Molecular biomarkers in urothelial bladder cancer

MicroRNA-124-3p inhibits cell migration and invasion in bladder cancer cells by targeting ROCK1

Background

Increasing evidence has suggested that dysregulation of certain microRNAs (miRNAs) may contribute to human disease including carcinogenesis and tumor metastasis in human. miR-124-3p is down-regulated in various cancers, and modulates proliferation and aggressiveness of cancer cells. However, the roles of miR-124-3p in human bladder cancer are elusive. Thus, this study was conducted to investigate the biological functions and its molecular mechanisms of miR-124-3p in human bladder cancer cell lines, discussing whether it has a potential to be a therapeutic biomarker of bladder cancer.

Methods

Three human bladder cancer cell lines and samples from ten patients with bladder cancer were analyzed for the expression of miR-124-3p by quantitative RT--PCR. Exogenetic overexpression of miR-124-3p was established by transfecting mimics into T24, UM-UC-3 and J82 cells, after that cell proliferation and cell cycle were assessed by MTT assay, flow cytometry and Colony-forming assay. Cell motility and invasion ability were evaluated by wound healing assay and transwell assay. Tissue microarray, and immunohistochemistry with antibodies against ROCK1, MMP2 and MMP9 was performed using the peroxidase and DAB methods. The target gene of miR-124-3p was determined by luciferase assays, quantitative RT--PCR and western blot. The regulation of epithelial-to-mesenchymal transition by miR-124-3p was analyzed by western blot.

Results

miR-124-3p is frequently down-regulated in bladder cancer both in three bladder cancer cell lines, T24, UM-UC-3, J82 and clinical samples. Overexpression of miR-124-3p induced G1-phase arrest in T24, UM-UC-3 and J82 cell lines and suppressed cell growth in colony-forming assay. miR-124-3p significantly repressed the capability of migration and invasion of bladder cancer cells. In addition, ROCK1 was identified as a new target of miR-124-3p. ROCK1, MMP2, MMP9 were up-regulated in bladder cancer tissues. Furthermore, we demonstrated miR-124-3p could inhibit bladder cancer cell epithelial mesenchymal transfer, and regulated the expression of c-Met, MMP2, MMP9.

Conclusions

miR-124-3p can repress the migration and invasion of bladder cancer cells via regulating ROCK1. Our data indicate that miR-124-3p could be a tumor suppressor and may have a potential to be a diagnostics or predictive biomarker in bladder cancer.

Hsa-miR-125b suppresses bladder cancer development by down-regulating oncogene SIRT7 and oncogenic long noncoding RNA MALAT1

MicroRNAs mainly inhibit coding genes and long non-coding RNA expression. Here, we report that hsa-miR-125b and oncogene SIRT7/ oncogenic long noncoding RNA MALAT1 were inversely expressed in bladder cancer. Hsa-miR-125b mimic downregulated, whereas hsa-miR-125b inhibitor upregulated the expression of SIRT7 and MALAT1. Binding sites were confirmed between hsa-miR-125b and SIRT7/MALAT1. Upregulation of hsa-miR-125b or downregulation of SIRT7 inhibited proliferation, motility and increased apoptosis. The effects of upregulation of hsa-miR-125b were similar to that of silencing MALAT1 in bladder cancer as we had previously described. These data suggest that hsa-miR-125b suppresses bladder cancer development via inhibiting SIRT7 and MALAT1.

The Lin28/let-7a/c-Myc pathway plays a role in non-muscle invasive bladder cancer

We investigate the role of the Lin28/let-7a/c-Myc pathway in non-muscle invasive bladder cancer (NMIBC). Using RT-PCR, western blot and immunohistochemistry techniques, the levels of pre-let-7a, let-7a, Lin28 and c-Myc RNA and/or proteins were determined in samples of normal bladder tissue and bladder cancer. Expression of pre-let-7a was found to be negatively correlated with the pathological grade of bladder cancer, while let-7a showed a positive correlation with bladder cancer pathological grade. Expression of Lin28 RNA and protein was not significantly different between normal bladder tissue and low-grade transitional cell carcinoma of bladder (TCC) but the expression levels in high-grade TCC were remarkably increased. Expression of c-Myc RNA and protein was significantly higher in bladder cancer samples in comparison to normal bladder tissue without correlation with cancer differentiation. Expression of all the above RNAs and proteins showed no significant difference in Ta and T1 stages. The Lin28/let-7a/c-Myc pathway plays an important role in NMIBC. In particular, expression levels of let-7a correlate with the degree of cancer differentiation but not cancer stage.

