Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia

BACKGROUND

Expansion of genome-wide association studies across population groups is needed to improve our understanding of shared and unique genetic contributions to breast cancer. We performed association and replication studies guided by a priori linkage findings from African ancestry (AA) relative pairs.

METHODS

We performed fixed-effect inverse-variance weighted meta-analysis under three significant AA breast cancer linkage peaks (3q26-27, 12q22-23, and 16q21-22) in 9241 AA cases and 10 193 AA controls. We examined associations with overall breast cancer as well as estrogen receptor (ER)-positive and negative subtypes (193,132 SNPs). We replicated associations in the African-ancestry Breast Cancer Genetic Consortium (AABCG).

RESULTS

In AA women, we identified two associations on chr12q for overall breast cancer (rs1420647, OR = 1.15, p = 2.50×10-6; rs12322371, OR = 1.14, p = 3.15×10-6), and one for ER-negative breast cancer (rs77006600, OR = 1.67, p = 3.51×10-6). On chr3, we identified two associations with ER-negative disease (rs184090918, OR = 3.70, p = 1.23×10-5; rs76959804, OR = 3.57, p = 1.77×10-5) and on chr16q we identified an association with ER-negative disease (rs34147411, OR = 1.62, p = 8.82×10-6). In the replication study, the chr3 associations were significant and effect sizes were larger (rs184090918, OR: 6.66, 95% CI: 1.43, 31.01; rs76959804, OR: 5.24, 95% CI: 1.70, 16.16).

CONCLUSION

The two chr3 SNPs are upstream to open chromatin ENSR00000710716, a regulatory feature that is actively regulated in mammary tissues, providing evidence that variants in this chr3 region may have a regulatory role in our target organ. Our study provides support for breast cancer variant discovery using prioritization based on linkage evidence.

Single-nucleotide polymorphisms of the adherent junction component cadherin gene are associated with leukoaraiosis

BACKGROUND

Leukoaraiosis (LA) is one of the manifestations of cerebral small vessel disease. Blood-brain barrier (BBB) disruption plays a key role in LA. Cadherin is a component of adherent junctions (AJ), which play a crucial role in cell-cell adhesion, cell-cell recognition and homeostasis in BBB development. We hypothesized that alterations in cadherin genes might be a potential cause of BBB abnormalities that result in LA.

METHODS

A total of 339 LA individuals (LA-PVWM, 183; LA-DWM 156) were enrolled, who underwent brain magnetic resonance imaging with obtainable vascular risk factors. Genotyping of cadherin single-nucleotide polymorphisms (SNPs) (rs5030625, rs1801026, and rs16260) was performed by real-time polymerase chain reaction with LightSNiP reagents (coupled primer and probe) and FastStart DNAMaster HybProbe (Roche Diagnostic, GmBH, Mannheim, Germany) on a LightCycler 2.0 instrument.

RESULTS

Two SNPs, rs1801026 and rs16260, were significantly different between the control and LA groups. The combinatorial effects of the three SNPs were also significant. The haplotypes G-T-C and GA-T-A increased the development of LA-PVWM (OR = 1.76 and OR = 40.7, respectively). The haplotypes G-T-A and GA-T-A increased the development of LA-DWM (OR = 2.56 and OR = 10.48, respectively), but G-C-C decreased the development of LA-DWM (OR = 17.57).

CONCLUSION

This study provides evidence for genetic polymorphisms of the AJ component cadherin gene and the association of its haplotypes with LA.

The -160 (C>A) CDH1 Gene Promoter Polymorphism and Its Relationship with Survival of Patients with Gastric Cancer in Kurdistan

Introduction:

Gastric cancer (GC) is the fourth most common type of neoplasm and the second cause of malignancy-related death across much of the world. Complex multi-factorial processes are involved in its genesis, classified in two determinant clusters: non-genetic and genetic. Variation in CDH1 gene expression may play an important role in increasing risk of diffuse and intestinal subtypes of GC. This tumor suppressor gene, located on chromosome 16q22.1, encodes a trans membrane glycoprotein called epithelial cadherin (E-cadherin).

Materials and Methods:

In this historical cohort study, from June 2004 to Journey 2005 we collected 50 samples from Kurdish patients with stage II pathologically diagnosed gastric cancer that underwent surgery. Tumor tissues were paraffin-embedded along with 54 control samples from non-ulcer dyspepsia (NUD) cases undergoing upper gastrointestinal endoscopy. Three biopsies were captured by endoscopy from each individual’s gastric antrum.

