 controls recruited in the Nordic-UK Interphone study, were analysed in association with three polymorphisms in p53 (rs2287499, rs1042533, rs1625895) and five polymorphisms in ATM ( rs228599, rs3092992, rs664143, rs170548, rs3092993). Haplotypes were constructed using the HAPLOSTAT program.

RESULTS

The global statistical test of glioblastoma and p53 haplotypes was p = 0.02. The haplotype analysis on glioblastoma revealed the 1-2-2 haplotype (promotor-codon72-intron 6) had a frequency of 6.1% in cases compared with 9.8% in controls (p = 0.003). The 1-2-1 haplotype was significantly more frequent in GBM cases, 10.2%, than in controls, 7.3% (p = 0.02). The haplotype analysis in ATM revealed an increased frequency of the 1-1-1-2-1 haplotype in meningioma cases (33.8%) compared with controls (30.3%) (p = 0.03). The 2-1-2-1-1 haplotype had a lower frequency in meningioma cases (36.1%) than controls (40.7%) (p = 0.009).

CONCLUSIONS

This study found both positive and negative associations of haplotypes in p53 for glioblastoma and ATM for meningioma. This study provides new data that could add to our understanding of brain tumour susceptibility.

Systematic replication study of reported genetic associations in prostate cancer: Strong support for genetic variation in the androgen pathway

BACKGROUND

Association studies have become a common and popular method to identify genetic variants predisposing to complex diseases. Despite considerable efforts and initial promising findings, the field of prostate cancer genetics is characterized by inconclusive reports and no prostate cancer gene has yet been established.

METHODS

We performed a literature review and identified 79 different polymorphisms reported to influence prostate cancer risk. Of these, 46 were selected and tested for association in a large Swedish population-based case-control prostate cancer population.

RESULTS

We observed significant (P < 0.05) confirmation for six polymorphisms located in five different genes. Three of them coded for key enzymes in the androgen biosynthesis and response pathway; the CAG repeat in the androgen receptor (AR) gene (P = 0.03), one SNP in the CYP17 gene (P = 0.04), two SNPs in the SRD5A2 gene (P = 0.02 and 0.02, respectively), a deletion of the GSTT1 gene (P = 0.006), and one SNP in the MSR1 gene, IVS5-59C > A, (P = 0.009).

CONCLUSIONS

Notwithstanding the difficulties to replicate findings in genetic association studies, our results strongly support the importance of androgen pathway genes in prostate cancer etiology.

Polymorphisms in the E-cadherin (CDH1) gene promoter and the risk of bladder cancer

AIM

E-cadherin plays a role in carcinogenesis. For two genetic polymorphisms in the gene (CDH1) promoter, a reduced transcription has been reported: a C/A single nucleotide polymorphism (SNP) and a G/GA SNP at -160 bp and -347 bp, respectively, upstream of the transcriptional start site. We studied the association between both polymorphisms and the risk of bladder cancer.

METHODS

One hundred and ninety-seven patients with bladder cancer and 344 population controls were genotyped and haplotyped for both SNPs.

RESULTS

A borderline significantly increased risk for bladder cancer was found for A allele carriers (OR 1.36; 95% CI: 0.96-1.94). We did not find any association between the -347 G/GA SNP and bladder cancer. Haplotype analyses did not yield much stronger associations with bladder cancer than the -160 C/A genotype analyses.

CONCLUSION

This study supports earlier suggestions that the -160 C/A SNP in the CDH1 promoter is a risk factor for bladder cancer.