The E-cadherin (CDH1)--160 C/A polymorphism and prostate cancer risk: a meta-analysis. Eur J Hum Genet. 2009;17:244-249. [PMID: 18781193 DOI: 10.1038/ejhg.2008.157]

Transcriptomic analysis of castration, chemo-resistant and metastatic prostate cancer elucidates complex genetic crosstalk leading to disease progression

Prostate adenocarcinoma, with its rising numbers and high fatality rate, is a daunting healthcare challenge to clinicians and researchers alike. The mainstay of our meta-analysis was to decipher differentially expressed genes (DEGs), their corresponding transcription factors (TFs), miRNAs (microRNA) and interacting pathways underlying the progression of prostate cancer (PCa). We have chosen multiple datasets from primary, castration-resistant, chemo-resistant and metastatic prostate cancer stages for investigation. From our tissue-specific and disease-specific co-expression networks, fifteen hub genes such as ACTB, ACTN1, CDH1, CDKN1A, DDX21, ELF3, FLNA, FLNC, IKZF1, ILK, KRT13, KRT18, KRT19, SVIL and TRIM29 were identified and validated by molecular complex detection analysis as well as survival analysis. In our attempt to highlight hub gene-associated mutations and drug interactions, FLNC was found to be most commonly mutated and CDKN1A gene was found to have highest druggability. Moreover, from DAVID and gene set enrichment analysis, the focal adhesion and oestrogen signalling pathways were found enriched which indicates the involvement of hub genes in tumour invasiveness and metastasis. Finally by Enrichr tool and miRNet, we identified transcriptional factors SNAI2, TP63, CEBPB and KLF11 and microRNAs, namely hsa-mir-1-3p, hsa-mir-145-5p, hsa-mir-124-3p and hsa-mir-218-5p significantly controlling the hub gene expressions. In a nutshell, our report will help to gain a deeper insight into complex molecular intricacies and thereby unveil the probable biomarkers and therapeutic targets involved with PCa progression.

Identification of potential biomarkers and pivotal biological pathways for prostate cancer using bioinformatics analysis methods

Background

Prostate cancer (PCa) is a common urinary malignancy, whose molecular mechanism has not been fully elucidated. We aimed to screen for key genes and biological pathways related to PCa using bioinformatics method.

Methods

Differentially expressed genes (DEGs) were filtered out from the GSE103512 dataset and subjected to the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The protein–protein interactions (PPI) network was constructed, following by the identification of hub genes. The results of former studies were compared with ours. The relative expression levels of hub genes were examined in The Cancer Genome Atlas (TCGA) and Oncomine public databases. The University of California Santa Cruz Xena online tools were used to study whether the expression of hub genes was correlated with the survival of PCa patients from TCGA cohorts.

Results

Totally, 252 (186 upregulated and 66 downregulated) DEGs were identified. GO analysis enriched mainly in “oxidation-reduction process” and “positive regulation of transcription from RNA polymerase II promoter”; KEGG pathway analysis enriched mostly in “metabolic pathways” and “protein digestion and absorption.” Kallikrein-related peptidase 3, cadherin 1 (CDH1), Kallikrein-related peptidase 2 (KLK2), forkhead box A1 (FOXA1), and epithelial cell adhesion molecule (EPCAM) were identified as hub genes from the PPI network. CDH1, FOXA1, and EPCAM were validated by other relevant gene expression omnibus datasets. All hub genes were validated by both TCGA and Oncomine except KLK2. Two additional top DEGs (ABCC4 and SLPI) were found to be associated with the prognosis of PCa patients.

Conclusions

This study excavated the key genes and pathways in PCa, which might be biomarkers for diagnosis, prognosis, and potential therapeutic targets.

