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Isali I, McClellan P, Calaway A, Prunty M, Abbosh P, Mishra K, Ponsky L, Markt S, Psutka SP, Bukavina L. Gene network profiling in muscle-invasive bladder cancer: A systematic review and meta-analysis. Urol Oncol 2022; 40:197.e11-197.e23. [PMID: 35039218 PMCID: PMC10123538 DOI: 10.1016/j.urolonc.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/17/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
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.
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Affiliation(s)
- Ilaha Isali
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH
| | - Phillip McClellan
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, OH
| | - Adam Calaway
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH; Case Comprehensive Cancer Center, Case Western Reserve School of Medicine, Cleveland, OH
| | - Megan Prunty
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH
| | - Phillip Abbosh
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA
| | - Kirtishri Mishra
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA
| | - Lee Ponsky
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH; Case Comprehensive Cancer Center, Case Western Reserve School of Medicine, Cleveland, OH
| | - Sarah Markt
- Department of Population and Quantitative Health Science, Case Western Reserve School of Medicine, Cleveland, OH
| | - Sarah P Psutka
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Laura Bukavina
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH; Case Comprehensive Cancer Center, Case Western Reserve School of Medicine, Cleveland, OH.
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Effect of prior radiation on stage, differentiation, and survival in bladder cancer. World J Urol 2022; 40:719-725. [PMID: 34988649 DOI: 10.1007/s00345-021-03901-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022] Open
Abstract
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.
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Ghassemi H, Hashemnia M, Mousavibahar SH, Mahmoodzadeh Hosseini H, Mirhosseini SA. Positive Association of Matrix Proteins Alteration with TAZ and The Progression of High-Grade Bladder Cancer. CELL JOURNAL 2021; 23:742-749. [PMID: 34979063 PMCID: PMC8753103 DOI: 10.22074/cellj.2021.7661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/31/2020] [Indexed: 11/25/2022]
Abstract
Objective Bladder cancer is the 9th cause of human urologic malignancy and the 13th 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.
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Affiliation(s)
- Hadi Ghassemi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Department of Clinical Biochemistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Hashemnia
- Department of Pathobiology, Veterinary Medicine Faculty Razi University, Kermanshah, Iran
| | | | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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4
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Dubois J, Rueger J, Haubold B, Far RKK, Sczakiel G. Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection. Oncotarget 2021; 12:1011-1023. [PMID: 34012513 PMCID: PMC8121610 DOI: 10.18632/oncotarget.27954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
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.
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Affiliation(s)
- Josephine Dubois
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck D-23538, Germany
| | - Jacqueline Rueger
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck D-23538, Germany
| | - Bernhard Haubold
- Max-Planck-Institute for Evolutionary Biology, Department of Evolutionary Genetics, Ploen 24306, Germany
| | | | - Georg Sczakiel
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck D-23538, Germany
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5
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Raja SA, Abbas S, Shah STA, Tariq A, Bibi N, Yousuf A, Khawaja A, Nawaz M, Mehmood A, Khan MJ, Hussain A. Increased expression levels of Syntaxin 1A and Synaptobrevin 2/Vesicle-Associated Membrane Protein-2 are associated with the progression of bladder cancer. Genet Mol Biol 2019; 42:40-47. [PMID: 30672978 PMCID: PMC6428126 DOI: 10.1590/1678-4685-gmb-2017-0339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/09/2018] [Indexed: 01/11/2023] Open
Abstract
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.
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Affiliation(s)
- Sadaf Azad Raja
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Seher Abbas
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Syed Tahir Abbas Shah
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Aamira Tariq
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Nazia Bibi
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Arzu Yousuf
- Department of Urology and Kidney Transplant, Shifa International Hospital, Islamabad, Pakistan
| | - Athar Khawaja
- Department of Urology and Kidney Transplant, Shifa International Hospital, Islamabad, Pakistan
| | - Muhammad Nawaz
- Armed Forces Institute of Urology (AFIU), Rawalpindi, Pakistan
| | - Arshad Mehmood
- Armed Forces Institute of Urology (AFIU), Rawalpindi, Pakistan
| | - Muhammad Jadoon Khan
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Alamdar Hussain
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
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Abstract
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.
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7
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Kittler R, Shiang C, Hutchinson R, Kollipara RK, Kapur P, Franto F, Lotan Y. 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. Oncotarget 2018; 9:9415-9424. [PMID: 29507699 PMCID: PMC5823658 DOI: 10.18632/oncotarget.24072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/30/2017] [Indexed: 01/14/2023] Open
Abstract
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.
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Affiliation(s)
- Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christine Shiang
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ryan Hutchinson
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Francis Franto
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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8
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Risk Factors and Molecular Features Associated with Bladder Cancer Development. MOLECULAR PATHOLOGY LIBRARY 2018. [DOI: 10.1007/978-3-319-64769-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Abstract
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.