Result:

The mean age of the patients was 59.5±2 years. Some 23 cases (53.4%) had the CC genotype, 19 AC and 1 AA. H.pylori infection was noted in 30 patients (69%). Survival rates of gastric cancer patients were 90.7% in the first year, 39.5% in the second year and 6.9% in the third year. Female patients had higher survival rates (P=0.004).

Conclusion:

In this study we found that frequencies of -160(C>A) CDH1 genotypes were not comparable in H.pylori-infected and H.pylori-uninfected subjects in both case and control groups. These findings suggest that -160 (C>A) CDH1 polymorphism is not related with H.pylori infection susceptibility. In addition we found no significant relationship between the CDH1 -160(C/A) promoter polymorphism with predisposition to gastric cancer.

Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma

The regulation of transcriptome expression level is a complex process involving multiple-level interactions among molecules such as protein coding RNA (mRNA), long noncoding RNA (lncRNA), and microRNA (miRNA), which are essential for the transcriptome stability and maintenance and regulation of body homeostasis. The availability of multilevel expression data enables a comprehensive view of the regulatory network. In this study, we analyzed the coding and noncoding gene expression profiles of 301 patients with uterine corpus endometrial carcinoma (UCEC). A new method was proposed to construct a genome-wide integrative network based on variance inflation factor (VIF) regression method. The cross-regulation relations of mRNA, lncRNA, and miRNA were then selected based on clique-searching algorithm from the network, when any two molecules of the three were shown as interacting according to the integrative network. Such relation, which we call the mRNA-lncRNA-miRNA triplet, demonstrated the complexity in transcriptome regulation process. Finally, six UCEC-related triplets were selected in which the mRNA participates in endometrial carcinoma pathway, such as CDH1 and TP53. The multi-type RNAs are proved to be cross-regulated as to each of the six triplets according to literature. All the triplets demonstrated the association with the initiation and progression of UCEC. Our method provides a comprehensive strategy for the investigation of transcriptome regulation mechanism.

Genetic variations in the Hippo signaling pathway and breast cancer risk in African American women in the AMBER Consortium

The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. Dysfunction of the Hippo pathway components has been linked with breast cancer stem cell regulation, as well as breast tumor progression and metastasis. TAZ, a key component of the Hippo pathway, is highly expressed in triple negative breast cancer; however, the associations of genetic variations in this important pathway with breast cancer risk remain largely unexplored. Here, we analyzed 8309 germline variants in 15 genes from the Hippo pathway with a total of 3663 cases and 4687 controls from the African American Breast Cancer Epidemiology and Risk Consortium. Odds ratios (ORs) were estimated using logistic regression for overall breast cancer, by estrogen receptor (ER) status (1983 ER positive and 1098 ER negative), and for case-only analyses by ER status. The Hippo signaling pathway was significantly associated with ER-negative breast cancer (pathway level P = 0.02). Gene-based analyses revealed that CDH1 was responsible for the pathway association (P < 0.01), with rs4783673 in CDH1 statistically significant after gene-level adjustment for multiple comparisons (P = 9.2×10(-5), corrected P = 0.02). rs142697907 in PTPN14 was associated with ER-positive breast cancer and rs2456773 in CDK1 with ER-negativity in case-only analysis after gene-level correction for multiple comparisons (corrected P < 0.05). In conclusion, common genetic variations in the Hippo signaling pathway may contribute to both ER-negative and ER+ breast cancer risk in AA women.

miR-199a-5p induces cell invasion by suppressing E-cadherin expression in cutaneous squamous cell carcinoma

A growing quantity of evidence exists to suggest that microRNAs are significant regulators of multiple cellular processes. When expressed aberrantly in different types of cancer, including cutaneous squamous cell carcinoma (cSCC), they play key roles in tumorigenesis and progression. The aberrant expression of miR-199a-5p has been observed to contribute to carcinogenesis in various types of cancer. However, the role of miR-199a-5p in the progression of cSCC metastasis remains largely unknown. In this study, we determined that miR-199a-5p was the upstream regulator of CDH1 (E-cadherin) and that it could suppress the expression of E-cadherin in cSCC cells. In addition, miR-199a-5p mimics significantly induced cell invasion and the activity of matrix metalloproteinase (MMP)2 and MMP9 in cSCC cells. In conclusion, these results are likely to aid in elucidating the molecular mechanisms of cSCC progression. In addition, the findings provide a new theoretical basis to further investigate miR-199a-5p as a potential biomarker and a promising approach in cSCC treatment.