Genetic polymorphisms in CDH1 and Exo1 genes elevate the prostate cancer risk in Bangladeshi population

The polymorphisms of invasion suppressor gene CDH1 and DNA mismatch repair gene Exo1 have been reported to play critical role in the development, tumorigenesis, and progression of several kinds of cancers including prostate cancer. This study was designed to analyze the contribution of single-nucleotide polymorphisms of the CDH1 (-160C/A) and Exo1 (K589E) to prostate cancer susceptibility in Bangladeshi population. The study included 100 prostate cancer cases and age-matched 100 healthy controls. Polymerase chain reaction-restriction fragment length polymorphism analysis was used to determine the genetic polymorphisms. A significant association was found between CDH1 -160C/A (rs16260) and Exo1 (rs1047840, K589E) polymorphisms and prostate cancer risk. In case of CDH1 -160C/A polymorphism, the frequencies of the three genotypes C/C,C/A, and A/A were 45%, 48%, and 7% in cases and 63%, 32%, and 5% in controls, respectively. The heterozygote C/A genotype and combined C/A + A/A genotypes showed 2.10-fold (odds ratio = 2.1000, 95% confidence interval = 1.2956-4.0905, p = 0.013) and 2.08-fold (odds ratio = 2.0811, 95% confidence interval = 1.1820-3.6641, p = 0.011) increased risk of prostate cancer, respectively, when compared with homozygous C/C genotypes. The variant A allele also was associated with increased risk of prostate cancer (odds ratio = 1.6901, 95% confidence interval = 1.0740-2.6597, p = 0.0233). In case of Exo1 (K589E) polymorphism, G/A heterozygote, A/A homozygote, and combined G/A + A/A genotypes were found to be associated with 2.30-, 4.85-, and 3.04-fold higher risk of prostate cancer, respectively (odds ratio = 2.3021, 95% confidence interval = 2.956-4.0905, p = 0.0031; odds ratio = 4.8462, 95% confidence interval = 1.0198-23.0284, p = 0.0291; OR = 3.0362, 95% confidence interval = 1.7054-5.4053, p = 0.0001, respectively). The "A" allele showed significant association with increased susceptibility (2.29-fold) to prostate cancer (odds ratio = 2.2955, 95% confidence interval = 1.4529-3.6270, p = 0.0004). Our results suggest that CDH1 -160C/A and Exo1 K589E polymorphisms are associated with increased susceptibility to prostate cancer in Bangladeshi population.

Exploration of the diagnostic value and molecular mechanism of miR‑1 in prostate cancer: A study based on meta‑analyses and bioinformatics

Prostate cancer (PCa) remains a principal issue to be addressed in male cancer-associated mortality. Therefore, the present study aimed to examine the clinical value and associated molecular mechanism of microRNA (miR)-1 in PCa. A meta-analysis was conducted to evaluate the diagnosis of miR-1 in PCa via Gene Expression Omnibus and ArrayExpress datasets, The Cancer Genome Atlas miR-1 expression data and published literature. It was identified that expression of miR-1 was significantly downregulated in PCa. Decreased miR-1 expression possessed moderate diagnostic value, with area under the curve, sensitivity, specificity and odds ratio values at 0.73, 0.77, 0.57 and 4.60, respectively. Using bioinformatics methods, it was revealed that a number of pathways, including the ‘androgen receptor signaling pathway’, ‘androgen receptor activity’, ‘transcription factor binding’ and ‘protein processing in the endoplasmic reticulum’, were important in PCa. A total of seven hub genes, including phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccin ocarboxamide synthase (PAICS), cadherin 1 (CDH1), SRC proto-oncogene, non-receptor tyrosine kinase, twist family bHLH transcription factor 1 (TWIST1), ZW10 interacting kinetochore protein (ZWINT), PCNA clamp associated factor (KIAA0101) and androgen receptor, among which, five (PAICS, CDH1, TWIST1, ZWINT and KIAA0101) were significantly upregulated and negatively correlated with miR-1, were identified as key miR-1 target genes in PCa. Additionally, it was investigated whether miR-1 and its hub genes were associated with clinical features, including age, tumor status, residual tumor, lymph node metastasis, pathological T stage and prostate specific antigen level. Collectively the results suggest that miR-1 may be involved in the progression of PCa, and consequently be a promising diagnostic marker. The ‘androgen receptor signaling pathway’, ‘androgen receptor activity’, ‘transcription factor binding’ and ‘protein processing in the endoplasmic reticulum’ may be crucial interactive pathways in PCa. Furthermore, PAICS, CDH1, TWIST1, ZWINT and KIAA0101 may serve as crucial miR-1 target genes in PCa.