Overexpression of Rab25 contributes to metastasis of bladder cancer through induction of epithelial-mesenchymal transition and activation of Akt/GSK-3β/Snail signaling

Rab25, an epithelial-specific member of the Rab family of small guanosine triphosphatases, is associated with several human cancers. The goal of this study was to determine its function in bladder cancer (BC). We examined the Rab25 expression pattern in two different cohorts of BC patients treated with radical cystectomy by quantitative PCR, western blotting and immunohistochemical staining. A series of in vitro and in vivo assays were performed to elucidate the function of Rab25 in BC and its underlying mechanisms. Rab25 expression was significantly elevated at both the messenger RNA and protein levels in BCs compared with normal bladder tissues. High Rab25 expression was closely associated with lymph node (LN) metastasis and was an independent predictor for poor disease-free survival in BC patients. Downregulation of Rab25 in BC cells markedly inhibited invasive motility in vitro and metastatic potential in vivo. In addition, downregulation of Rab25 in BC EJ and T24 cells increased the expression levels of epithelial markers (E-cadherin and α-catenin) and decreased the levels of mechamechy markers (vimentin and fibronectin). Simultaneously, downregulation of Rab25 in EJ and T24 cells resulted in the inactivation of downstream phosphorylated protein kinase B (p-Akt), phosphorylated glycogen synthase kinase-β (p-GSK-3β) and snail signaling. This study demonstrates that Rab25 can promote BC metastasis through induction of epithelial-mesenchymal transition process and activation of Akt/GSK-3β/Snail signaling pathway; Rab25 expression level can predict LN metastasis and inferior clinical outcome in BC patients.

Republished: non-invasive urine based tests for the detection of bladder cancer

Bladder cancer is the fourth most frequently diagnosed malignant neoplasm and cause of cancer-related deaths in men and eighth in women. Patients with bladder cancer undergo repeated cystoscopic examinations of the bladder to monitor for tumour recurrence which is invasive, costly and lacks accuracy. Therefore, the development of non-invasive urine based tests for the early detection of bladder cancer would be of tremendous benefit to both patients and healthcare systems. A number of urine based markers are available for the early diagnosis of bladder cancer. The diagnosis of bladder cancer relies on identifying malignant cells in the urine. All urinary markers have a higher sensitivity as compared with cytology but they score lower in specificity. Many soluble and cell based markers have been developed. Only two of the soluble and cell based markers have obtained the Food and Drug Administration approval. In the current review, the most recent literature of urinary markers is summarised. This article reports some of the more prominent urine markers and new technologies used nowadays.

Twist1 and Y-box-binding protein-1 are potential prognostic factors in bladder cancer

OBJECTIVE

To investigate the expression and possible roles of Twist1 and Y-box-binding protein-1 (YB-1) in bladder cancer tissue. Twist1 belongs to the family of basic helix-loop-helix transcription factors. A functional link between Twist1 and YB-1 has recently been determined to play an important role in bladder cancer cell lines.

MATERIALS AND METHODS

Frozen samples from 75 patients with bladder cancer were analyzed by quantitative real-time polymerase chain reaction (PCR). Formalin-fixed and paraffin-embedded tissues from 53 patients with bladder cancer were examined by immunohistochemistry.

RESULTS

Twist1 transcript levels were positively correlated with YB-1 transcript levels (coefficient of correlation = 0.42, P<0.001), tumor grade (low grade vs. high grade; P<0.001), invasiveness (non-muscle-invasive bladder cancer vs. muscle invasive bladder cancer; P = 0.0018), and metastasis (meta- vs. meta+; P<0.001). YB-1 transcript level was also correlated with grade (P = 0.029) and invasiveness (P = 0.006). By immunohistochemistry, Twist1 expression was also correlated with YB-1 expression (P<0.001). Further, both Twist1 and YB-1 expression were positively correlated with invasiveness (P = 0.007 and P = 0.002, respectively). Patients with high Twist1 expression and high YB-1 expression had lower overall survival rates, compared with patients with low expression (log-rank test, P = 0.040 and P<0.001, respectively).

CONCLUSIONS

These results suggest a functional link between Twist1 and YB-1, and they indicate that Twist1 and YB-1 promote bladder cancer progression.

Inducing cell proliferation inhibition, apoptosis, and motility reduction by silencing long noncoding ribonucleic acid metastasis-associated lung adenocarcinoma transcript 1 in urothelial carcinoma of the bladder

OBJECTIVE

To study the expression patterns of long noncoding ribonucleic acid (RNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and the cell proliferation inhibition, apoptosis, and motility changes induced by silencing MALAT1 in urothelial carcinoma of the bladder.

MATERIALS AND METHODS

The expression levels of MALAT1 were determined using real-time quantitative polymerase chain reaction in cancerous tissues and paired normal tissues in a total of 36 patients with urothelial carcinoma of the bladder. Expression differences were analyzed according to the grade and stage. Bladder urothelial carcinoma T24 and 5637 cells were transfected with MALAT1 small interfering RNA or negative control small interfering RNA. The cell proliferation changes of the transfected bladder urothelial carcinoma cells were determined using the MTT assay. Apoptosis caused by silencing MALAT1 was evaluated using the flow cytometry assay and enzyme-linked immunosorbent assay. The motility changes induced by silencing MALAT1 were measured using the wound healing assay.

RESULTS

MALAT1 was upregulated in bladder urothelial carcinoma compared with matched normal urothelium (P=.008). The MALAT1 expression levels were greater in high-grade carcinomas than in low-grade carcinoma (P=.001). The MALAT1 expression levels were greater in invasive carcinoma than in noninvasive carcinoma (P=.018). Cell proliferation inhibition, increased apoptosis, and decreased motility were observed in MALAT1 small interfering RNA-transfected bladder urothelial carcinoma T24 and 5637 cells.

