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Eturi A, Bhasin A, Zarrabi KK, Tester WJ. Predictive and Prognostic Biomarkers and Tumor Antigens for Targeted Therapy in Urothelial Carcinoma. Molecules 2024; 29:1896. [PMID: 38675715 PMCID: PMC11054340 DOI: 10.3390/molecules29081896] [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: 02/27/2024] [Revised: 04/01/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Urothelial carcinoma (UC) is the fourth most prevalent cancer amongst males worldwide. While patients with non-muscle-invasive disease have a favorable prognosis, 25% of UC patients present with locally advanced disease which is associated with a 10-15% 5-year survival rate and poor overall prognosis. Muscle-invasive bladder cancer (MIBC) is associated with about 50% 5 year survival when treated by radical cystectomy or trimodality therapy; stage IV disease is associated with 10-15% 5 year survival. Current therapeutic modalities for MIBC include neoadjuvant chemotherapy, surgery and/or chemoradiation, although patients with relapsed or refractory disease have a poor prognosis. However, the rapid success of immuno-oncology in various hematologic and solid malignancies offers new targets with tremendous therapeutic potential in UC. Historically, there were no predictive biomarkers to guide the clinical management and treatment of UC, and biomarker development was an unmet need. However, recent and ongoing clinical trials have identified several promising tumor biomarkers that have the potential to serve as predictive or prognostic tools in UC. This review provides a comprehensive summary of emerging biomarkers and molecular tumor targets including programmed death ligand 1 (PD-L1), epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor (FGFR), DNA damage response and repair (DDR) mutations, poly (ADP-ribose) polymerase (PARP) expression and circulating tumor DNA (ctDNA), as well as their clinical utility in UC. We also evaluate recent advancements in precision oncology in UC, while illustrating limiting factors and challenges related to the clinical application of these biomarkers in clinical practice.
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Affiliation(s)
- Aditya Eturi
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; (K.K.Z.); (W.J.T.)
| | - Amman Bhasin
- Department of Internal Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Kevin K. Zarrabi
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; (K.K.Z.); (W.J.T.)
| | - William J. Tester
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; (K.K.Z.); (W.J.T.)
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Wu S, Li R, Jiang Y, Yu J, Zheng J, Li Z, Li M, Xin K, Wang Y, Xu Z, Li S, Chen X. Liquid biopsy in urothelial carcinoma: Detection techniques and clinical applications. Biomed Pharmacother 2023; 165:115027. [PMID: 37354812 DOI: 10.1016/j.biopha.2023.115027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023] Open
Abstract
The types of urothelial carcinoma (UC) include urothelial bladder cancer and upper tract urothelial carcinoma. Current diagnostic techniques cannot meet the needs of patients. Liquid biopsy is an accurate method of determining the molecular profile of UC and is a cutting-edge and popular technique that is expected to complement existing detection techniques and benefit patients with UC. Circulating tumor cells, cell-free DNA, cell-free RNA, extracellular vesicles, proteins, and metabolites can be found in the blood, urine, or other bodily fluids and are examined during liquid biopsies. This article focuses on the components of liquid biopsies and their clinical applications in UC. Liquid biopsies have tremendous potential in multiple aspects of precision oncology, from early diagnosis and treatment monitoring to predicting prognoses. They may therefore play an important role in the management of UC and precision medicine.
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Affiliation(s)
- Siyu Wu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Rong Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yuanhong Jiang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jiazheng Yu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Mingyang Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
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Claps F, Mir MC, Zargar H. Molecular markers of systemic therapy response in urothelial carcinoma. Asian J Urol 2021; 8:376-390. [PMID: 34765445 PMCID: PMC8566362 DOI: 10.1016/j.ajur.2021.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/07/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
Identification of reliable molecular biomarkers that can complement clinical practice represents a fascinating challenge in any cancer field. Urothelial carcinoma is a very heterogeneous disease and responses to systemic therapies, and outcomes after radical cystectomy are difficult to predict. Advances in molecular biology such as next generation sequencing and whole genome or transcriptomic analysis provide promising platforms to achieve a full understanding of the biology behind the disease and can identify emerging predictive biomarkers. Moreover, the ability to categorize patients' risk of recurrence after curative treatment, or even predict benefit from a conventional or targeted therapies, represents a compelling challenge that may reshape both selection for tailored treatment and disease monitoring. Progress has been made but currently no molecular biomarkers are used in the clinical setting to predict response to systemic agents in either neoadjuvant or adjuvant settings highlighting a relevant unmet need. Here, we aim to present the emerging role of molecular biomarkers in predicting response to systemic agents in urothelial carcinoma.
