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Picard LC, Rich FJ, Kenwright DN, Stevens AJ. Epigenetic changes associated with Bacillus Calmette-Guerin (BCG) treatment in bladder cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189123. [PMID: 38806074 DOI: 10.1016/j.bbcan.2024.189123] [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: 12/06/2023] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
Bacillus Calmette-Guérin (BCG) treatment for non-muscle invasive bladder cancer (NMIBC) is an established immunotherapeutic, however, a significant portion of patients do not respond to treatment. Despite extensive research into the therapeutic mechanism of BCG, gaps remain in our understanding. This review specifically focuses on the epigenomic contributions in the immune microenvironment, in the context of BCG treatment for NMIBC. We also summarise the current understanding of NMIBC epigenetic characteristics, and discuss how future targeted strategies for BCG therapy should incorporate epigenomic biomarkers in conjunction with genomic biomarkers.
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Affiliation(s)
- Lucy C Picard
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand
| | - Fenella J Rich
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand
| | - Diane N Kenwright
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand
| | - Aaron J Stevens
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand.
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2
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Koukourikis P, Papaioannou M, Pervana S, Apostolidis A. Exploring the DNA Methylation Profile of Genes Associated with Bladder Cancer in Bladder Tissue of Patients with Neurogenic Lower Urinary Tract Dysfunction. Int J Mol Sci 2024; 25:5660. [PMID: 38891848 PMCID: PMC11171624 DOI: 10.3390/ijms25115660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/12/2024] [Accepted: 05/19/2024] [Indexed: 06/21/2024] Open
Abstract
DNA methylation is an epigenetic process that commonly occurs in genes' promoters and results in the transcriptional silencing of genes. DNA methylation is a frequent event in bladder cancer, participating in tumor initiation and progression. Bladder cancer is a major health issue in patients suffering from neurogenic lower urinary tract dysfunction (NLUTD), although the pathogenetic mechanisms of the disease remain unclear. In this population, bladder cancer is characterized by aggressive histopathology, advanced stage during diagnosis, and high mortality rates. To assess the DNA methylation profiles of five genes' promoters previously known to be associated with bladder cancer in bladder tissue of NLUTD patients, we conducted a prospective study recruiting NLUTD patients from the neuro-urology unit of a public teaching hospital. Cystoscopy combined with biopsy for bladder cancer screening was performed in all patients following written informed consent being obtained. Quantitative methylation-specific PCR was used to determine the methylation status of RASSF1, RARβ, DAPK, hTERT, and APC genes' promoters in bladder tissue samples. Twenty-four patients suffering from mixed NLUTD etiology for a median duration of 10 (IQR: 12) years were recruited in this study. DNA hypermethylation was detected in at least one gene of the panel in all tissue samples. RAR-β was hypermethylated in 91.7% samples, RASSF and DAPK were hypermethylated in 83.3% samples, APC 37.5% samples, and TERT in none of the tissue samples. In 45.8% of the samples, three genes of the panel were hypermethylated, in 29.2% four genes were hypermethylated, and in 16.7% and in 8.3% of the samples, two and one gene were hypermethylated, respectively. The number of hypermethylated genes of the panel was significantly associated with recurrent UTIs (p = 0.0048). No other significant association was found between DNA hypermethylation or the number of hypermethylated genes and the clinical characteristics of the patients. Histopathological findings were normal in 8.3% of patients, while chronic inflammation was found in 83.3% of patients and squamous cell metaplasia in 16.7% of patients. In this study, we observed high rates of DNA hypermethylation of genes associated with bladder cancer in NLUTD patients, suggesting an epigenetic field effect and possible risk of bladder cancer development. Recurrent UTIs seem to be associated with increased DNA hypermethylation. Further research is needed to evaluate the impact of recurrent UTIs and chronic inflammation in DNA hypermethylation and bladder cancer etiopathogenesis in NLUTD patients.
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Affiliation(s)
- Periklis Koukourikis
- 2nd Department of Urology, Aristotle University of Thessaloniki, General Hospital ‘Papageorgiou’, 56403 Thessaloniki, Greece;
| | - Maria Papaioannou
- Department of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Stavroula Pervana
- Department of Pathology, General Hospital ‘Papageorgiou’, 56403 Thessaloniki, Greece;
| | - Apostolos Apostolidis
- 2nd Department of Urology, Aristotle University of Thessaloniki, General Hospital ‘Papageorgiou’, 56403 Thessaloniki, Greece;
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de Jong FC, Iflé IG, van der Made AC, Kooper D, de Jong JJ, Franckena M, Zuiverloon TC, van Criekinge W, Incrocci L, Zwarthoff EC, Boormans JL. A Genomic Urine Assay for Surveillance of Patients with Bladder Cancer Treated with Radiotherapy. EUR UROL SUPPL 2024; 62:131-139. [PMID: 38496820 PMCID: PMC10940129 DOI: 10.1016/j.euros.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Background Patients with muscle-invasive bladder cancer (MIBC) who receive radiotherapy with curative intent are followed by imaging, cystoscopy, and urine cytology. However, interpretation of cytology and cystoscopy is hampered by the impact of ionizing radiation on cells. Objective To assess the diagnostic performance of a genomic urine assay to detect urinary tract recurrences in patients with MIBC treated by (chemo)radiation. Design setting and participants Patients with nonmetastatic MIBC who underwent (chemo)radiation with curative intent from 2016 to 2020 were prospectively included. Follow-up consisted of cystoscopy and upper tract imaging. Prior to cystoscopy, a urine sample was analyzed to assess mutations in the genes FGFR3, HRAS, and TERT and methylation of OTX1, TWIST1, and ONECUT2. The treating physician was blinded for the assay result. Outcome measurements and statistical analysis The primary endpoint was a urinary tract recurrence. Cross-sectional sensitivity, specificity, and negative predictive value (NPV) were analyzed using a previously developed logistic regression model for the detection of bladder cancer with this assay. The secondary endpoint was the risk of a future urinary tract recurrence following a positive test and negative cystoscopy/imaging, using a time-dependent Cox proportional hazard analysis. Results and limitations A total of 143 patients were included, and 503 urine samples were analyzed. The median study duration was 20 mo (interquartile range [IQR] 10-33), and the median time to a recurrence was 16 mo (IQR 12-26). In 27 patients, 32 urinary tract recurrences were diagnosed, including three upper tract tumors. Of 32 recurrences, 18 (56%) had a concomitant urine test available. The diagnostic model had an area under the curve of 0.80 (95% confidence interval [CI] 0.69-0.90) with corresponding sensitivity, specificity, and NPV of 78 (95% CI 52-94), 77% (95% CI 73-81), and 99% (95% CI 97-100). When taking into account the anticipatory effect of the test, 28/32 (88%) recurrences were detected. A Cox regression analysis showed a hazard ratio of 14.8 for the development of a future recurrence (p < 0.001). A major limitation was the lack of a concomitant urine test result in 14/32 (44%) recurrences. Conclusions A genomic urine assay detected urinary tract recurrences after (chemo)radiation in patients with MIBC, and a positive test was strongly associated with future recurrences. Although validation in a large cohort is warranted, the test has the potential to limit frequent cystoscopies. Patient summary Radiotherapy is a bladder-sparing treatment in patients with bladder cancer. After treatment, these patients undergo visual inspection of the bladder by cystoscopy to detect possible recurrences. However, interpretation of cystoscopy is difficult due to the effects of radiation on the bladder lining. Hence, we analyzed the diagnostic value of a molecular urine test to detect recurrent disease in bladder cancer patients treated by radiotherapy, and we showed that the urine test has the potential to limit the number of cystoscopies.
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Affiliation(s)
- Florus C. de Jong
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Iris G. Iflé
- Department of Pathology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Angelique C. van der Made
- Department of Pathology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Denise Kooper
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joep J. de Jong
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Martine Franckena
- Department of Radiotherapy, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Tahlita C.M. Zuiverloon
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wim van Criekinge
- Laboratory of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Luca Incrocci
- Department of Radiotherapy, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ellen C. Zwarthoff
- Department of Pathology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joost L. Boormans
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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Pilala KM, Kotronopoulos G, Levis P, Giagkos GC, Stravodimos K, Vassilacopoulou D, Scorilas A, Avgeris M. MIR145 Core Promoter Methylation in Pretreatment Cell-Free DNA: A Liquid Biopsy Tool for Muscle-Invasive Bladder Cancer Treatment Outcome. JCO Precis Oncol 2024; 8:e2300414. [PMID: 38579191 DOI: 10.1200/po.23.00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/06/2024] [Accepted: 02/13/2024] [Indexed: 04/07/2024] Open
Abstract
PURPOSE The lack of personalized management of bladder cancer (BlCa) results in patients' lifelong post-treatment monitoring with invasive interventions, underlying the urgent need for tailored and minimally invasive health care services. On the basis of our previous findings on miR-143/145 cluster methylation in bladder tumors, we evaluated its clinical significance in pretreatment cell-free DNA (cfDNA) of patients with BlCa. MATERIALS AND METHODS Methylation analysis was performed in our screening cohort (120 patients with BlCa; 20 age-matched healthy donors) by bisulfite-based pyrosequencing. Tumor recurrence/progression for patients with non-muscle-invasive bladder cancer, and progression and mortality for patients with muscle-invasive bladder cancer (MIBC) were used as clinical end point events in survival analysis. Bootstrap analysis was applied for internal validation of Cox regression models and decision curve analysis for assessment of clinical benefit on disease prognosis. RESULTS Decreased methylation of MIR145 core promoter in pretreatment cfDNA was associated with short-term disease progression (multivariate Cox: hazard ratio [HR], 2.027 [95% CI, 1.157 to 3.551]; P = .010) and poor overall survival (multivariate Cox: HR, 2.098 [95% CI, 1.154 to 3.817]; P = .009) of patients with MIBC after radical cystectomy (RC). Multivariate models incorporating MIR145 promoter methylation in cfDNA with tumor stage clearly ameliorated patients' risk stratification, highlighting superior clinical benefit in MIBC prognostication. CONCLUSION Reduced pretreatment cfDNA methylation of MIR145 core promoter was markedly correlated with increased risk for short-term progression and worse survival of patients with MIBC after RC and adjuvant therapy, supporting modern personalized and minimally invasive prognosis. Methylation profiling of MIR145 core promoter in pretreatment cfDNA could serve as a minimally invasive and independent predictor of MIBC treatment outcome and emerge as a promising marker for blood-based test in BlCa.
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Affiliation(s)
- Katerina-Marina Pilala
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotronopoulos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Levis
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios-Christos Giagkos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dido Vassilacopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
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Pierconti F, Rossi ED, Fiorentino V, Bakacs A, Carlino A, Navarra E, Sacco E, Totaro A, Palermo G, Larocca LM, Martini M. Methylation Analysis of Urinary Sample in Non-Muscle-Invasive Bladder Carcinoma: Frequency and Management of Invalid Result. Biomedicines 2023; 11:3288. [PMID: 38137509 PMCID: PMC10741688 DOI: 10.3390/biomedicines11123288] [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: 11/16/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Numerous studies showed that methylation analysis represents a newly developed urinary marker based on DNA methylation changes in a panel of genomic biomarkers and it could represent a valid tool in terms of the diagnosis and prediction of high-grade urothelial carcinoma recurrences. One of the limits of the use of this new molecular method during a follow-up is represented by the number of invalid tests in routine practice. METHOD A total of 782 patients with a diagnosis of non-muscle-invasive high-grade carcinoma (NMIBC) was studied. The Bladder EpiCheck test (BE) was performed together with cytology in all cases within 1 year after the end of treatment. In 402 patients, the urinary samples were voided urine (UV), while, in 380 cases, the samples were collected after bladder washing (IU). For all the patients with invalid BE results, a second BE test was performed following the instructions for use that indicated the test should be repeated with a new urinary sample in the case of an invalid result. RESULTS Analyzing the two different groups (UV and IU), we found the invalid BE results seemed to be not related to urinary samples (p = 0.13 Fisher's exact test), suggesting that the collection method was not relevant in order to reduce the number of invalid tests. CONCLUSIONS In the follow-up for NMIBC, for patients for whom a BE test is planned, a combined approach of cytology and a methylation test is recommended in order to repeat the BE test with an invalid result only in those cases with a cytological diagnosis of atypical urothelial cells (AUC) suspicious for high-grade urothelial carcinoma (SHGUC) and high-grade urothelial carcinoma (HGUC).
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Affiliation(s)
- Francesco Pierconti
- Institute of Pathology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00153 Rome, Italy; (E.D.R.); (A.B.); (E.N.)
| | - E. D. Rossi
- Institute of Pathology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00153 Rome, Italy; (E.D.R.); (A.B.); (E.N.)
| | - V. Fiorentino
- Institute of Pathology, University of Messina, 98125 Messina, Italy; (V.F.); (M.M.)
| | - A. Bakacs
- Institute of Pathology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00153 Rome, Italy; (E.D.R.); (A.B.); (E.N.)
| | - A. Carlino
- Institute of Pathology, UniCamillus Rome, 00131 Rome, Italy; (A.C.); (L.M.L.)
| | - E. Navarra
- Institute of Pathology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00153 Rome, Italy; (E.D.R.); (A.B.); (E.N.)
| | - E. Sacco
- Institute of Urology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00168 Rome, Italy; (E.S.); (A.T.); (G.P.)
| | - A. Totaro
- Institute of Urology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00168 Rome, Italy; (E.S.); (A.T.); (G.P.)
| | - G. Palermo
- Institute of Urology, Catholic University of Rome, Fondazione Policlinico Gemelli Roma, 00168 Rome, Italy; (E.S.); (A.T.); (G.P.)
| | - L. M. Larocca
- Institute of Pathology, UniCamillus Rome, 00131 Rome, Italy; (A.C.); (L.M.L.)
| | - M. Martini
- Institute of Pathology, University of Messina, 98125 Messina, Italy; (V.F.); (M.M.)