CONCLUSION

MALAT1 plays an oncogenic role in urothelial carcinoma of the bladder. Silencing MALAT1 is a potential novel therapeutic approach for this cancer.

HERV-E-mediated modulation of PLA2G4A transcription in urothelial carcinoma

Human endogenous retroviruses (HERV) and related elements account for more than 8% of the human genome and significantly contribute to the human transcriptome by long terminal repeat (LTR) promoter activity. In this context, HERVs are thought to intervene in the expression of adjacent genes by providing regulatory sequences (cis-effect) or via noncoding RNA including natural antisense transcripts. To address the potential impact of HERV activity in urothelial carcinoma, we comparatively analyzed the HERV transcription profiles in paired samples of non-malignant urothelium and urothelial carcinoma derived from 13 patients with bladder cancer by means of a retrovirus-specific microarray (RetroArray). We established a characteristic HERV signature consisting of six ubiquitously active HERV subgroups (E4-1, HERV-Rb, ERV9, HERV-K-T47D, NMWV3, HERV-KC4). The transcription pattern is largely identical in human urothelial carcinoma, non-malignant urothelial tissue, four tumor-derived cell lines and in a non-malignant urothelial cell line (UROtsa). Quantitative reverse transcriptase PCR (qRT-PCR) of HERV-E4-1, HERV-K(HML-6) and HERV-T(S71-TK1) revealed a bias to lower HERV activity in carcinoma samples compared to non-malignant tissue. Determination of active HERV-E4-1 loci by cloning and sequencing revealed six HERV-E4-1 proviral loci that are differentially regulated in urothelial carcinoma cells and normal tissue. Two full-length HERV-E4-1 proviruses, HERV-Ec1 and HERV-Ec6, are located in antisense orientation in introns of the genes PLA2G4A and RNGTT, respectively. PLA2G4A encodes a cytosolic phospholipase A2 (cPLA2) that is dysregulated in many human tumors. PLA2G4A and HERV-Ec1 displayed reciprocal transcript levels in 7 of 11 urothelial carcinoma patients. Moreover, reciprocal shifts were observed after treatment of UROtsa cells with HERV-Ec1 and PLA2G4A-directed siRNAs or 5-aza-2′-deoxycytidine (aza-dC) pointing to an antagonistic regulation of PLA2G4A and HERV-Ec1 transcription in human urothelial cells. We suggest that transcription of HERV-Ec1 contributes to fine tuning of cPLA2 expression, thereby facilitating tumorigenesis.

Long intergenic non-coding RNA TUG1 is overexpressed in urothelial carcinoma of the bladder

BACKGROUND AND OBJECTIVES

Long intergenic non-coding RNAs (lincRNAs) are a class of non-coding RNAs that regulate gene expression via chromatin reprogramming. Taurine Up-regulated Gene 1 (TUG1) is a lincRNA that is associated with chromatin-modifying complexes and plays roles in gene regulation. In this study, we determined the expression patterns of TUG1 and the cell proliferation inhibition and apoptosis induced by silencing TUG1 in urothelial carcinoma of the bladder.

METHODS

The expression levels of TUG1 were determined using Real-Time qPCR in a total of 44 patients with bladder urothelial carcinomas. Bladder urothelial carcinoma T24 and 5637 cells were transfected with TUG1 siRNA or negative control siRNA. Cell proliferation was evaluated using MTT assay. Apoptosis was determined using ELISA assay.

RESULTS

TUG1 was up-regulated in bladder urothelial carcinoma compared to paired normal urothelium. High TUG1 expression levels were associated with high grade and stage carcinomas. Cell proliferation inhibition and apoptosis induction were observed in TUG1 siRNA-transfected bladder urothelial carcinoma T24 and 5637 cells.

CONCLUSIONS

Our data suggest that lincRNA TUG1 is emerging as a novel player in the disease state of bladder urothelial carcinoma. TUG1 may have potential roles as a biomarker and/or a therapeutic target in bladder urothelial carcinoma.

Inducing cell proliferation inhibition and apoptosis via silencing Dicer, Drosha, and Exportin 5 in urothelial carcinoma of the bladder

BACKGROUND AND OBJECTIVES

MicroRNAs (miRNAs) are aberrantly expressed in cancers. Dicer, Drosha, and Exportin 5 are essential for miRNA processing. In this study, the expression patterns of Dicer, Drosha, and Exportin 5 and the cell proliferation inhibition and apoptosis induced by silencing these genes in urothelial carcinoma of the bladder were determined.

METHODS

The expression levels of Dicer, Drosha, and Exportin 5 were determined using Real-Time qPCR in 40 patients with urothelial carcinoma of the bladder. Bladder urothelial carcinoma T24 and 5637 cells were transfected with Dicer, Drosha, or Exportin 5 siRNA or negative control siRNA. Cell proliferation was determined using MTT assay. Apoptosis was evaluated using ELISA assay.

