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Tran MA, Youssef D, Shroff S, Chowhan D, Beaumont KG, Sebra R, Mehrazin R, Wiklund P, Lin JJ, Horowitz A, Farkas AM, Galsky MD, Sfakianos JP, Bhardwaj N. Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment. J Exp Med 2024; 221:e20240045. [PMID: 38847806 PMCID: PMC11157455 DOI: 10.1084/jem.20240045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/04/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
Due to bladder tumors' contact with urine, urine-derived cells (UDCs) may serve as a surrogate for monitoring the tumor microenvironment (TME) in bladder cancer (BC). However, the composition of UDCs and the extent to which they mirror the tumor remain poorly characterized. We generated the first single-cell RNA-sequencing of BC patient UDCs with matched tumor and peripheral blood mononuclear cells (PBMC). BC urine was more cellular than healthy donor (HD) urine, containing multiple immune populations including myeloid cells, CD4+ and CD8+ T cells, natural killer (NK) cells, B cells, and dendritic cells (DCs) in addition to tumor and stromal cells. Immune UDCs were transcriptionally more similar to tumor than blood. UDCs encompassed cytotoxic and activated CD4+ T cells, exhausted and tissue-resident memory CD8+ T cells, macrophages, germinal-center-like B cells, tissue-resident and adaptive NK cells, and regulatory DCs found in tumor but lacking or absent in blood. Our findings suggest BC UDCs may be surrogates for the TME and serve as therapeutic biomarkers.
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Affiliation(s)
- Michelle A. Tran
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dina Youssef
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanjana Shroff
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Disha Chowhan
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin G. Beaumont
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Wiklund
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jenny J. Lin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Department of Immunology and Immunotherapy, The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam M. Farkas
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D. Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John P. Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Extramural Member, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
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Yang Z, Chen Q, Dong S, Xu P, Zheng W, Mao Z, Qian C, Zheng X, Dai L, Wang C, Shi H, Li J, Yuan J, Yu W, Xu C. Hypermethylated TAGMe as a universal-cancer-only methylation marker and its application in diagnosis and recurrence monitoring of urothelial carcinoma. J Transl Med 2024; 22:608. [PMID: 38956589 PMCID: PMC11218302 DOI: 10.1186/s12967-024-05420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Urothelial carcinoma (UC) is the second most common urological malignancy. Despite numerous molecular markers have been evaluated during the past decades, no urothelial markers for diagnosis and recurrence monitoring have shown consistent clinical utility. METHODS The methylation level of tissue samples from public database and clinical collected were analyzed. Patients with UC and benign diseases of the urinary system (BUD) were enrolled to establish TAGMe (TAG of Methylation) assessment in a training cohort (n = 567) using restriction enzyme-based bisulfite-free qPCR. The performance of TAGMe assessment was further verified in the validation cohort (n = 198). Urine samples from 57 UC patients undergoing postoperative surveillance were collected monthly for six months after surgery to assess the TAGMe methylation. RESULTS We identified TAGMe as a potentially novel Universal-Cancer-Only Methylation (UCOM) marker was hypermethylated in multi-type cancers and investigated its application in UC. Restriction enzyme-based bisulfite-free qPCR was used for detection, and the results of which were consistent with gold standard pyrosequencing. Importantly, hypermethylated TAGMe showed excellent sensitivity of 88.9% (95% CI: 81.4-94.1%) and specificity of 90.0% (95% CI: 81.9-95.3%) in efficiently distinguishing UC from BUD patients in urine and also performed well in different clinical scenarios of UC. Moreover, the abnormality of TAGMe as an indicator of recurrence might precede clinical recurrence by three months to one year, which provided an invaluable time window for timely and effective intervention to prevent UC upstaging. CONCLUSION TAGMe assessment based on a novel single target in urine is effective and easy to perform in UC diagnosis and recurrence monitoring, which may reduce the burden of cystoscopy. Trial registration ChiCTR2100052507. Registered on 30 October 2021.
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Affiliation(s)
- Zhicong Yang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qing Chen
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shihua Dong
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Peng Xu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Wanxiang Zheng
- Department of Urology, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Zhanrui Mao
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chengchen Qian
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Xiangyi Zheng
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Lihe Dai
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Chengyang Wang
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Haoqing Shi
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jing Li
- Department of Bioinformatics, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Jianlin Yuan
- Department of Urology, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China.
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China.
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Tan WY, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Curr Issues Mol Biol 2024; 46:6533-6565. [PMID: 39057032 PMCID: PMC11276574 DOI: 10.3390/cimb46070390] [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: 05/27/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/28/2024] Open
Abstract
Technological advancements in cell-free DNA (cfDNA) liquid biopsy have triggered exponential growth in numerous clinical applications. While cfDNA-based liquid biopsy has made significant strides in personalizing cancer treatment, the exploration and translation of epigenetics in liquid biopsy to clinical practice is still nascent. This comprehensive review seeks to provide a broad yet in-depth narrative of the present status of epigenetics in cfDNA liquid biopsy and its associated challenges. It highlights the potential of epigenetics in cfDNA liquid biopsy technologies with the hopes of enhancing its clinical translation. The momentum of cfDNA liquid biopsy technologies in recent years has propelled epigenetics to the forefront of molecular biology. We have only begun to reveal the true potential of epigenetics in both our understanding of disease and leveraging epigenetics in the diagnostic and therapeutic domains. Recent clinical applications of epigenetics-based cfDNA liquid biopsy revolve around DNA methylation in screening and early cancer detection, leading to the development of multi-cancer early detection tests and the capability to pinpoint tissues of origin. The clinical application of epigenetics in cfDNA liquid biopsy in minimal residual disease, monitoring, and surveillance are at their initial stages. A notable advancement in fragmentation patterns analysis has created a new avenue for epigenetic biomarkers. However, the widespread application of cfDNA liquid biopsy has many challenges, including biomarker sensitivity, specificity, logistics including infrastructure and personnel, data processing, handling, results interpretation, accessibility, and cost effectiveness. Exploring and translating epigenetics in cfDNA liquid biopsy technology can transform our understanding and perception of cancer prevention and management. cfDNA liquid biopsy has great potential in precision oncology to revolutionize conventional ways of early cancer detection, monitoring residual disease, treatment response, surveillance, and drug development. Adapting the implementation of liquid biopsy workflow to the local policy worldwide and developing point-of-care testing holds great potential to overcome global cancer disparity and improve cancer outcomes.
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Affiliation(s)
- Wan Ying Tan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
- Hematology & Oncology, Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030, USA
| | | | - Olivia Ang-Olson
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Paromita Das
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Luisa Ladel
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
| | - Bethsebie Sailo
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Linda He
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Anup Sharma
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Nita Ahuja
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520-8000, USA
- Biological and Biomedical Sciences Program (BBS), Yale University, New Haven, CT 06520-8084, USA
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Silva-Ferreira M, Carvalho JA, Salta S, Henriques TS, Pereira Rodrigues P, Monteiro-Reis S, Henrique R, Jerónimo C. Diagnostic Test Accuracy of Urinary DNA Methylation-based Biomarkers for the Detection of Primary and Recurrent Bladder Cancer: A Systematic Review and Meta-analysis. Eur Urol Focus 2024:S2405-4569(24)00088-9. [PMID: 38897871 DOI: 10.1016/j.euf.2024.05.024] [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: 03/21/2024] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND AND OBJECTIVE Diagnosis of primary and relapsed bladder carcinomas is accomplished by urethrocystoscopy, an invasive procedure, combined with urinary cytology, with limited sensitivity, resulting in a substantial burden. Thus, noninvasive biomarkers have been investigated, among which DNA methylation has shown promise. This systematic review and meta-analysis sought to assess the diagnostic accuracy of DNA methylation biomarkers reported in the literature for bladder cancer detection, pinpointing the most informative one. METHODS The search for this systematic review and meta-analysis was conducted on PubMed, Scopus, and Cochrane Library for relevant studies published until December 31, 2022. A meta-analysis was performed using a random-effect model, to compute the pooled sensitivity and specificity of the markers. PROSPERO's registration ID for the study is CRD42023397703. KEY FINDINGS AND LIMITATIONS Out of the 2297 studies retrieved, 68 were included in the final analysis, despite considerable heterogeneity. These involved 12 696 participants, of whom 5557 were diagnosed with bladder cancer. Using diagnostic odds ratio (DOR) as a comparative measure, the five most promising markers (pooled sensitivity, specificity, and DOR) were SALL3 (61%, 97%, and 55.67, respectively), PENK (77%, 93%, and 47.90, respectively), ZNF154 (87%, 90%, and 45.07, respectively), VIM (82%, 90%, and 44.81, respectively), and POU4F2 (81%, 89%, and 34.89, respectively). Urinary cytology identified bladder cancer with 55% sensitivity, 92% specificity, and 14.37 DOR. CONCLUSIONS AND CLINICAL IMPLICATIONS DNA methylation biomarkers disclose high accuracy for bladder cancer detection in urine. Nonetheless, validation studies in different clinical settings are scarce, hampering clinical use. The identified biomarkers should be prioritized in future validation studies. PATIENT SUMMARY In this meta-analysis, we include previously published studies that used urine samples of bladder cancer patients' from all around the globe. We were able to compare the diagnostic accuracy of noninvasive markers across different populations. We were able to conclude on the most promising DNA methylation markers to detect bladder cancer using urine.
