51
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Abstract
Renal masses are diagnosed with an increasing frequency. However, a significant proportion of these masses are benign, and the majority of malignant tumors are biologically indolent. Furthermore, renal tumors are often harbored by the elderly and comorbid patients. As such, matching of renal tumor biology to appropriate treatment intensity is an urgent clinical need. Renal mass biopsy is currently a very useful clinical tool that can assist with critical clinical decision-making in patients with renal mass. Yet, renal mass biopsy is associated with limitations and, as such, may not be appropriate for all patients.
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52
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Feber A, Dhami P, Dong L, de Winter P, Tan WS, Martínez-Fernández M, Paul DS, Hynes-Allen A, Rezaee S, Gurung P, Rodney S, Mehmood A, Villacampa F, de la Rosa F, Jameson C, Cheng KK, Zeegers MP, Bryan RT, James ND, Paramio JM, Freeman A, Beck S, Kelly JD. UroMark-a urinary biomarker assay for the detection of bladder cancer. Clin Epigenetics 2017; 9:8. [PMID: 28163793 PMCID: PMC5282868 DOI: 10.1186/s13148-016-0303-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Bladder cancer (BC) is one of the most common cancers in the western world and ranks as the most expensive to manage, due to the need for cystoscopic examination. BC shows frequent changes in DNA methylation, and several studies have shown the potential utility of urinary biomarkers by detecting epigenetic alterations in voided urine. The aim of this study is to develop a targeted bisulfite next-generation sequencing assay to diagnose BC from urine with high sensitivity and specificity. Results We defined a 150 CpG loci biomarker panel from a cohort of 86 muscle-invasive bladder cancers and 30 normal urothelium. Based on this panel, we developed the UroMark assay, a next-generation bisulphite sequencing assay and analysis pipeline for the detection of bladder cancer from urinary sediment DNA. The 150 loci UroMark assay was validated in an independent cohort (n = 274, non-cancer (n = 167) and bladder cancer (n = 107)) voided urine samples with an AUC of 97%. The UroMark classifier sensitivity of 98%, specificity of 97% and NPV of 97% for the detection of primary BC was compared to non-BC urine. Conclusions Epigenetic urinary biomarkers for detection of BC have the potential to revolutionise the management of this disease. In this proof of concept study, we show the development and utility of a novel high-throughput, next-generation sequencing-based biomarker for the detection of BC-specific epigenetic alterations in urine. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0303-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Feber
- UCL Cancer Institute, University College London, London, UK
| | - Pawan Dhami
- UCL Cancer Institute, University College London, London, UK
| | - Liqin Dong
- UCL Cancer Institute, University College London, London, UK
| | - Patricia de Winter
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Wei Shen Tan
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Mónica Martínez-Fernández
- Molecular Oncology Unit, CIEMAT (ed70A), Madrid, Spain & Biomedical Research Institute I+12, Universitary Hospistal 12 de Octubre, Av Cordoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Dirk S Paul
- UCL Cancer Institute, University College London, London, UK
| | - Antony Hynes-Allen
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Sheida Rezaee
- UCL Cancer Institute, University College London, London, UK
| | - Pratik Gurung
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK.,School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Simon Rodney
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Ahmed Mehmood
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Felipe Villacampa
- Uro-oncology Section & Biomedical Research Institute I+12, Universitary Hospital 12 de Octubre, Av Córdoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Federico de la Rosa
- Uro-oncology Section & Biomedical Research Institute I+12, Universitary Hospital 12 de Octubre, Av Córdoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Charles Jameson
- Department of Histopathology, University College London Hospital, London, UK
| | - Kar Keung Cheng
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Maurice P Zeegers
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK.,School for Public Health and Primary Care, Maastricht University, Maastricht, Netherlands
| | - Richard T Bryan
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | | | - Jesus M Paramio
- Molecular Oncology Unit, CIEMAT (ed70A), Madrid, Spain & Biomedical Research Institute I+12, Universitary Hospistal 12 de Octubre, Av Cordoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Alex Freeman
- Department of Histopathology, University College London Hospital, London, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK
| | - John D Kelly
- UCL Cancer Institute, University College London, London, UK.,Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
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53
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Genetic and Epigenetic Alterations in Bladder Cancer. Int Neurourol J 2016; 20:S84-94. [PMID: 27915480 PMCID: PMC5169086 DOI: 10.5213/inj.1632752.376] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/27/2016] [Indexed: 12/11/2022] Open
Abstract
Bladder cancer is one of the most common cancers worldwide, with a high rate of recurrence and poor outcomes as a result of relapse. Bladder cancer patients require lifelong invasive monitoring and treatment, making bladder cancer one of the most expensive malignancies. Lines of evidence increasingly point to distinct genetic and epigenetic alteration patterns in bladder cancer, even between the different stages and grades of disease. In addition, genetic and epigenetic alterations have been demonstrated to play important roles during bladder tumorigenesis. This review will focus on bladder cancer-associated genomic and epigenomic alterations, which are common in bladder cancer and provide potential diagnostic markers and therapeutic targets for bladder cancer treatment.