RESULTS

All the three genes were up-regulated in bladder urothelial carcinoma compared to matched normal urothelium. Dicer, Drosha, and Exportin 5 expression levels were higher in high grade carcinomas than that in low grade carcinomas. Invasive carcinomas had higher expression levels than non-invasive carcinomas. Silencing Dicer, Drosha, or Exportin 5 induced cell proliferation inhibition and apoptosis in bladder urothelial carcinoma T24 and 5637 cells.

CONCLUSIONS

Dicer, Drosha, and Exportin 5 are promising biomarkers and therapeutic targets for urothelial carcinoma of the bladder.

Non-invasive urine based tests for the detection of bladder cancer

Bladder cancer is the fourth most frequently diagnosed malignant neoplasm and cause of cancer-related deaths in men and eighth in women. Patients with bladder cancer undergo repeated cystoscopic examinations of the bladder to monitor for tumour recurrence which is invasive, costly and lacks accuracy. Therefore, the development of non-invasive urine based tests for the early detection of bladder cancer would be of tremendous benefit to both patients and healthcare systems. A number of urine based markers are available for the early diagnosis of bladder cancer. The diagnosis of bladder cancer relies on identifying malignant cells in the urine. All urinary markers have a higher sensitivity as compared with cytology but they score lower in specificity. Many soluble and cell based markers have been developed. Only two of the soluble and cell based markers have obtained the Food and Drug Administration approval. In the current review, the most recent literature of urinary markers is summarised. This article reports some of the more prominent urine markers and new technologies used nowadays.

Significant Correlation between Chromosomal Aberration and Nuclear Morphology in Urothelial Carcinoma

We aimed to identify whether there is any correlation between chromosomal/genetic changes, nuclear morphology and the histological grade of urothelial carcinomas of the urinary bladder. Morphometry and multicolour fluorescence in situ hybridisation (FISH) techniques were applied to 250 cells in five low-grade cases and 350 cells in seven high-grade cases of urothelial carcinoma. Compared with low-grade carcinomas, most high-grade cases showed larger and more variable nuclear size, more frequent polysomy of centromere enumeration probes (CEPs) 3, 7 and 17, and the loss of the 9p21 locus. The number of CEP signals in cells was increased as the nuclear area of the cells became larger. Cells with gains in two or more types of CEP had significantly larger nuclei than cells with normal FISH signal patterns. In conclusion, the present study indicates that there was a correlation between nuclear morphology and chromosomal/genetic changes which were related to histological grading. Thus, we show that differences in the chromosomal/genetic aberrations present in low- and high-grade tumours can affect not only nuclear morphology but also the histopathological and clinical behaviour of urothelial carcinomas.

Ras association domain family 1A: a promising prognostic marker in recurrent nonmuscle invasive bladder cancer

The aim of this study was to investigate the value of RASSF1A methylation as a prognostic marker in bladder cancer. RASSF1A hypermethylation from 301 specimens of primary BC tissue was assessed using methylation-specific PCR. Among patients with recurrent NMIBC, RASSF1A methylation was identified as an independent predictor of cancer progression.

INTRODUCTION

Aberrant methylation of promoter CpG islands is an important inactivation mechanism of tumor suppressors and tumor-related genes. Ras association domain family 1A (RASSF1A) promoter hypermethylation was shown to be associated with bladder cancer (BC), but its prognostic value remains unclear. The aim of the present study was to investigate the value of RASSF1A methylation as a prognostic marker in BC.

MATERIALS AND METHODS

Primary BC tissues were obtained from 301 patients and included 186 specimens of nonmuscle invasive bladder cancer (NMIBC) and 115 specimens of muscle invasive bladder cancers (MIBC). RASSF1A hypermethylation was assessed using methylation-specific polymerase chain reaction (MS-PCR). The association between RASSF1A hypermethylation and clinicopathologic features, and the prognostic significance of RASSF1A hypermethylation were evaluated by Kaplan-Meier and multivariate Cox regression analyses.

RESULTS

RASSF1A promoter hypermethylation was detected in 33.6% of BCs and occurred more frequently in MIBC (46.1%) than in NMIBC (25.8%) (P < .001). In NMIBC, RASSF1A methylation was associated with advanced tumor stage (P = .026) and high grade (P < .001). Among patients with recurrent NMIBC, RASSF1A methylation was associated with shorter time to progression by Kaplan-Meier analysis (log-rank test; P = .004) and identified as an independent predictor of cancer progression by multivariate Cox regression analysis (hazard ratio [HR], 8.559; P = .014).

CONCLUSIONS

Our results suggest that methylated RASSF1A may be a potential prognostic marker in patients with recurrent NMIBC.