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Affiliation(s)
- Mariana Silva-Ferreira
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Master Program in Oncology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - João A Carvalho
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Doctoral Program in Medical Science, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Doctoral Program in Pathology and Molecular Genetics, ICBAS - School of Medicine and Biomedical Sciences - University of Porto, Porto, Portugal
| | - Teresa S Henriques
- CINTESIS@RISE - Health Research Network & MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Pedro Pereira Rodrigues
- CINTESIS@RISE - Health Research Network & MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Sara Monteiro-Reis
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Institute of Science and Innovation in Mechanical and Industrial Engineering (INEGI), Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [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] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
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Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
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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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Tomiyama E, Fujita K, Hashimoto M, Uemura H, Nonomura N. Urinary markers for bladder cancer diagnosis: A review of current status and future challenges. Int J Urol 2024; 31:208-219. [PMID: 37968825 DOI: 10.1111/iju.15338] [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: 09/10/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023]
Abstract
Bladder cancer is a common urological cancer with a high recurrence rate that requires long-term follow-up, and early detection positively affects prognosis. To date, the initial diagnosis and follow-up for bladder cancer rely on cystoscopy, which is an invasive and expensive procedure. Therefore, urinary markers for the detection of bladder cancer have attracted research attention for decades to reduce unnecessary cystoscopies. Urine, which is in continuous contact with bladder cancer, is considered a suitable fluid for providing tumor information. Urinary cytology is the only widely used urinary marker in clinical practice; however, it has poor sensitivity for low-grade tumors; indicating the need for novel urinary markers. Considerable research has been conducted on this topic over the years, resulting in a complex landscape with a wide range of urinary markers, including protein-, exfoliated cell-, RNA-, DNA-, and extracellular vesicle-based markers. Although some of these markers have been approved by the U.S. Food and Drug Administration and are commercially available, their use in clinical practice is limited. To facilitate clinical application, potential urinary markers must withstand prospective clinical trials and be easy for patients and clinicians to understand and utilize in a clinical context. This review provides a comprehensive overview of currently available and recently reported promising urinary markers for bladder cancer. Additionally, the challenges and the prospects of these urinary markers for clinical implementation in bladder cancer treatment were discussed.
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Affiliation(s)
- Eisuke Tomiyama
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazutoshi Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Mamoru Hashimoto
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Hirotsugu Uemura
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
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9
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Jiang YH, Liu YS, Wei YC, Jhang JF, Kuo HC, Huang HH, Chan MWY, Lin GL, Cheng WC, Lin SC, Wang HJ. Hypermethylation Loci of ZNF671, IRF8, and OTX1 as Potential Urine-Based Predictive Biomarkers for Bladder Cancer. Diagnostics (Basel) 2024; 14:468. [PMID: 38472940 DOI: 10.3390/diagnostics14050468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Bladder cancer (BCa) is a significant health issue and poses a healthcare burden on patients, highlighting the importance of an effective detection method. Here, we developed a urine DNA methylation diagnostic panel for distinguishing between BCa and non-BCa. In the discovery stage, an analysis of the TCGA database was conducted to identify BCa-specific DNA hypermethylation markers. In the validation phase, DNA methylation levels of urine samples were measured with real-time quantitative methylation-specific PCR (qMSP). Comparative analysis of the methylation levels between BCa and non-BCa, along with the receiver operating characteristic (ROC) analyses with machine learning algorithms (logistic regression and decision tree methods) were conducted to develop practical diagnostic panels. The performance evaluation of the panel shows that the individual biomarkers of ZNF671, OTX1, and IRF8 achieved AUCs of 0.86, 0.82, and 0.81, respectively, while the combined yielded an AUC of 0.91. The diagnostic panel using the decision tree algorithm attained an accuracy, sensitivity, and specificity of 82.6%, 75.0%, and 90.9%, respectively. Our results show that the urine-based DNA methylation diagnostic panel provides a sensitive and specific method for detecting and stratifying BCa, showing promise as a standard test that could enhance the diagnosis and prognosis of BCa in clinical settings.
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Affiliation(s)
- Yuan-Hong Jiang
- Department of Urology, Hualien Tzu Chi Hospital, Tzu Chi University, Hualien 970374, Taiwan
| | - Yu-Shu Liu
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
- Phalanx Biotech, Hsinchu City 302041, Taiwan
| | - Yu-Chung Wei
- Graduate Institute of Statistics and Information Science, National Changhua University of Education, Changhua City 500207, Taiwan
| | - Jia-Fong Jhang
- Department of Urology, Hualien Tzu Chi Hospital, Tzu Chi University, Hualien 970374, Taiwan
| | - Hann-Chorng Kuo
- Department of Urology, Hualien Tzu Chi Hospital, Tzu Chi University, Hualien 970374, Taiwan
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
| | - Hsin-Hui Huang
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
- Phalanx Biotech, Hsinchu City 302041, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi 621301, Taiwan
| | - Guan-Ling Lin
- Department of Biomedical Sciences, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi 621301, Taiwan
| | - Wen-Chi Cheng
- Institute of Medical Sciences, Tzu Chi University, Hualien 970374, Taiwan
| | - Shu-Chuan Lin
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
- Phalanx Biotech, Hsinchu City 302041, Taiwan
| | - Hung-Jung Wang
- Institute of Medical Sciences, Tzu Chi University, Hualien 970374, Taiwan
- Doctoral Degree Program in Translational Medicine, Tzu Chi University and Academia Sinica, Hualien 97004, Taiwan
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien 970374, Taiwan
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10
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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: 17] [Impact Index Per Article: 17.0] [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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11
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Flores Monar GV, Reynolds T, Gordon M, Moon D, Moon C. Molecular Markers for Bladder Cancer Screening: An Insight into Bladder Cancer and FDA-Approved Biomarkers. Int J Mol Sci 2023; 24:14374. [PMID: 37762677 PMCID: PMC10531979 DOI: 10.3390/ijms241814374] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Bladder cancer is one of the most financially burdensome cancers globally, from its diagnostic to its terminal stages. The impact it imposes on patients and the medical community is substantial, exacerbated by the absence of disease-specific characteristics and limited disease-free spans. Frequent recurrences, impacting nearly half of the diagnosed population, require frequent and invasive monitoring. Given the advancing comprehension of its etiology and attributes, bladder cancer is an appealing candidate for screening strategies. Cystoscopy is the current gold standard for bladder cancer detection, but it is invasive and has the potential for undesired complications and elevated costs. Although urine cytology is a supplementary tool in select instances, its efficacy is limited due to its restricted sensitivity, mainly when targeting low-grade tumors. Although most of these assays exhibit higher sensitivity than urine cytology, clinical guidelines do not currently incorporate them. Consequently, it is necessary to explore novel screening assays to identify distinctive alterations exclusive to bladder cancer. Thus, integrating potential molecular assays requires further investigation through more extensive validation studies. Within this article, we offer a comprehensive overview of the critical features of bladder cancer while conducting a thorough analysis of the FDA-approved assays designed to diagnose and monitor its recurrences.
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Affiliation(s)
| | - Thomas Reynolds
- NEXT Bio-Research Services, LLC, 11601 Ironbridge Road, Suite 101, Chester, VA 23831, USA;
| | - Maxie Gordon
- BCD Innovations USA, 10606 Candlewick Road, Lutherville, MD 2109, USA
| | - David Moon
- HJM Cancer Research Foundation Corporation, 10606 Candlewick Road, Lutherville, MD 2109, USA
| | - Chulso Moon
- HJM Cancer Research Foundation Corporation, 10606 Candlewick Road, Lutherville, MD 2109, USA
- BCD Innovations USA, 10606 Candlewick Road, Lutherville, MD 2109, USA
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins Medical Institution, Cancer Research Building II, 5M3, 1550 Orleans Street, Baltimore, MD 21205, USA
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12
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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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13
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Oh TJ, Lee JY, Seo Y, Woo MA, Lim JS, Na YG, Song KH, Bang BR, Lee JJ, Shin JH, An S. Evaluation of Sensitive Urine DNA-Based PENK Methylation Test for Detecting Bladder Cancer in Patients with Hematuria. J Mol Diagn 2023; 25:646-654. [PMID: 37330048 DOI: 10.1016/j.jmoldx.2023.05.003] [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: 02/04/2023] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023] Open
Abstract
Hematuria is a prevalent symptom associated with bladder cancer (BC). However, the invasiveness and cost of cystoscopy, the current gold standard for BC diagnosis in patients with hematuria, necessitate the development of a sensitive and accurate noninvasive test. This study introduces and validates a highly sensitive urine-based DNA methylation test. The test improves sensitivity in detecting PENK methylation in urine DNA using linear target enrichment followed by quantitative methylation-specific PCR. In a case-control study comprising 175 patients with BC and 143 patients without BC with hematuria, the test's optimal cutoff value was determined by distinguishing between two groups, achieved an overall sensitivity of 86.9% and a specificity of 91.6%, with an area under the curve of 0.892. A prospective validation clinical study involving 366 patients with hematuria scheduled for cystoscopy assessed the test's performance. The test demonstrated an overall sensitivity of 84.2% in detecting 38 cases of BC, a specificity of 95.7%, and an area under the curve of 0.900. Notably, the sensitivity for detecting Ta high grade and higher stages of BC reached 92.3%. The test's negative predictive value was 98.2%, and the positive predictive value was 68.7%. These findings highlight the potential of the PENK methylation in urine DNA using linear target enrichment followed by quantitative methylation-specific PCR test in urine as a promising molecular diagnostic tool for detecting primary BC in patients with hematuria, which may reduce the need for cystoscopy.