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54
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An epigenetic biomarker combination of PCDH17 and POU4F2 detects bladder cancer accurately by methylation analyses of urine sediment DNA in Han Chinese. Oncotarget 2016; 7:2754-64. [PMID: 26700620 PMCID: PMC4823069 DOI: 10.18632/oncotarget.6666] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/20/2015] [Indexed: 12/03/2022] Open
Abstract
To develop a routine and effectual procedure of detecting bladder cancer (BlCa), an optimized combination of epigenetic biomarkers that work synergistically with high sensitivity and specificity is necessary. In this study, methylation levels of seven biomarkers (EOMES, GDF15, NID2, PCDH17, POU4F2, TCF21, and ZNF154) in 148 individuals—which including 58 urothelial cell carcinoma (UCC) patients, 20 infected urinary calculi (IUC) patients, 20 kidney cancer (KC) patients,20 prostate cancer (PC) patients, and 30 healthy volunteers (HV)—were quantified by qMSP using the urine sediment DNA. Receiver operating characteristic (ROC) curves were generated for each biomarker. The combining predictors of possible combinations were calculated through logistic regression model. Subsequently, ROC curves of the three best performing combinations were constructed. Then, we validated the three best performing combinations and POU4F2 in another 72 UCC, 21 IUC, 26 KC and 22 PC, and 23 HV urine samples. The combination of POU4F2/PCDH17 has yielded the highest sensitivity and specificity of 90.00% and 93.96% in all the 312 individuals, showing the capability of detecting BlCa effectively among pathologically varied sample groups.
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55
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Krabbe LM, Woldu SL, Shariat SF, Lotan Y. Improving diagnostic molecular tests to monitor urothelial carcinoma recurrence. Expert Rev Mol Diagn 2016; 16:1189-1199. [PMID: 27696932 DOI: 10.1080/14737159.2016.1244006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The high recurrence rates associated with non-muscle invasive bladder cancer require close surveillance with cystoscopy, an invasive and expensive procedure with risk of missing cancer. Finding an accurate urinary biomarker that can detect recurrent disease would represent a significant advancement in management. Areas covered: This review summarizes the commercially-available urinary biomarkers including cytology, UroVysion, BTA, NMP22, uCyt+, and Cxbladder assays. Additionally, we review recent investigational urinary biomarkers that hold promise in bladder cancer surveillance. Expert commentary: The quest for a reliable urinary biomarker for bladder cancer is decades-old and seems intuitive given the direct contact of urine with malignant urothelium. Beyond urine cytology, there are many commercially-available products approved for surveillance. However, none of the assays are routinely used due to lack of sensitivity and/or specificity. As such, emerging technologies, in particular the '-omic' technologies have resulted in a proliferation of promising reports on novel biomarkers in recent literature.