MicroRNA-195-5p suppresses glucose uptake and proliferation of human bladder cancer T24 cells by regulating GLUT3 expression

It has been reported that expression of glucose transporter member 3 (GLUT3) is up-regulated in bladder cancers. However, the regulating mechanism remains unknown. Here, we assessed whether microRNAs (miRNAs) regulate GLUT3 expression in bladder cancers. In our study, miR-195-5p was identified to directly targeted GLUT3 3'-untranslated region (UTR) in bladder cancer T24 cells. Small interfering RNA (siRNA)- and miR-195-5p-mediated GLUT3 knockdown experiments revealed that miR-195-5p decreased T24 cells glucose uptake, inhibited cell growth and promoted cell apoptosis through suppression of GLUT3 expression. Therefore, miR-195-5p is a novel and also the first identified miRNA that targets GLUT3, and the aberrant decreased expression of miR-195-5p and consequent GLUT3 up-regulation may contribute to bladder carcinogenesis.

Epigenetics of bladder cancer

Epigenetic changes are closely associated with tumor development and prognosis of bladder cancer, and its detection in specimens (tissue/body fluid) may be feasible and more sensitive than conventional methods. Additionally, the epigenetic changes are interesting from a clinical point of view because it may be possible to reverse epigenetic changes and restore the gene function. Epigenetic markers might therefore be more useful than conventional molecular markers for the detection, prediction of prognosis, and treatment of bladder cancer.

Urothelial carcinoma of the bladder: definition, treatment and future efforts

The identification of patients with high-risk bladder cancer is important for the timely and appropriate treatment of this lethal disease. The understanding of the natural history of bladder cancer has improved; however, the criteria used to define high-risk disease and the relevant treatment strategies have remained the same for the past several decades, despite multiple large, randomized, prospective clinical trials that have evaluated the use of intravesical, surgical and systemic therapies. The genetic signature of high-risk bladder cancer has been a focus of investigation and has led to the discovery of potential molecular targets for disease identification, risk stratification and therapy. These advances, combined with a comprehensive risk assessment profile that incorporates available pathological and clinical characteristics, might improve the diagnosis and treatment of patients with bladder cancer.

MicroRNA expression signatures of bladder cancer revealed by deep sequencing

Background

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression. They are aberrantly expressed in many types of cancers. In this study, we determined the genome-wide miRNA profiles in bladder urothelial carcinoma by deep sequencing.

Methodology/Principal Findings

We detected 656 differentially expressed known human miRNAs and miRNA antisense sequences (miRNA*s) in nine bladder urothelial carcinoma patients by deep sequencing. Many miRNAs and miRNA*s were significantly upregulated or downregulated in bladder urothelial carcinoma compared to matched histologically normal urothelium. hsa-miR-96 was the most significantly upregulated miRNA and hsa-miR-490-5p was the most significantly downregulated one. Upregulated miRNAs were more common than downregulated ones. The hsa-miR-183, hsa-miR-200b∼429, hsa-miR-200c∼141 and hsa-miR-17∼92 clusters were significantly upregulated. The hsa-miR-143∼145 cluster was significantly downregulated. hsa-miR-182, hsa-miR-183, hsa-miR-200a, hsa-miR-143 and hsa-miR-195 were evaluated by Real-Time qPCR in a total of fifty-one bladder urothelial carcinoma patients. They were aberrantly expressed in bladder urothelial carcinoma compared to matched histologically normal urothelium (p<0.001 for each miRNA).

Conclusions/Significance

To date, this is the first study to determine genome-wide miRNA expression patterns in human bladder urothelial carcinoma by deep sequencing. We found that a collection of miRNAs were aberrantly expressed in bladder urothelial carcinoma compared to matched histologically normal urothelium, suggesting that they might play roles as oncogenes or tumor suppressors in the development and/or progression of this cancer. Our data provide novel insights into cancer biology.

Prognostic value of opioid binding protein/cell adhesion molecule-like promoter methylation in bladder carcinoma

The OPCML gene (opioid binding protein/cell adhesion molecule-like), a putative tumour suppressor gene, is frequently inactivated in carcinomas, namely through aberrant promoter methylation. Herein, we aimed to determine whether OPCML altered expression mediated by epigenetic mechanisms was implicated in bladder carcinogenesis and to assess its potential as a bladder cancer epi-marker. OPCML promoter methylation levels from 91 samples of bladder urothelial carcinoma, 25 normal bladder tissues and bladder cancer cell lines were assessed by quantitative methylation-specific polymerase chain reaction, and correlated with OPCML mRNA expression, determined by quantitative reverse-transcription polymerase chain reaction. To prove the epigenetic regulation of OPCML, five bladder cancer cell lines were exposed to 5-aza-2'deoxycytidine (5-aza-dC), a specific DNA methyltransferase inhibitor and trichostatin A (TSA), a histone deacetylase inhibitor. In bladder tumours, the overall frequency of methylation was 60% and methylation levels were significantly higher when compared with normal mucosa (P=0.0001). No correlation was found between methylation levels and clinicopathological parameters. Interestingly, OPCML promoter methylation was associated with worse disease-specific survival (P=0.022) in univariate analysis. Furthermore, a significant inverse correlation between OPCML promoter methylation and mRNA expression levels was found, although a significant re-expression was only achieved when 5-aza-dC and TSA were used simultaneously. The high frequency of OPCML promoter methylation in urothelial carcinomas suggests an important role for this epigenetic alteration in bladder carcinogenesis, highlighting its potential as an epigenetic biomarker for bladder urothelial carcinoma with prognostic significance.

