Expression profiling for bladder cancer: strategies to uncover prognostic factors

Gene network profiling in muscle-invasive bladder cancer: A systematic review and meta-analysis

BACKGROUND

Determining meta-analysis of transcriptional profiling of muscle-invasive bladder cancer (MIBC) through Gene Expression Omnibus (GEO) datasets has not been investigated. This study aims to define gene expression profiles in MIBC and to identify potential candidate genes and pathways.

OBJECTIVES

To review and evaluate gene expression studies in MIBC through publicly available RNA sequencing (RNA-Seq) and microarray data in order to identify potential prognostic and therapeutic targets for MIBC.

METHODS

A systematic literature search of the Ovid MEDLINE, PubMed, and Wiley Cochrane Central Register of Controlled Trials databases was performed using the terms "gene," "gene expression," and "bladder cancer" January 1, 1990 through March 2021 focused on populations with MIBC.

RESULTS

In the final analysis, GEO datasets were included. Fixed effect model was employed in the meta-analysis. Gene networking connections and gene-set functional analyses of the identified genes as differentially expressed in MIBC were performed using ImaGEO and GeneMANIA software. A heatmap for the upregulated and downregulated genes was generated along with the correlated pathways.

CONCLUSION

A total of 9 genes were reported in this analysis. Six genes were reported as upregulated (ProTα, SPINT1, UBE2E1, RAB25, KPNB1, HDAC1) and 3 genes as downregulated (NUP188, IPO13, NUP124). Genes were found to be involved in "ubiquitin mediated proteolysis," "protein processing in endoplasmic reticulum," "transcriptional misregulation in cancer," and "RNA transport" pathways.

Effect of prior radiation on stage, differentiation, and survival in bladder cancer

PURPOSE

Clinically significant differences in radiation-related bladder tumors are not well-characterized, and survival analyses are needed. In this study, we aimed to utilize a national cancer database to evaluate the effect of prior radiation on tumor characteristics and survival in bladder cancer patients.

METHODS

The Surveillance, Epidemiology, and End Results (SEER) 9 database was queried to identify patients diagnosed with bladder cancer as a second malignancy. Patients having undergone radiation prior to developing bladder cancer were selected for comparative analysis. Logistic regression was used to generate odds ratios to evaluate differences in differentiation, stage, grade, and tumor size. Kaplan-Meier analysis and Cox non-proportional hazards regression models were used to assess the association between previous radiation and bladder cancer survival.

RESULTS

A total of 25,408 patients were identified, of which 14,570 patients had sufficient data for analysis. Of these, 5968 (41.0%) received radiation for their primary malignancy. Prior radiation conferred a lower risk of developing moderately- or poorly-differentiated bladder tumors and muscle invasive or node-positive disease. An increased risk of squamous cell carcinoma was noted (OR 1.43, CI 1.06-1.93). Prior radiation led to an increased risk of bladder cancer-specific (HR 1.13, CI 1.03-1.24) mortality at 5 years. The greatest effect of prior radiation was an increased risk of bladder cancer-specific mortality for carcinoma in situ at 5 years (OR 2.37, CI 1.45-3.86).

CONCLUSION

Prior radiation is associated with lower grade and stage of bladder tumors in addition to worse cancer-specific survival.

Positive Association of Matrix Proteins Alteration with TAZ and The Progression of High-Grade Bladder Cancer

Objective

Bladder cancer is the 9^th cause of human urologic malignancy and the 13^th of death worldwide. Increased collagen cross-linking, NIDOGEN1 expression and consequently stiffness of extracellular matrix (ECM) may be responsible for the mechanotransduction and regulation of transcriptional co-activator with PDZ-binding motif (TAZ) and transforming growth factor β1 (TGF-β1) signaling pathways, resulting in progression of tumorigenesis. The present study aimed to assess whether type 1 collagen expression is associated with TAZ nuclear localization.

Materials and Methods

In this case-control study, real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunohistochemical analysis were performed to evaluate the activation of the TAZ pathway in patients with bladder cancer (n=40) and healthy individuals (n=20). The ELISA method was also conducted to measure the serum concentrations of TGF-β1. Masson’s trichrome staining was carried out to histologically evaluate the density of type 1 collagen.