The CDH1 -160C/A polymorphism is associated with breast cancer: evidence from a meta-analysis

Background

Numerous epidemiological studies have evaluated the association between the CDH1 -160C/A polymorphism and the risk of breast cancers. However, these studies have yielded conflicting results. To derive a more precise estimation of this association, this meta-analysis was conducted.

Methods

A comprehensive search using the keywords “CDH1,” “E-Cadherin,” “polymorphism,” “SNP,” and “variant” combined with “breast,” “cancer,” “tumor,” or “carcinomas” was conducted. Pooled odds ratios (ORs) with 95 % confidence intervals (CIs) were appropriately calculated using a fixed effect or random effect model. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2009 checklist was used for this meta-analysis.

Results

Four publications including five studies were identified. It was found that the CDH1 -160C/A polymorphism was significantly associated with breast cancer risk in the dominant model (CA + AA vs. CC: OR = 1.207, 95 % CI = 1.031–1.412, P = 0.019).

Conclusions

Our meta-analysis demonstrated that the -160C/A polymorphism in the CDH1 gene might contribute to breast cancer susceptibility. Further investigations using a much larger sample including different ethnicities are still needed to verify this association.

Electronic supplementary material

The online version of this article (doi:10.1186/s12957-016-0927-0) contains supplementary material, which is available to authorized users.

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.

Key regulators in prostate cancer identified by co-expression module analysis

Background

Prostate cancer (PrCa) is the most commonly diagnosed cancer in men in the world. Despite the fact that a large number of its genes have been investigated, its etiology remains poorly understood. Furthermore, most PrCa candidate genes have not been rigorously replicated, and the methods by which they biologically function in PrCa remain largely unknown.

Results

Aiming to identify key players in the complex prostate cancer system, we reconstructed PrCa co-expressed modules within functional gene sets defined by the Gene Ontology (GO) annotation (biological process, GO_BP). We primarily identified 118 GO_BP terms that were well-preserved between two independent gene expression datasets and a consequent 55 conserved co-expression modules within them. Five modules were then found to be significantly enriched with PrCa candidate genes collected from expression Quantitative Trait Loci (eQTL), somatic copy number alteration (SCNA), somatic mutation data, or prognostic analyses. Specifically, two transcription factors (TFs) (NFAT and SP1) and three microRNAs (hsa-miR-19a, hsa-miR-15a, and hsa-miR-200b) regulating these five candidate modules were found to be critical to the development of PrCa.

Conclusions

Collectively, our results indicated that genes with similar functions may play important roles in disease through co-expression, and modules with different functions could be regulated by similar genetic components, such as TFs and microRNAs, in a synergistic manner.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1015) contains supplementary material, which is available to authorized users.

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.

KCTD11 tumor suppressor gene expression is reduced in prostate adenocarcinoma

Prostate cancer is the most common noncutaneous cancer among men in the United States. A genetic contribution to prostate cancer risk has been documented, but knowledge of the molecular mechanisms involved in prostate cancer initiation is still not well understood. Loss of heterozygosity (LOH) of chromosomal regions is crucial in tumor progression. In human prostate cancer, several chromosomal regions demonstrating a high frequency of LOH have been previously identified. KCTD11 (REN) is a tumor suppressor gene mapping on human chromosome 17p13.2, whose expression is frequently lost in human medulloblastoma and in several other cancer types. KCTD11 acts as a negative regulator of the Hedgehog (Hh) signaling. Here, we demonstrated that KCTD11 LOH is a common genetic lesion in human prostate adenocarcinoma. Indeed, nuclear KCTD11 protein expression is strongly reduced in primary prostate cancer, and this event correlated with overexpression of proteins acting into the Hedgehog pathway. Low levels of KCTD11 mRNA have been also observed in prostatic cancer cells, and ectopic overexpression of KCTD11 led to growth arrest. Our study demonstrates and supports that KCTD11, as well as negatively regulated downstream effectors belonging to Hh signaling, plays a role in prostate cancer pathogenesis. This could be suitable to characterize new diagnostic and therapeutic markers.