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Affiliation(s)
- Anirban P Mitra
- Institute of Urology, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, Suite 7416, MC 9178, Los Angeles, CA, 90033, USA.
| | - Siamak Daneshmand
- Institute of Urology, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, Suite 7416, MC 9178, Los Angeles, CA, 90033, USA
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10
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Mitra AP. Molecular substratification of bladder cancer: moving towards individualized patient management. Ther Adv Urol 2016; 8:215-33. [PMID: 27247631 DOI: 10.1177/1756287216638981] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
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.
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Affiliation(s)
- Anirban P Mitra
- Institute of Urology, University of Southern California, 1441 Eastlake Avenue, Suite 7416, MC 9178, Los Angeles, CA 90033, USA
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11
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Bartsch G, Mitra AP, Mitra SA, Almal AA, Steven KE, Skinner DG, Fry DW, Lenehan PF, Worzel WP, Cote RJ. Use of Artificial Intelligence and Machine Learning Algorithms with Gene Expression Profiling to Predict Recurrent Nonmuscle Invasive Urothelial Carcinoma of the Bladder. J Urol 2016; 195:493-8. [DOI: 10.1016/j.juro.2015.09.090] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Georg Bartsch
- University of Southern California, Los Angeles, California
- Goethe University Frankfurt, Frankfurt, Germany
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12
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Sapre N, Macintyre G, Clarkson M, Naeem H, Cmero M, Kowalczyk A, Anderson PD, Costello AJ, Corcoran NM, Hovens CM. A urinary microRNA signature can predict the presence of bladder urothelial carcinoma in patients undergoing surveillance. Br J Cancer 2016; 114:454-62. [PMID: 26812572 PMCID: PMC4815774 DOI: 10.1038/bjc.2015.472] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/28/2015] [Accepted: 12/03/2015] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
- Nikhil Sapre
- Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Geoff Macintyre
- NICTA Victoria Research Laboratory, Department of Electronic Engineering, University of Melbourne, Melbourne, Victoria, Australia.,Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Clarkson
- Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Haroon Naeem
- NICTA Victoria Research Laboratory, Department of Electronic Engineering, University of Melbourne, Melbourne, Victoria, Australia.,Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia
| | - Marek Cmero
- NICTA Victoria Research Laboratory, Department of Electronic Engineering, University of Melbourne, Melbourne, Victoria, Australia
| | - Adam Kowalczyk
- NICTA Victoria Research Laboratory, Department of Electronic Engineering, University of Melbourne, Melbourne, Victoria, Australia.,Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul D Anderson
- Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Anthony J Costello
- Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Niall M Corcoran
- Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Christopher M Hovens
- Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
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13
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Mitra AP, Lerner SP. Potential Role for Targeted Therapy in Muscle-Invasive Bladder Cancer. Urol Clin North Am 2015; 42:201-15, viii. [DOI: 10.1016/j.ucl.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Liu Y, Noon AP, Aguiar Cabeza E, Shen J, Kuk C, Ilczynski C, Ni R, Sukhu B, Chan K, Barbosa-Morais NL, Hermanns T, Blencowe BJ, Azad A, van der Kwast TH, Catto JWF, Zlotta AR, Wrana JL. Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer. Eur Urol 2014; 66:982-6. [PMID: 25199720 DOI: 10.1016/j.eururo.2014.07.045] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/30/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED 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.
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Affiliation(s)
- Yu Liu
- The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aidan P Noon
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada
| | - Eduardo Aguiar Cabeza
- The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jess Shen
- The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Cynthia Kuk
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada
| | - Christine Ilczynski
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ruoyu Ni
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Balram Sukhu
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kin Chan
- The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nuno L Barbosa-Morais
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Thomas Hermanns
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Azar Azad
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Theodorus H van der Kwast
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - James W F Catto
- The Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, UK
| | - Alexandre R Zlotta
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada
| | - Jeffrey L Wrana
- The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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15
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Mubarak M. A step towards refining prognostication in individual patients with bladder cancer. Urol Ann 2013; 5:85-7. [PMID: 23798863 PMCID: PMC3685751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Muhammed Mubarak
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi, Pakistan,Address for correspondence: Dr. Muhammed Mubarak, Associate Professor, Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi - 74200, Pakistan. E-mail:
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Wu D, Tao J, Ding J, Qu P, Lu Q, Zhang W. Interleukin-11, an interleukin-6-like cytokine, is a promising predictor for bladder cancer prognosis. Mol Med Rep 2012. [PMID: 23179440 DOI: 10.3892/mmr.2012.1199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
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.
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Affiliation(s)
- Deyao Wu
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People's Hospital, Nanjing, P.R. China
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Mitra AP, Cote RJ. Molecular signatures that predict nodal metastasis in bladder cancer: does the primary tumor tell tales? Expert Rev Anticancer Ther 2011; 11:849-52. [PMID: 21707281 DOI: 10.1586/era.11.60] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
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.
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Affiliation(s)
- Anirban P Mitra
- University of Southern California Keck School of Medicine, Center for Personalized Medicine, 4650 Sunset Blvd, SRT 1014, Los Angeles, CA 90027, USA
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