Results

Our findings that the expression levels of COL1A1, COL1A2, NIDOGEN1, TAZ, and TGF-β1 genes were overexpressed in patients with bladder cancer, and their expression levels were positively associated with the grade of bladder cancer. The immunohistochemical analysis demonstrated that the nuclear localization of TAZ was markedly correlated with high-grade bladder cancer. We also found that TAZ nuclear localization was substantially higher in cancerous tissues as compared with normal bladder tissues. Masson's trichrome staining showed that the tissue density of type I collagen was considerably increased in patients with bladder cancer as compared with healthy subjects.

Conclusion

According to our findings, it seems the alterations in the expression of type I collagen and NIDOGEN1, as well as TAZ nuclear localization influence the progression of bladder cancer. The significance of TGF-β1 and TAZ expression in tumorigenesis and progression to high-grade bladder cancer was also highlighted. However, a possible relationship between TGF-β1 expression and the Hippo pathway needs further investigations.

Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection

Non-invasive clinical diagnostics of bladder cancer is feasible via a set of chemically distinct molecules including macromolecular tumor markers such as polypeptides and nucleic acids. In terms of tumor-related aberrant gene expression, RNA transcripts are the primary indicator of tumor-specific gene expression as for polypeptides and their metabolic products occur subsequently. Thus, in case of bladder cancer, urine RNA represents an early potentially useful diagnostic marker. Here we describe a systematic deep transcriptome analysis of representative pools of urine RNA collected from healthy donors versus bladder cancer patients according to established SOPs. This analysis revealed RNA marker candidates reflecting coding sequences, non-coding sequences, and circular RNAs. Next, we designed and validated PCR amplicons for a set of novel marker candidates and tested them in human bladder cancer cell lines. We identified linear and circular transcripts of the S100 Calcium Binding Protein 6 (S100A6) and translocation associated membrane protein 1 (TRAM1) as highly promising potential tumor markers. This work strongly suggests exploiting urine RNAs as diagnostic markers of bladder cancer and it suggests specific novel markers. Further, this study describes an entry into the tumor-biology of bladder cancer and the development of gene-targeted therapeutic drugs.

Increased expression levels of Syntaxin 1A and Synaptobrevin 2/Vesicle-Associated Membrane Protein-2 are associated with the progression of bladder cancer

Gene expression is tightly regulated in time and space through a multitude of factors consisting of signaling molecules. Soluble N-ethylmaleimide-sensitive-factor attachment protein receptors (SNARE) are membrane proteins responsible for the intercellular trafficking of signals through endocytosis and exocytosis of vesicles. Altered expression of SNARE proteins in cellular communication is the major hallmark of cancer phenotypes as indicated in recent studies. SNAREs play an important role in maintaining cell growth and epithelial membrane permeability of the bladder and are not only involved in cancer progression but also metastatic cell invasion through SNARE-mediated trafficking. Synaptobrevin2/Vesicle associated membrane protein-2 (v-SNARE) and Syntaxin (t-SNARE) form a vesicular docking complex during endocytosis. Some earlier studies have shown a critical role of SNARE in colon, lungs, and breast cancer progression and metastasis. In this study, we analyzed the relative expression of the STX1A and VAMP2 (SYB2) for their possible association in the progression and metastasis of bladder cancer. The profiling of the genes showed a significant increase in STX1A and VAMP2 expression (p < 0.001) in high-grade tumor cells compared to normal and low-grade tumors. These findings suggest that elevated expression of STX1A and VAMP2 might have caused the abnormal progression and invasion of cancer cells leading to the transformation of cells into high-grade tumor in bladder cancer.

Molecular markers in bladder cancer

Purpose

Use of molecular markers in urine, tissue or blood offers potential opportunities to improve understanding of bladder cancer biology which may help identify disease earlier, risk stratify patients, improve prediction of outcomes or help target therapy.

Methods

A review of the published literature was performed, without restriction of time.