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Xu Z, Wu Y, Zhao G, Jin B, Jiang P. A novel DNA methylation signature revealed GDF6 and RCC1 as potential prognostic biomarkers correlated with cell proliferation in clear cell renal cell carcinoma. Mol Biol Rep 2023; 51:16. [PMID: 38087057 DOI: 10.1007/s11033-023-09003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) accounts for the majority (80%-90%) of renal cell carcinoma (RCC) patients at the time of diagnosis, and approximately 15% of ccRCC patients will develop distant metastasis or recurrence during their lifetime. Increasing number of studies have revealed that the aberrant DNA methylations is closely correlated with the tumorigenesis in ccRCC. RESULTS In this study, we utilized a LASSO (least absolute shrinkage and selection operator) model to identify a combination of 13 probes-based DNA methylation signature that associated with the progression-free survival (PFS) of ccRCC patients. First, differentially methylated regions (CpGs) related to PFS and phenotypes were identified. Next, prognostic DNA methylation probes were selected from the differentially methylated probes (DMPs) and calculated risk scores to stratify patients with ccRCC. The performance of this signature was validated in an independent testing set using various analyses, including Kaplan-Meier analysis for PFS and receiver operating characteristic (ROC) curve analysis. Based on our 13-DNA methylation probes signature, ccRCC patients were successfully stratified into high- and low-risk groups. Combining DNA methylation signature with clinical variables such as T stage, M stage and tumor grade could further improve the accuracy of prediction. Moreover, we highlight two molecular biomarkers (RCC1 and GDF6) corresponding to our probes. Invitro experiments showed that knockdown of RCC1 or GDF6 in ccRCC cell lines reduced cell proliferation, which indicated that both biomarkers are associated with tumorigenesis. CONCLUSIONS The 13-probes-based DNA methylation signature has the potential to serve as an independent tool for survival outcome improvement and treatment strategy selection for ccRCC patients. In addition, our findings suggest that RCC1 and GDF6 may serve as promising markers for ccRCC.
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Affiliation(s)
- Zhijie Xu
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, 31003, Zhejiang, China
| | - Yunfei Wu
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, 31003, Zhejiang, China
| | - Guanan Zhao
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Department of Urology, Lishui People's Hospital, Lishui, 323050, Zhejiang, China
| | - Baiye Jin
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, 31003, Zhejiang, China
| | - Peng Jiang
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
- Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, 31003, Zhejiang, China.
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Maas M, Todenhöfer T, Black PC. Urine biomarkers in bladder cancer - current status and future perspectives. Nat Rev Urol 2023; 20:597-614. [PMID: 37225864 DOI: 10.1038/s41585-023-00773-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 05/26/2023]
Abstract
Urine markers to detect bladder cancer have been the subject of research for decades. The idea that urine - being in continuous contact with tumour tissue - should provide a vector of tumour information remains an attractive concept. Research on this topic has resulted in a complex landscape of many different urine markers with varying degrees of clinical validation. These markers range from cell-based assays to proteins, transcriptomic markers and genomic signatures, with a clear trend towards multiplex assays. Unfortunately, the number of different urine markers and the efforts in research and development of clinical grade assays are not reflected in the use of these markers in clinical practice, which is currently limited. Numerous prospective trials are in progress with the aim of increasing the quality of evidence about urinary biomarkers in bladder cancer to achieve guideline implementation. The current research landscape suggests a division of testing approaches. Some efforts are directed towards addressing the limitations of current assays to improve the performance of urine markers for a straightforward detection of bladder cancer. Additionally, comprehensive genetic analyses are emerging based on advances in next-generation sequencing and are expected to substantially affect the potential application of urine markers in bladder cancer.
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Affiliation(s)
- Moritz Maas
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Urology, University of Tübingen, Tübingen, Germany
| | - Tilman Todenhöfer
- Clinical Trials Unit Studienpraxis Urologie, Nürtingen, Germany
- Eberhard-Karls-University, Tübingen, Germany
| | - Peter C Black
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
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Wang P, Shi Y, Zhang J, Shou J, Zhang M, Zou D, Liang Y, Li J, Tan Y, Zhang M, Bi X, Zhou L, Ci W, Li X. UCseek: ultrasensitive early detection and recurrence monitoring of urothelial carcinoma by shallow-depth genome-wide bisulfite sequencing of urinary sediment DNA. EBioMedicine 2023; 89:104437. [PMID: 36758479 PMCID: PMC9941055 DOI: 10.1016/j.ebiom.2023.104437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Current methods for the detection and surveillance of urothelial carcinomas (UCs) are often invasive, costly, and not effective for low-grade, early-stage, and minimal residual disease (MRD) tumors. We aimed to develop and validate a model from urine sediments to predict different grade and stage UCs with low cost and high accuracy. METHODS We collected 167 samples, including 90 tumors and 77 individuals without tumors, as a discovery cohort. We assessed copy number variations and methylation values for them and constructed a diagnostic classifier to detect UC, UCseek, by using an individual read-based method and support vector machine. The performance of UCseek was validated in an independent cohort derived from three hospitals (n = 206) and a relapse cohort (n = 42) for monitoring recurrence. FINDINGS We constructed UCseek, which could predict UCs with high sensitivity (92.7%), high specificity (90.7%), and high accuracy (91.7%) in the independent validation set. The accuracy of UCseek in low-grade and early-stage patients reached 91.8% and 94.3%, respectively. Notably, UCseek retained great performance at ultralow sequencing depths (0.3X-0.5X). It also demonstrated a powerful ability to monitor recurrence in a surveillance cohort compared with cystoscopy (90.91% vs. 59.09%). INTERPRETATION We optimized an improved approach named UCseek for the noninvasive diagnosis and monitoring of UCs in both low- and high-grade tumors and in early- and advanced-stage tumors, even at ultralow sequencing depths, which may reduce the burden of cystoscopy and blind second surgery. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgments section.
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Affiliation(s)
- Ping Wang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jianye Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China
| | - Jianzhong Shou
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Daojia Zou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Juan Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Xingang Bi
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China; National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China; National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
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Musangile FY, Matsuzaki I, Iwamoto R, Sagan K, Nishikawa M, Mikasa Y, Takahashi Y, Kojima F, Hara I, Murata SI. Targeted Next-Generation Sequencing of Flat Urothelial Lesions Reveals Putative Pathobiological Pathways, Potential Biomarkers, and Rational Therapeutic Targets. Mod Pathol 2023; 36:100120. [PMID: 36812689 DOI: 10.1016/j.modpat.2023.100120] [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: 10/04/2022] [Revised: 01/05/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Flat urothelial lesions are controversial diagnostic and prognostic urologic entities whose importance relies mainly on their ability to progress to muscle-invasive tumors via urothelial carcinoma in situ (CIS). However, the carcinogenetic progression of preneoplastic flat urothelial lesions is not well established. Moreover, predictive biomarkers and therapeutic targets of the highly recurrent and aggressive urothelial CIS lesion are lacking. Using a targeted next-generation sequencing (NGS) panel of 17 genes directly involved in bladder cancer pathogenesis, we investigated alterations of genes and pathways with clinical and carcinogenic implications on 119 samples of flat urothelium, including normal urothelium (n = 7), reactive atypia (n = 10), atypia of unknown significance ( n = 34), dysplasia ( n = 23), and CIS (n = 45). The majority of the flat lesions were tumor-associated but grossly/microscopically or temporally separated from the main tumor. Mutations were compared across flat lesions and concerning the concomitant urothelial tumor. Associations between genomic mutations and recurrence after intravesical bacillus Calmette-Guerin treatment were estimated with Cox regression analysis. TERT promoter mutations were highly prevalent in intraurothelial lesions but not in the normal or reactive urothelium, suggesting that it is a critical driver mutation in urothelial tumorigenesis. We found that synchronous atypia of unknown significance-dysplasia-CIS lesions without concomitant papillary urothelial carcinomas had a similar genomic profile that differed from atypia of unknown significance-dysplasia lesions associated with papillary urothelial carcinomas, which harbored significantly more FGFR3, ARID1A, and PIK3CA mutations. KRAS G12C and ERBB2 S310F/Y mutations were exclusively detected in CIS and were associated with recurrence after bacillus Calmette-Guerin treatment (P = .0006 and P = .01, respectively). This targeted NGS study revealed critical mutations involved in the carcinogenetic progression of flat lesions with putative pathobiological pathways. Importantly, KRAS G12C and ERBB2 S310F/Y mutations were identified as potential prognostic and therapeutic biomarkers for urothelial carcinoma.
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Affiliation(s)
- Fidele Y Musangile
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Ibu Matsuzaki
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Ryuta Iwamoto
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Kanako Sagan
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Mizuki Nishikawa
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Yurina Mikasa
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Yuichi Takahashi
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Fumiyoshi Kojima
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Isao Hara
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | - Shin-Ichi Murata
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan.
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10
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Zhou S, Li M, Ostrow D, Ruble D, Mascarenhas L, Pawel B, Buckley JD, Triche TJ. Potential methylation-regulated genes and pathways in hepatocellular neoplasm, not otherwise specified. Front Oncol 2022; 12:952325. [PMID: 36212481 PMCID: PMC9532972 DOI: 10.3389/fonc.2022.952325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Aims The molecular basis of hepatocellular neoplasm, not otherwise specified (HCN-NOS) is unknown. We aimed to identify gene expression patterns, potential methylation-regulated genes and pathways that characterize the tumor, and its possible relationship to hepatoblastoma and hepatocellular carcinoma (HCC). Approach & Results Parallel genome-wide profiling of gene expression (RNAseq) and DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls. 2530 significantly differentially expressed genes (DEGs) were identified between tumors and controls. Many of these DEGs were associated with hepatoblastoma and/or HCC. Analysis Match in Ingenuity Pathway Analysis determined that the gene expression profile of HCN-NOS was unique but significantly similar to that of both hepatoblastoma and HCC. A total of 27,195 CpG sites (CpGs) were significantly differentially methylated (DM) between tumors and controls, with a global hypomethylation pattern and predominant CpG island hypermethylation in promotor regions. Aberrant DNA methylation predominated in Developmental Process and Molecular Function Regulator pathways. Embryonic stem cell pathways were significantly enriched. In total, 1055 aberrantly methylated (at CpGs) and differentially expressed genes were identified, including 25 upstream regulators and sixty-one potential CpG island methylation-regulated genes. Eight methylation-regulated genes (TCF3, MYBL2, SRC, HMGA2, PPARGC1A, SLC22A1, COL2A1 and MYCN) had highly consistent gene expression patterns and prognostic value in patients with HCC, based on comparison to publicly available datasets. Conclusions HCN-NOS has a unique, stem-cell like gene expression and DNA methylation profile related to both hepatoblastoma and HCC but distinct therefrom. Further, 8 methylation-regulated genes associated with prognosis in HCC were identified.
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Affiliation(s)
- Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Shengmei Zhou,
| | - Meng Li
- USC Libraries Bioinformatics Services, University of Southern California, Los Angeles, CA, United States
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - David Ruble
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Leo Mascarenhas
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Cancer and Blood Disease Institute, Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Bruce Pawel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jonathan David Buckley
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Timothy J. Triche
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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11
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Li J, Liang Y, Fan J, Xu C, Guan B, Zhang J, Guo B, Shi Y, Wang P, Tan Y, Zhang Q, Yuan C, Wu Y, Zhou L, Ci W, Li X. DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma. BMC Med 2022; 20:222. [PMID: 35843958 PMCID: PMC9290251 DOI: 10.1186/s12916-022-02426-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND At present, the extent and clinical relevance of epigenetic differences between upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) remain largely unknown. Here, we conducted a study to describe the global DNA methylation landscape of UTUC and UCB and to address the prognostic value of DNA methylation subtype and responses to the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma (UC). METHODS Using whole-genome bisulfite sequencing (n = 49 samples), we analyzed epigenomic features and profiles of UTUC (n = 36) and UCB (n = 9). Next, we characterized potential links between DNA methylation, gene expression (n = 9 samples), and clinical outcomes. Then, we integrated an independent UTUC cohort (Fujii et al., n = 86) and UCB cohort (TCGA, n = 411) to validate the prognostic significance. Furthermore, we performed an integrative analysis of genome-wide DNA methylation and gene expression in two UC cell lines following transient DNA methyltransferase inhibitor SGI-110 treatment to identify potential epigenetic driver events that contribute to drug efficacy. RESULTS We showed that UTUC and UCB have very similar DNA methylation profiles. Unsupervised DNA methylation classification identified two epi-clusters, Methy-High and Methy-Low, associated with distinct muscle-invasive statuses and patient outcomes. Methy-High samples were hypermethylated, immune-infiltrated, and enriched for exhausted T cells, with poor clinical outcome. SGI-110 inhibited the migration and invasion of Methy-High UC cell lines (UMUC-3 and T24) by upregulating multiple antitumor immune pathways. CONCLUSIONS DNA methylation subtypes pave the way for predicting patient prognosis in UC. Our results provide mechanistic rationale for evaluating SGI-110 in treating UC patients in the clinic.