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Affiliation(s)
- Francesco Claps
- Department of Urology, Fundacion Instituto Valenciano de Oncologia, Valencia, Spain
- Urological Clinic, Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Maria Carmen Mir
- Department of Urology, Fundacion Instituto Valenciano de Oncologia, Valencia, Spain
| | - Homayoun Zargar
- Department of Urology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
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Crocetto F, Cimmino A, Ferro M, Terracciano D. Circulating tumor cells in bladder cancer: a new horizon of liquid biopsy for precision medicine. J Basic Clin Physiol Pharmacol 2021; 33:525-527. [PMID: 34563104 DOI: 10.1515/jbcpp-2021-0233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Felice Crocetto
- Department of Neurosciences, Sciences of Reproduction and Odontostomatology, University of Naples Federico II, Naples, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Matteo Ferro
- Department of Urology of European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
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Uygun ZO, Yeniay L, Gi Rgi N Sağın F. CRISPR-dCas9 powered impedimetric biosensor for label-free detection of circulating tumor DNAs. Anal Chim Acta 2020; 1121:35-41. [PMID: 32493587 DOI: 10.1016/j.aca.2020.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 12/20/2022]
Abstract
Label-free biosensors which can be integrated into lab-on-a-chip platforms have the advantage of using small volumes for rapid and inexpensive measurements contrary to label-based technologies which are often more costly and time-consuming. In this study, graphene oxide screen printed electrodes (GPHOXE) were modified by deactivated Cas9 (dCas9) proteins and synthetic guide RNA (sgRNA) as the biorecognition receptor for label-free detection of circulating tumor DNAs (ctDNA). This was achieved by detection of a tumor related mutation (PIK3CA exon 9 mutation) via sequence-specific recognition followed by electrochemical impedance spectroscopy (EIS) analysis. The biosensor showed high specificity as there was no impedance signal for other ctDNA sequences, even the single nucleotide mismatch. dCas9-sgRNA modified biosensor demonstrated linear detection limits between 2 and 20 nM for 120 bp ctDNA's in 40 s. The calibration curve showed good linearity, LOD was calculated as 0.65 nM and LOQ was calculated as 1.92 nM. Selectivity and repeatability studies were carried out in real blood samples and the recovery was higher than 96%. In conclusion, dCas9-sgRNA was effectively immobilized and optimized on GPHOXE as the selective biorecognition receptor of this ultrafast impedimetric biosensor. The CRISPR-dCas9 powered impedimetric system showed good selectivity, high repeatability and good recovery properties. This is the first literature to report the use of CRISPR/Cas technology as a label-free tool that can be used in an impedimetric system for detection of ctDNA's.
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Affiliation(s)
- Zihni Onur Uygun
- Ege University, Faculty of Medicine, Department of Medical Biochemistry, Bornova, 35100, İzmir, Turkey.
| | - Levent Yeniay
- Ege University, Faculty of Medicine, Department of General Surgery, Bornova, 35100, İzmir, Turkey
| | - Ferhan Gi Rgi N Sağın
- Ege University, Faculty of Medicine, Department of Medical Biochemistry, Bornova, 35100, İzmir, Turkey
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Ou Z, Li K, Yang T, Dai Y, Chandra M, Ning J, Wang Y, Xu R, Gao T, Xie Y, He Q, Li Y, Lu Q, Wang L, Song Z. Detection of bladder cancer using urinary cell-free DNA and cellular DNA. Clin Transl Med 2020; 9:4. [PMID: 31938901 PMCID: PMC6960275 DOI: 10.1186/s40169-020-0257-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/05/2020] [Indexed: 01/29/2023] Open
Abstract
Background The present study sought to identify a panel of DNA markers for noninvasive diagnosis using cell-free DNA (cfDNA) from urine supernatant or cellular DNA from urine sediments of hematuria patients. A panel of 48 bladder cancer-specific genes was selected. A next-generation sequencing-based assay with a cfDNA barcode-enabled single-molecule test was employed. Mutation profiles of blood, urine, and tumor sample from 16 bladder cancer patients were compared. Next, urinary cellular DNA and cfDNA were prospectively collected from 125 patients (92 bladder cancer cases and 33 controls) and analyzed using the 48-gene panel. The individual gene markers and combinations of markers were validated according to the pathology results. The mean areas under the receiver operating characteristic (ROC) curves (AUCs) obtained with the various modeling approaches were calculated and compared. Results This pilot study of 16 bladder cancer patients demonstrated that gene mutations in urine supernatant and sediments had better concordance with cancer tissue as compared with plasma. Logistic analyses suggested two powerful combinations of genes for genetic diagnostic modeling: five genes for urine supernatant (TERT, FGFR3, TP53, PIK3CA, and KRAS) and seven genes for urine sediments (TERT, FGFR3, TP53, HRAS, PIK3CA, KRAS, and ERBB2). The accuracy of the five-gene panel and the seven-gene panel in the validation cohort yielded AUCs of 0.94 [95% confidence interval (CI) 0.91–0.97] and 0.91 (95% CI 0.86–0.96), respectively. With the addition of age and gender, the diagnostic power of the urine supernatant five-gene model and the urine sediment seven-gene model improved as the revised AUCs were 0.9656 (95% CI 0.9368–0.9944) and 0.9587 (95% CI 0.9291–0.9883). Conclusions cfDNA from urine bears great diagnostic potential. A five-gene panel for urine supernatant and a seven-gene panel for urine sediments are promising options for identifying bladder cancer in hematuria patients.