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Affiliation(s)
| | - Ji Yong Lee
- Department of Urology, Chungnam National University College of Medicine, Daejeon, South Korea
| | | | - Min A Woo
- Genomictree, Inc., Daejeon, South Korea
| | - Jae Sung Lim
- Department of Urology, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Yong Gil Na
- Department of Urology, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Ki Hak Song
- Department of Urology, Chungnam National University College of Medicine, Daejeon, South Korea
| | | | | | - Ju Hyun Shin
- Department of Urology, Chungnam National University College of Medicine, Daejeon, South Korea.
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14
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Chin FW, Chan SC, Veerakumarasivam A. Homeobox Gene Expression Dysregulation as Potential Diagnostic and Prognostic Biomarkers in Bladder Cancer. Diagnostics (Basel) 2023; 13:2641. [PMID: 37627900 PMCID: PMC10453580 DOI: 10.3390/diagnostics13162641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/27/2023] Open
Abstract
Homeobox genes serve as master regulatory transcription factors that regulate gene expression during embryogenesis. A homeobox gene may have either tumor-promoting or tumor-suppressive properties depending on the specific organ or cell lineage where it is expressed. The dysregulation of homeobox genes has been reported in various human cancers, including bladder cancer. The dysregulated expression of homeobox genes has been associated with bladder cancer clinical outcomes. Although bladder cancer has high risk of tumor recurrence and progression, it is highly challenging for clinicians to accurately predict the risk of tumor recurrence and progression at the initial point of diagnosis. Cystoscopy is the routine surveillance method used to detect tumor recurrence. However, the procedure causes significant discomfort and pain that results in poor surveillance follow-up amongst patients. Therefore, the development of reliable non-invasive biomarkers for the early detection and monitoring of bladder cancer is crucial. This review provides a comprehensive overview of the diagnostic and prognostic potential of homeobox gene expression dysregulation in bladder cancer.
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Affiliation(s)
- Fee-Wai Chin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Soon-Choy Chan
- School of Liberal Arts, Science and Technology, Perdana University, Kuala Lumpur 50490, Malaysia
| | - Abhi Veerakumarasivam
- School of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
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15
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Coppedè F, Bhaduri U, Stoccoro A, Nicolì V, Di Venere E, Merla G. DNA Methylation in the Fields of Prenatal Diagnosis and Early Detection of Cancers. Int J Mol Sci 2023; 24:11715. [PMID: 37511475 PMCID: PMC10380460 DOI: 10.3390/ijms241411715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The central objective of the metamorphosis of discovery science into biomedical applications is to serve the purpose of patients and curtail the global disease burden. The journey from the discovery of DNA methylation (DNAm) as a biological process to its emergence as a diagnostic tool is one of the finest examples of such metamorphosis and has taken nearly a century. Particularly in the last decade, the application of DNA methylation studies in the clinic has been standardized more than ever before, with great potential to diagnose a multitude of diseases that are associated with a burgeoning number of genes with this epigenetic alteration. Fetal DNAm detection is becoming useful for noninvasive prenatal testing, whereas, in very preterm infants, DNAm is also shown to be a potential biological indicator of prenatal risk factors. In the context of cancer, liquid biopsy-based DNA-methylation profiling is offering valuable epigenetic biomarkers for noninvasive early-stage diagnosis. In this review, we focus on the applications of DNA methylation in prenatal diagnosis for delivering timely therapy before or after birth and in detecting early-stage cancers for better clinical outcomes. Furthermore, we also provide an up-to-date commercial landscape of DNAm biomarkers for cancer detection and screening of cancers of unknown origin.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- Interdepartmental Research Center of Biology and Pathology of Aging, University of Pisa, 56126 Pisa, Italy
| | - Utsa Bhaduri
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Eleonora Di Venere
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
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16
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Jordaens S, Oeyen E, Willems H, Ameye F, De Wachter S, Pauwels P, Mertens I. Protein Biomarker Discovery Studies on Urinary sEV Fractions Separated with UF-SEC for the First Diagnosis and Detection of Recurrence in Bladder Cancer Patients. Biomolecules 2023; 13:932. [PMID: 37371512 DOI: 10.3390/biom13060932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Urinary extracellular vesicles (EVs) are an attractive source of bladder cancer biomarkers. Here, a protein biomarker discovery study was performed on the protein content of small urinary EVs (sEVs) to identify possible biomarkers for the primary diagnosis and recurrence of non-muscle-invasive bladder cancer (NMIBC). The sEVs were isolated by ultrafiltration (UF) in combination with size-exclusion chromatography (SEC). The first part of the study compared healthy individuals with NMIBC patients with a primary diagnosis. The second part compared tumor-free patients with patients with a recurrent NMIBC diagnosis. The separated sEVs were in the size range of 40 to 200 nm. Based on manually curated high quality mass spectrometry (MS) data, the statistical analysis revealed 69 proteins that were differentially expressed in these sEV fractions of patients with a first bladder cancer tumor vs. an age- and gender-matched healthy control group. When the discriminating power between healthy individuals and first diagnosis patients is taken into account, the biomarkers with the most potential are MASP2, C3, A2M, CHMP2A and NHE-RF1. Additionally, two proteins (HBB and HBA1) were differentially expressed between bladder cancer patients with a recurrent diagnosis vs. tumor-free samples of bladder cancer patients, but their biological relevance is very limited.
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Affiliation(s)
- Stephanie Jordaens
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Eline Oeyen
- Health Unit, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
- Centre for Proteomics (CfP), University of Antwerp, 2020 Antwerp, Belgium
| | - Hanny Willems
- Health Unit, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
| | - Filip Ameye
- Department of Urology, AZ Maria Middelares, 9000 Ghent, Belgium
| | - Stefan De Wachter
- Department of Urology, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Inge Mertens
- Health Unit, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
- Centre for Proteomics (CfP), University of Antwerp, 2020 Antwerp, Belgium
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17
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Papavasiliou E, Sills VA, Calanzani N, Harrison H, Snudden C, di Martino E, Cowan A, Behiyat D, Boscott R, Tan S, Bovaird J, Stewart GD, Walter FM, Zhou Y. Diagnostic Performance of Biomarkers for Bladder Cancer Detection Suitable for Community and Primary Care Settings: A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:709. [PMID: 36765672 PMCID: PMC9913596 DOI: 10.3390/cancers15030709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Evidence on the use of biomarkers to detect bladder cancer in the general population is scarce. This study aimed to systematically review evidence on the diagnostic performance of biomarkers which might be suitable for use in community and primary care settings [PROSPERO Registration: CRD42021258754]. Database searches on MEDLINE and EMBASE from January 2000 to May 2022 resulted in 4914 unique citations, 44 of which met inclusion criteria. Included studies reported on 112 biomarkers and combinations. Heterogeneity of designs, populations and outcomes allowed for the meta-analysis of three biomarkers identified in at least five studies (NMP-22, UroVysion, uCyt+). These three biomarkers showed similar discriminative ability (adjusted AUC estimates ranging from 0.650 to 0.707), although for NMP-22 and UroVysion there was significant unexplained heterogeneity between included studies. Narrative synthesis revealed the potential of these biomarkers for use in the general population based on their reported clinical utility, including effects on clinicians, patients, and the healthcare system. Finally, we identified some promising novel biomarkers and biomarker combinations (N < 3 studies for each biomarker/combination) with negative predictive values of ≥90%. These biomarkers have potential for use as a triage tool in community and primary care settings for reducing unnecessary specialist referrals. Despite promising emerging evidence, further validation studies in the general population are required at different stages within the diagnostic pathway.
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Affiliation(s)
- Evie Papavasiliou
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Valerie A. Sills
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Natalia Calanzani
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Hannah Harrison
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Claudia Snudden
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Erica di Martino
- Division of Primary Care, Public Health & Palliative Care, Leeds Institute of Health Sciences, University of Leeds, Leeds LS2 3AA, UK
| | - Andy Cowan
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Dawnya Behiyat
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Rachel Boscott
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Sapphire Tan
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jennifer Bovaird
- Patient & Public Representative c/o The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Fiona M. Walter
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK
| | - Yin Zhou
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
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18
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Zhang J, Xu R, Lu Q, Xu Z, Liu J, Li P, Zhang Y, Zhou C, Luo L, Tang W, Wang Z, Cao M, Cao J, Xu G, Wang L. A Novel Methylation Marker NRN1 plus TERT and FGFR3 Mutation Using Urine Sediment Enables the Detection of Urothelial Bladder Carcinoma. Cancers (Basel) 2023; 15:cancers15030615. [PMID: 36765573 PMCID: PMC9913436 DOI: 10.3390/cancers15030615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation is an early event during tumorigenesis. In the present study, we aimed to construct a methylation diagnostic tool using urine sediment for the detection of urothelial bladder carcinoma, and improved the diagnostic performance of the model by incorporating single-nucleotide polymorphism (SNP) sites. METHODS A three-stage analysis was carried out to construct the model and evaluate the diagnostic performance. In stage I, two small cohorts from Xiangya hospital were recruited to validate and identify the detailed regions of collected methylation biomarkers. In stage II, proof-of-concept study cohorts from the Hunan multicenter were recruited to construct a diagnostic tool. In stage III, a blinded cohort comprising suspicious UBC patients was recruited from Beijing single center to further test the robustness of the model. RESULTS In stage I, single NRN1 exhibited the highest AUC compared with six other biomarkers and the Random Forest model. At the best cutoff value of 5.16, a single NRN1 biomarker gave a diagnosis with a sensitivity of 0.93 and a specificity of 0.97. In stage II, the Random Forest algorithm was applied to construct a diagnostic tool, consisting of NRN1, TERT C228T and FGFR3 p.S249C. The tool exhibited AUC values of 0.953, 0.946 and 0.951 in training, test and all cohorts. At the best cutoff value, the model resulted in a sensitivity of 0.871 and a specificity of 0.947. In stage III, the diagnostic tool achieved a good discrimination in the external validation cohort, with an overall AUC of 0.935, sensitivity of 0.864 and specificity of 0.895. Additionally, the model exhibited a superior sensitivity and comparable specificity compared with conventional cytology and FISH. CONCLUSIONS The diagnostic tool exhibited a highly specific and robust performance. It may be used as a replaceable approach for the detection of UBC.