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Affiliation(s)
- Juan Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jian Fan
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Jianye Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Bin Guo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Ping Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changwei Yuan
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Yucai Wu
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, China. .,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, China. .,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
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12
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Lokeshwar SD, Lopez M, Sarcan S, Aguilar K, Morera DS, Shaheen DM, Lokeshwar BL, Lokeshwar VB. Molecular Oncology of Bladder Cancer from Inception to Modern Perspective. Cancers (Basel) 2022; 14:cancers14112578. [PMID: 35681556 PMCID: PMC9179261 DOI: 10.3390/cancers14112578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
Within the last forty years, seminal contributions have been made in the areas of bladder cancer (BC) biology, driver genes, molecular profiling, biomarkers, and therapeutic targets for improving personalized patient care. This overview includes seminal discoveries and advances in the molecular oncology of BC. Starting with the concept of divergent molecular pathways for the development of low- and high-grade bladder tumors, field cancerization versus clonality of bladder tumors, cancer driver genes/mutations, genetic polymorphisms, and bacillus Calmette-Guérin (BCG) as an early form of immunotherapy are some of the conceptual contributions towards improving patient care. Although beginning with a promise of predicting prognosis and individualizing treatments, "-omic" approaches and molecular subtypes have revealed the importance of BC stem cells, lineage plasticity, and intra-tumor heterogeneity as the next frontiers for realizing individualized patient care. Along with urine as the optimal non-invasive liquid biopsy, BC is at the forefront of the biomarker field. If the goal is to reduce the number of cystoscopies but not to replace them for monitoring recurrence and asymptomatic microscopic hematuria, a BC marker may reach clinical acceptance. As advances in the molecular oncology of BC continue, the next twenty-five years should significantly advance personalized care for BC patients.
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Affiliation(s)
- Soum D. Lokeshwar
- Department of Urology, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Maite Lopez
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Semih Sarcan
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | - Karina Aguilar
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Daley S. Morera
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Devin M. Shaheen
- Yale School of Nursing, Yale University, New Haven, CT 06520, USA;
| | - Bal L. Lokeshwar
- Georgia Cancer Center, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA
- Research Service, Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
- Correspondence: (B.L.L.); (V.B.L.)
| | - Vinata B. Lokeshwar
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
- Correspondence: (B.L.L.); (V.B.L.)
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13
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Cadherin switches during epithelial-mesenchymal transition: CDH4/RCAD downregulation reduces bladder cancer progression. Cell Oncol (Dordr) 2022; 45:135-149. [DOI: 10.1007/s13402-021-00657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2021] [Indexed: 11/03/2022] Open
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14
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Bošković M, Roje B, Chung FFL, Gelemanović A, Cahais V, Cuenin C, Khoueiry R, Vilović K, Herceg Z, Terzić J. DNA Methylome Changes of Muscle- and Neuronal-Related Processes Precede Bladder Cancer Invasiveness. Cancers (Basel) 2022; 14:487. [PMID: 35158756 PMCID: PMC8833512 DOI: 10.3390/cancers14030487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is the ninth leading cause of cancer death with one of the highest recurrence rates among all cancers. One of the main risks for BC development is exposure to nitrosamines present in tobacco smoke or in other products. Aberrant epigenetic (DNA methylation) changes accompanied by deregulated gene expression are an important element of cancer pathogenesis. Therefore, we aimed to determine DNA methylation signatures and their impacts on gene expression in mice treated with N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN), a carcinogen similar to compounds found in tobacco smoke. Following BBN administration mice developed non-invasive or invasive bladder cancers. Surprisingly, muscle- and neuronal-related pathways emerged as the most affected in those tumors. Hypo- and hypermethylation changes were present within non-invasive BC, across CpGs mapping to the genes involved in muscle- and neuronal-related pathways, however, methylation differences were not sufficient to affect the expression of the majority of associated genes. Conversely, invasive tumors displayed hypermethylation changes that were linked with alterations in gene expression profiles. Together, these findings indicate that bladder cancer progression could be revealed through methylation profiling at the pre-invasive cancer stage that could assist monitoring of cancer patients and guide novel therapeutic approaches.
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Affiliation(s)
- Maria Bošković
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Blanka Roje
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Felicia Fei-Lei Chung
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia
| | - Andrea Gelemanović
- Biology of Robustness Group, Mediterranean Institute for Life Sciences (MedILS), Šetalište Ivana Meštrovića 45, 21000 Split, Croatia;
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Rita Khoueiry
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Katarina Vilović
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Janoš Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
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15
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Zhou Q, Chen Q, Chen X, Hao L. Bioinformatics analysis to screen DNA methylation-driven genes for prognosis of patients with bladder cancer. Transl Androl Urol 2021; 10:3604-3619. [PMID: 34733656 PMCID: PMC8511533 DOI: 10.21037/tau-21-326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
Background Bladder cancer (BLCA) is the most prevalent tumor affecting the urinary system, and has contributed to a rise in morbidity and mortality rates. Herein, we sought to identify the methylation-driven genes (MDGs)of BLCA in an effort to develop prognostic biomarkers suitable for the individualized assessment of patients with this particular cancer. Methods The Cancer Genome Atlas (TCGA) dataset was distributed into training set (n=272) and testing set(n=117). The ConsensusClusterPluspackage was used to identify BLCA subtypes. The ChAMP package was used to analyze differential methylation probe (DMP) and differential methylation region (DMR). The differentially expressed genes (DEGs) were detected using DESeq2. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were utilized to identify the pathways enriched of DEGs. Correlation analysis between 5’-C-phosphate-G-3’s (CpGs) and DEGs was employed to identify the MDGs. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) was used to build the protein-protein interaction (PPI) network of MDGs. Screening for BLCA prognosis-related MDGs and clinical features was conducted via the Cox regression model. A prognosis-related nomogram was developed and validated for prediction of the BLCA patients’ survival. Results We identified 2 BLCA clusters. Differential methylations at CpGs sites (dm-CpGs) were observed between cluster2 and cluster1, with 14,189 of them hypermethylated and 878 hypomethylated, predominantly in the CpG islands. In addition, a total 4,234 DEGs were identified between cluster2 and cluster1. The KEGG pathway and GO term enrichment analyses found that some DEGs were significantly enriched in multiple cancer-related pathways. A total of 33 MDGs were detected from correlation analysis between CpGs and DEGs. We selected BLCA-specific prognostic DMGs signatures for risk model development. The nomogram comprised a risk model to predict survival for BLCA patients. The efficiency of the prognostic prediction model was validated in the training and testing set. Conclusions This study discovered differential methylation patterns and MDGs in BLCA patients, which provided a bioinformatics basis for guiding BLCA early diagnosis and prognosis analyses.
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Affiliation(s)
- Qing Zhou
- Central Laboratory, People's Hospital of Baoan District, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiuyan Chen
- Science and Education Department, Shenzhen Baoan Shiyan People's Hospital, Shenzhen, China
| | - Xi Chen
- Central Laboratory, People's Hospital of Baoan District, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lu Hao
- Science and Education Department, Shenzhen Baoan Shiyan People's Hospital, Shenzhen, China
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16
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Gu Y, Zeng J, Zou Y, Liu C, Fu H, Chang H. Folate Intake and Risk of Urothelial Carcinoma: A Systematic Review and Meta-Analysis of Epidemiological Studies. Nutr Cancer 2021; 74:1593-1605. [PMID: 34472414 DOI: 10.1080/01635581.2021.1973518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We aimed to investigate the association between folate intake and the risk of urothelial carcinoma (UC). A systematic literature search using Pubmed and EMBASE databases was performed to find prospective cohort studies, population-based case-control study or hospital-based case-control study investigating the association of folate intake and the risk of UC. A total of 19 studies involving 11,175 cases and 656,161 individuals were included. High intake of folate was associated with a decreased risk of UC, with a pooled OR of 0.78 (95% CI: 0.66-0.93, P = 0.006) for the highest category of intake vs. the lowest. The data suggested that folate may contribute to the prevention of urothelial cancer. However, the association was observed only in case-control studies (OR = 0.56, 95% CI: 0.39-0.79, P = 0.001), but not in cohort studies (RR = 0.97, 95% CI: 0.87-1.09, P = 0.638). Dose-response meta-analysis showed that an increment of folate intake (100 μg/day) corresponded to an 8% deceased risk of invasive UC (RR = 0.92, 95% CI: 0.87-0.98, P = 0.004). High folate intake might be inversely associated with risk of UC particularly invasive UC, which needs to be confirmed.
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Affiliation(s)
- Yi Gu
- College of Food Science, Southwest University, Chongqing, China
| | - Jie Zeng
- College of Food Science, Southwest University, Chongqing, China
| | - Yixin Zou
- College of Food Science, Southwest University, Chongqing, China
| | - Chang Liu
- College of Food Science, Southwest University, Chongqing, China
| | - Hongjuan Fu
- College of Food Science, Southwest University, Chongqing, China
| | - Hui Chang
- College of Food Science, Southwest University, Chongqing, China
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17
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Loras A, Segovia C, Ruiz-Cerdá JL. Epigenomic and Metabolomic Integration Reveals Dynamic Metabolic Regulation in Bladder Cancer. Cancers (Basel) 2021; 13:2719. [PMID: 34072826 PMCID: PMC8198168 DOI: 10.3390/cancers13112719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) represents a clinical, social, and economic challenge due to tumor-intrinsic characteristics, limitations of diagnostic techniques and a lack of personalized treatments. In the last decade, the use of liquid biopsy has grown as a non-invasive approach to characterize tumors. Moreover, the emergence of omics has increased our knowledge of cancer biology and identified critical BC biomarkers. The rewiring between epigenetics and metabolism has been closely linked to tumor phenotype. Chromatin remodelers interact with each other to control gene silencing in BC, but also with stress-inducible factors or oncogenic signaling cascades to regulate metabolic reprogramming towards glycolysis, the pentose phosphate pathway, and lipogenesis. Concurrently, one-carbon metabolism supplies methyl groups to histone and DNA methyltransferases, leading to the hypermethylation and silencing of suppressor genes in BC. Conversely, α-KG and acetyl-CoA enhance the activity of histone demethylases and acetyl transferases, increasing gene expression, while succinate and fumarate have an inhibitory role. This review is the first to analyze the interplay between epigenome, metabolome and cell signaling pathways in BC, and shows how their regulation contributes to tumor development and progression. Moreover, it summarizes non-invasive biomarkers that could be applied in clinical practice to improve diagnosis, monitoring, prognosis and the therapeutic options in BC.
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Affiliation(s)
- Alba Loras
- Unidad Mixta de Investigación en TICs Aplicadas a la Reingeniería de Procesos Socio-Sanitarios (eRPSS), Universitat Politècnica de València-Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
| | - Cristina Segovia
- Epithelial Carcinogenesis Group, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - José Luis Ruiz-Cerdá
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València-Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
- Servicio de Urología, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Departamento de Cirugía, Facultad de Medicina y Odontología, Universitat de València, 46010 Valencia, Spain
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18
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Crabb SJ, Danson S, Catto JWF, Hussain S, Chan D, Dunkley D, Downs N, Marwood E, Day L, Saunders G, Light M, Whitehead A, Ellis D, Sarwar N, Enting D, Birtle A, Johnson B, Huddart R, Griffiths G. Phase I Trial of DNA Methyltransferase Inhibitor Guadecitabine Combined with Cisplatin and Gemcitabine for Solid Malignancies Including Urothelial Carcinoma (SPIRE). Clin Cancer Res 2021; 27:1882-1892. [PMID: 33472913 PMCID: PMC7611191 DOI: 10.1158/1078-0432.ccr-20-3946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 01/02/2023]
Abstract
PURPOSE Preclinical data indicate that DNA methyltransferase inhibition will circumvent cisplatin resistance in various cancers. PATIENT AND METHODS SPIRE comprised a dose-escalation phase for incurable metastatic solid cancers, followed by a randomized dose expansion phase for neoadjuvant treatment of T2-4a N0 M0 bladder urothelial carcinoma. The primary objective was a recommended phase II dose (RP2D) for guadecitabine combined with gemcitabine and cisplatin. Treatment comprised 21-day gemcitabine and cisplatin cycles (cisplatin 70 mg/m2, i.v., day 8 and gemcitabine 1,000 mg/m2, i.v., days 8 + 15). Guadecitabine was injected subcutaneously on days 1-5, within escalation phase cohorts, and to half of 20 patients in the expansion phase. Registration ID: ISRCTN 16332228. RESULTS Within the escalation phase, dose-limiting toxicities related predominantly to myelosuppression requiring G-CSF prophylaxis from cohort 2 (guadecitabine 20 mg/m2, days 1-5). The most common grade ≥3 adverse events in 17 patients in the dose-escalation phase were neutropenia (76.5%), thrombocytopenia (64.7%), leukopenia (29.4%), and anemia (29.4%). Addition of guadecitabine to gemcitabine and cisplatin in the expansion phase resulted in similar rates of severe hematologic adverse events, similar cisplatin dose intensity, but modestly reduced gemcitabine dose intensity. Radical treatment options after chemotherapy were not compromised. Pharmacodynamics evaluations indicated guadecitabine maximal target effect at the point of cisplatin administration. Pharmacokinetics were consistent with prior data. No treatment-related deaths occurred. CONCLUSIONS The guadecitabine RP2D was 20 mg/m2, days 1-5, in combination with gemcitabine and cisplatin and required GCSF prophylaxis. Gene promoter methylation pharmacodynamics are optimal with this schedule. Addition of guadecitabine to gemcitabine and cisplatin was tolerable, despite some additional myelosuppression, and warrants further investigation to assess efficacy.