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Affiliation(s)
- Laura-Maria Krabbe
- a Department of Urology , UT Southwestern Medical Center , Dallas , TX , USA.,b Department of Urology , University of Muenster Medical Center , Muenster , Germany
| | - Solomon L Woldu
- a Department of Urology , UT Southwestern Medical Center , Dallas , TX , USA
| | - Shahrokh F Shariat
- a Department of Urology , UT Southwestern Medical Center , Dallas , TX , USA.,c Department of Urology, Comprehensive Cancer Center , Medical University of Vienna , Vienna , Austria.,d Department of Urology and Medical Oncology , Weill Medical College of Cornell University , New York , NY , USA
| | - Yair Lotan
- a Department of Urology , UT Southwestern Medical Center , Dallas , TX , USA
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56
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Abstract
DNA methylation alterations are common in urothelial carcinoma, a prevalent cancer worldwide caused predominantly by chemical carcinogens. Recent studies have proposed sets of hypermethylated genes as promising diagnostic and prognostic biomarkers from urine or tissue samples, which require validation. Other studies have revealed intriguing links between specific carcinogens and DNA methylation alterations in cancer tissues or blood that might clarify carcinogenesis mechanisms and aid prevention. Like DNA methylation alterations, mutations in chromatin regulators are frequent, underlining the importance of epigenetic changes. However, the relations between the two changes and their functions in urothelial carcinogenesis remain unclear. Transcription factor genes with altered methylation deserve particular interest. Elucidating the functional impact of methylation changes is a prerequisite for their therapeutic targeting.
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Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Pathology, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
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57
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Yeh CM, Chen PC, Hsieh HY, Jou YC, Lin CT, Tsai MH, Huang WY, Wang YT, Lin RI, Chen SS, Tung CL, Wu SF, Chang DC, Shen CH, Hsu CD, Chan MWY. Methylomics analysis identifies ZNF671 as an epigenetically repressed novel tumor suppressor and a potential non-invasive biomarker for the detection of urothelial carcinoma. Oncotarget 2016; 6:29555-72. [PMID: 26320192 PMCID: PMC4745746 DOI: 10.18632/oncotarget.4986] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/16/2015] [Indexed: 11/25/2022] Open
Abstract
The molecular mechanism underlying the lethal phenomenon of urothelial carcinoma (UC) tumor recurrence remains unresolved. Here, by methylation microarray, we identified promoter methylation of the zinc-finger protein gene, ZNF671 in bladder UC tumor tissue samples, a finding that was independently validated by bisulphite pyrosequencing in cell lines and tissue samples. Subsequent assays including treatment with epigenetic depressive agents and in vitro methylation showed ZNF671 methylation to result in its transcriptional repression. ZNF671 re-expression in UC cell lines, via ectopic expression, inhibited tumor growth and invasion, in possible conjunction with downregulation of cancer stem cell markers (c-KIT, NANOG, OCT4). Clinically, high ZNF671 methylation in UC tumor tissues (n=96; 63 bladder, 33 upper urinary tract) associated with tumor grade and poor locoregional disease-free survival. Quantitative MSP analysis in a training (n=97) and test (n=61) sets of voided urine samples from bladder UC patients revealed a sensitivity and specificity of 42%-48% and 89%-92.8%, respectively, for UC cancer detection. Moreover, combining DNA methylation of ZNF671 and 2 other genes (IRF8 and sFRP1) further increased the sensitivity to 96.2%, suggesting a possible three-gene UC biomarker. In summary, ZNF671, an epigenetically silenced novel tumor suppressor, represents a potential predictor for UC relapse and non-invasive biomarker that could assist in UC clinical decision-making.