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Affiliation(s)
- Zhenyu Ou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.,Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Kai Li
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Ting Yang
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Ying Dai
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Mohan Chandra
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204-5060, USA
| | - Jun Ning
- Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yongli Wang
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Ran Xu
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Tangjie Gao
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Yu Xie
- Department of Urology, Hunan Provincial Tumor Hospital and Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
| | - Qing He
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Yuanwei Li
- Department of Urology, Hunan Provincial People's Hospital, Changsha, 410002, Hunan, China
| | - Qin Lu
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China. .,Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Zhuo Song
- GeneTalks Biotech Co., Ltd., Changsha, 410010, Hunan, China.
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Su H, Jiang H, Tao T, Kang X, Zhang X, Kang D, Li S, Li C, Wang H, Yang Z, Zhang J, Li C. Hope and challenge: Precision medicine in bladder cancer. Cancer Med 2019; 8:1806-1816. [PMID: 30907072 PMCID: PMC6488142 DOI: 10.1002/cam4.1979] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 12/21/2022] Open
Abstract
Bladder cancer (BC) is a complex disease and could be classified into nonmuscle‐invasive BC (NMIBC) or muscle‐invasive BC (MIBC) subtypes according to the distinct genetic background and clinical prognosis. Until now, the golden standard and confirmed diagnosis of BC is cystoscopy and the major problems of BC are the high rate of recurrence and high costs in the clinic. Recent molecular and genetic studies have provided perspectives on the novel biomarkers and potential therapeutic targets of BC. In this article, we provided an overview of the traditional diagnostic approaches of BC, and introduced some new imaging, endoscopic, and immunological diagnostic technology in the accurate diagnosis of BC. Meanwhile, the minimally invasive precision treatment technique, immunotherapy, chemotherapy, gene therapy, and targeted therapy of BC were also included. Here, we will overview the diagnosis and therapy methods of BC used in clinical practice, focusing on their specificity, efficiency, and safety. On the basis of the discussion of the benefits of precision medicine in BC, we will also discuss the challenges and limitations facing the non‐invasive methods of diagnosis and precision therapy of BC. The molecularly targeted and immunotherapeutic approaches, and gene therapy methods to BC treatment improved the prognosis and overall survival of BC patients.