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Affiliation(s)
- Simon J Crabb
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom.
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
- Southampton Experimental Cancer Medicine Centre, University of Southampton, Southampton, England, United Kingdom
| | - Sarah Danson
- Sheffield Experimental Cancer Medicine Centre, Weston Park Hospital, University of Sheffield, Sheffield, England, United Kingdom
| | - James W F Catto
- Academic Urology Unit, University of Sheffield, Sheffield, England, United Kingdom
| | - Syed Hussain
- Sheffield Experimental Cancer Medicine Centre, Weston Park Hospital, University of Sheffield, Sheffield, England, United Kingdom
| | - Danna Chan
- Astex Pharmaceuticals, Inc., Pleasanton, California
| | - Denise Dunkley
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
- Southampton Experimental Cancer Medicine Centre, University of Southampton, Southampton, England, United Kingdom
| | - Nichola Downs
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Ellice Marwood
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Laura Day
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Geoff Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Michelle Light
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Amy Whitehead
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Deborah Ellis
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Naveed Sarwar
- Department of Oncology, Charing Cross Hospital, London, England, United Kingdom
| | - Deborah Enting
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, England, United Kingdom
| | - Alison Birtle
- Lancashire Teaching Hospitals NHS Foundation Trust, Preston, England, United Kingdom
| | | | - Robert Huddart
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
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19
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Hayashi Y, Fujita K. Toward urinary cell-free DNA-based treatment of urothelial carcinoma: a narrative review. Transl Androl Urol 2021; 10:1865-1877. [PMID: 33968675 PMCID: PMC8100839 DOI: 10.21037/tau-20-1259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsy technique targeting urinary cell-free DNA (cfDNA) is getting a lot of attention to overcome limitations of the present treatment strategy for urothelial carcinoma, including urothelial bladder carcinoma (UBC) and upper tract urothelial carcinoma (UTUC). Analysis of tumor-derived DNA in urine focusing either on genomic or epigenomic alterations, holds great potential as a noninvasive method for the detection of urothelial carcinoma with high accuracy. It is also predictive of prognosis and response to drugs, and reveals the underlying characteristics of different stages of urothelial carcinoma. Although cfDNA methylation analyses based on a combination of several methylation profiles have demonstrated high sensitivity for UBC diagnosis, there have been few reports involving epigenomic studies of urinary cfDNA. In mutational analyses, frequent gene mutations (TERT promoter, TP53, FGFR3, PIK3CA, RAS, etc.) have been detected in urine supernatant by using remarkable technological innovations such as next-generation sequencing and droplet digital PCR. These methods allow highly sensitive detection of rare mutation alleles while minimizing artifacts. In this review, we summarize the current insights into the clinical applications of urinary cfDNA from patients with urothelial carcinoma. Although it is necessary to conduct prospective multi-institutional clinical trials, noninvasive urine biopsy is expected to play an important role in the realization of precision medicine in patients with urothelial carcinoma in the near future.
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Affiliation(s)
- Yujiro Hayashi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazutoshi Fujita
- Department of Urology, Kindai University Faculty of Medicine, Osakasayama, Japan
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20
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Tripathi K, Goel A, Singhai A, Garg M. Promoter hypomethylation as potential confounder of Ras gene overexpression and their clinical significance in subsets of urothelial carcinoma of bladder. Mol Biol Rep 2021; 48:2183-2199. [PMID: 33620658 DOI: 10.1007/s11033-021-06227-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/10/2021] [Indexed: 12/31/2022]
Abstract
Overexpression of normal Ras and its aberrant CpG island methylation in the promoter regions have been shown to direct cells for uncontrolled abnormal growth and bladder tumor formation and therefore, fetched recent attention as a marker of diagnosis and prognosis to predict the biological behavior of urothelial carcinoma of bladder (UCB). Methylation pattern at CpG islands of the promoter regions of rat sarcoma (Ras) gene homologues namely Kristen-Ras (K-Ras), Harvey (H-Ras), and Neuroblastoma (N-Ras) were examined by methylation specific polymerase chain reaction (MSP). Real time-quantitative polymerase chain reaction (RT-qPCR) was done to determine transcriptomic expressions of these Ras isoforms in the prospective series of 42 NMIBC (non-muscle invasive bladder cancer) and 45 MIBC (muscle invasive bladder cancer) biopsies. CpG loci in H-Ras and K-Ras were observed to be more hypomethylated in MIBC, whereas more hypomethylation in N-Ras was noted in NMIBC. Strong association of hypomethylation index with tumor stage, grade, type and size validate them it as marker of diagnosis in UCB patients. Differential overexpression of H-Ras, N-Ras and K-Ras genes in NMIBC and MIBC and their association with patients' demographics identify them as important diagnostic markers in pathogenesis of UCB. Given the reported ability of promoter hypomethylation to activate Ras expression, correlation studies examined positive significant association between hypomethylation index and expression. Study concludes that promoter hypomethylation of N-Ras and K-Ras could be a potential confounder of their increased expression in NMIBC. Biological significance of simultaneous presence of higher expression and promoter hypomethylation of Ras gene isoforms in MIBC is difficult to resolve in a given cohort of patients.
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Affiliation(s)
- Kiran Tripathi
- Department of Biochemistry, University of Lucknow, Lucknow, 226007, India
| | - Apul Goel
- Department of Urology, King George Medical University, Lucknow, 226003, India
| | - Atin Singhai
- Department of Pathology, King George Medical University, Lucknow, 226003, India
| | - Minal Garg
- Department of Biochemistry, University of Lucknow, Lucknow, 226007, India.
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21
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Xu Z, Gujar H, Fu G, Ahmadi H, Bhanvadia S, Weisenberger DJ, Jin B, Gill PS, Gill I, Daneshmand S, Siegmund KD, Liang G. A Novel DNA Methylation Signature as an Independent Prognostic Factor in Muscle-Invasive Bladder Cancer. Front Oncol 2021; 11:614927. [PMID: 33659216 PMCID: PMC7917237 DOI: 10.3389/fonc.2021.614927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Background Muscle-invasive bladder cancer (MIBC) accounts for approximately 20% of all urothelial bladder carcinomas (UBC) at time of diagnosis, and up to 30% of patients with non-muscle invasive UBC will progress to MIBC over time. An increasing body of evidence has revealed a strong correlation between aberrant DNA methylation and tumorigenesis in MIBC. Results Using The Cancer Genome Atlas (TCGA) molecular data for 413 patients, we described a DNA methylation-based signature as a prognostic factor for overall survival (OS) in MIBC patients. By using a least absolute shrinkage and selection operator (LASSO) model, differentially methylated regions were first identified using multiple criteria followed by survival and LASSO analyses to identify DNA methylation probes related to OS and build a classifier to stratify patients with MIBC. The prognostic value of the classifier, referred to as risk score (RS), was validated in a held-out testing set from the TCGA MIBC cohort. Finally, receiver operating characteristic (ROC) analysis was used to compare the prognostic accuracy of the models built with RS alone, RS plus clinicopathologic features, and clinicopathologic features alone. We found that our seven-probe classifier-based RS stratifies patients into high- and low-risk groups for overall survival (OS) in the testing set (n = 137) (AUC at 3 years, 0.65; AUC at 5 years, 0.65). In addition, RS significantly improved the prognostic model when it was combined with clinical information including age, smoking status, Tumor (T) stage, and Lymph node metastasis (N) stage. Conclusions The DNA methylation-based RS can be a useful tool to predict the accuracy of preoperative and/or post-cystectomy models of OS in MIBC patients.
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Affiliation(s)
- Zhijie Xu
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Hemant Gujar
- USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Guanghou Fu
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Hamed Ahmadi
- USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sumeet Bhanvadia
- USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Baiye Jin
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Parkash S Gill
- Division of Hematology in Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Inderbir Gill
- USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Siamak Daneshmand
- USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Kimberly D Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Gangning Liang
- USC Institute of Urology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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22
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Su X, Lu X, Bazai SK, Compérat E, Mouawad R, Yao H, Rouprêt M, Spano JP, Khayat D, Davidson I, Tannir NN, Yan F, Malouf GG. Comprehensive integrative profiling of upper tract urothelial carcinomas. Genome Biol 2021; 22:7. [PMID: 33397444 PMCID: PMC7780630 DOI: 10.1186/s13059-020-02230-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Crosstalk between genetic, epigenetic, and immune alterations in upper tract urothelial carcinomas and their role in shaping muscle invasiveness and patient outcome are poorly understood. RESULTS We perform an integrative genome- and methylome-wide profiling of diverse non-muscle-invasive and muscle-invasive upper tract urothelial carcinomas. In addition to mutations of FGFR3 and KDM6A, we identify ZFP36L1 as a novel, significantly mutated tumor suppressor gene. Overall, mutations of ZFP36 family genes (ZFP36, ZFP36L1, and ZFP36L2) are identified in 26.7% of cases, which display a high mutational load. Unsupervised DNA methylation subtype classification identifies two epi-clusters associated with distinct muscle-invasive status and patient outcome, namely, EpiC-low and EpiC-high. While the former is hypomethylated, immune-depleted, and enriched for FGFR3-mutated, the latter is hypermethylated, immune-infiltrated, and tightly associated with somatic mutations of SWI/SNF genes. CONCLUSIONS Our study delineates for the first time the key role for convergence between genetic and epigenetic alterations in shaping clinicopathological and immune upper tract urothelial carcinoma features.
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Affiliation(s)
- Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaofan Lu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Sehrish Khan Bazai
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Eva Compérat
- Department of Pathology, GRC No. 5, Predictive Onco Uro, AP-HP, Hôpital Tenon, Sorbonne University, Paris, France
| | - Roger Mouawad
- Department of Medical Oncology, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Morgan Rouprêt
- Department of Urology, GRC No. 5, Predictive Onco Uro, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Jean-Philippe Spano
- Department of Medical Oncology, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - David Khayat
- Department of Medical Oncology, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Irwin Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Nizar N Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fangrong Yan
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Gabriel G Malouf
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France.
- Department of Medical Oncology, Institut de Cancérologie de Strasbourg-Europe, Strasbourg, France.
- Centre Hospitalier Régional Universitaire de Strasbourg, Strasbourg, France.
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23
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24
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DNA Methylation as a Therapeutic Target for Bladder Cancer. Cells 2020; 9:cells9081850. [PMID: 32784599 PMCID: PMC7463638 DOI: 10.3390/cells9081850] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Bladder cancer (BC) is the tenth most frequent cancer worldwide and is associated with high mortality when diagnosed in its most aggressive form, which is not reverted by the current treatment options. Thus, the development of new therapeutic strategies, either alternative or complementary to the current ones, is of major importance. The disruption of normal epigenetic mechanisms, namely, DNA methylation, is a known early event in cancer development. Consequently, DNA methyltransferase (DNMT) inhibitors constitute a promising therapeutic target for the treatment of BC. Although these inhibitors, mainly nucleoside analogues such as 5-azacytidine (5-aza) and decitabine (DAC), cause re-expression of tumor suppressor genes, inhibition of tumor cell growth, and increased apoptosis in BC experimental models and clinical trials, they also show important drawbacks that prevent their use as a valuable option for the treatment of BC. However, their combination with chemotherapy and/or immune-checkpoint inhibitors could aid in their implementation in the clinical practice. Here, we provide a comprehensive review of the studies exploring the effects of DNA methylation inhibition using DNMTs inhibitors in BC, from in vitro and in vivo studies to clinical trials.
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25
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Lozano F, Raventos CX, Carrion A, Trilla E, Morote J. Current status of genetic urinary biomarkers for surveillance of non-muscle invasive bladder cancer: a systematic review. BMC Urol 2020; 20:99. [PMID: 32664878 PMCID: PMC7362437 DOI: 10.1186/s12894-020-00670-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/08/2020] [Indexed: 01/22/2023] Open
Abstract
Background Genetic biomarkers are a promising and growing field in the management of bladder cancer in all stages. The aim of this paper is to understand the role of genetic urinary biomarkers in the follow up of patients with non muscle invasive bladder cancer where there is increasing evidence that they can play a role in avoiding invasive techniques. Methods Following PRISMA criteria, we have performed a systematic review. The search yielded 164 unique articles, of which 21 articles were included involving a total of 7261 patients. Sixteen of the articles were DNA based biomarkers, analyzing different methylations, microsatellite aberrations and gene mutations. Five articles studied the role of RNA based biomarkers, based on measuring levels of different combinations of mRNA. QUADAS2 critical evaluation of each paper has been reported. Results There are not randomized control trials comparing any biomarker with the gold standard follow-up, and the level of evidence is 2B in almost all the studies. Negative predictive value varies between 55 and 98.5%, being superior in RNA based biomarkers. Conclusions Although cystoscopy and cytology are the gold standard for non muscle invasive bladder cancer surveillance, genetic urinary biomarkers are a promising tool to avoid invasive explorations to the patients with a safe profile of similar sensitivity and negative predictive value. The accuracy that genetic biomarkers can offer should be taken into account to modify the paradigm of surveillance in non muscle invasive bladder cancer patients, especially in high-risk ones where many invasive explorations are recommended and biomarkers experiment better results.