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Affiliation(s)
- Junjie Zhang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha 410013, China
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ran Xu
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410028, China
| | - Qiang Lu
- Department of Urology, Hunan Provincial People’s Hospital, First Affiliated Hospital of Hunan Normal University, Changsha 410002, China
| | - Zhenzhou Xu
- Department of Urology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medical, Central South University, Changsha 410013, China
| | - Jianye Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Pei Li
- Hunan Yearth Biotechnology Co., Ltd., Changsha 410205, China
| | - Yaqun Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Chuanchi Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Lufeng Luo
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Wei Tang
- Hunan Yearth Biotechnology Co., Ltd., Changsha 410205, China
| | - Zhenting Wang
- Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Changsha 410017, China
| | - Manman Cao
- Hunan Yearth Biotechnology Co., Ltd., Changsha 410205, China
| | - Jian Cao
- Department of Urology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medical, Central South University, Changsha 410013, China
| | - Genming Xu
- Hunan Yearth Biotechnology Co., Ltd., Changsha 410205, China
- Correspondence: (G.X.); (L.W.)
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha 410013, China
- Correspondence: (G.X.); (L.W.)
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19
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Ibrahim J, Peeters M, Van Camp G, Op de Beeck K. Methylation biomarkers for early cancer detection and diagnosis: Current and future perspectives. Eur J Cancer 2023; 178:91-113. [PMID: 36427394 DOI: 10.1016/j.ejca.2022.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/17/2022] [Indexed: 11/25/2022]
Abstract
The increase in recent scientific studies on cancer biomarkers has brought great new insights into the field. Moreover, novel technological breakthroughs such as long read sequencing and microarrays have enabled high throughput profiling of many biomarkers, while advances in bioinformatic tools have made the possibility of developing highly reliable and accurate biomarkers a reality. These changes triggered renewed interest in biomarker research and provided tremendous opportunities for enhancing cancer management and improving early disease detection. DNA methylation alterations are known to accompany and contribute to carcinogenesis, making them promising biomarkers for cancer, namely due to their stability, frequency and accessibility in bodily fluids. The advent of newer minimally invasive experimental methods such as liquid biopsies provide the perfect setting for methylation-based biomarker development and application. Despite their huge potential, accurate and robust biomarkers for the conclusive diagnosis of most cancer types are still not routinely used, hence a strong need for sustained research in this field is still needed. This review provides a brief exposition of current methylation biomarkers for cancer diagnosis and early detection, including markers already in clinical use as well as various upcoming ones. It also outlines how recent big data and novel technologies will revolutionise the next generation of cancer tests in supplementing or replacing currently existing invasive techniques.
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Affiliation(s)
- Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium; Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
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20
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Davalos V, Esteller M. Cancer epigenetics in clinical practice. CA Cancer J Clin 2022. [PMID: 36512337 DOI: 10.3322/caac.21765] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/07/2022] [Accepted: 10/20/2022] [Indexed: 12/15/2022] Open
Abstract
Cancer development is driven by the accumulation of alterations affecting the structure and function of the genome. Whereas genetic changes disrupt the DNA sequence, epigenetic alterations contribute to the acquisition of hallmark tumor capabilities by regulating gene expression programs that promote tumorigenesis. Shifts in DNA methylation and histone mark patterns, the two main epigenetic modifications, orchestrate tumor progression and metastasis. These cancer-specific events have been exploited as useful tools for diagnosis, monitoring, and treatment choice to aid clinical decision making. Moreover, the reversibility of epigenetic modifications, in contrast to the irreversibility of genetic changes, has made the epigenetic machinery an attractive target for drug development. This review summarizes the most advanced applications of epigenetic biomarkers and epigenetic drugs in the clinical setting, highlighting commercially available DNA methylation-based assays and epigenetic drugs already approved by the US Food and Drug Administration.
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Affiliation(s)
- Veronica Davalos
- Josep Carreras Leukaemia Research Institute, Badalona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer, Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avancats, Barcelona, Catalonia, Spain
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21
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Buckley DN, Gooden G, Feng K, Enk J, Salhia B. Targeted DNA methylation from cell-free DNA using hybridization probe capture. NAR Genom Bioinform 2022; 4:lqac099. [PMID: 36601578 PMCID: PMC9803870 DOI: 10.1093/nargab/lqac099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 01/01/2023] Open
Abstract
Cell-free (cf)DNA signatures are quickly becoming the target of choice for non-invasive screening, diagnosis, treatment and monitoring of human tumors. DNA methylation changes occur early in tumorigenesis and are widespread, making cfDNA methylation an attractive cancer biomarker. Already a proven technology for targeted genome sequencing, hybridization probe capture is emerging as a method for high-throughput targeted methylation profiling suitable to liquid biopsy samples. However, to date there are no reports describing the performance of this approach in terms of reproducibility, scalability, and accuracy. In the current study we performed hybridization probe capture using the myBaits® Custom Methyl-seq kit on 172 plasma samples and standards to evaluate its performance on cfDNA methylation analysis. The myBaits® assay showed high target recovery (>90%), demonstrated excellent reproducibility between captures (R 2 = 0.92 on average), and was unaffected by increasing the number of targets in a capture. Finally, myBaits® accurately replicated 'gold standard' beta values from WGBS (average R 2 = 0.79). The results of this study show that custom targeted methylation sequencing with myBaits® offers a cost-effective, reliable platform to profile DNA methylation at a set of discrete custom regions, with potential applicability to liquid biopsies for cancer monitoring.
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Affiliation(s)
- David N Buckley
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gerald Gooden
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kuan Feng
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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22
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Pharo HD, Jeanmougin M, Ager-Wick E, Vedeld HM, Sørbø AK, Dahl C, Larsen LK, Honne H, Brandt-Winge S, Five MB, Monteiro-Reis S, Henrique R, Jeronimo C, Steven K, Wahlqvist R, Guldberg P, Lind GE. BladMetrix: a novel urine DNA methylation test with high accuracy for detection of bladder cancer in hematuria patients. Clin Epigenetics 2022; 14:115. [PMID: 36115961 PMCID: PMC9482155 DOI: 10.1186/s13148-022-01335-2] [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: 07/06/2022] [Accepted: 09/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cystoscopy is the gold standard for bladder cancer detection, but is costly, invasive and has imperfect diagnostic accuracy. We aimed to identify novel and accurate DNA methylation biomarkers for non-invasive detection of bladder cancer in urine, with the potential to reduce the number of cystoscopies among hematuria patients. Results Biomarker candidates (n = 32) were identified from methylome sequencing of urological cancer cell lines (n = 16) and subjected to targeted methylation analysis in tissue samples (n = 60). The most promising biomarkers (n = 8) were combined into a panel named BladMetrix. The performance of BladMetrix in urine was assessed in a discovery series (n = 112), consisting of bladder cancer patients, patients with other urological cancers and healthy individuals, resulting in 95.7% sensitivity and 94.7% specificity. BladMetrix was furthermore evaluated in an independent prospective and blinded series of urine from patients with gross hematuria (n = 273), achieving 92.1% sensitivity, 93.3% specificity and a negative predictive value of 98.1%, with the potential to reduce the number of cystoscopies by 56.4%. Conclusions We here present BladMetrix, a novel DNA methylation urine test for non-invasive detection of bladder cancer, with high accuracy across tumor grades and stages, and the ability to spare a significant number of cystoscopies among patients with gross hematuria. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01335-2.