Results

Despite the fast-growing literature about the topic and the approval of several urinary biomarkers for use in clinical practice, they have not reached the level of evidence for widespread utilization. Biomarkers could be used in different clinical scenarios, mainly to overcome the limitations of current diagnostic, predictive, and prognostic tools. They have been evaluated to detect bladder cancer in asymptomatic populations or those with hematuria and in surveillance of disease as adjuncts to cystoscopy. There is also a potential role as prognosticators of disease recurrence, progression and survival both in patients with non-invasive cancers and in those with advanced disease. Finally, they promise to be helpful in predicting the response to local and/or systemic chemotherapy and/or immunotherapy.

Conclusions

To date, due to the lack of high-quality prospective trials, the level of evidence provided by the current literature remains low and, therefore, the potential of biomarkers exceeds utilization in clinical practice.

Grade progression in urothelial carcinoma can occur with high or low mutational homology: a first-step toward tumor-specific care in initial low-grade bladder cancer

Purpose

Low-grade (LG) urothelial carcinomas of the bladder (UCB) are common malignancies that are costly to surveil and rarely progress to life threatening, high-grade (HG) malignancies. It is unknown if the progression of LG to HG is a result of second primary tumors or transformation of existing LG tumors. We examined tumor genetics in patients with grade progression in urothelial carcinoma and compared to patients with no progression.

Results

Five patients were identified with progression. Median time from initial LG diagnosis to HG diagnosis in those experiencing progression was 19 months. Progression with both high and low mutational homology was identified. Gene alterations associated with tumor grade progression in initial low grade tumors include FBN3, CIT and HECTD4.

Materials and Methods

An institutional cancer database at a tertiary referral center in the United States identified patients who progressed from LG to HG UCB. Histologic re-review was performed by a genitourinary pathologist. Whole exome sequencing with correction for germline mutations by buffy coat subtraction was performed. Mutations were assessed between LG tumors and subsequent same-patient HG tumors and for LG patients who did not progress. Individual genes were assessed as potential predictors of risk for progression.

Conclusions

Tumor grade progression occurred with both high mutational homology and low mutational homology, which may represent both true tumor progression and de-novo growth. Validation of the identified tumor genes that appeared associated with progression may provide a clinically valuable tool to providers managing patients with LG urothelial carcinomas.

Molecular Prognostication in Bladder Cancer

Clinical outcomes for patients with bladder cancer have largely remained unchanged over the last three decades despite improvements in surgical techniques, perioperative therapies, and postoperative management. Current management still heavily relies on pathologic staging that does not always reflect an individual patient's risk. The genesis and progression of bladder cancer is now increasingly recognized as being a result of alterations in several pathways that affect the cell cycle, apoptosis, cellular signaling, gene regulation, immune modulation, angiogenesis, and tumor cell invasion. Multiplexed assessment of biomarkers associated with alterations in these pathways offers novel insights into tumor behavior while identifying panels that are capable of reproducibly predicting patient outcomes. Future management of bladder cancer will likely incorporate such prognostic molecular models for risk stratification and treatment personalization.

Molecular substratification of bladder cancer: moving towards individualized patient management

Despite advances in surgical techniques, perioperative therapies and postoperative management, outcomes for patients with bladder cancer have largely remained unchanged. Current management of bladder cancer still relies on pathologic staging that does not always reflect the risk for an individual patient. Studies assessing molecular alterations in individual tumors are offering insights into the myriad of cellular pathways that are deregulated in bladder tumorigenesis and progression. Alterations in pathways involved in cell-cycle regulation, apoptosis, cell signaling, angiogenesis and tumor-cell invasion have been shown to influence disease behavior. High-throughput assays are now allowing multiplexed assessment of biomarker alterations, thereby enabling characterization of novel molecular subtypes of bladder cancer. Such approaches have also been used for discovery and validation of robust prognostic molecular signatures. The future of bladder cancer management will rely on the use of validated multimarker panels for risk stratification, optimal surgical management, and theranostic strategies to identify and target specific alterations in individual tumors.