Discovery of novel bladder cancer biomarkers by comparative urine proteomics using iTRAQ technology

A urine sample preparation workflow for the iTRAQ (isobaric tag for relative and absolute quantitation) technique was established. The reproducibility of this platform was evaluated and applied to discover proteins with differential levels between pooled urine samples from nontumor controls and three bladder cancer patient subgroups with different grades/stages (a total of 14 controls and 23 cancer cases in two multiplex iTRAQ runs). Combining the results of two independent clinical sample sets, a total of 638 urine proteins were identified. Among them, 55 proteins consistently showed >2-fold differences in both sample sets. Western blot analyses of individual urine samples confirmed that the levels of apolipoprotein A-I (APOA1), apolipoprotein A-II, heparin cofactor 2 precursor and peroxiredoxin-2 were significantly elevated in bladder cancer urine specimens (n = 25-74). Finally, we quantified APOA1 in a number of urine samples using a commercial ELISA and confirmed again its potential value for diagnosis (n = 126, 94.6% sensitivity and 92.0% specificity at a cutoff value of 11.16 ng/mL) and early detection (n = 71, 83.8% sensitivity and 94.0% specificity). Collectively, our results provide the first iTRAQ-based quantitative profile of bladder cancer urine proteins and represent a valuable resource for the discovery of bladder cancer markers.

Glioblastoma-specific protein interaction network identifies PP1A and CSK21 as connecting molecules between cell cycle-associated genes

Glioblastoma (GBM; grade IV astrocytoma) is a very aggressive form of brain cancer with a poor survival and few qualified predictive markers. This study integrates experimentally validated genes that showed specific upregulation in GBM along with their protein-protein interaction information. A system level analysis was used to construct GBM-specific network. Computation of topological parameters of networks showed scale-free pattern and hierarchical organization. From the large network involving 1,447 proteins, we synthesized subnetworks and annotated them with highly enriched biological processes. A careful dissection of the functional modules, important nodes, and their connections identified two novel intermediary molecules CSK21 and protein phosphatase 1 alpha (PP1A) connecting the two subnetworks CDC2-PTEN-TOP2A-CAV1-P53 and CDC2-CAV1-RB-P53-PTEN, respectively. Real-time quantitative reverse transcription-PCR analysis revealed CSK21 to be moderately upregulated and PP1A to be overexpressed by 20-fold in GBM tumor samples. Immunohistochemical staining revealed nuclear expression of PP1A only in GBM samples. Thus, CSK21 and PP1A, whose functions are intimately associated with cell cycle regulation, might play key role in gliomagenesis.

Pathobiologic implications of methylation and expression status of Runx3 and CHFR genes in gastric cancer

Runx3 and CHFR genes were defined as tumor suppressor genes in gastric cancer (GC) recently. This paper was to investigate the roles of methylation and expression status of Runx3 and CHFR genes in GC patients. Methylation-specific polymerase chain reaction (MSP) and bisulfite DNA sequencing (BSP) were used to detect methylation status of Runx3 and CHFR genes in GC patients. The expression of Runx3 and CHFR in GC patients was analyzed by reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemical analysis. The expression of the protein and mRNA decreased remarkably in the patients with aberrant promoter methylation of Runx3 and CHFR genes. The methylation status of Runx3 and CHFR were inversely related to the tumor size, tumor invasion depth and tumor differentiation in GC patients. Moreover, the protein expression of Runx3 and CHFR were significantly correlated with tumor invasion depth and tumor differentiation, respectively. Aberrant promoter methylation of Runx3 and CHFR genes may be involved in the carcinogenesis and development of GC and may provide useful clues for the prediction of the malignant behaviors of GC.

A novel XPF -357A>C polymorphism predicts risk and recurrence of bladder cancer

Xeroderma pigmentosum group F (XPF) has an essential role in the nucleotide excision repair pathway that removes a wide variety of DNA lesions. We hypothesized that genetic variants in XPF are associated with bladder cancer risk and recurrence. We selected three tagging single nucleotide polymorphisms (tagSNPs) from the HapMap database for the Chinese and genotyped them in a two-stage case-control study to evaluate the association and further examined the functionality of a novel polymorphism in the promoter. The two-stage analysis found that the rs744154 tagSNP in the XPF intron 1, which was linkage disequilibrium with the -357A>C polymorphism in the promoter region, was associated with a protective effect on bladder cancer risk. Electrophoretic mobility shift assay (EMSA) further revealed that the -357C allele decreased the binding ability of transcriptional factors to the XPF promoter. The vector construct containing the -357C allele had a lower luciferase expression than did the -357A allele. The -357C allele in the transcription factor-binding site was also associated with decreased expression levels of both XPF mRNA and protein in bladder cancer tissues. Furthermore, patients with the -357C allele had a shorter overall recurrence-free survival than did patients with the -357A allele. Our results suggest that the XPF promoter -357A>C polymorphism may regulate the expression of XPF and thereby contribute to susceptibility to and prognosis of bladder cancer. Further larger studies with different populations are warranted to confirm these findings.

Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer

Background

While several molecular markers of bladder cancer prognosis have been identified, the limited value of current prognostic markers has created the need for new molecular indicators of bladder cancer outcomes. The aim of this study was to identify genetic signatures associated with disease prognosis in bladder cancer.

Results

We used 272 primary bladder cancer specimens for microarray analysis and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analysis. Microarray gene expression analysis of randomly selected 165 primary bladder cancer specimens as an original cohort was carried out. Risk scores were applied to stratify prognosis-related gene classifiers. Prognosis-related gene classifiers were individually analyzed with tumor invasiveness (non-muscle invasive bladder cancer [NMIBC] and muscle invasive bladder cancer [MIBC]) and prognosis. We validated selected gene classifiers using RT-PCR in the original (165) and independent (107) cohorts. Ninety-seven genes related to disease progression among NMIBC patients were identified by microarray data analysis. Eight genes, a progression-related gene classifier in NMIBC, were selected for RT-PCR. The progression-related gene classifier in patients with NMIBC was closely correlated with progression in both original and independent cohorts. Furthermore, no patient with NMIBC in the good-prognosis signature group experienced cancer progression.

Conclusions

We identified progression-related gene classifier that has strong predictive value for determining disease outcome in NMIBC. This gene classifier could assist in selecting NMIBC patients who might benefit from more aggressive therapeutic intervention or surveillance.

Potential new urinary markers in the early detection of bladder cancer

PURPOSE OF REVIEW

Bladder cancer remains a highly prevalent and lethal malignancy. Early diagnosis and prompt treatment have been shown to improve survival at both initial diagnosis and recurrence. A vast number of tumor markers have been identified and rigorously evaluated in attempts to improve noninvasive diagnostic accuracy of bladder cancer. Hematuria was the first tumor marker in a field that has grown to include soluble markers, cell-surface antigens, cell-cycle-related proteins, and genetic alterations. We aim to provide a critical appraisal of newer markers and the current state of research.

RECENT FINDINGS

The number of tumor markers identified has been exponentially increasing. For a variety of reasons, many are unsuitable for clinical practice. More promising recent markers include those discovered in the fields of genomics, proteomics, and epigenetics. Much of the recent work is focused on molecular genetic pathways in bladder cancer.

SUMMARY

The field of bladder cancer tumor markers remains a rapidly evolving area in which newer markers are constantly identified, evaluated, and often discarded if they do not add significantly to the urologists' armamentarium. Newer markers rely on genetic rearrangements, molecular changes, and cell-cycle-related proteins. Work is currently being done to identify the most promising markers.

Comparative genomic hybridization analysis reveals new different subgroups in early-stage bladder tumors

OBJECTIVES

To classify bladder tumors according to their genomic imbalances and evaluate their association with patient's outcome.

METHODS

Sixty-three superficially and minimally invasive bladder tumors were analyzed by conventional comparative genomic hybridization. Subtelomeric screening in 15 of these tumors was performed by multiplex ligation-dependent probe amplification.

RESULTS

Losses of 9q and 9p (32% and 25% of all cases, respectively) as well as gains of chromosomes Xq and Xp (28% and 25%, respectively) were the most frequent chromosome imbalances. Losses of 8p and gains in 1q and 8q were detected in >20% of cases. Tumors were classified into 3 groups according to their individualized pattern of gains and losses. The largest group was characterized by few chromosome imbalances, presenting 77% and 49% of the Ta and T1 tumors, respectively. Another group characterized by chromosomal gains, was composed of equal number of Ta and T1 tumors, with +1q and +17q gains being the most common imbalances. A minority group was characterized by chromosomal losses on 11q, 5q, and 6q. The multiplex ligation-dependent probe amplification study showed good correlation with comparative genomic hybridization results. With regard to the biological significance of this classification, a remarkable fact is that this minority group composed mainly of T1 tumors, showed a significant decrease in patient overall survival.

CONCLUSIONS

Our data suggest that superficial carcinomas of the bladder can be subdivided into a larger number of subclasses than had previously been expected. Our results also demonstrate a decreased survival among patients whose tumors show more genomic losses than gains.

Molecular biomarkers for urothelial carcinoma of the bladder: challenges in clinical use

Conventional clinical and pathological parameters are limited in their capacity to detect patients with urothelial carcinoma of the bladder (UCB) who are at high risk for recurrence or mortality. The assessment of molecular biomarkers in surgical UCB specimens offers additional information on the biology of the disease, and might improve the prediction of oncologic end points. A wide range of candidate biomarkers, including key cell-cycle regulators, apoptotic markers and specific growth factors, have been reported to be of prognostic value. To date, however, no molecular biomarker for UCB has been introduced into clinical practice, mainly owing to insufficient validation and the absence of prospective studies. Knowledge about the value of molecular biomarkers in predicting the response to adjuvant or neoadjuvant therapies is also lacking. Prospective trials need to be initiated in high-risk patients selected on the basis of the expression patterns of molecular biomarkers that have already passed the initial steps towards clinical utility.