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Affiliation(s)
- F Lozano
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain. .,Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - C X Raventos
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - A Carrion
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - E Trilla
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - J Morote
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
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26
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Yang L, Zhang J, Yang G, Xu H, Lin J, Shao L, Li J, Guo C, Du Y, Guo L, Li X, Han-Zhang H, Wang C, Chuai S, Ye J, Kang Q, Liu H, Ying J, Wang Y. The prognostic value of a Methylome-based Malignancy Density Scoring System to predict recurrence risk in early-stage Lung Adenocarcinoma. Theranostics 2020; 10:7635-7644. [PMID: 32685009 PMCID: PMC7359091 DOI: 10.7150/thno.44229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Current NCCN guidelines do not recommend the use of adjuvant chemotherapy for stage IA lung adenocarcinoma patients with R0 surgery. However, 25% to 40% of patients with stage IA disease experience recurrence. Stratifying patients according to the recurrence risk may tailor adjuvant therapy and surveillance imaging for those with a higher risk. However, prognostic markers are often identified by comparing high-risk and low-risk cases which might introduce bias due to the widespread interpatient heterogeneity. Here, we developed a scoring system quantifying the degree of field cancerization in adjacent normal tissues and revealed its association with disease-free survival (DFS). Methods: We recruited a cohort of 44 patients with resected stage IA lung adenocarcinoma who did not receive adjuvant therapy. Both tumor and adjacent normal tissues were obtained from each patient and subjected to capture-based targeted genomic and epigenomic profiling. A novel methylome-based scoring system namely malignancy density ratio (MD ratio) was developed based on 39 patients by comparing tumor and corresponding adjacent normal tissues of each patient. A MD score was then obtained by Wald statistics. The correlations of MD ratio, MD score, and genomic features with clinical outcome were investigated. Results: Patients with a high-risk MD ratio showed a significantly shorter postsurgical DFS compared with those with a low-risk MD ratio (HR=4.47, P=0.01). The MD ratio was not associated with T stage (P=1), tumor cell fraction (P=0.748) nor inflammatory status (p=0.548). Patients with a high-risk MD score also demonstrated an inferior DFS (HR=4.69, P=0.039). In addition, multivariate analysis revealed EGFR 19 del (HR=5.39, P=0.012) and MD score (HR= 7.90, P=0.01) were independent prognostic markers. Conclusion: The novel methylome-based scoring system, developed by comparing the signatures between tumor and corresponding adjacent normal tissues of individual patients, largely minimizes the bias of interpatient heterogeneity and reveals a robust prognostic value in patients with resected lung adenocarcinoma.
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27
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Tian Z, Meng L, Long X, Diao T, Hu M, Wang M, Liu M, Wang J. DNA methylation-based classification and identification of bladder cancer prognosis-associated subgroups. Cancer Cell Int 2020; 20:255. [PMID: 32565739 PMCID: PMC7302382 DOI: 10.1186/s12935-020-01345-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Bladder cancer (BCA) is the most common urinary tumor, but its pathogenesis is unclear, and the associated treatment strategy has rarely been updated. In recent years, a deeper understanding of tumor epigenetics has been gained, providing new opportunities for cancer detection and treatment. METHODS We identified prognostic methylation sites based on DNA methylation profiles of BCA in the TCGA database and constructed a specific prognostic subgroup. RESULTS Based on the consistent clustering of 402 CpGs, we identified seven subgroups that had a significant association with survival. The difference in DNA methylation levels was related to T stage, N stage, M stage, grade, sex, age, stage and prognosis. Finally, the prediction model was constructed using a Cox regression model and verified using the test dataset; the prognosis was consistent with that of the training set. CONCLUSIONS The classification based on DNA methylation is closely related to the clinicopathological characteristics of BCA and determines the prognostic value of each epigenetic subtype. Therefore, our findings provide a basis for the development of DNA methylation subtype-specific therapeutic strategies for human bladder cancer.
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Affiliation(s)
- Zijian Tian
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730 China
| | - Lingfeng Meng
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730 China
| | - Xingbo Long
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
| | - Tongxiang Diao
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
| | - Maolin Hu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
| | - Miao Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730 China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730 China
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28
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Abstract
PURPOSE OF REVIEW Molecular characterization of cancer allows us to understand oncogenesis and clinical prognosis as well as facilitates development of biomarkers and treatment. Our aim was to review the current literature on genomic characterization of bladder cancer, and how far we are in implementing genomics into clinical practice. RECENT FINDINGS Bladder cancers are molecularly diverse tumors with a high mutational rate. On molecular level, bladder cancer can be categorized into at least six subtypes called luminal-papillary, luminal-unstable, luminal non-specified, basal-squamous, neuroendocrine-like, and stroma-rich. These subtypes have characteristic genomic and transcriptomic profiles and appear to have different prognoses. Several molecular subtypes have been identified in bladder cancer. Prospective trials are underway to validate the applicability of genomic subtypes for clinical decision making. Further integrative analyses of genomic alterations, gene expression, epigenetics, and proteomics need to be performed before genomic subtyping can be attained in clinical practice.
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Affiliation(s)
- Tuomas Jalanko
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada.,Department of Urology, Helsinki University, Helsinki, Finland
| | - Joep J de Jong
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Roland Seiler
- Department of Urology, University of Bern, Bern, Switzerland
| | - Peter C Black
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada.
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29
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Xu T, Li HT, Wei J, Li M, Hsieh TC, Lu YT, Lakshminarasimhan R, Xu R, Hodara E, Morrison G, Gujar H, Rhie SK, Siegmund K, Liang G, Goldkorn A. Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype. Int J Cancer 2020; 146:3065-3076. [PMID: 32017074 DOI: 10.1002/ijc.32904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
Abstract
Highly tumorigenic, drug-resistant cancer stem-like cells drive cancer progression. These aggressive cells can arise repeatedly from bulk tumor cells independently of mutational events, suggesting an epigenetic mechanism. To test this possibility, we studied bladder cancer cells as they cyclically shifted to and from a cancer stem-like phenotype, and we discovered that these two states exhibit distinct DNA methylation and chromatin accessibility. Most differential chromatin accessibility was independent of methylation and affected the expression of driver genes such as E2F3, a cell cycle regulator associated with aggressive bladder cancer. Cancer stem-like cells exhibited increased E2F3 promoter accessibility and increased E2F3 expression that drove cell migration, invasiveness and drug resistance. Epigenetic interference using a DNA methylation inhibitor blocked the transition to a cancer stem-like state and reduced E2F3 expression. Our findings indicate that epigenetic plasticity plays a key role in the transition to and from an aggressive, drug-resistant phenotype.
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Affiliation(s)
- Tong Xu
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Hong-Tao Li
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jenny Wei
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Meng Li
- Norris Bioinformatics Core, Health Sciences Libraries, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Tien-Chan Hsieh
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Yi-Tsung Lu
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Rong Xu
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Emmanuelle Hodara
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Gareth Morrison
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Hemant Gujar
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Kimberly Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
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30
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Zhang C, Shen K, Zheng Y, Qi F, Luo J. Genome-wide screening of abberant methylated drivers combined with relative risk loci in bladder cancer. Cancer Med 2019; 9:768-782. [PMID: 31794632 PMCID: PMC6970050 DOI: 10.1002/cam4.2665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022] Open
Abstract
Background To explore important methylation‐driven genes (MDGs) and risk loci to construct risk model for prognosis of bladder cancer (BCa). Methods We utilized TCGA‐Assembler package to download 450K methylation data and corresponding transcriptome profiles. MethylMix package was used for identifying methylation‐driven genes and functional analysis was mainly performed based on ConsensusPathDB database. Then, Cox regression method was utilized to find prognostic MDGs, and we selected 17 hub genes via stepwise regression and multivariate Cox models. Kruskal‐Wallis test was implemented for comparisons between risk with other clinical variables. Moreover, we constructed the risk model and validated it in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507. Gene set enrichment analysis was performed using the levels of risk score as the phenotype. Additionally, we further screened out the relative methylation sites associated with the 17 hub genes. Cox regression and Survival analysis were conducted to find the specifically prognostic sites. Results Two hundred and twenty‐eight MDGs were chosen by ConsensusPathDB database. Results revealed that most conspicuous pathways were transcriptional mis‐regulation pathways in cancer and EMT. After Cox regression analysis, 17 hub epigenetic MDGs were identified. We calculated the risk score and found satisfactory predictive efficiency by ROC curve (AUC = 0.762). In the validation group from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507, 17 hub genes remained higher predictive value with AUC = 0.723 and patients in high‐risk group. Meanwhile, Kruskal‐Wallis test revealed that higher risk score correlated with a higher level of TNM stage, tumor grade, and advanced pathological stages. Then, identified 38 risk methylated loci that highly associated with prognosis. Last, gene set enrichment analysis revealed that high‐risk level of MDGs may correlate with several important pathways, including MAPK signaling pathway and so on. Conclusion Our study indicated several hub‐MDGs, calculated novel risk score and explored the prognostic value in BCa, which provided a promising approach to BCA prognosis assessment.
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Affiliation(s)
- Chuanjie Zhang
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Kangjie Shen
- First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yuxiao Zheng
- Department of Urology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Qi
- Department of Urology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Luo
- Department of Urology, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, China
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31
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Yang B, Etheridge T, McCormick J, Schultz A, Khemees TA, Damaschke N, Leverson G, Woo K, Sonn GA, Klein EA, Fumo M, Huang W, Jarrard DF. Validation of an epigenetic field of susceptibility to detect significant prostate cancer from non-tumor biopsies. Clin Epigenetics 2019; 11:168. [PMID: 31779677 PMCID: PMC6883627 DOI: 10.1186/s13148-019-0771-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
Background An epigenetic field of cancer susceptibility exists for prostate cancer (PC) that gives rise to multifocal disease in the peripheral prostate. In previous work, genome-wide DNA methylation profiling identified altered regions in the normal prostate tissue of men with PC. In the current multicenter study, we examined the predictive strength of a panel of loci to detect cancer presence and grade in patients with negative biopsy tissue. Results Four centers contributed benign prostate biopsy tissues blocks from 129 subjects that were either tumor associated (TA, Grade Group [GG] ≥ 2, n = 77) or non-tumor associated (NTA, n = 52). Biopsies were analyzed using pyrosequencing for DNA methylation encompassing CpG loci near CAV1, EVX1, FGF1, NCR2, PLA2G16, and SPAG4 and methylation differences were detected within all gene regions (p < 0.05). A multiplex regression model for biomarker performance incorporating a gene combination discriminated TA from NTA tissues (area under the curve [AUC] 0.747, p = 0.004). A multiplex model incorporating all the above genes and clinical information (PSA, age) identified patients with GG ≥ 2 PC (AUC 0.815, p < 0.0001). In patients with cancer, increased variation in gene methylation levels occurs between biopsies across the prostate. Conclusions A widespread epigenetic field defect is utilized to detect GG ≥ 2 PC in patients with histologically negative biopsies. These alterations in non-tumor cells display increased heterogeneity of methylation extent and are spatially distant from tumor foci. These findings have the potential to decrease the need for repeated prostate biopsy.
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Affiliation(s)
- Bing Yang
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Tyler Etheridge
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Johnathon McCormick
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Adam Schultz
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Tariq A Khemees
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA.,Department of Urology, University of Wisconsin, Madison, WI, 53705, USA
| | - Nathan Damaschke
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Glen Leverson
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Kaitlin Woo
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | | | - Eric A Klein
- Cleveland Clinic, Glickman Urological and Kidney Institute, Cleveland, OH, USA
| | - Mike Fumo
- Rockford Urologic, Rockford, IL, USA
| | - Wei Huang
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA.,Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, WI, 53705, USA
| | - David F Jarrard
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA. .,Department of Urology, University of Wisconsin, Madison, WI, 53705, USA. .,Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, WI, 53705, USA. .,Molecular and Environmental Toxicology Program, University of Wisconsin, Madison, WI, 53705, USA.
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32
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Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M, Paramio JM. Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet. Front Genet 2019; 10:1125. [PMID: 31850055 PMCID: PMC6902278 DOI: 10.3389/fgene.2019.01125] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is the most common neoplasia of the urothelial tract. Due to its high incidence, prevalence, recurrence and mortality, it remains an unsolved clinical and social problem. The treatment of BC is challenging and, although immunotherapies have revealed potential benefit in a percentage of patients, it remains mostly an incurable disease at its advanced state. Epigenetic alterations, including aberrant DNA methylation, altered chromatin remodeling and deregulated expression of non-coding RNAs are common events in BC and can be driver events in BC pathogenesis. Accordingly, these epigenetic alterations are now being used as potential biomarkers for these disorders and are being envisioned as potential therapeutic targets for the future management of BC. In this review, we summarize the recent findings in these emerging and exciting new aspects paving the way for future clinical treatment of this disease.
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Affiliation(s)
- Victor G. Martinez
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Ester Munera-Maravilla
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandra Bernardini
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carolina Rubio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristian Suarez-Cabrera
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Cristina Segovia
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Iris Lodewijk
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Marta Dueñas
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mónica Martínez-Fernández
- Genomes & Disease Lab, CiMUS (Center for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesus Maria Paramio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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33
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Gkountela S, Castro-Giner F, Szczerba BM, Vetter M, Landin J, Scherrer R, Krol I, Scheidmann MC, Beisel C, Stirnimann CU, Kurzeder C, Heinzelmann-Schwarz V, Rochlitz C, Weber WP, Aceto N. Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding. Cell 2019; 176:98-112.e14. [PMID: 30633912 PMCID: PMC6363966 DOI: 10.1016/j.cell.2018.11.046] [Citation(s) in RCA: 516] [Impact Index Per Article: 103.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/31/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023]
Abstract
The ability of circulating tumor cells (CTCs) to form clusters has been linked to increased metastatic potential. Yet biological features and vulnerabilities of CTC clusters remain largely unknown. Here, we profile the DNA methylation landscape of single CTCs and CTC clusters from breast cancer patients and mouse models on a genome-wide scale. We find that binding sites for stemness- and proliferation-associated transcription factors are specifically hypomethylated in CTC clusters, including binding sites for OCT4, NANOG, SOX2, and SIN3A, paralleling embryonic stem cell biology. Among 2,486 FDA-approved compounds, we identify Na+/K+ ATPase inhibitors that enable the dissociation of CTC clusters into single cells, leading to DNA methylation remodeling at critical sites and metastasis suppression. Thus, our results link CTC clustering to specific changes in DNA methylation that promote stemness and metastasis and point to cluster-targeting compounds to suppress the spread of cancer.