Role of rare variants in undetermined multiple adenomatous polyposis and early-onset colorectal cancer

Some 15-20% of multiple adenomatous polyposis have no genetic explanation and 20-30% of colorectal cancer (CRC) cases are thought to be due to inherited multifactorial causes. Accumulation of deleterious effects of low-frequency dominant and independently acting variants may be a partial explanation for such patients. The aim of this study was to type a selection of rare and low-frequency variants (<5%) to elucidate their role in CRC susceptibility. A total of 1181 subjects were included (866 controls; 315 cases). Cases comprised UK (n=184) and French (n=131) patients with MAP (n=187) or early-onset CRC (n=128). Seventy variants in 17 genes were examined in cases and controls. The effect of the variant effect on protein function was investigated in silico. Out of the 70 variants typed, 36 (51%) were tested for association. Twenty-one variants were rare (minor allele frequency (MAF) <1%). Four rare variants were found to have a significantly higher MAF in cases (EXO1-12, MLH1-1, CTNNB1-1 and BRCA2-37, P<0.05) than in controls. Pooling all rare variants with a MAF <0.5% showed an excess risk in cases (odds ratio=3.2; 95% confidence interval=1.1-9.5; P=0.04). Rare variants are important risk factors in CRC and, as such, should be systematically assayed alongside common variation in the search for the genetic basis of complex diseases.

E-cadherin (CDH1) gene promoter polymorphism and the risk of colorectal cancer : a meta-analysis

OBJECTIVE

Published data on the relationship between E-cadherin (CDH1) gene promoter polymorphisms and colorectal cancer (CRC) risk are inconclusive. To derive a more precise estimation of the relationship, a meta-analysis was carried out.

METHODS

In this meta-analysis, we evaluated reported studies of associations between polymorphisms of CDH1 gene promoter -160 C > A and -347 G > GA site, and CRC risk using fixed-effects model and random-effects model.

RESULTS

We found decreased CRC risk among subjects carrying CDH1 -160AA (odds ratio [OR] = 0.86, 95 percent confidence interval [95% CI]: 0.75-0.98) and CA + AA (OR = 0.92, 95% CI: 0.87-0.98), using 4,652/4,428 cases/controls and 7,866/7,689 cases/controls from ten studies, respectively. We found a protective effect of the CDH1 -160CA + AA polymorphisms for CRC in distal site tumor population and population-based control in stratified analysis. We found a protective effect of the CDH1 -160AA and CA + AA polymorphisms for CRC in European and American population (OR = 0.87, 95% CI: 0.76-0.99 and OR = 0.91, 95% CI: 0.85-0.98, respectively). We observed that the CDH1 -347 G/GA + GA/GA carrier had an increased risk of CRC, the summary OR was 1.33 (95% CI: 1.08-1.62).

CONCLUSIONS

Data indicated that certain CDH1 gene promoter -160 C > A and -347 G > GA variants might affect the susceptibility of CRC. Recommendations for further studies include pooling of individual data to facilitate evaluation of multigenic effects and detailed analysis of effect modification by environmental and lifestyle factors.

The -1082A/G polymorphism in the Interleukin-10 gene and the risk of rheumatoid arthritis: a meta-analysis

A large number of studies have shown that the -1082A/G polymorphism (rs1800896) in the Interleukin-10 gene (IL-10) is implicated in the susceptibility to rheumatoid arthritis (RA). However, the results are inconsistent and inconclusive. The aim of this study is to analyze the association between the -1082A/G polymorphism in the IL-10 gene and the RA risk by meta-analysis. A total of 1480 cases and 1413 controls in 10 case-control studies were included in this meta-analysis. The results indicated that the G allele carriers (GG+GA) had a 25% decreased risk of RA, when compared with the homozygote AA (odds ratio (OR)=0.75, 95% confidence interval (CI): 0.59-0.93). In the analysis in Europeans, significant decreased risks were associated with the G allele carriers (OR=0.73 and 95% CI: 0.57-0.93 for GG+GA vs. AA). The results from this meta-analysis provide evidence for the association between the IL-10 -1082A/G polymorphism and the risk of RA. To further evaluate gene×gene and gene×environment interactions between the polymorphisms in the IL-10 gene and RA risk, more studies with large groups of patients are required.