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Affiliation(s)
- Chia-Ming Yeh
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Pi-Che Chen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Hsiao-Yen Hsieh
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Yeong-Chin Jou
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Chang-Te Lin
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Hsuan Tsai
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Wen-Yu Huang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Yi-Ting Wang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Ru-Inn Lin
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Departments of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Chia Yi, Taiwan
| | - Szu-Shan Chen
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Chun-Liang Tung
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Shu-Fen Wu
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - D Ching Chang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Cheng-Da Hsu
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Michael W Y Chan
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
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58
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Kim YJ, Kim WJ. Can we use methylation markers as diagnostic and prognostic indicators for bladder cancer? Investig Clin Urol 2016; 57 Suppl 1:S77-88. [PMID: 27326410 PMCID: PMC4910760 DOI: 10.4111/icu.2016.57.s1.s77] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/17/2016] [Indexed: 12/21/2022] Open
Abstract
Urothelial carcinomas of the urinary bladder have diverse biological and functional characteristics, and numerous factors are likely to be involved in recurrence, progression, and patient survival. While several molecular markers used to evaluate the development and prognosis of bladder cancer have been studied, they are of limited value; therefore, new molecular parameters useful for predicting the prognosis of bladder cancer patients (particularly patients at high risk of progression and recurrence) are required. Recent progress in the understanding of epigenetic modification and gene silencing has provided new opportunities for the detection, treatment, and prevention of cancer. Methylation is an important molecular mechanism in bladder cancer and may have utility as a prognostic and/or diagnostic marker. This review discusses the epigenetic issues involved in the detection and prediction of bladder cancer.
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Affiliation(s)
- Yong-June Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Wun-Jae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
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59
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Niegisch G, Hoffmann MJ, Koutsogiannouli EA, Schulz WA. [Epigenetics in urothelial cancer: Pathogenesis, improving diagnostics and developing novel treatment options]. Urologe A 2016; 54:526-32. [PMID: 25784269 DOI: 10.1007/s00120-014-3756-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Urothelial carcinoma of the bladder is a common tumor for which improvements in diagnostic markers and new therapy approaches, in addition to or combined with standard chemotherapy, are urgently required. Epigenetic alterations could provide both novel diagnostic markers and therapeutic targets as they are emerging as crucial factors in the development and progression of this tumor type, likely contributing to altered differentiation and metastatic potential. These alterations affect DNA methylation, histone modifications, chromatin remodeling, long noncoding RNAs, and microRNAs. Factors involved in histone modifications and chromatin remodeling appear to be particularly frequently inactivated by mutations. Thus, histone-modifying enzymes may represent good targets for rational new therapeutic approaches, although thorough investigation of their complex functions is a prerequisite. DNA methylation changes and altered miRNA expression provide promising biomarkers for diagnosis and prognosis that need further validation in comprehensive and well-standardized studies.
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Affiliation(s)
- G Niegisch
- Medizinische Fakultät, Urologische Klinik, Heinrich-Heine-Universität Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Deutschland,
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60
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Blanca A, Requena MJ, Alvarez J, Cheng L, Montironi R, Raspollini MR, Reymundo C, Lopez-Beltran A. FGFR3 and Cyclin D3 as urine biomarkers of bladder cancer recurrence. Biomark Med 2016; 10:243-53. [PMID: 26861974 DOI: 10.2217/bmm.15.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To assess the diagnostic performance of FGFR3 and Cyclin D3 urinary protein levels in detecting bladder cancer recurrence. PATIENTS & METHODS Urine of 321 patients in follow-up for bladder cancer and 150 non-neoplastic urine controls was included. Cytology, cystoscopy and FGFR3 and Cyclin D3 expression by western blot were performed. RESULTS One hundred ten (34.3%) patients had evidence of tumor recurrence. The sensitivity and specificity of cytology/cystoscopy was 80 and 84%, and for FGFR3/Cyclin D3 was of 73 and 90%. CONCLUSION Combined urinary FGFR3/Cyclin D3 expression shows improved detection rates for bladder cancer recurrence with high specificity and sensitivity, and within the same range of detection shown by cystoscopy, therefore supporting its potential use as noninvasive diagnostic biomarker for bladder cancer recurrence.