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23
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Harsanyi S, Novakova ZV, Bevizova K, Danisovic L, Ziaran S. Biomarkers of Bladder Cancer: Cell-Free DNA, Epigenetic Modifications and Non-Coding RNAs. Int J Mol Sci 2022; 23:13206. [PMID: 36361996 PMCID: PMC9653602 DOI: 10.3390/ijms232113206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/29/2022] Open
Abstract
Bladder cancer (BC) is the 10th most frequent cancer in the world. The initial diagnosis and surveillance of BC require a combination of invasive and non-invasive methods, which are costly and suffer from several limitations. Cystoscopy with urine cytology and histological examination presents the standard diagnostic approach. Various biomarkers (e.g., proteins, genes, and RNAs) have been extensively studied in relation to BC. However, the new trend of liquid biopsy slowly proves to be almost equally effective. Cell-free DNA, non-coding RNA, and other subcellular structures are now being tested for the best predictive and diagnostic value. In this review, we focused on published gene mutations, especially in DNA fragments, but also epigenetic modifications, and non-coding RNA (ncRNA) molecules acquired by liquid biopsy. We performed an online search in PubMed/Medline, Scopus, and Web of Science databases using the terms "bladder cancer", in combination with "markers" or "biomarkers" published until August 2022. If applicable, we set the sensitivity and specificity threshold to 80%. In the era of precision medicine, the development of complex laboratory techniques fuels the search and development of more sensitive and specific biomarkers for diagnosis, follow-up, and screening of BC. Future efforts will be focused on the validation of their sensitivity, specificity, predictive value, and their utility in everyday clinical practice.
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Affiliation(s)
- Stefan Harsanyi
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Zuzana Varchulova Novakova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Katarina Bevizova
- Institute of Anatomy, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 2, 811 08 Bratislava, Slovakia
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Stanislav Ziaran
- Department of Urology, Faculty of Medicine, Comenius University in Bratislava, Limbova 5, 833 05 Bratislava, Slovakia
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24
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Malinaric R, Mantica G, Lo Monaco L, Mariano F, Leonardi R, Simonato A, Van der Merwe A, Terrone C. The Role of Novel Bladder Cancer Diagnostic and Surveillance Biomarkers-What Should a Urologist Really Know? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159648. [PMID: 35955004 PMCID: PMC9368399 DOI: 10.3390/ijerph19159648] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/29/2022] [Accepted: 07/31/2022] [Indexed: 05/20/2023]
Abstract
The aim of this review is to analyze and describe the current landscape of bladder cancer diagnostic and surveillance biomarkers. We researched the literature from 2016 to November 2021 to find the most promising new molecules and divided them into seven different subgroups based on their function and location in the cell. Although cystoscopy and cytology are still the gold standard for diagnosis and surveillance when it comes to bladder cancer (BCa), their cost is quite a burden for national health systems worldwide. Currently, the research is focused on finding a biomarker that has high negative predictive value (NPV) and can exclude with a certainty the presence of the tumor, considering missing it could be disastrous for the patient. Every subgroup has its own advantages and disadvantages; for example, protein biomarkers cost less than genomic ones, but on the other hand, they seem to be less precise. We tried to simplify this complicated topic as much as possible in order to make it comprehensible to doctors and urologists that are not as familiar with it, as well as encourage them to actively participate in ongoing research.
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Affiliation(s)
- Rafaela Malinaric
- Department of Urology, IRCCS Policlinic Hospital San Martino, 16132 Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate (DISC), University of Genoa, 16132 Genoa, Italy
- Correspondence:
| | - Guglielmo Mantica
- Department of Urology, IRCCS Policlinic Hospital San Martino, 16132 Genoa, Italy
| | - Lorenzo Lo Monaco
- Department of Urology, IRCCS Policlinic Hospital San Martino, 16132 Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate (DISC), University of Genoa, 16132 Genoa, Italy
| | - Federico Mariano
- Department of Urology, IRCCS Policlinic Hospital San Martino, 16132 Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate (DISC), University of Genoa, 16132 Genoa, Italy
| | - Rosario Leonardi
- Department of Urology, Casa di Cura Musumeci GECAS, 95030 Gravina di Catania, Italy
| | - Alchiede Simonato
- Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, 90133 Palermo, Italy
| | - André Van der Merwe
- Department of Urology, Tygerberg Academic Hospital, Stellenbosch University, Cape Town 7600, South Africa
| | - Carlo Terrone
- Department of Urology, IRCCS Policlinic Hospital San Martino, 16132 Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate (DISC), University of Genoa, 16132 Genoa, Italy
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25
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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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26
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Schulz A, Loloi J, Pina Martina L, Sankin A. The Development of Non-Invasive Diagnostic Tools in Bladder Cancer. Onco Targets Ther 2022; 15:497-507. [PMID: 35529887 PMCID: PMC9075009 DOI: 10.2147/ott.s283891] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Bladder cancer is a common urinary tract cancer with a difficult clinical course. With frequent recurrence, patients with a history of bladder cancer often undergo surveillance that involves invasive cystoscopies and biopsies. Not only is this financially burdensome for patients but it is also mentally and physically intensive. Given this predicament, the field has shifted towards the use of non-invasive urinary tests to detect bladder cancer earlier in the disease course and to avoid unnecessary procedures. The first non-invasive test developed was urine cytology; however, that was found to have a low sensitivity, especially for low-grade lesions. There are many tests that are available that utilize common protein biomarkers to enhance the sensitivity of detection. However, many of these tests lack the specificity seen with cytology. With recent technological and research advancements, there are newer detection systems such as RNA sequencing and microfluidics along with novel bladder cancer biomarkers including mRNAs, methylation patterns and exosomes, which have potential to be used in clinical practice. The aim of this review is to highlight established non-invasive bladder cancer diagnostic tests as well as innovative methodologies that are on the horizon for use in bladder cancer detection.
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Affiliation(s)
- Alison Schulz
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Justin Loloi
- Department of Urology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 11061, USA
| | - Luis Pina Martina
- Department of Urology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 11061, USA
| | - Alexander Sankin
- Department of Urology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 11061, USA
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27
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Crocetto F, Barone B, Ferro M, Busetto GM, La Civita E, Buonerba C, Di Lorenzo G, Terracciano D, Schalken JA. Liquid biopsy in bladder cancer: State of the art and future perspectives. Crit Rev Oncol Hematol 2022; 170:103577. [PMID: 34999017 DOI: 10.1016/j.critrevonc.2022.103577] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 01/01/2023] Open
Abstract
Bladder cancer is the most common malignancy of the urinary tract. Cystoscopy represents the gold standard in the diagnosis of suspicious bladder lesions. However, the procedure is invasive and burdened by pain, discomfort and infective complications. Cytology, which represents an alternative diagnostic possibility is limited by poor sensitivity. Considering the limitations of both procedures, and the necessity to perform multiple evaluations in patients who are in follow-up for bladder cancer, an improved non-invasive methodology is required in the clinical management of this disease. Liquid biopsy, e.g. the detection of clinical biomarkers in urine, represent a promising novel and non-invasive approach that could overcome those limitations and be integrated into the current clinical practice. The aim of this review is to summarize the state of the art of this approach and the latest novelties regarding detection, prognosis and surveillance of bladder cancer.
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Affiliation(s)
- Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples "Federico II", Naples, Italy
| | - Biagio Barone
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples "Federico II", Naples, Italy.
| | - Matteo Ferro
- Department of Urology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Gian Maria Busetto
- Urology and Renal Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
| | - Carlo Buonerba
- Oncology Unit, Hospital "Andrea Tortora", ASL Salerno, Pagani, Italy
| | - Giuseppe Di Lorenzo
- Oncology Unit, Hospital "Andrea Tortora", ASL Salerno, Pagani, Italy; Department of Medicine and Health Science, University of Molise, Campobasso, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
| | - Jack A Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
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28
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Sugeeta SS, Sharma A, Ng K, Nayak A, Vasdev N. Biomarkers in Bladder Cancer Surveillance. Front Surg 2021; 8:735868. [PMID: 34651010 PMCID: PMC8506024 DOI: 10.3389/fsurg.2021.735868] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/25/2021] [Indexed: 01/15/2023] Open
Abstract
Aim: This is a narrative review with an aim to summarise and describe urinary biomarkers in the surveillance of non-muscle-invasive bladder cancer (NMIBC). It provides a summary of FDA-approved protein biomarkers along with emerging ones which utilise genetic, epigenetic and exosomal markers. We discuss the current limitations of the available assays. Background: Current guidelines advice a combination of cystoscopy, imaging,and urine cytology in diagnosis and surveillance. Although cytology has a high specificity, it is limited by low sensitivity particularly in low grade tumours. There are six FDA-approved urinary assays for diagnosis and surveillance of bladder cancer. They have shown to improve sensitivity and specificity to be used alongside cytology and cystoscopy but have a lower specificity in comparison to cytology and false positives often occur in benign conditions. Recent developments in laboratory techniques has allowed for use of markers which are RNA-, DNA-based as well as extracellular vesicles in the past decade. Methods: Using the PubMed/Medline search engines as well as Google Scholar, we performed an online search using the terms "bladder cancer," "non-muscle invasive bladder cancer," and "urine biomarkers" with filter for articles in English published up to May 2021. Systematic reviews and original data of clinical trials or observational studies which contributed to the development of the biomarkers were collated. Results: Biomarkers identified were divided into FDA-approved molecular biomarkers, protein biomarkers and gene-related biomarker with a table summarising the findings of each marker with the most relevant studies. The studies conducted were mainly retrospective. Due to the early stages of development, only a few prospective studies have been done for more recently developed biomarkers and limited meta-analyses are available.Therefore a detailed evaluation of these markers are still required to decide on their clinical use. Conclusion: Advancements of analytical methods in BC has driven the research towards non-invasive liquid-based biomarkers in adjunct to urine cytology. Further large prospective studies are required to determine its feasibility in a clinical setting as they are not effective when used in isolation as they have their limitation. With the ongoing pandemic, other than reduction in costs and increased accuracy, the need for biomarkers to cope with delay in cystoscopies in diagnosis and surveillance is crucial. Thus clinical trials with direct comparison is required to improve patient care.