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Affiliation(s)
- Sofia Gkountela
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Francesc Castro-Giner
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Barbara Maria Szczerba
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Marcus Vetter
- Gynecologic Cancer Center, University Hospital Basel, 4056 Basel, Switzerland; Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland
| | - Julia Landin
- Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland; Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Ramona Scherrer
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Ilona Krol
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Manuel C Scheidmann
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Christian Kurzeder
- Gynecologic Cancer Center, University Hospital Basel, 4056 Basel, Switzerland; Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | | | - Christoph Rochlitz
- Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland
| | - Walter Paul Weber
- Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Nicola Aceto
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
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Vrieling A, Bueno‐De‐Mesquita HB, Ros MM, Kampman E, Aben KK, Büchner FL, Jansen EH, Roswall N, Tjønneland A, Boutron‐Ruault M, Cadeau C, Chang‐Claude J, Kaaks R, Weikert S, Boeing H, Trichopoulou A, Lagiou P, Trichopoulos D, Sieri S, Palli D, Panico S, Peeters PH, Weiderpass E, Skeie G, Jakszyn P, Chirlaque M, Ardanaz E, Sánchez M, Ehrnström R, Malm J, Ljungberg B, Khaw K, Wareham NJ, Brennan P, Johansson M, Riboli E, Kiemeney LA. One-carbon metabolism biomarkers and risk of urothelial cell carcinoma in the European prospective investigation into cancer and nutrition. Int J Cancer 2019; 145:2349-2359. [PMID: 30694528 PMCID: PMC6899898 DOI: 10.1002/ijc.32165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/24/2018] [Accepted: 01/04/2019] [Indexed: 01/10/2023]
Abstract
Published associations between dietary folate and bladder cancer risk are inconsistent. Biomarkers may provide more accurate measures of nutrient status. This nested case-control analysis within the European Prospective Investigation into Cancer and Nutrition (EPIC) investigated associations between pre-diagnostic serum folate, homocysteine, vitamins B6 and B12 and the risk of urothelial cell carcinomas of the bladder (UCC). A total of 824 patients with newly diagnosed UCC were matched with 824 cohort members. Serum folate, homocysteine, and vitamins B6 and B12 were measured. Odds ratios (OR) and 95% confidence intervals (CI) for total, aggressive, and non-aggressive UCC were estimated using conditional logistic regression with adjustment for smoking status, smoking duration and intensity, and other potential confounders. Additionally, statistical interaction with smoking status was assessed. A halving in serum folate concentrations was moderately associated with risk of UCC (OR: 1.18; 95% CI: 0.98-1.43), in particular aggressive UCC (OR: 1.34; 95% CI: 1.02-1.75; p-heterogeneity = 0.19). Compared to never smokers in the highest quartile of folate concentrations, this association seemed only apparent among current smokers in the lowest quartile of folate concentrations (OR: 6.26; 95% CI: 3.62-10.81, p-interaction = 0.07). Dietary folate was not associated with aggressive UCC (OR: 1.26; 95% CI: 0.81-1.95; p-heterogeneity = 0.14). No association was observed between serum homocysteine, vitamins B6 and B12 and risk of UCC. This study suggests that lower serum folate concentrations are associated with increased UCC risk, in particular aggressive UCC. Residual confounding by smoking cannot be ruled out and these findings require confirmation in future studies with multiple measurements.
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Affiliation(s)
- Alina Vrieling
- Radboud University Medical CenterRadboud Institute for Health SciencesNijmegenThe Netherlands
| | - H. Bas Bueno‐De‐Mesquita
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of MedicineImperial College LondonLondonUnited Kingdom
- Department of Gastroenterology and HepatologyUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of Social & Preventive Medicine, Faculty of MedicineUniversity of MalayaKuala LumpurMalaysia
| | - Martine M. Ros
- Radboud University Medical CenterRadboud Institute for Health SciencesNijmegenThe Netherlands
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Ellen Kampman
- Radboud University Medical CenterRadboud Institute for Health SciencesNijmegenThe Netherlands
- Division of Human NutritionWageningen UniversityWageningenThe Netherlands
| | - Katja K. Aben
- Radboud University Medical CenterRadboud Institute for Health SciencesNijmegenThe Netherlands
- Netherlands Comprehensive Cancer OrganisationUtrechtThe Netherlands
| | - Frederike L. Büchner
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Eugène H. Jansen
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Nina Roswall
- Danish Cancer Society Research CenterCopenhagenDenmark
| | | | - Marie‐Christine Boutron‐Ruault
- Inserm, Center for Research in Epidemiology and Population Health (CESP), U1018, NutritionHormones and Women's Health teamVillejuifFrance
- Université of Paris‐SudVillejuifFrance
- IGRVillejufFrance
| | - Claire Cadeau
- Inserm, Center for Research in Epidemiology and Population Health (CESP), U1018, NutritionHormones and Women's Health teamVillejuifFrance
- Université of Paris‐SudVillejuifFrance
- IGRVillejufFrance
| | - Jenny Chang‐Claude
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)Germany
- Cancer Epidemiology GroupUniversity Medical Centre Hamburg‐Eppendorf, University Cancer Centre Hamburg (UCCH)HamburgGermany
| | - Rudolf Kaaks
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)Germany
| | - Steffen Weikert
- Department of EpidemiologyGerman Institute of Human NutritionNuthetalGermany
- Department of UrologyVivantes Humboldt HospitalBerlinGermany
| | - Heiner Boeing
- Department of EpidemiologyGerman Institute of Human NutritionNuthetalGermany
| | - Antonia Trichopoulou
- WHO Collaborating Center for Food and Nutrition Policies, Department of HygieneEpidemiology and Medical Statistics University of Athens Medical SchoolAthensGreece
- Hellenic Health FoundationAthensGreece
| | - Pagona Lagiou
- WHO Collaborating Center for Food and Nutrition Policies, Department of HygieneEpidemiology and Medical Statistics University of Athens Medical SchoolAthensGreece
- Department of EpidemiologyHarvard School of Public HealthBostonMA
- Bureau of Epidemiologic ResearchAcademy of AthensAthensGreece
| | - Dimitrios Trichopoulos
- Hellenic Health FoundationAthensGreece
- Department of EpidemiologyHarvard School of Public HealthBostonMA
- Bureau of Epidemiologic ResearchAcademy of AthensAthensGreece
| | - Sabina Sieri
- Epidemiology and Prevention UnitFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Domenico Palli
- Molecular and Nutritional Epidemiology UnitCancer and Prevention Institute (ISPO)FlorenceItaly
| | - Salvatore Panico
- Department of Clinical and Experimental MedicineFederico II University, Medical SchoolNaplesItaly
| | - Petra H. Peeters
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of MedicineImperial College LondonLondonUnited Kingdom
- Julius Center for Health Sciences and Primary CareUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health SciencesUniversity of Tromsø, The Artic University of NorwayTromsøNorway
- Department of ResearchCancer Registry of Norway – Institute of Population‐based Cancer ResearchOsloNorway
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Genetic Epidemiology Group, Folkhälsan Research Center and Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Guri Skeie
- Department of Community Medicine, Faculty of Health SciencesUniversity of Tromsø, The Artic University of NorwayTromsøNorway
| | - Paula Jakszyn
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research ProgrammeCatalan Institute of Oncology (ICO)BarcelonaSpain
| | - María‐Dolores Chirlaque
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER de Epidemiologia y Salud Pública)MadridSpain
- Department of Epidemiology, Murcia Health AuthorityIMIB‐Arrixaca. Murcia UniversitySpain
| | - Eva Ardanaz
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER de Epidemiologia y Salud Pública)MadridSpain
- Instituto de Salud Pública de Navarra, IdiSNAPamplonaSpain
| | - María‐José Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER de Epidemiologia y Salud Pública)MadridSpain
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADAHospitales Universitarios de Granada/Universidad de GranadaGranadaSpain
| | - Roy Ehrnström
- Laboratory Medicine, Department of PathologySkåne University Hospital MalmöMalmöSweden
| | - Johan Malm
- Department of Translational Medicine, Division of Clinical ChemistryLund UniversityMalmöSweden
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and AndrologyUmeå UniversityUmeåSweden
| | - Kay‐Tee Khaw
- Department of Public Health and Primary CareUniversity of CambridgeCambridgeUnited Kingdom
| | - Nick J. Wareham
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUnited Kingdom
| | - Paul Brennan
- Genetic Epidemiology GroupInternational Agency for Research on Cancer (IARC)LyonFrance
| | - Mattias Johansson
- Genetic Epidemiology GroupInternational Agency for Research on Cancer (IARC)LyonFrance
- Department of Biobank ResearchUmeå UniversityUmeåSweden
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of MedicineImperial College LondonLondonUnited Kingdom
| | - Lambertus A. Kiemeney
- Radboud University Medical CenterRadboud Institute for Health SciencesNijmegenThe Netherlands
- Department of UrologyRadboud University Medical CenterNijmegenThe Netherlands
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Zhang N, Chen S, Wu L, Wu Y, Jiang G, Shao J, Chen L, Sun J, Na R, Wang X, Xu J. Identification of Cancer-Specific Methylation of Gene Combination for the Diagnosis of Bladder Cancer. J Cancer 2019; 10:6761-6766. [PMID: 31777606 PMCID: PMC6856882 DOI: 10.7150/jca.28192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 05/27/2019] [Indexed: 01/30/2023] Open
Abstract
Here we conducted an evidence-based study in developing and validating a urinary biomarker combination of gene methylation assays in patients with hematuria. A number of 99 urine samples were obtained and detected from Chinese patients with hematuria. The Cancer Genome Atlas cohort with methylation (HM450) beta-values and clinical data of 412 bladder cancer and 21 matching normal tissue was included as a validation series. A risk score formula was then developed and calculated by the targeted genes, weighted by their estimated regression coefficients from the multivariable binary logistic regression analyses, and evaluated by receiver operating characteristic (ROC) curves analysis. The combination assay of HOXA9, ONECUT2, PCDH17, PENK, TWIST1, VIM and ZNF154 was singled out according to the results of multivariate logistic regression analysis. The higher probability of DNA methylation of all the selected 7 genes was found in bladder cancer group than the control group. Remarkable higher DNA methylation beta-values of all the selected 7 genes were also displayed in bladder cancer tissues compared with their matching normal bladder tissues. And the AUC value of our risk score model were 0.894 and 0.851 in respective cohort, revealing highlighted predictive value of our risk score model on bladder cancer diagnosis. In conclusions, a urinary combined methylation assay of HOXA9, ONECUT2, PCDH17, PENK, TWIST1, VIM and ZNF154 displayed accurate prediction of bladder cancer in hematuria patients, which provided the guidance for the patients at early stage tumor and during the follow-up after operation. Of course, prospective study based on a hematuria cohort with a large sample size should be conducted to validate these findings in the future.
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Affiliation(s)
- Ning Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siteng Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingfeng Wu
- Department of Urology, Songjiang District Central Hospital, Shanghai, China
| | - Yishuo Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Guangliang Jiang
- Department of Urology, Shengzhen Second People's Hospital, Guangdong, China
| | - Jialiang Shao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixin Chen
- Department of Urology, Songjiang District Central Hospital, Shanghai, China
| | - Jishan Sun
- Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201
| | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201
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High Detection Rate for Non-Muscle-Invasive Bladder Cancer Using an Approved DNA Methylation Signature Test. Clin Genitourin Cancer 2019; 18:210-221. [PMID: 32139301 DOI: 10.1016/j.clgc.2019.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/25/2019] [Accepted: 10/06/2019] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Cystoscopy and transurethral resection are the current reference standard tests to diagnose and histologically confirm non-muscle-invasive bladder cancer (NMIBC). In other tumor entities (ie, colon carcinoma, cervical cancer), DNA methylation markers have been approved as diagnostic tests with high diagnostic power. In our case-control study, we used an approved molecular cervical cancer diagnostics test that includes 6 DNA methylation markers (GynTect) for the detection of bladder cancer. PATIENTS AND METHODS We included samples from 40 patients with bladder cancer and 34 control subjects. In a pilot study, we analyzed DNA methylation in 38 tumor tissues and 4 healthy ureters using methylation-specific polymerase chain reaction. Subsequently, we determined the sensitivity and specificity of the GynTect for the detection of bladder cancer in urine sediments from 40 patients with bladder cancer and 30 control subjects with benign prostatic hyperplasia or urolithiasis. RESULTS The markers showed very different methylation rates in the NMIBC tissues, ranging from 2.6% to 78.9%. No methylation of any of the markers was detectable in the healthy ureters. Using the urine sediments from the patients with cancer and control subjects, we found surprisingly high sensitivity and specificity for the GynTect assay (60% and 96.7%, respectively). The application of different algorithms for evaluation of the markers included in GynTect resulted in a sensitivity of ≤ 90% and specificity of ≤ 100%. CONCLUSION The GynTect assay, originally designed for cervical cancer diagnostics, showed unexpectedly high diagnostic accuracy for bladder cancer detection. The inclusion of additional methylation markers might allow for the development of a suitable diagnostic marker set based on the GynTect test for NMIBC diagnostics.