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Affiliation(s)
- Ana Blanca
- Urology Department, Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain
| | - Maria J Requena
- Urology Department, Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain
| | - Jose Alvarez
- Urology Department, Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain
| | - Liang Cheng
- Departments of Pathology & Laboratory Medicine, and Urology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rodolfo Montironi
- Institute of Pathological Anatomy & Histopathology, Polytechnic University of the Marche Region, Ancona, Italy
| | - Maria R Raspollini
- Histopathology & Molecular Diagnostics, Careggi University Hospital, 50134, Florence, Italy
| | - Carlos Reymundo
- Department of Pathology & Surgery, Cordoba University Medical School, 14004 Cordoba, Spain
| | - Antonio Lopez-Beltran
- Department of Pathology & Surgery, Cordoba University Medical School, 14004 Cordoba, Spain
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61
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Current Status of Urinary Biomarkers for Detection and Surveillance of Bladder Cancer. Urol Clin North Am 2016; 43:47-62. [DOI: 10.1016/j.ucl.2015.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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62
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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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63
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Lakshminarasimhan R, Liang G. The Role of DNA Methylation in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:151-172. [PMID: 27826838 PMCID: PMC7409375 DOI: 10.1007/978-3-319-43624-1_7] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The malignant transformation of normal cells is driven by both genetic and epigenetic changes. With the advent of next-generation sequencing and large-scale multinational consortium studies, it has become possible to profile the genomes and epigenomes of thousands of primary tumors from nearly every cancer type. From these genome-wide studies, it became clear that the dynamic regulation of DNA methylation is a critical epigenetic mechanism of cancer initiation, maintenance, and progression. Proper control of DNA methylation is not only crucial for regulating gene transcription, but its broader consequences include maintaining the integrity of the genome and modulating immune response. Here, we describe the aberrant DNA methylation changes that take place in cancer and how they contribute to the disease phenotype. Further, we highlight potential clinical implications of these changes in the context of prognostic and diagnostic biomarkers, as well as therapeutic targets.
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Affiliation(s)
- Ranjani Lakshminarasimhan
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA
| | - Gangning Liang
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA.
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64
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Jandaghi P, Hoheisel JD, Riazalhosseini Y. GHSR hypermethylation: a promising pan-cancer marker. Cell Cycle 2015; 14:689-90. [PMID: 25603164 DOI: 10.1080/15384101.2015.1006051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Pouria Jandaghi
- a Department of Human Genetics ; McGill University ; Montreal , QC Canada
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65
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Cheng C, Varn FS, Marsit CJ. E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer. Mol Cancer Res 2015; 13:1316-24. [PMID: 26032289 PMCID: PMC4734892 DOI: 10.1158/1541-7786.mcr-15-0120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/19/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Bladder cancer is a common malignant disease, with non-muscle-invasive bladder cancer (NMIBC) representing the majority of tumors. This cancer subtype is typically treated by transurethral resection. In spite of treatment, up to 70% of patients show local recurrences. Intravesical BCG (Bacillus Calmette-Guerin) immunotherapy has been widely used to treat NMIBC, but it fails to suppress recurrence of bladder tumors in up to 40% of patients. Therefore, the development of prognostic markers is needed to predict the progression of bladder cancer and the efficacy of intravesical BCG treatment. This study demonstrates the effectiveness of an E2F4 signature for prognostic prediction of bladder cancer. E2F4 scores for each sample in a bladder cancer expression dataset were calculated by summarizing the relative expression levels of E2F4 target genes identified by ChIP-seq, and then the scores were used to stratify patients into good- and poor-outcome groups. The molecular signature was investigated in a single bladder cancer dataset and then its effectiveness was confirmed in two meta-bladder datasets consisting of specimens from multiple independent studies. These results were consistent in different datasets and demonstrate that the E2F4 score is predictive of clinical outcomes in bladder cancer, with patients whose tumors exhibit an E2F4 score >0 having significantly shorter survival times than those with an E2F4 score <0, in both non-muscle-invasive, and muscle-invasive bladder cancer. Furthermore, although intravesical BCG immunotherapy can significantly improve the clinical outcome of NMIBC patients with positive E2F4 scores (E2F4>0 group), it does not show significant treatment effect for those with negative scores (E2F4<0 group). IMPLICATIONS The E2F4 signature can be applied to predict the progression/recurrence and the responsiveness of patients to intravesical BCG immunotherapy in bladder cancer.