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Affiliation(s)
- Sukumar S. Sugeeta
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, United Kingdom
| | - Anand Sharma
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, United Kingdom
| | - Kenrick Ng
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, United Kingdom
| | - Arvind Nayak
- Department of Urology and Surgery, Lister Hospital, East and North Herts NHS Trust, Stevenage, United Kingdom
| | - Nikhil Vasdev
- Department of Urology and Surgery, Lister Hospital, East and North Herts NHS Trust, Stevenage, United Kingdom
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
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29
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Piao XM, Kang H, Kim WJ, Yun SJ. Prominence of urinary biomarkers for bladder cancer in the COVID-19 era: From the commercially available to new prospective candidates. Investig Clin Urol 2021; 62:500-519. [PMID: 34488250 PMCID: PMC8421991 DOI: 10.4111/icu.20210194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Molecular markers detected in urine may improve our understanding of the evolution of bladder cancer (BCa) and its micro- and macroenvironment. Detection of such markers will identify disease earlier, allow stratification of patients according to risk, and improve prognostication and prediction of outcomes, thereby facilitating targeted therapy. However, current guidelines have yet to embrace such markers for routine management of BCa, and most research studies have focused on urine-based tumor markers. In this review, we summarize known urinary biomarkers for BCa and highlight newly identified molecules. We then discuss the challenges that must be overcome to incorporate these markers into clinical care.
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Affiliation(s)
- Xuan-Mei Piao
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Howon Kang
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Wun-Jae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
- Institute of Urotech, Cheongju, Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea.
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Bladder cancer risk stratification using a urinary mRNA biomarker panel - A path towards cystoscopy triaging. Urol Oncol 2021; 39:497.e9-497.e15. [PMID: 33766467 DOI: 10.1016/j.urolonc.2021.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/02/2021] [Accepted: 02/09/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES The risk of bladder cancer (BCa) diagnosis and recurrence necessitates cystoscopy. Improved risk stratification may inform personalized triage and surveillance strategies. We aim to develop a urinary mRNA biomarker panel for risk stratification in patients undergoing BCa screening and surveillance. METHODS AND MATERIALS Urine samples were collected from patients undergoing cystoscopy for BCa screening or surveillance. In patients who underwent transurethral resection of bladder tumor, urine samples were categorized based on tumor histopathology, size, and focality. Subjects with intermediate and high-risk BCa based on American Urological Association (AUA) guideline for non-muscle invasive bladder cancer were classified as "increased-risk"; those with no cancer and AUA low-risk BCa were classified as "low-risk". Urine was evaluated for ROBO1, WNT5A, CDC42BPB, ABL1, CRH, IGF2, ANXA10, and UPK1B expression. A diagnostic model to detect "increased-risk" BCa was created using forward logistic regression analysis of cycle threshold values. Model validation was performed with ten-fold cross-validation. Sensitivity and specificity for detection of "increased-risk" BCa was determined and net benefit analysis performed. RESULTS Urine samples (n = 257) were collected from 177 patients (95 screening, 76 surveillance, 6 both). There were 65 diagnoses of BCa (12 low, 22 intermediate, 31 high risk). ROBO1, CRH, and IGF2 expression correlated with "increased-risk" disease yielding sensitivity of 92.5% (95% CI, 84.9%-98.1%) and specificity of 73.5% (95% CI, 67.7-79.9%). The overall calculated standardized net benefit of the model was 0.81 (95%CI, 0.71-0.90). CONCLUSIONS A 3-marker urinary mRNA panel allows for non-invasive identification of "increased-risk" BCa and with further validation may prove to be a tool to reduce the need for cystoscopies in low-risk patients.
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Ferro M, La Civita E, Liotti A, Cennamo M, Tortora F, Buonerba C, Crocetto F, Lucarelli G, Busetto GM, Del Giudice F, de Cobelli O, Carrieri G, Porreca A, Cimmino A, Terracciano D. Liquid Biopsy Biomarkers in Urine: A Route towards Molecular Diagnosis and Personalized Medicine of Bladder Cancer. J Pers Med 2021; 11:jpm11030237. [PMID: 33806972 PMCID: PMC8004687 DOI: 10.3390/jpm11030237] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
Bladder cancer (BC) is characterized by high incidence and recurrence rates together with genomic instability and elevated mutation degree. Currently, cystoscopy combined with cytology is routinely used for diagnosis, prognosis and disease surveillance. Such an approach is often associated with several side effects, discomfort for the patient and high economic burden. Thus, there is an essential demand of non-invasive, sensitive, fast and inexpensive biomarkers for clinical management of BC patients. In this context, liquid biopsy represents a very promising tool that has been widely investigated over the last decade. Liquid biopsy will likely be at the basis of patient selection for precision medicine, both in terms of treatment choice and real-time monitoring of therapeutic effects. Several different urinary biomarkers have been proposed for liquid biopsy in BC, including DNA methylation and mutations, protein-based assays, non-coding RNAs and mRNA signatures. In this review, we summarized the state of the art on different available tests concerning their potential clinical applications for BC detection, prognosis, surveillance and response to therapy.
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Affiliation(s)
- Matteo Ferro
- Department of Urology of European Institute of Oncology (IEO), IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (M.F.); (O.d.C.)
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
| | - Antonietta Liotti
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
| | - Fabiana Tortora
- Institute of Protein Biochemistry, National Research Council, 80131 Naples, Italy;
| | - Carlo Buonerba
- CRTR Rare Tumors Reference Center, AOU Federico II, 80131 Naples, Italy;
- Environment & Health Operational Unit, Zoo-Prophylactic Institute of Southern Italy, 80055 Portici, Italy
| | - Felice Crocetto
- Department of Neurosciences, Sciences of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy;
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation, Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy;
| | - Gian Maria Busetto
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy;
| | - Francesco Del Giudice
- Department of Urology, Sapienza University of Rome, 00185 Rome, Italy; (F.D.G.); (G.C.)
| | - Ottavio de Cobelli
- Department of Urology of European Institute of Oncology (IEO), IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (M.F.); (O.d.C.)
- Dipartimento di Oncologia ed Ematoncologia-DIPO-Università degli Studi di Milano, 20122 Milan, Italy
| | - Giuseppe Carrieri
- Department of Urology, Sapienza University of Rome, 00185 Rome, Italy; (F.D.G.); (G.C.)
| | - Angelo Porreca
- Department of Urology, Veneto Institute of Oncology, 31033 Padua, Italy;
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, 80131 Naples, Italy
- Correspondence: or (A.C.); (D.T.); Tel.: +39-81-746-3617 (D.T.)
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
- Correspondence: or (A.C.); (D.T.); Tel.: +39-81-746-3617 (D.T.)
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Zeng Q, Wang S, Tan J, Chen L, Wang J. The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study. PeerJ 2021; 9:e10830. [PMID: 33717678 PMCID: PMC7934648 DOI: 10.7717/peerj.10830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022] Open
Abstract
Tumor-derived circulating tumor DNA (ctDNA) has demonstrated its excellent potential for cancer diagnosis by DNA methylome; therefore, this study aimed to identify the retinoblastoma (RB) specific methylated CpG loci as the RB diagnostic biomarkers and design a methylation specific assay to detect these biomarker from aqueous humor of RB patients. Through a genome-wide methylation profiling of tissue samples from patients with RB, normal retina and other retinal diseases, we shortlisted two CpG loci were only methylated in RB but not in normal retina or other retinal diseases. Both of these two CpG loci were located in the genome of TFAP2A. Through the screening, a primer and probe set for the two CpG loci were tested in fully methylated standards and RB tissues with a significant differentiation of RB. Our results of this assay tested in aqueous humor from RB revealed an accuracy of 92.7% for RB diagnosis. These results suggested our assay targeting the TFAP2A ctDNA methylation can be utilized for RB diagnosis and cancer monitoring.
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Affiliation(s)
- Qi Zeng
- Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Sha Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, China
| | - Jia Tan
- Eye Center of Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, China
| | - Lu Chen
- Eye Center of Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, China
| | - Jinwei Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, China
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Xu Y, Ma X, Ai X, Gao J, Liang Y, Zhang Q, Ma T, Mao K, Zheng Q, Wang S, Jiao Y, Zhang X, Li H. A Urine-Based Liquid Biopsy Method for Detection of Upper Tract Urinary Carcinoma. Front Oncol 2021; 10:597486. [PMID: 33634022 PMCID: PMC7901537 DOI: 10.3389/fonc.2020.597486] [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: 08/21/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Background Conventional clinical detection methods such as CT, urine cytology, and ureteroscopy display low sensitivity and/or are invasive in the diagnosis of upper tract urinary carcinoma (UTUC), a factor precluding their use. Previous studies on urine biopsy have not shown satisfactory sensitivity and specificity in the application of both gene mutation or gene methylation panels. Therefore, these unfavorable factors call for an urgent need for a sensitive and non-invasive method for the diagnosis of UTUC. Methods In this study, a total of 161 hematuria patients were enrolled with (n = 69) or without (n = 92) UTUC. High-throughput sequencing of 17 genes and methylation analysis for ONECUT2 CpG sites were combined as a liquid biopsy test panel. Further, a logistic regression prediction model that contained several significant features was used to evaluate the risk of UTUC in these patients. Results In total, 86 UTUC− and 64 UTUC+ case samples were enrolled for the analysis. A logistic regression analysis of significant features including age, the mutation status of TERT promoter, and ONECUT2 methylation level resulted in an optimal model with a sensitivity of 94.0%, a specificity of 93.1%, the positive predictive value of 92.2% and a negative predictive value of 94.7%. Notably, the area under the curve (AUC) was 0.957 in the training dataset while internal validation produced an AUC of 0.962. It is worth noting that during follow-up, a patient diagnosed with ureteral inflammation at the time of diagnosis exhibiting both positive mutation and methylation test results was diagnosed with ureteral carcinoma 17 months after his enrollment. Conclusion This work utilized the epigenetic biomarker ONECUT2 for the first time in the detection of UTUC and discovered its superior performance. To improve its sensitivity, we combined the biomarker with high-throughput sequencing of 17 genes test. It was found that the selected logistic regression model diagnosed with ureteral cancer can evaluate upper tract urinary carcinoma risk of patients with hematuria and outperform other existing panels in providing clinical recommendations for the diagnosis of UTUC. Moreover, its high negative predictive value is conducive to rule to exclude patients without UTUC.