Biomarkers for evaluation of prostate cancer prognosis

Prostate cancer, with a lifetime prevalence of one in six men, is the second cause of malignancy-related death and the most prevalent cancer in men in many countries. Nowadays, prostate cancer diagnosis is often based on the use of biomarkers, especially prostate-specific antigen (PSA) which can result in enhanced detection at earlier stage and decreasing in the number of metastatic patients. However, because of the low specificity of PSA, unnecessary biopsies and mistaken diagnoses frequently occur. Prostate cancer has various features so prognosis following diagnosis is greatly variable. There is a requirement for new prognostic biomarkers, particularly to differentiate between inactive and aggressive forms of disease, to improve clinical management of prostate cancer. Research continues into finding additional markers that may allow this goal to be attained. We here selected a group of candidate biomarkers including PSA, PSA velocity, percentage free PSA, TGFβ1, AMACR, chromogranin A, IL-6, IGFBPs, PSCA, biomarkers related to cell cycle regulation, apoptosis, PTEN, androgen receptor, cellular adhesion and angiogenesis, and also prognostic biomarkers with Genomic tests for discussion. This provides an outline of biomarkers that are presently of prognostic interest in prostate cancer investigation.

Breast cancer risk in relation to TP53 codon 72 and CDH1 gene polymorphisms in the Bangladeshi women

Pharmacogenomic studies play a significant role in understanding the risk of breast cancer where genetic abnormalities are implicated as the etiology of cancer. Various polymorphisms of tumor suppressor gene TP53 and E-cadherin (CDH1) have been found to be associated with increased breast cancer risk worldwide. This study aimed to analyze the contribution of TP53 and CDH1 gene anomalies in breast cancer risk in the Bangladeshi breast cancer patients. For risk determination, 310 patients with breast cancer and 250 controls from Bangladeshi women were recruited who are matched up with age and use of contraceptives with patients. Genetic polymorphisms were detected by using polymerase chain reaction restriction fragment length polymorphism. A significant association was found between TP53Arg72Pro (rs1042522) and CDH1 -160 C/A (rs16260) polymorphisms and breast cancer risk. In case of P53rs1042522 polymorphism, Arg/Pro (P = 0.0053, odds ratio (OR) = 1.69) and Pro/Pro (P = 0.018, OR = 1.83) genotypes were associated with increased risk of breast cancer in comparison to the Arg/Arg genotype. Arg/Pro + Pro/Pro genotype and Pro allele also increased the risk of breast cancer (P = 0.002, OR = 1.73; P = 0.004, OR = 1.43, respectively). In case of CDH1rs16260 polymorphism, C/A heterozygote and combined C/A + A/A genotypes were found to be strongly associated (P = 0.005, OR = 1.67; P = 0.0037, OR = 1.68) with increased risk of breast cancer. The variant A allele also increased the breast cancer risk (P = 0.0058, OR = 1.52). The present study demonstrates that P53Arg72Pro and CDH1rs16260 polymorphisms are associated with elevated breast cancer risk in the Bangladeshi population.

CDH1/E-cadherin and solid tumors. An updated gene-disease association analysis using bioinformatics tools

Cancer is a group of diseases that causes millions of deaths worldwide. Among cancers, Solid Tumors (ST) stand-out due to their high incidence and mortality rates. Disruption of cell-cell adhesion is highly relevant during tumor progression. Epithelial-cadherin (protein: E-cadherin, gene: CDH1) is a key molecule in cell-cell adhesion and an abnormal expression or/and function(s) contributes to tumor progression and is altered in ST. A systematic study was carried out to gather and summarize current knowledge on CDH1/E-cadherin and ST using bioinformatics resources. The DisGeNET database was exploited to survey CDH1-associated diseases. Reported mutations in specific ST were obtained by interrogating COSMIC and IntOGen tools. CDH1 Single Nucleotide Polymorphisms (SNP) were retrieved from the dbSNP database. DisGeNET analysis identified 609 genes annotated to ST, among which CDH1 was listed. Using CDH1 as query term, 26 disease concepts were found, 21 of which were neoplasms-related terms. Using DisGeNET ALL Databases, 172 disease concepts were identified. Of those, 80 ST disease-related terms were subjected to manual curation and 75/80 (93.75%) associations were validated. On selected ST, 489 CDH1 somatic mutations were listed in COSMIC and IntOGen databases. Breast neoplasms had the highest CDH1-mutation rate. CDH1 was positioned among the 20 genes with highest mutation frequency and was confirmed as driver gene in breast cancer. Over 14,000 SNP for CDH1 were found in the dbSNP database. This report used DisGeNET to gather/compile current knowledge on gene-disease association for CDH1/E-cadherin and ST; data curation expanded the number of terms that relate them. An updated list of CDH1 somatic mutations was obtained with COSMIC and IntOGen databases and of SNP from dbSNP. This information can be used to further understand the role of CDH1/E-cadherin in health and disease.