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Affiliation(s)
- Hongwei Su
- Department of Urology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Haitao Jiang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, China
| | - Tao Tao
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Department of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Xing Kang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xu Zhang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Danyue Kang
- Michigan State University, East Lansing, Michigan
| | - Shucheng Li
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chengxi Li
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haifeng Wang
- Department of Urology, The Second Affliated Hospital of Kunming Medical University, Kunming, China
| | - Zhao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jinku Zhang
- Department of pathology, First Central Hospital of Baoding, Baoding, Hebei, China
| | - Chong Li
- Department of Urology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China.,Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Department of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen, China.,Beijing Jianlan Institute of Medicine, Beijing, China
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Wach S, Weigelt K, Michalke B, Lieb V, Stoehr R, Keck B, Hartmann A, Wullich B, Taubert H, Chaudhri A. Diagnostic potential of major and trace elements in the serum of bladder cancer patients. J Trace Elem Med Biol 2018; 46:150-155. [PMID: 29413105 DOI: 10.1016/j.jtemb.2017.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/17/2022]
Abstract
Major and trace elements may play a role in the diagnosis of diseases. In this study, we investigated the concentration of 26 major and trace elements in the serum by inductively coupled plasma (ICP) - optical emission spectrometry (OES) and ICP-sector field-mass spectrometry (sf-MS). We analyzed the serum from a discovery cohort of 6 bladder cancer (BCa) patients and 12 healthy controls as well as from a validation cohort of 21 BCa patients, 29 non-tumor bladder patients (with acute and chronic inflammation) and 18 healthy controls. Patients were recruited after written consent was obtained at one medical center. Serum was prepared from peripheral blood prior to surgical treatment. Differences in the levels of major and trace elements were determined by a nonparametric Mann-Whitney test and Kruskal-Wallis statistics. In the discovery cohort, we measured significantly increased levels of calcium, mercury, potassium, lithium, nickel, phosphorus and strontium and a significantly decreased level of sodium in BCa patients compared with healthy controls. These findings were reassessed in our validation cohort. We measured significantly increased levels of boron, calcium, cadmium, copper, chromium, lead, lithium, potassium, magnesium, nickel, sulfur, strontium, titan, vanadium and zinc and significantly decreased levels of iron and molybdenum. When we studied the concordance for the discovery and validation cohorts, concentrations of five elements were detected as significantly increased in BCa patients compared with healthy controls: calcium, lithium, potassium, nickel, and strontium. Interestingly, the levels of three elements (calcium, potassium and strontium) were also significantly increased in non-tumor bladder patients compared with healthy controls. But no element was significantly altered between non-tumor bladder patients and BCa patients. In summary, we suggest that determination of the elements calcium, lithium, nickel and strontium in the serum could be a new and promising tool for the early diagnosis of BCa.
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Affiliation(s)
- Sven Wach
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Katrin Weigelt
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Analytical BioGeoChemistry, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Germany.
| | - Verena Lieb
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany
| | - Robert Stoehr
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 8-10, D-91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Bastian Keck
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 8-10, D-91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Bernd Wullich
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Helge Taubert
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Anwar Chaudhri
- Institute for Surface Science and Corrosion, Department of Materials Science, Friedrich Alexander-University Erlangen-Nürnberg, Martensstraße 7, D-91058 Erlangen, Germany
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Copy number variations of circulating, cell-free DNA in urothelial carcinoma of the bladder patients treated with radical cystectomy: a prospective study. Oncotarget 2017; 8:56398-56407. [PMID: 28915599 PMCID: PMC5593570 DOI: 10.18632/oncotarget.17657] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/26/2017] [Indexed: 12/18/2022] Open
Abstract
The aim of the present study was to establish a rapid profiling method using multiplex ligation-dependent probe amplification (MLPA) and characterize copy number variations (CNV) in circulating, cell-free DNA (cfDNA) in 85 urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC). MLPA was tested for the use of cfDNA extracted from serum and plasma by various commercial extraction kits. Eighteen probes served as reference to control denaturation, ligation and amplification efficiency. MLPA was exclusively suitable for cfDNA extracted from serum. Serum from 72 patients (84.7%) could be analyzed. Thirty-five patients (48.6%) had presence of CNV in cfDNA. The median CNV count in patients with presence of CNV was 2. Predominantly, CNV were located in the genes CDH1, ZFHX3, RIPK2 and PTEN in 15 patients (20.8%), 12 patients (16.7%), 9 patients (12.5%) and 7 patients (9.7%), respectively. CNV in TSG1, RAD21, KIAA0196, ANXA7 and TMPRSS2 were associated with presence of variant UCB histology (p = 0.029, 0.029, 0.029, 0.029, 0.043, respectively). Furthermore, CNV in miR-15a, CDH1 and ZFHX3 were associated with presence of incidental prostate cancer (p = 0.023, 0.003, 0.025, respectively). Patients with CNV in KLF5, ZFHX3 and CDH1 had reduced cancer-specific survival, compared to patients without CNV in these genes (pairwise p = 0.028, 0.026, 0.044, respectively). MLPA represents an efficient method for the detection of CNV among numerous genes on various chromosomal regions. CNV in specific genes seem to be associated with aggressive UCB biologic features and presence of incidental prostate cancer, and may have a negative impact on cancer-specific survival.
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