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Affiliation(s)
- Yansheng Xu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China.,Department of Urology, The Sixth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xin Ma
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xing Ai
- Department of Urology, The Seventh Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiangping Gao
- Department of Urology, The Fourth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yiming Liang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Qin Zhang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Tonghui Ma
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Kaisheng Mao
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Qiaosong Zheng
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Sizhen Wang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xu Zhang
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hongzhao Li
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
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Hong M, He G, Goh S, Low AWX, Tay KJ, Lim TKH, Yeong J, Khor LY, Lim TS. Biomarkers for Precision Urothelial Carcinoma Diagnosis: Current Approaches and the Application of Single-Cell Technologies. Cancers (Basel) 2021; 13:cancers13020260. [PMID: 33445605 PMCID: PMC7827267 DOI: 10.3390/cancers13020260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Urothelial carcinoma (UC) is the most frequently diagnosed cancer of the urinary tract and is ranked the sixth most diagnosed cancer in men worldwide. About 70–75% of newly diagnosed UCs are non-invasive or low grade. Different tests such as urine cytology and cystoscopy are used to detect UC. If abnormal tissue is found during cystoscopy, then a biopsy will be performed. Cytology has low sensitivity for low-grade cancer while cystoscopy is invasive and costly. Detecting UC early improves the chances of treatment success. Therefore, many researchers have painstakingly identified urine biological markers for non-invasive UC diagnosis. In this review, we summarize some of the latest and most promising biological markers (including FDA-approved and investigational markers). We also discuss some new technologies that can aid research efforts in biological marker discovery for early UC detection. Abstract Urothelial carcinoma (UC) is the most frequent malignancy of the urinary system and is ranked the sixth most diagnosed cancer in men worldwide. Around 70–75% of newly diagnosed UC manifests as the non-muscle invasive bladder cancer (NMIBC) subtype, which can be treated by a transurethral resection of the tumor. However, patients require life-long monitoring due to its high rate of recurrence. The current gold standard for UC diagnosis, prognosis, and disease surveillance relies on a combination of cytology and cystoscopy, which is invasive, costly, and associated with comorbidities. Hence, there is considerable interest in the development of highly specific and sensitive urinary biomarkers for the non-invasive early detection of UC. In this review, we assess the performance of current diagnostic assays for UC and highlight some of the most promising biomarkers investigated to date. We also highlight some of the recent advances in single-cell technologies that may offer a paradigm shift in the field of UC biomarker discovery and precision diagnostics.
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Affiliation(s)
- Michelle Hong
- A. Menarini Biomarkers Singapore Pte Ltd., Singapore 117440, Singapore;
| | - George He
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore; (G.H.); (S.G.); (T.K.H.L.)
| | - Siting Goh
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore; (G.H.); (S.G.); (T.K.H.L.)
| | - Alvin Wei Xiang Low
- Department of Urology, Singapore General Hospital, Singapore 169854, Singapore; (A.W.X.L.); (K.J.T.)
| | - Kae Jack Tay
- Department of Urology, Singapore General Hospital, Singapore 169854, Singapore; (A.W.X.L.); (K.J.T.)
| | - Tony Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore; (G.H.); (S.G.); (T.K.H.L.)
| | - Joe Yeong
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore; (G.H.); (S.G.); (T.K.H.L.)
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Correspondence: (J.Y.); (L.Y.K.); (T.S.L.)
| | - Li Yan Khor
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore; (G.H.); (S.G.); (T.K.H.L.)
- Correspondence: (J.Y.); (L.Y.K.); (T.S.L.)
| | - Tong Seng Lim
- A. Menarini Biomarkers Singapore Pte Ltd., Singapore 117440, Singapore;
- Correspondence: (J.Y.); (L.Y.K.); (T.S.L.)
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Hentschel AE, van der Toom EE, Vis AN, Ket JC, Bosschieter J, Heymans MW, van Moorselaar RJA, Steenbergen RD, Nieuwenhuijzen JA. A systematic review on mutation markers for bladder cancer diagnosis in urine. BJU Int 2021; 127:12-27. [PMID: 32539176 PMCID: PMC7818192 DOI: 10.1111/bju.15137] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVES To systematically summarise the available evidence on urinary bladder cancer (BC) mutation markers. Gene mutations are expected to provide novel biomarkers for urinary BC diagnosis. To date, evidence on urinary BC mutation markers has not proven sufficient to be adopted by clinical guidelines. In the present systematic review, diagnostic accuracy of urinary mutation analysis is separately assessed for primary BC diagnosis (BC detection) and for follow-up of BC patients (BC surveillance). METHODS A literature search (PubMed, Embase.com and Wiley/Cochrane Library) and systematic review was performed up to 31 October 2019. As studies were too heterogeneous, no quantitative analysis could be performed. RESULTS In total, 25 studies were summarised by qualitative analysis. For BC detection, diagnostic accuracy differed considerably for single mutation markers (sensitivity 1-85%, specificity 84-100%), and for marker panels (sensitivity 50-94%, specificity 43-97%). Similarly, for BC surveillance, diagnostic accuracy was highly variable for single mutation markers (sensitivity 0-85%, specificity 66-100%), and for marker panels (sensitivity 51-84%, specificity 66-96%). CONCLUSION Urinary mutation analysis showed to be a promising diagnostic tool for non-invasive BC diagnosis. Nonetheless, we observed substantial differences in diagnostic accuracy of urinary BC mutation markers among publications. To translate the data summarised in the present review to future clinical practice, heterogeneity in research design, BC population, mutation analysis technique and urinary DNA should be considered. Eventual clinical implementation of urinary BC mutation markers can only be achieved by collecting more and stronger evidence. Combining different molecular assays might overcome current shortcomings of urinary mutation analysis.
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Affiliation(s)
- Anouk E. Hentschel
- Department ofUrologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Emma E. van der Toom
- Department ofUrologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - André N. Vis
- Department ofUrologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | | | - Judith Bosschieter
- Department ofUrologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Martijn W. Heymans
- Amsterdam, Epidemiology & BiostatisticsAmsterdam Public HealthAmsterdamThe Netherlands
| | - R. Jeroen A. van Moorselaar
- Department ofUrologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Renske D.M. Steenbergen
- Department ofPathologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Jakko A. Nieuwenhuijzen
- Department ofUrologyAmsterdam University Medical CentersCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
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36
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Ghandour RA, Singla N, Lotan Y. Using Urinary Biomarkers in Urothelial Carcinoma of the Bladder and Upper Tracts. Bladder Cancer 2021. [DOI: 10.1007/978-3-030-70646-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Bladder cancer has a very high frequency of recurrence and therefore requires close clinical surveillance throughout its life, with cystoscopies and serial cytological examinations. These tests are both invasive and expensive, with considerable interpersonal and inter-institutional variability. Moreover, cytological examination used for the diagnosis of low-grade tumors has a low sensitivity; thus, there is an increasing focus on the research for new, accurate, urinary markers. Herein, the biological basis, methodologies, and diagnostic performance of biomarkers are discussed.
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Affiliation(s)
- Matteo Costantini
- Department of Pathology, Azienda Ospedaliera-Universitaria Policlinico di Modena, Modena, Italy.
| | - Graziana Gallo
- Department of Pathology, Azienda Ospedaliera-Universitaria Policlinico di Modena, Modena, Italy
| | - Giovanna Attolini
- Department of Pathology, Azienda Ospedaliera-Universitaria Policlinico di Modena, Modena, Italy
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Galardi F, De Luca F, Romagnoli D, Biagioni C, Moretti E, Biganzoli L, Di Leo A, Migliaccio I, Malorni L, Benelli M. Cell-Free DNA-Methylation-Based Methods and Applications in Oncology. Biomolecules 2020; 10:E1677. [PMID: 33334040 PMCID: PMC7765488 DOI: 10.3390/biom10121677] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy based on cell-free DNA (cfDNA) enables non-invasive dynamic assessment of disease status in patients with cancer, both in the early and advanced settings. The analysis of DNA-methylation (DNAm) from cfDNA samples holds great promise due to the intrinsic characteristics of DNAm being more prevalent, pervasive, and cell- and tumor-type specific than genomics, for which established cfDNA assays already exist. Herein, we report on recent advances on experimental strategies for the analysis of DNAm in cfDNA samples. We describe the main steps of DNAm-based analysis workflows, including pre-analytics of cfDNA samples, DNA treatment, assays for DNAm evaluation, and methods for data analysis. We report on protocols, biomolecular techniques, and computational strategies enabling DNAm evaluation in the context of cfDNA analysis, along with practical considerations on input sample requirements and costs. We provide an overview on existing studies exploiting cell-free DNAm biomarkers for the detection and monitoring of cancer in early and advanced settings, for the evaluation of drug resistance, and for the identification of the cell-of-origin of tumors. Finally, we report on DNAm-based tests approved for clinical use and summarize their performance in the context of liquid biopsy.