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Epigenetic loss of AOX1 expression via EZH2 leads to metabolic deregulations and promotes bladder cancer progression. Oncogene 2019; 39:6265-6285. [PMID: 31383940 DOI: 10.1038/s41388-019-0902-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/24/2022]
Abstract
Advanced Bladder Cancer (BLCA) remains a clinical challenge that lacks effective therapeutic measures. Here, we show that distinct, stage-wise metabolic alterations in BLCA are associated with the loss of function of aldehyde oxidase (AOX1). AOX1 associated metabolites have a high predictive value for advanced BLCA and our findings demonstrate that AOX1 is epigenetically silenced during BLCA progression by the methyltransferase activity of EZH2. Knockdown (KD) of AOX1 in normal bladder epithelial cells re-wires the tryptophan-kynurenine pathway resulting in elevated NADP levels which may increase metabolic flux through the pentose phosphate (PPP) pathway, enabling increased nucleotide synthesis, and promoting cell invasion. Inhibition of NADP synthesis rescues the metabolic effects of AOX1 KD. Ectopic AOX1 expression decreases NADP production, PPP flux and nucleotide synthesis, while decreasing invasion in cell line models and suppressing growth in tumor xenografts. Further gain and loss of AOX1 confirm the EZH2-dependent activation, metabolic deregulation, and tumor growth in BLCA. Our findings highlight the therapeutic potential of AOX1 and provide a basis for the development of prognostic markers for advanced BLCA.
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Bunch B, Krishnan N, Greenspan RD, Ramakrishnan S, Attwood K, Yan L, Qi Q, Wang D, Morrison C, Omilian A, Bshara W, Pili R, Trump DL, Johnson C, Woloszynska A. TAp73 expression and P1 promoter methylation, a potential marker for chemoresponsiveness to cisplatin therapy and survival in muscle-invasive bladder cancer (MIBC). Cell Cycle 2019; 18:2055-2066. [PMID: 31318640 DOI: 10.1080/15384101.2019.1638693] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Intrinsic and/or acquired resistance to cisplatin is a significant obstacle in the treatment of muscle-invasive bladder cancer. p73, a p53 homolog and determinant of chemosensitivity, is rarely mutated in bladder cancer (BC). However p73 expression and therefore function can be repressed through epigenetic changes. In this study, we sought to identify DNA methylation status of p73, expression of TAp73 isoform, and their role in cisplatin sensitivity in BC. Primary tumor samples from 338 bladder cancer patients showed decreased TAp73 expression in MIBC compared to superficial BC. Low TAp73 protein expression was associated with shorter overall survival. To investigate if the loss of expression was methylation dependent, we utilized Illumina 450K methylation arrays to interrogate over 150 BC patient samples. We found 12 distinct CpGs in the p73 gene locus that were hypermethylated in tumors compared to adjacent normal tissues. Patients with high p73 promoter methylation specifically at CpG site cg07382920 had worse survival. In vitro, treatment with a DNA demethylating agent, decitabine (DAC), decreased TAp73 methylation and upregulated expression in both CR-T24 (cisplatin resistant T24 cells) and wild type T24 cells. Furthermore, treatment with DAC increased cisplatin response in wild type T24 and CR-T24. Our studies indicate that TAp73 expression and P1 promoter methylation, specifically at the cg073892920 site, may have prognostic and diagnostic value in MIBC. In the setting of P1 promoter hypermethylation, DAC could be used as a potentiating agent of cisplatin-based chemotherapy.
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Affiliation(s)
- Brittany Bunch
- a Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Nithya Krishnan
- a Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Rebecca D Greenspan
- a Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Swathi Ramakrishnan
- a Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Kristopher Attwood
- b Department of Bioinformatics and BioStatistics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Li Yan
- b Department of Bioinformatics and BioStatistics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Qianya Qi
- b Department of Bioinformatics and BioStatistics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Dan Wang
- b Department of Bioinformatics and BioStatistics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Carl Morrison
- c Department of Pathology, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Angela Omilian
- c Department of Pathology, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Wiam Bshara
- c Department of Pathology, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Roberto Pili
- d Department of Medicine, Indiana University , Buffalo , USA
| | - Donald L Trump
- e Inova Schar Cancer Institute , Falls Church , VA , USA
| | - Candace Johnson
- a Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
| | - Anna Woloszynska
- a Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center , Buffalo , USA
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Yang Z, Liu A, Xiong Q, Xue Y, Liu F, Zeng S, Zhang Z, Li Y, Sun Y, Xu C. Prognostic value of differentially methylated gene profiles in bladder cancer. J Cell Physiol 2019; 234:18763-18772. [PMID: 30953370 DOI: 10.1002/jcp.28515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 01/03/2023]
Abstract
DNA methylation can regulate gene expression and is pivotal in the occurrence and development of bladder cancer. In this study, we analyzed whole-genome DNA methylation on the basis of data from The Cancer Genome Atlas to select epigenetic biomarkers predictive of survival and further understand the molecular mechanisms underlying methylation patterns in bladder cancer. We identified 540 differentially methylated genes between tumor and normal tissues, including a number of independent prognostic factors based on univariate analysis. Genes (MIR6732, SOWAHC, SERPINI1, OR10W1, OR7G3, AIM1, and ZFAND5) were integrated to establish a risk model for prognostic assessment based on multivariate Cox analysis. The methylation of SOWAHC was negatively correlated with its messenger RNA expression, and together these were significantly correlated with prognosis. This study took advantage of high-throughput data mining to provide new bioinformatics evidence and ideas for further study into the pathogenesis and prognosis of bladder cancer.
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Affiliation(s)
- Zeyu Yang
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Anwei Liu
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Qiao Xiong
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Yongping Xue
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Fei Liu
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Shuxiong Zeng
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Zhensheng Zhang
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Yunfei Li
- Department of Urology, The Thrid Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yinghao Sun
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
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40
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Young FP, Ende D, Epstein RJ. Beyond BCG: the approaching era of personalised bladder-sparing therapies for non-muscle-invasive urothelial cancers. Future Oncol 2019; 15:409-420. [DOI: 10.2217/fon-2018-0565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Progress in the management of non-muscle invasive bladder cancer has been slow. Despite longstanding use of intravesical therapies (e.g., Bacille Calmette-Guerin; BCG) to complement cystoscopic resection of high-grade lesions, many patients still develop recurrences requiring cystectomy, while others suffer side-effects of BCG without definite benefit. Many questions remain: for example, how many patients receive intravesical prophylaxis without efficacy? Which high-risk patients are best managed with early cystectomy? Could systemic therapies and/or radiotherapy extend bladder preservation times? Such questions may soon be refined by clinicopathologic non-muscle invasive bladder cancer signatures that predict sensitivity to cytotoxic, immune and targeted therapies. Hypothesis-based trials using these signatures should lead to more rational adjuvant treatments, longer bladder preservation times, and better quality of life for patients.
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Affiliation(s)
- Francis P Young
- University of New South Wales Clinical School, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010, Sydney, Australia
| | - David Ende
- Department of Urologic Surgery, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010, Sydney, Australia
| | - Richard J Epstein
- University of New South Wales Clinical School, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010, Sydney, Australia
- The Kinghorn Cancer Centre, Clinical Informatics & Research Centre, St Vincent's Hospital, 370 Victoria St, Darlinghurst 2010, Sydney, Australia
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Abstract
PURPOSE OF REVIEW Bladder cancer (BC) is the second most common genitourinary malignancy, with a growing population of survivors globally. Over the past two decades, there has been a growing awareness of not only the oncologic, but also the quality of life ramifications of a BC diagnosis, treatment, and surveillance. In the current review, the literature surrounding the many domains that encompass bladder cancer survivorship is summarized and analyzed. RECENT FINDINGS There have been ongoing efforts to decrease perioperative morbidity, particularly in patients undergoing radical cystectomy, with mixed results. There is a growing emphasis on the short and long-term health-related quality of life (HR-QoL) impacts of bladder cancer spanning the domains of physical and mental QoL related to urinary function, sexual function, and financial and psychological burden, with validated measures specific to BC patients. There continue to be disparities in oncologic outcomes by race and gender. The impact of BC is prolonged and there is an unmet need for long term support and survivorship resources to address this. There is a growing global population of bladder cancer patients, and their needs are complex and vary by stage, treatment, and certain demographic features. Outcome-centered perioperative strategies show potential to diminish treatment morbidity, and validated BC specific HR-QoL tools have helped to define the impact and burden of BC, but there continue to be large areas of unmet need that warrant greater study and intervention.
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Affiliation(s)
- Sumeet K Bhanvadia
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, USC Institute of Urology, 1441 Eastlake Ave, Suite 7416, Los Angeles, CA, 90094, USA.
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Abstract
PURPOSE OF REVIEW Epigenetics refers to processes that alter gene expression without altering primary DNA. Over that past decade, there is a growing focus on epigenetic mechanisms in cancer research and its importance in cancer biology. This review summarizes epigenetic dysregulation in bladder cancer. RECENT FINDINGS Epigenetic alterations are overall shared across various grades and stages of bladder cancer. High grade invasive tumors demonstrate a greater degree and intensity of methylation and may have a unique methylation pattern. Environmental exposures may influence epigenetic alterations directly independent of genomic change. Non-coding RNAs play an important role in cancer phenotype, especially in the context of integrative genomic analyses. DNA hypermethylation and non-coding RNAs have potential as robust bladder cancer biomarkers; however, they require further study and validation. Changes in chromatin and histone modification are attractive targets for therapy and are currently in clinical trials. Epigenetic dysregulation may be an important key in improving the understanding of bladder cancer pathogenesis, especially through integrative genomic analyses. Deeper understanding of these pathways can help identify clinically relevant biomarkers and therapeutic targets to validate for diagnosis, monitoring, prognosis, and treatment for bladder cancer.
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Affiliation(s)
- Sima P Porten
- Department of Urology, University of California San Francisco (UCSF), Mailbox Code 1695, 550 16th Street, 6th Floor, San Francisco, CA, 94143, USA.
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Santoni G, Morelli MB, Amantini C, Battelli N. Urinary Markers in Bladder Cancer: An Update. Front Oncol 2018; 8:362. [PMID: 30245975 PMCID: PMC6137202 DOI: 10.3389/fonc.2018.00362] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is ones of the most common cancer worldwide. It is classified in muscle invasive (MIBC) and muscle non-invasive (NMIBC) BC. NMIBCs frequently recur and progress to MIBCs with a reduced survival rate and frequent distant metastasis. BC detection require unpleasant and expensive cystoscopy and biopsy, which are often accompanied by several adverse effects. Thus, there is an urgent need to develop novel diagnostic methods for initial detection and surveillance in both MIBCs and NMIBCs. Multiple urine-based tests approved by FDA for BC detection and surveillance are commercially available. However, at present, sensitivity, specificity and diagnostic accuracy of these urine-based assays are still suboptimal and, in the attend to improve them, novel molecular markers as well as multiple-assays must to be translated in clinic. Now there are growing evidence toward the use of minimally invasive “liquid biopsy” to identify biomarkers in urologic malignancy. DNA- and RNA-based markers in body fluids such as blood and urine are promising potential markers in diagnostic, prognostic, predictive and monitoring urological malignancies. Thus, circulating cell-free DNA, DNA methylation and mutations, circulating tumor cells, miRNA, IncRNA and mRNAs, cell-free proteins and peptides, and exosomes have been assessed in urine specimens. However, proteomic and genomic data must to be validated in well-designed multicenter clinical studies, before to be employed in clinic oncology.
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Affiliation(s)
- Giorgio Santoni
- Immunopathology Laboratory, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Maria B Morelli
- Immunopathology Laboratory, School of Pharmacy, University of Camerino, Camerino, Italy.,Immunopathology Laboratory, School of Biosciences, Biotechnology and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Consuelo Amantini
- Immunopathology Laboratory, School of Biosciences, Biotechnology and Veterinary Medicine, University of Camerino, Camerino, Italy
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Jordahl KM, Randolph TW, Song X, Sather CL, Tinker LF, Phipps AI, Kelsey KT, White E, Bhatti P. Genome-Wide DNA Methylation in Prediagnostic Blood and Bladder Cancer Risk in the Women's Health Initiative. Cancer Epidemiol Biomarkers Prev 2018; 27:689-695. [PMID: 29540343 PMCID: PMC5984694 DOI: 10.1158/1055-9965.epi-17-0951] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/31/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022] Open
Abstract
Background: Differential DNA methylation as measured in blood is a promising marker of bladder cancer susceptibility. However, previous studies have exclusively used postdiagnostic blood samples, meaning that observed associations may be markers of disease rather than susceptibility.Methods: Genome-wide methylation was measured in prediagnostic blood samples, using the Illumina Infinium HumanMethylation450 Bead Array, among 440 bladder cancer cases with the transitional cell carcinoma (TCC) subtype and 440 matched cancer-free controls from the Women's Health Initiative cohort. After normalization and probe filtering, we used conditional logistic regression models to test for associations between methylation measurements at 361,184 CpG sites and bladder cancer risk.Results: Increased methylation at cg22748573, located in a CpG island within the 5'-UTR/first exon of the CITED4 gene, was associated with an 82% decreased risk of bladder cancer after adjusting for race/ethnicity, smoking status, pack-years of smoking, and leukocyte cell profile and accounting for multiple testing (OR = 0.18, q-value = 0.05). The result was robust to sensitivity analyses accounting for time between enrollment and diagnosis, race, tumor subtype, and secondhand smoke exposure.Conclusions: Although results need to be confirmed in additional prospective studies, differential methylation in CITED4, as measured in blood, is a promising marker of bladder cancer susceptibility.Impact: Identification of biomarkers of bladder cancer susceptibility in easily accessible tissues may allow targeting of screening efforts so as to improve bladder cancer prognosis. This is particularly important among women, who tend to have poorer bladder cancer outcomes than men. Cancer Epidemiol Biomarkers Prev; 27(6); 689-95. ©2018 AACR.