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Affiliation(s)
- Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire. Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire. Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire.
| | - Frederick S Varn
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Carmen J Marsit
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Lucca I, de Martino M, Klatte T, Shariat SF. Novel biomarkers to predict response and prognosis in localized bladder cancer. Urol Clin North Am 2015; 42:225-33, ix. [PMID: 25882564 DOI: 10.1016/j.ucl.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This review summarizes recent developments in diagnostic and prognostic biomarkers for nonmuscle invasive bladder cancer (NMIBC). Although the number of new biomarkers increases continuously, none are included in practice guidelines. Most NMIBC biomarkers show a higher sensitivity than urinary cytology, but lower specificity. Some protein and chromosome markers have been approved for screening and follow-up of patients in combination with cystoscopy. The long interval required for validation, testing, and approval of the assays and the lack of standardization could explain present issues in biomarker research. To enhance the development of new biomarkers, a more structured approach is required.
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Affiliation(s)
- Ilaria Lucca
- Department of Urology, Comprehensive Cancer Center, Vienna General Hospital, Medical University of Vienna, Währinger Gürtel 18-20, Vienna A-1090, Austria; Department of Urology, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 46, Lausanne CH-1010, Switzerland
| | - Michela de Martino
- Department of Urology, Comprehensive Cancer Center, Vienna General Hospital, Medical University of Vienna, Währinger Gürtel 18-20, Vienna A-1090, Austria
| | - Tobias Klatte
- Department of Urology, Comprehensive Cancer Center, Vienna General Hospital, Medical University of Vienna, Währinger Gürtel 18-20, Vienna A-1090, Austria
| | - Shahrokh F Shariat
- Department of Urology, Comprehensive Cancer Center, Vienna General Hospital, Medical University of Vienna, Währinger Gürtel 18-20, Vienna A-1090, Austria; Department of Urology, University of Texas Southwestern Medical Center, 1801 Inwood Road, Dallas, TX 75235, USA; Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, Cornell University, 1300 York Avenue, New York, NY 10065, USA.
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Peter S, Borkowska E, Drayton RM, Rakhit CP, Noon A, Chen W, Catto JW. Identification of differentially expressed long noncoding RNAs in bladder cancer. Clin Cancer Res 2014; 20:5311-21. [PMID: 25165097 DOI: 10.1158/1078-0432.ccr-14-0706] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE Loss of epigenetic gene regulation through altered long noncoding RNA (lncRNA) expression seems important in human cancer. LncRNAs have diagnostic and therapeutic potential, and offer insights into the biology disease, but little is known of their expression in urothelial cancer. Here, we identify differentially expressed lncRNAs with potential regulatory functions in urothelial cancer. EXPERIMENTAL DESIGN The expression of 17,112 lncRNAs and 22,074 mRNAs was determined using microarrays in 83 normal and malignant urothelial (discovery) samples and selected RNAs with qPCR in 138 samples for validation. Significantly differentially expressed RNAs were identified and stratified according to tumor phenotype. siRNA knockdown, functional assays, and whole-genome transcriptomic profiling were used to identify potential roles of selected lncRNAs. RESULTS We observed upregulation of many lncRNAs in urothelial cancer that was distinct to corresponding, more balanced changes for mRNAs. In general, lncRNA expression reflected disease phenotype. We identified 32 lncRNAs with potential roles in disease progression. Focusing upon a promising candidate, we implicate upregulation of AB074278 in apoptosis avoidance and the maintenance of a proproliferative state in cancer through a potential interaction with EMP1, a tumor suppressor and a negative regulator of cell proliferation. CONCLUSIONS We report differential expression profiles for numerous lncRNA in urothelial cancer. We identify phenotype-specific expression and a potential mechanistic target to explain this observation. Further studies are required to validate lncRNAs as prognostic biomarkers in this disease.
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Affiliation(s)
- Stefan Peter
- Academic Urology Unit and Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Edyta Borkowska
- Academic Urology Unit and Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Ross M Drayton
- Academic Urology Unit and Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Callum P Rakhit
- Academic Urology Unit and Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Aidan Noon
- Academic Urology Unit and Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom. Department of Urology, University of Toronto, Toronto, Canada
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - James Wf Catto
- Academic Urology Unit and Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom.
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