Immunohistochemical assessment of E-cadherin and β-catenin in the histological differentiations of oral squamous cell carcinoma

The aim of this study was to establish the expression and localization of E-cadherin and β-catenin in oral squamous cell carcinomas (OSCC) so that we could correlate the findings with prognostic-relevant histopathological variables. E-cadherin and β-catenin expression in normal oral epithelia and in oral squamous cell carcinomas was examined immunohistochemically, and associations with histopathological differentiation and prognosis were then analyzed in 33 patients who had been operated on for OSCC. E-cadherin expression was found in (82%) of the squamous cells of well differentiated OSCC, (61%) of moderately differentiated and (39%) of poorly differentiated. E-cadherin expression was significantly associated with histological grade (p=0.000). No nuclear staining was detected. In (19.5%) of the cells E-cadherin localized in the cytoplasm, with no correlation to the histological grade (p=0.106). β-Catenin expression was found in 87% of the squamous cells of well differentiated OSCC, 67% of moderately differentiated and 43% of poorly differentiated, the expression was significantly associated with histological grade (p=0.000). the nuclear β-Catenin expression appeared in 3.3% of the cells and it was correlated to the histological grade (p=0.000). In (23.5%) of the cells β-Catenin localized in the cytoplasm, with correlation to the histological grade (p=0.002). According to this study the expression of β-catenin and E-cadherin were independent prognostic factors for histological grade. E-cadherin was closely linked to β-catenin expression in OSCC (p=0.000) and to tumor differentiation. That reflects a structural association and the role of both in tumor progression.

Estrogen receptor 1 (ESR1) genetic variations in cancer risk: a systematic review and meta-analysis

BACKGROUND

Emerging published data on the association between single nucleotide polymorphisms (SNPs) in the estrogen receptor 1 (ESR1) gene and cancer susceptibility are inconsistent. This review and meta-analysis is performed to derive a more precise evaluation of this relationship.

METHODS

The literature search of PubMed, Embase, Web of Science and CNKI databases was conducted from their inception through June 2014. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association.

RESULTS

Twenty-two literatures were enrolled in this meta-analysis. The results indicated that ESR1 rs1801132 (C>G) was associated with cancer risk in Caucasian populations. However, the results of stratified analysis by cancer type and source of controls indicated that no significant association was found. Furthermore, rs2077647 (A>G) was only associated with an increased risk of hepatocellular carcinoma, but was an adverse effect on cancer risk in Caucasian populations.

CONCLUSIONS

This present meta-analysis indicated that rs1801132 (C>G) and rs2077647 (A>G) may be protective factors in Caucasian populations. Meanwhile, rs2077647 (A>G) may be closely related with hepatocellular carcinoma.

Association of common variations of the E-cadherin with endometriosis

Endometriosis is a polygenic and multifactorial disease. E-cadherin (CDH1) gene encodes an epithelial cell-cell adhesion glycoprotein that modulates a wide variety of processes, including cell polarization, migration and cancer metastasis. Decreased expression of CDH1 in epithelial cells in peritoneal endometriosis has been reported in advanced stages of endometriotic lesions. We investigated the CDH1 -160C/A and +54C/T variations with susceptibility to endometriosis in an Iranian population. In this case-control study, 149 patients with endometriosis (stages I-IV) and 151 healthy women as controls were included. Genotyping was performed using PCR-RFLP method. A p value of <0.05 was considered statistically significant. The CDH1 + 54TT genotype was significantly lower (p = 0.012; OR = 0.30, 95% CI: 0.12-0.77) in the patients (11.6%) than the control group (26.7%). The CDH1 + 54T allele was significantly lower (p = 0.001; OR = 0.55, 95% CI: 0.38-0.77) in the cases (35.7%) compared with the control group (50.3%). No association was found between CDH1 - 160C/A polymorphism and endometriosis. The CDH1 +54C/T was associated with susceptibility to endometriosis in Iranian population, and +54T allele may have a protective role in progression of endometriosis.

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.