CDH1 promoter polymorphism and stomach cancer susceptibility

The relationship of stomach cancer susceptibility and the presence of E-cadherin (CDH1) promoter -160 C/A polymorphism had been reported with conflicting results. To further explore the association of this polymorphism with stomach cancer susceptibility, we performed an extensive search of relevant studies and carried out a meta-analysis to obtain a more precise estimate. A total of 16 studies including 2,611 cases and 3,788 controls were involved in this meta-analysis. When all studies involved, the meta-analysis results suggest no statistically significant association between CDH1 -160 C/A polymorphism and stomach cancer risk (CA vs. CC: OR = 1.01, 95% CI: 0.85-1.19; AA vs. CC: OR = 1.05, 95% CI: 0.75-1.46; dominant model: OR = 1.02, 95% CI: 0.86-1.20; recessive model: OR = 1.04, 95% CI: 0.76-1.41). When subgroup analyses were performed by ethnicity, the A-allele carriers conferred a decreased stomach cancer risk in Asians (AA vs. CC: OR = 0.67, 95% CI: 0.47-0.96; dominant model: OR = 0.85, 95% CI: 0.72-0.99), but no statistically significant association was found in Caucasians. In conclusion, this meta-analysis suggests that CDH1 -160 A-allele may play a protective role of stomach cancer development in Asians but not in Caucasians.

Role of E-cadherin in antimigratory and antiinvasive efficacy of silibinin in prostate cancer cells

The epithelial-to-mesenchymal transition (EMT) in prostate cancer (PCA) cells is considered prerequisite for acquiring migratory/invasive phenotype, and subsequent metastasis. We hypothesized that promoting the E-cadherin expression in PCA cells by using nontoxic phytochemicals, like silibinin, would prevent EMT and consequently invasiveness. Our results showed that silibinin treatment (5-90 μmol/L) significantly inhibits migratory and invasive potential of advance human PCA PC3, PC3MM2, and C4-2B cells in in vitro assays. Importantly, the antimigratory/antiinvasive efficacy of silibinin was not due to its cytotoxicity toward PCA cells. Molecular analyses showed that silibinin increases E-cadherin level that was localized mainly at cellular membrane as evidenced by subcellular fractional and confocal analyses in PC3 cells, which might be responsible for morphologically observed shift toward epithelial character. Silibinin also decreased the levels of Slug, Snail, phospho-Akt(ser(473)), nuclear β-catenin, phospho-Src(tyr(419)) and Hakai; together they play an important role in regulating E-cadherin expression/function and EMT. Similar silibinin effects on E-cadherin, β-catenin, phospho-Src(tyr(419)), and Hakai levels were also observed in PC3MM2 and C4-2B PCA cells. Selective Src inhibition by dasatinib also showed increased E-cadherin expression in PC3 cells suggesting a possible involvement of Src inhibition in silibinin-caused increase in E-cadherin level. Additional studies in PC3 cells with stable knock-down of E-cadherin expression revealed that antimigratory/antiinvasive efficacy of silibinin is in-part dependent on E-cadherin expression. Together, our results showing antimigratory/antiinvasive effects of silibinin and associated mechanisms suggest that silibinin should be tested further in clinically relevant animal models toward exploiting its potential benefits against metastatic PCA.

The I/D polymorphism of angiotensin-converting enzyme gene and asthma risk: a meta-analysis

BACKGROUND

  The insertion/deletion (I/D) polymorphism of angiotensin-converting enzyme (ACE) gene has been implicated in susceptibility to asthma, but a large number of studies have reported inconclusive results. The aim of this study is to investigate the association between the I/D polymorphism of ACE gene and asthma risk by meta-analysis.