A urinary microRNA signature can predict the presence of bladder urothelial carcinoma in patients undergoing surveillance

BACKGROUND

The objective of this study was to determine whether microRNA (miRNA) profiling of urine could identify the presence of urothelial carcinoma of the bladder (UCB) and to compare its performance characteristics to that of cystoscopy.

METHODS

In the discovery cohort we screened 81 patients, which included 21 benign controls, 30 non-recurrers and 30 patients with active cancer (recurrers), using a panel of 12 miRNAs. Data analysis was performed using a machine learning approach of a Support Vector Machine classifier with a Student's t-test feature selection procedure. This was trained using a three-fold cross validation approach and performance was measured using the area under the receiver operator characteristic curve (AUC). The miRNA signature was validated in an independent cohort of a further 50 patients.

RESULTS

The best predictor to distinguish patients with UCB from non-recurrers was achieved using a combination of six miRNAs (AUC=0.85). This validated in an independent cohort (AUC=0.74) and detected UCB with a high sensitivity (88%) and sufficient specificity (48%) with all significant cancers identified. The performance of the classifier was best in detecting clinically significant disease such as presence of T1 Stage disease (AUC=0.92) and high-volume disease (AUC=0.81). Cystoscopy rates in the validation cohort would have been reduced by 30%.

CONCLUSIONS

Urinary profiling using this panel of miRNAs shows promise for detection of tumour recurrence in the surveillance of UCB. Such a panel may be useful in reducing the morbidity and costs associated with cystoscopic surveillance, and now merits prospective evaluation.

Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer

Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives. In this paper, we establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. We obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. We find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, we compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. We found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous.

PATIENT SUMMARY

In this report, we show that it is now possible to use universally available bladder cancer samples that have been fixed in formalin to perform high-quality transcriptome analysis. This ability will facilitate the development of transcriptome-wide tests based on gene expression correlated with clinical outcome.

Interleukin-11, an interleukin-6-like cytokine, is a promising predictor for bladder cancer prognosis

Numerous studies have suggested that interleukin 11 (IL-11) has roles in human gastric, prostate and bone cancer and endometrial carcinoma. Hence, we evaluated the expression of IL-11 in bladder cancer and the correlation of IL-11 levels and clinico-pathological features. The expression of IL-11 in primary human bladder cell culture, human bladder cancer cell lines, transitional cell carcinoma (TCC) and non-cancerous bladder tissues (NATs) were analyzed by western blotting. Enzyme-linked immunosorbent assay (ELISA) for urinary IL-11 was performed to compare the IL-11 levels in healthy subjects and subjects diagnosed with bladder cancer. Our study suggested that the expression of IL-11 in human bladder cancer cell lines and TCC was downregulated compared with primary human bladder cell culture and matched NATs. We also demonstrated reduced urinary levels of IL-11 in subjects with bladder cancer compared with healthy subjects. Furthermore, we revealed that the levels of IL-11 were associated with tumor grade and stage. The results suggested that reduced levels of IL-11 may play an important role in the carcinogenesis and progression of TCC. They also indicated that IL-11 may be a promising predictor for prognosis of TCC.

Molecular signatures that predict nodal metastasis in bladder cancer: does the primary tumor tell tales?

Evaluation of: Smith SC, Baras AS, Dancik G et al. A 20-gene model for molecular nodal staging of bladder cancer: development and prospective assessment. Lancet Oncol. 12, 137-143 (2011). Accurate identification of nodal status in patients with bladder cancer is important in determining their prognosis and administration of perioperative chemotherapy. In this article, we review the study by Smith and colleagues, documenting the identification of a 20-gene model that can predict nodal stage in patients with bladder cancer based on the profiles of their primary tumors. The gene-expression model generated in this study was able to identify node-positive disease based on tumor tissues obtained from patients in a Phase III bladder cancer trial cohort. The model was able to predict nodal status independent of standard clinicopathologic prognostic criteria. This study adds the agnostic profiling dimension to prior investigations that have attempted to define molecular signatures that predict nodal metastasis in bladder cancer patients based on the primary tumors' gene-expression profiles.