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Affiliation(s)
- Kristina M Jordahl
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Timothy W Randolph
- Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaoling Song
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cassandra L Sather
- Genomics Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lesley F Tinker
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Amanda I Phipps
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Karl T Kelsey
- Department of Community Health, Brown University, Providence, Rhode Island
| | - Emily White
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Parveen Bhatti
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington.
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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van der Heijden AG, Mengual L, Ingelmo-Torres M, Lozano JJ, van Rijt-van de Westerlo CCM, Baixauli M, Geavlete B, Moldoveanud C, Ene C, Dinney CP, Czerniak B, Schalken JA, Kiemeney LALM, Ribal MJ, Witjes JA, Alcaraz A. Urine cell-based DNA methylation classifier for monitoring bladder cancer. Clin Epigenetics 2018; 10:71. [PMID: 29854012 PMCID: PMC5975622 DOI: 10.1186/s13148-018-0496-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/03/2018] [Indexed: 01/12/2023] Open
Abstract
Background Current standard methods used to detect and monitor bladder cancer (BC) are invasive or have low sensitivity. This study aimed to develop a urine methylation biomarker classifier for BC monitoring and validate this classifier in patients in follow-up for bladder cancer (PFBC). Methods Voided urine samples (N = 725) from BC patients, controls, and PFBC were prospectively collected in four centers. Finally, 626 urine samples were available for analysis. DNA was extracted from the urinary cells and bisulfite modificated, and methylation status was analyzed using pyrosequencing. Cytology was available from a subset of patients (N = 399). In the discovery phase, seven selected genes from the literature (CDH13, CFTR, NID2, SALL3, TMEFF2, TWIST1, and VIM2) were studied in 111 BC and 57 control samples. This training set was used to develop a gene classifier by logistic regression and was validated in 458 PFBC samples (173 with recurrence). Results A three-gene methylation classifier containing CFTR, SALL3, and TWIST1 was developed in the training set (AUC 0.874). The classifier achieved an AUC of 0.741 in the validation series. Cytology results were available for 308 samples from the validation set. Cytology achieved AUC 0.696 whereas the classifier in this subset of patients reached an AUC 0.768. Combining the methylation classifier with cytology results achieved an AUC 0.86 in the validation set, with a sensitivity of 96%, a specificity of 40%, and a positive and negative predictive value of 56 and 92%, respectively. Conclusions The combination of the three-gene methylation classifier and cytology results has high sensitivity and high negative predictive value in a real clinical scenario (PFBC). The proposed classifier is a useful test for predicting BC recurrence and decrease the number of cystoscopies in the follow-up of BC patients. If only patients with a positive combined classifier result would be cystoscopied, 36% of all cystoscopies can be prevented. Electronic supplementary material The online version of this article (10.1186/s13148-018-0496-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Lourdes Mengual
- 2Laboratory and Department of Urology, Hospital Clinic of Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain.,Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, office B22, C/Casanova, 143, 08036 Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- 2Laboratory and Department of Urology, Hospital Clinic of Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Juan J Lozano
- 3CIBERehd, Plataforma de Bioinformática, Centro de Investigación Biomédica en red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | | | - Montserrat Baixauli
- 2Laboratory and Department of Urology, Hospital Clinic of Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
| | | | | | - Cosmin Ene
- 4Saint John Emergency Clinical Hospital, Bucharest, Romania
| | | | | | - Jack A Schalken
- 1Department of Urology Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Maria J Ribal
- 2Laboratory and Department of Urology, Hospital Clinic of Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - J Alfred Witjes
- 1Department of Urology Radboud University Medical Center, Nijmegen, The Netherlands
| | - Antonio Alcaraz
- 2Laboratory and Department of Urology, Hospital Clinic of Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
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Zhang Y, Fang L, Zang Y, Xu Z. Identification of Core Genes and Key Pathways via Integrated Analysis of Gene Expression and DNA Methylation Profiles in Bladder Cancer. Med Sci Monit 2018; 24:3024-3033. [PMID: 29739919 PMCID: PMC5968840 DOI: 10.12659/msm.909514] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development. Material/Methods Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R. Gene Ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID database and KOBAS 3.0. STRING and Cytoscape software were used to construct protein–protein interaction (PPI) networks and analyze modules of the PPI network. Results A total of 71 hypomethylated/upregulated genes were significantly enriched in cell–cell adhesion and blood vessel development. KEGG pathway analysis highlighted p53 signaling and metabolic pathways. Five core genes in the PPI network were determined: CDH1, DDOST, CASP8, DHX15, and PTPRF. Additionally, 89 hypermethylated/downregulated genes were found. These genes were enriched mostly in cell adhesion and signal transduction. KEGG pathway analysis revealed enrichment in focal adhesion. The top 5 core genes in the PPI network were GNG4, ADCY9, NPY, ADRA2B, and PENK. We found most of the core genes were also significantly altered in the Cancer Genome Atlas database. Conclusions Abnormal methylated/expressed genes and key signaling pathways involved in BC were identified through integrated bioinformatics analysis. In the future, these genes may serve as biomarkers for diagnosis and therapeutic targets in BC.
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Affiliation(s)
- Yongzhen Zhang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Liang Fang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yuanwei Zang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Zhonghua Xu
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
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Marques-Magalhães Â, Graça I, Henrique R, Jerónimo C. Targeting DNA Methyltranferases in Urological Tumors. Front Pharmacol 2018; 9:366. [PMID: 29706891 PMCID: PMC5909196 DOI: 10.3389/fphar.2018.00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/28/2018] [Indexed: 12/14/2022] Open
Abstract
Urological cancers are a heterogeneous group of malignancies accounting for a considerable proportion of cancer-related morbidity and mortality worldwide. Aberrant epigenetic traits, especially altered DNA methylation patterns constitute a hallmark of these tumors. Nonetheless, these alterations are reversible, and several efforts have been carried out to design and test several epigenetic compounds that might reprogram tumor cell phenotype back to a normal state. Indeed, several DNMT inhibitors are currently under evaluation for therapeutic efficacy in clinical trials. This review highlights the critical role of DNA methylation in urological cancers and summarizes the available data on pre-clinical assays and clinical trials with DNMT inhibitors in bladder, kidney, prostate, and testicular germ cell cancers.
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Affiliation(s)
- Ângela Marques-Magalhães
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Inês Graça
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
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Ilijazi D, Abufaraj M, Hassler MR, Ertl IE, D'Andrea D, Shariat SF. Waiting in the wings: the emerging role of molecular biomarkers in bladder cancer. Expert Rev Mol Diagn 2018. [PMID: 29542328 DOI: 10.1080/14737159.2018.1453808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Bladder cancer (BCa) is the fifth most frequently diagnosed cancer worldwide and is, in fact, the most expensive cancer on a per-patient to treat basis. There is a critical need to implement new tests into clinical practice to improve the quality of clinical care, decrease unnecessary invasive therapies and ultimately save costs. Currently, no molecular or genetic biomarker has been widely integrated into daily clinical practice. However, major milestones have been achieved in our understanding of the molecular alterations in BCa that will provide the basis for integrating molecular and genetic biomarkers into clinical decision making to guide management. Clinical implementation of such novel molecular and genetic concepts is the cornerstone in an effort to usher the age of precision medicine into patient care. Areas covered: In this review, the authors discuss the emerging role of molecular biomarkers in patients receiving BCG immunotherapy as well as neoadjuvant and adjuvant chemotherapy in BCa. Expert commentary: Molecular predictive and prognostic biomarkers in BCa are promising diagnostic options that will pave the way for molecular-based personalized medicine.
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Affiliation(s)
- Dafina Ilijazi
- a Department of Urology , Medical University of Vienna , Vienna , Austria
| | - Mohammad Abufaraj
- a Department of Urology , Medical University of Vienna , Vienna , Austria.,b Department of Special Surgery , Jordan University Hospital, The University of Jordan , Amman , Jordan
| | - Melanie R Hassler
- a Department of Urology , Medical University of Vienna , Vienna , Austria
| | - Iris E Ertl
- a Department of Urology , Medical University of Vienna , Vienna , Austria
| | - David D'Andrea
- a Department of Urology , Medical University of Vienna , Vienna , Austria
| | - Shahrokh F Shariat
- a Department of Urology , Medical University of Vienna , Vienna , Austria.,c Karl Landsteiner Institute of Urology and Andrology , Vienna , Austria.,d Department of Urology , University of Texas Southwestern Medical Center , Dallas , TX , USA.,e Department of Urology , Weill Cornell Medical College, New York-Presbyterian Hospital , New York , NY , USA
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Erichsen L, Ghanjati F, Beermann A, Poyet C, Hermanns T, Schulz WA, Seifert HH, Wild PJ, Buser L, Kröning A, Braunstein S, Anlauf M, Jankowiak S, Hassan M, Bendhack ML, Araúzo-Bravo MJ, Santourlidis S. Aberrant methylated key genes of methyl group metabolism within the molecular etiology of urothelial carcinogenesis. Sci Rep 2018; 8:3477. [PMID: 29472622 PMCID: PMC5823913 DOI: 10.1038/s41598-018-21932-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Urothelial carcinoma (UC), the most common cancer of the urinary bladder causes severe morbidity and mortality, e.g. about 40.000 deaths in the EU annually, and incurs considerable costs for the health system due to the need for prolonged treatments and long-term monitoring. Extensive aberrant DNA methylation is described to prevail in urothelial carcinoma and is thought to contribute to genetic instability, altered gene expression and tumor progression. However, it is unknown how this epigenetic alteration arises during carcinogenesis. Intact methyl group metabolism is required to ensure maintenance of cell-type specific methylomes and thereby genetic integrity and proper cellular function. Here, using two independent techniques for detecting DNA methylation, we observed DNA hypermethylation of the 5'-regulatory regions of the key methyl group metabolism genes ODC1, AHCY and MTHFR in early urothelial carcinoma. These hypermethylation events are associated with genome-wide DNA hypomethylation which is commonly associated with genetic instability. We therefore infer that hypermethylation of methyl group metabolism genes acts in a feed-forward cycle to promote additional DNA methylation changes and suggest a new hypothesis on the molecular etiology of urothelial carcinoma.
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Affiliation(s)
- Lars Erichsen
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Foued Ghanjati
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Agnes Beermann
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Cedric Poyet
- Department of Urology, University Hospital, University of Zurich, Zurich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital, University of Zurich, Zurich, Switzerland
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Peter J Wild
- Institute of Surgical Pathology, University Hospital, University of Zurich, 8091, Zurich, Switzerland
| | - Lorenz Buser
- Institute of Surgical Pathology, University Hospital, University of Zurich, 8091, Zurich, Switzerland
| | - Alexander Kröning
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Stefan Braunstein
- Department of Pathology, Medical Faculty, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Martin Anlauf
- Department of Pathology, Medical Faculty, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Silvia Jankowiak
- Department of Pathology, Medical Faculty, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Mohamed Hassan
- Department of Surgery, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Institut National de la Santé et de la Recherché Médicale, University of Strasbourg, 67000, Strasbourg, France
| | - Marcelo L Bendhack
- Department of Urology, University Hospital, Positivo University, Curitiba, Brazil
| | - Marcos J Araúzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
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Sanford T, Meng MV, Railkar R, Agarwal PK, Porten SP. Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma. Clin Epigenetics 2018; 10:19. [PMID: 29456764 PMCID: PMC5809922 DOI: 10.1186/s13148-018-0451-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
Background Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler. An R package MethylMix was used to perform an analysis incorporating both methylation and gene expression data on all samples, as well as a subset analysis comparing patients surviving less than 2 years and patients surviving more than 2 years. Genes associated with poor prognosis were individually queried. Pathway analysis was performed on statistically significant genes identified by MethylMix criteria using ConsensusPathDB. Validation was performed using flow cytometry on bladder cancer cell lines. Results A total of 408 patients met all inclusion criteria. There were a total of 240 genes differentially methylated by MethylMix criteria. Review of individual genes specific to poor-prognosis patients revealed the majority to be candidate tumor suppressors in other cancer types. Pathway analysis showed increase in methylation of genes involved in antioxidant pathways including glutathione and NRF2. Genes involved in estrogen metabolism were also hypermethylated while genes involved in the EGFR pathway were found to be hypomethylated. EGFR expression was confirmed to be elevated in six bladder cancer cell lines. Conclusions In patients with invasive urothelial carcinoma, we found differential methylation in patients with better and worse prognosis after cystectomy. Differentially methylated genes are involved in many relevant oncologic pathways, including EGFR and antioxidant pathways, that may be a target for therapy or chemoprevention.
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Affiliation(s)
- Thomas Sanford
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10—Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA
| | - Maxwell V. Meng
- Department of Urology, University of California, Mail code 1695, 550 16th Street, 6th Floor, San Francisco, CA 94143 USA
| | - Reema Railkar
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10—Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA
| | - Piyush K. Agarwal
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10—Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA
| | - Sima P. Porten
- Department of Urology, University of California, Mail code 1695, 550 16th Street, 6th Floor, San Francisco, CA 94143 USA
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