METHODS

  We searched Medline (Ovid), Pubmed, CNKI, Wanfang, and Weipu database, covering all papers until March 12, 2010. Statistical analysis was performed by using the software revman 4.2 (The Cochrane Collaboration, http://www.cochrane.org) and stata 10.0 (StataCorp, College Station, TX, USA, http://www.stata.com).

RESULTS

  A total of 1946 cases and 2152 controls in 18 case-control studies were included in this meta-analysis. The results indicated that the DD homozygote carriers had a 59% increased risk of asthma, when compared with the homozygotes II and heterozygote DI [odds ratio (OR)=1.59, 95% confidence interval (CI): 1.16-2.18]. In the subgroup analysis by ethnicity, significant elevated risks were associated with DD homozygote carriers in Asians (OR=2.02 and 95% CI: 1.29-3.16 for DD vs DI+II) but not in Caucasians (OR=1.14 and 95% CI: 0.76-1.72 for DD vs DI+II). In the subgroup analysis by age, significant elevated risks were associated with DD homozygote carriers in children (OR=2.44 and 95% CI: 1.36-4.38 for DD vs II+DI) but not in adults (OR=1.54 and 95% CI: 0.94-2.51 for DD vs II+DI).

CONCLUSIONS

  This meta-analysis suggested that the I/D polymorphism of ACE gene would be a risk factor of asthma. To further evaluate gene-to-gene and gene-to-environment interactions between polymorphisms of ACE gene and asthma risk, more studies with large groups of patients are required.

Gene expression correlation analysis predicts involvement of high- and low-confidence risk genes in different stages of prostate carcinogenesis

BACKGROUND

Whole genome association studies have identified many loci associated with the risk of prostate cancer (PC). However, very few of the genes associated with these loci have been related to specific processes of prostate carcinogenesis. Therefore I inferred biological functions associated with these risk genes using gene expression correlation analysis.

METHODS

PC risk genes reported in the literature were classified as having high (P<10(-6)), medium (P<10(-4)), or low (P<10(-2)) statistical confidence. Correlation coefficients of the expression levels between the risk genes and other genes in cancerous prostates samples were compared against those in normal prostates using a microarray dataset from Gene Expression Omnibus.

RESULTS

Overall, significant decrease of correlations in PC was observed between the levels of expression of the high-confidence genes and other genes in the microarray dataset, whereas correlation between low-confidence genes and other genes in PC showed smaller decrease. Genes involved in developmental processes were significantly correlated with all risk gene categories. Ectoderm development genes, which may be related to squamous metaplasia, and genes enriched in fetal prostate stem cells (PSCs) showed strong association with the high-confidence genes. The association between the PSC genes and the low-confidence genes was weak, but genes related to neural system genes showed strong association with low-confidence genes.

CONCLUSIONS

The high-confidence risk genes may be associated with an early stage of prostate carcinogenesis, possibly involving PSCs and squamous metaplasia. The low-confidence genes may be involved in a later stage of carcinogenesis.

RANTES gene polymorphisms and asthma risk: A meta-analysis

BACKGROUND AND AIMS

RANTES is a chemokine that assists the recruitment of inflammatory cells including eosinophils. Previous studies revealed that polymorphisms of RANTES were implicated in susceptibility to asthma, but a large number of studies reported apparently conflicting results. We performed a meta-analysis to investigate the association of these polymorphisms and asthma risk.

METHODS

Literature-based meta-analysis was supplemented by tabular data from investigation of all relevant studies regarding all polymorphisms of RANTES available before November 30, 2009, with investigation on potential sources of heterogeneity.