Epigenetic biomarkers in urothelial bladder cancer

Bladder cancers comprise heterogeneous cell populations, and numerous factors are likely to be involved in dictating recurrence, progression and patient survival. While several molecular markers that are used to evaluate the development and prognosis of bladder cancer have been studied, the limited value of these established markers has created the need for new molecular indicators of bladder cancer prognosis. Of particular interest is the silencing of tumor-suppressor genes by epigenetic alteration. Recent progress in understanding epigenetic modification and gene silencing has led to new opportunities for the understanding, detection, treatment and prevention of cancer. Moreover, epigenetic silencing of tumor-suppressor genes is interesting from a clinical standpoint, because of the possibility of reversing epigenetic changes and restoring gene function in a cell. This review focuses on the prognostic relevance of epigenetic markers in bladder cancer.

Overexpression of EIF-5A2 predicts tumor recurrence and progression in pTa/pT1 urothelial carcinoma of the bladder

The authors investigated the status of abnormalities of eIF-5A2 gene in superficial (pTa/pT1) urothelial carcinoma of the bladder (UC), as well as its correlation with clinicopathologic variables and patient outcome. The methods of immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting were utilized to examine protein/mRNA(messenger RNA) expression and amplification of eIF-5A2 in a cohort of pTa/pT1 UCs. Overexpression of EIF-5A2 was examined by IHC in 38/112 (33.9%) pTa/pT1 UCs. A significant association of overexpression of EIF-5A2 with shortened UC patient recurrence-free survival (P = 0.002), as well as with shortened progression-free survival (P = 0.004), was demonstrated. Importantly, multivariate Cox regression analysis revealed that EIF-5A2 expression provided a significant independent prognostic parameter either in tumor recurrence (P = 0.002) or in tumor progression (P = 0.007). FISH results demonstrated that eIF-5A2 amplification was detected in 5/59 of the informative UCs; in each of the five cases with eIF-5A2 amplification, overexpression of EIF-5A2 was observed. In the remaining 54 UCs without eIF-5A2 amplification, 16 cases were also observed to have overexpression of EIF-5A2. In 13 pairs of UC and adjacent normal tissues, eight UCs were examined and showed up-regulated eIF-5A2 mRNA by RT-PCR, while increased expression of EIF-5A2 protein was only detected in 4/8 UCs by Western blotting. These findings suggest that overexpression of EIF-5A2, as detected by IHC, may predict tumor recurrence and progression in pTa/pT1 UC patients, and the protein expression of eIF-5A2 might be regulated not only by gene amplification, but also by other molecular mechanisms.

Epigenetic markers as promising prognosticators for bladder cancer

Transitional cell carcinomas of the urinary bladder have diverse biological and functional characteristics. Surveillance strategies for bladder cancer recurrence have historically relied on the diagnostic combination of cystoscopy and urinary cytology. However, the accuracy of both tests depends on subjective and operator-dependent interpretations of the visible findings. In contrast, promoter hypermethylation of CpG islands is strongly associated with tumor development and prognosis of bladder cancer. Detection of DNA methylation in voided urine may be feasible and more sensitive than conventional urine cytology. Ultimately, all types of urological cancers may be screened in urine using a candidate panel of hypermethylated genes. The epigenetic silencing of tumor suppressor genes is interest from a clinical point of view because it is possible to reverse epigenetic changes and restore gene function to a cell. Methylation markers might therefore be more useful than conventional molecular markers for the treatment and prevention of bladder cancer.

Methylation of the RUNX3 promoter as a potential prognostic marker for bladder tumor

PURPOSE

DNA methylation is a key regulator of gene transcription and genomic stability, and alterations in DNA methylation patterns are frequently detected in human tumors. Previously we reported that inactivation of RUNX3 by primarily epigenetic alterations in DNA methylation is closely associated with bladder tumor development, recurrence and progression. In the current series we evaluated the association between RUNX3 inactivation and bladder tumors after a long-term followup study.

MATERIALS AND METHODS

We used previously published data on the methylation patterns of RUNX3 in bladder tumor samples as well as 25 new data sets obtained by methylation specific polymerase chain reaction and direct DNA sequencing. Of the 149 patients examined 118 were followed periodically and included in the final analysis. Median followup was 49.8 months (range 1 to 146).

RESULTS

RUNX3 promoter methylation was observed in 84 of the 118 tumor samples (71.2%) examined. RUNX3 methylation patterns correlated significantly with the development of invasive tumor, tumor progression, and overall and cancer specific survival (each p <0.05). Kaplan-Meyer curves showed identical results (p <0.05). Multivariate Cox regression models revealed that RUNX3 methylation status was a strong predictor of tumor progression and cancer specific survival.

CONCLUSIONS

Results strongly suggest that inactivation of RUNX3 by the methylation of its promoter region is a significant risk factor for invasive bladder tumors, tumor progression and cancer specific survival. RUNX3 promoter methylation status could be a promising marker for assessing the prognosis of human bladder tumors.