RESULTS

Ten case/control studies were included in the meta-analysis, involving a total of 1706 cases and 1685 controls. In a combined analysis, no significant associations with asthma risk were found on these two polymorphisms (-403G/A and -28C/G) without any publication bias. For the -403G/A polymorphism, in subgroup analysis by ethnicity, no significant associations were found in Asians, Europeans or African-Americans; in subgroup analysis by age, no significant associations were found in adults or children. In subgroup analysis by atopic status, the -403G/A polymorphism was significantly associated with asthma risk in atopic asthma (dominant model [OR = 1.38, 95% CI = 1.09-1.76, p = 0.009; P(het) = 0.10]; A vs. G model [OR = 1.25, 95% CI = 1.04-1.51, p = 0.02; P(het) = 0.11] and AG vs. GG model [OR = 1.37, 95% CI = 1.06-1.77, p = 0.02; P(het) = 0.14]).

CONCLUSIONS

This meta-analysis suggested that RANTES gene -403G/A polymorphism would be a risk factor among atopic asthma patients. To further evaluate gene-to-gene and gene-to-environment interactions on RANTES polymorphisms and asthma risk, more studies with thousands of patients are required.

CDH1 C-160A promoter polymorphism and genetic susceptibility to gastric cancer: a meta-analysis

AIM: To investigate the relationship between E-cadherin (CDH1) gene C-160A promoter polymorphism and genetic susceptibility to gastric cancer.

METHODS: Chinese biomedicine disc (CBM), Wanfang database, China National Knowledge Infrastructure (CNKI) and PubMed were searched for published case-control studies investigating the association between CDH1 C-160A promoter polymorphism and susceptibility to gastric cancer. The odds ratio was calculated to evaluate the genotypes of gastric cancer patients and control subjects. Fixed or random effect models were selected for pooled odds ratio calculation. Publication bias was assessed. All statistical analyses were conducted with Stata 10.0 software.

RESULTS: A total of 14 case-control studies involving 3 144 gastric cancer patients and 4 221 controls were analyzed in the study. Compared with the wild-type genotype (homozygote CC), the pooled odds ratio [and 95% confidence interval (CI)] for CA and AA genotypes was 0.98 (0.84-1.15). In the population subgroup analysis, the odds ratios for Asian and Caucasian populations were 0.92 (0.81-1.04) and 1.21 (0.88-1.67), respectively.

CONCLUSION: CDH1 C-160A promoter polymorphism is not associated with genetic susceptibility to gastric cancer.

Hereditary diffuse gastric cancer

Gastric cancer is one of the world's leading causes of cancer mortality. A small percentage of cases can be attributed to heritable mutations in highly penetrant cancer susceptibility genes. In this chapter we will focus on the genetic cause of hereditary diffuse gastric cancer (HDGC). Until 10 years ago, individuals from these families lived with the uncertainty of developing lethal gastric cancer. Today, HDGC families can be identified, tested for causative mutations in CDH1, and for those families where a pathogenic mutation can be identified, prophylactic total gastrectomy can be implemented in asymptomatic mutation carriers who elect to virtually eliminate their risk of developing this lethal disease.

E-cadherin polymorphisms and breast cancer susceptibility: a report from the Shanghai Breast Cancer Study

The epithelial transmembrane glycoprotein E-cadherin (CDH1) is necessary for intercellular adhesion, cell signaling, and maintenance of cellular differentiation; reduced expression contributes to cell proliferation, invasion, and cancer progression. Functional or potentially functional single nucleotide polymorphisms (SNPs) in E-cadherin have been previously identified and evaluated in relation to cancer risk; however, studies on breast cancer have been sparse. Forty-six SNPs were genotyped to capture genetic variation of the CDH1 gene among 2,290 Phase 1 and 1,944 Phase 2 participants of the Shanghai Breast Cancer Study (SBCS), a large, population-based, case-control study. No overall associations between E-cadherin SNPs and breast cancer risk were observed. When stratified by menopausal status, associations that were consistent between Phases 1 and 2 and significant when data from both phases were combined were observed for several SNPs. Although none of these associations retained statistical significance after correcting for the total number of polymorphisms evaluated, this study suggests that genetic variation in CDH1 may be associated with breast cancer risk, and that this relationship may vary by menopausal status.