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Affiliation(s)
- Francesca Galardi
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
| | - Francesca De Luca
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
| | - Dario Romagnoli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy; (D.R.); (C.B.)
| | - Chiara Biagioni
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy; (D.R.); (C.B.)
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Erica Moretti
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Laura Biganzoli
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Angelo Di Leo
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Ilenia Migliaccio
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
| | - Luca Malorni
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy; (D.R.); (C.B.)
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Report From the International Society of Urological Pathology (ISUP) Consultation Conference On Molecular Pathology Of Urogenital Cancers. II. Molecular Pathology of Bladder Cancer: Progress and Challenges. Am J Surg Pathol 2020; 44:e30-e46. [PMID: 32091435 DOI: 10.1097/pas.0000000000001453] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During the 2019 International Society of Urological Pathology Consultation Conference on Molecular Pathology of Urogenital Cancer, the Working Group on Bladder Cancer presented the current status and made recommendations on the diagnostic use of molecular pathology, incorporating a premeeting survey. Bladder cancers are biologically diverse and can be separated into "molecular subtypes," based on expression profiling. These subtypes associate with clinical behavior, histology, and molecular alterations, though their clinical utility has not been demonstrated at present and use in bladder cancer is not recommended. Mutations in the TERT promoter are present in the majority of bladder cancers, including the noninvasive stage of tumor evolution, but not in reactive conditions. Mutational analysis of the TERT promoter thus distinguishes histologically deceptive cancers from their benign mimics in some cases. A minority of pathologists employ this test. FGFR3 mutations are common in bladder cancer, and metastatic urothelial carcinoma (UC) with such mutations frequently responds to erdafitinib, an FGFR inhibitor. Testing for FGFR3 alterations is required before using this drug. Metastatic UC responds to immune-oncology (IO) agents in 20% of cases. These are approved as first and second-line treatments in metastatic UC. Several biological parameters associate with response to IO agents, including tumor mutational burden, molecular subtype, and infiltration by programmed death-ligand 1-positive lymphocytes, detected by immunohistochemistry. Programmed death-ligand 1 immunohistochemistry is mandatory before administering IO agents in the first-line setting. In conclusion, much has been learned about the biology of bladder cancer, and this understanding has improved the care of patients with the disease.
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Lee HH, Kim SH. Review of non-invasive urinary biomarkers in bladder cancer. Transl Cancer Res 2020; 9:6554-6564. [PMID: 35117265 PMCID: PMC8798424 DOI: 10.21037/tcr-20-1990] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022]
Abstract
Bladder cancer (BC) is the sixth-most prevalent cancer. The standard diagnostic tool of BC is cystoscopy, whereas cystoscopy has several disadvantages in terms of symptomatic invasiveness and operator-dependency. The urinary markers are attractive because the testing is non-invasive and cost-efficient, and sample collection is easy. Urinary marker is thereby a good tool to detect exfoliated tumor cell in the urine samples for the diagnosis and therapeutic surveillance of BC to supplement the limitations of the cystoscopy. However, they are not recommended as a population-based screening tool because of the low rate of BC prevalence. Although both cystoscopy and urine cytology improve BC diagnostic power, the field still needs additional non-invasive, cost-effective, and highly sensitive and specific diagnostic tools. Various urinary markers with different mechanisms and different targets have been developed and under investigation in these days. However, the accuracy of the urinary marker including its sensitivity and specificity is the most important factor for the diagnosis and surveillance in cancer that this review deals with multiple FDA-approved and non-FDA approved commercialized urinary markers with their accuracy in different purposes for BC. We then discuss more about the potential candidate targets for the future urinary markers in BC.
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Affiliation(s)
- Hyung-Ho Lee
- Department of Urology, Urological Cancer Center, Research Institute and Hospital of National Cancer Center, Goyang, Korea
| | - Sung Han Kim
- Department of Urology, Urological Cancer Center, Research Institute and Hospital of National Cancer Center, Goyang, Korea
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Ng K, Stenzl A, Sharma A, Vasdev N. Urinary biomarkers in bladder cancer: A review of the current landscape and future directions. Urol Oncol 2020; 39:41-51. [PMID: 32919875 DOI: 10.1016/j.urolonc.2020.08.016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/07/2020] [Accepted: 08/02/2020] [Indexed: 12/23/2022]
Abstract
AIM This narrative review aims to describe established and emerging urinary biomarkers in the diagnosis and surveillance of non-muscle invasive bladder cancer. It provides a comprehensive account of classical, FDA-approved protein biomarkers and discusses their limitations. Further, we discuss the role that epigenetic, genetic, and exosomal markers can play to enhance sensitivity and specificity of the available tests. BACKGROUND The initial diagnosis and surveillance of bladder cancer involves a combination of cystoscopy, upper urinary tract imaging, and urine cytology. Despite high specificity, cytology is limited by low sensitivity. There are currently 6 urinary assays approved by the FDA to enhance diagnosis and surveillance of bladder cancer. While these have improved diagnosis and surveillance when combined with cytology, these tests are still not sufficiently sensitive and false positives often occur in benign conditions which result in inflammation of the urinary tract. Advancements in laboratory techniques have produced significant advancements in epigenetic and genetic markers, as well as extracellular vesicles, with DNA- and RNA-based markers dominating the research in this area in recent years. METHODS We identified relevant published data, using the PubMed/ Medline search engines as well as Google Scholar. We performed an online search using the terms "bladder cancer", "non-muscle invasive bladder cancer" in combination with "urine biomarkers" and limited articles in English published up to February 2020. This review consolidated on all available narrative and systematic reviews published in the 5 years in this field, while also reviewing the original data of each clinical trial or observational study which led to the development of the biomarkers. CONCLUSION The development of laboratory techniques and understanding urine-based biomarkers in BC has fuelled the use of noninvasive liquid-based biomarkers to complement urine cytology. Nonetheless, none are sufficiently effective when used in isolation, and cytology remains the gold standard in many practices. Future efforts will be focused on using these markers in combination as a predictive signature, and moving on to validating them for use in everyday clinical practice.
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Affiliation(s)
- Kenrick Ng
- UCL Cancer Institute, London, United Kindom
| | - Arnulf Stenzl
- Department of Urology, Eberhard-Karls-University, Tübingen, Germany
| | - Anand Sharma
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, United Kindom
| | - Nikhil Vasdev
- Hertfordshire and Bedfordshire Urological Cancer Centre, Lister Hospital, Stevenage, United Kindom; School of Life and Medical Sciences, University of Hertfordshire, United Kindom.
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Lu T, Zhang L, Zhu W, Zhang Y, Zhang S, Wu B, Deng N. CRISPR/Cas9-Mediated OC-2 Editing Inhibits the Tumor Growth and Angiogenesis of Ovarian Cancer. Front Oncol 2020; 10:1529. [PMID: 32984003 PMCID: PMC7492522 DOI: 10.3389/fonc.2020.01529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer is the leading cancer-related cause of death in women worldwide. It is of great relevance to understand the mechanism responsible for tumor progression and identify unique oncogenesis markers for a higher chance of preventing this malignant disease. The high-expression OC-2 gene has been shown to be a potential candidate for regulating oncogenesis and angiogenesis in ovarian cancer. Hence, we wished to investigate the impact of OC-2 gene on ovarian cancer aggressiveness. CRISPR/Cas9, a gene editing tool, allows for direct ablation of OC-2 at the genomic level, and we successfully generated OC-2 KO cell lines from SKOV3 and CAOV3 cells. In an apoptosis assay, OC-2 KO induced the apoptosis activation of tumor cells, with the up-regulation of Bax/Caspase-8 and the down-regulation of Bcl-2. Consequently, the proliferation, migration, and invasion of OC-2 KO cell lines were significantly inhibited. Assays of qRT-PCR and Western blotting showed that the expression levels of pro-angiogenic growth factors VEGFA, FGF2, HGF, and HIF-1α and the activation of Akt/ERK pathways were significantly down-regulated at the loss of OC-2. In the xenograft model, OC-2 KO potently suppressed the subcutaneous tumor growth, with the inhibition exceeding 56%. The down-regulation of CD31 and relevant pro-angiogenic growth factors were observed in OC-2 KO tumor tissues. Taken together, OC-2 depletion negatively regulated the ovarian cancer progression possibly by apoptosis activation and angiogenesis inhibition. This work revealed a pivotal regulator of apoptosis and angiogenesis networks in ovarian cancer, and we applied the CRISPR/Cas9 system to the transcription factor pathway for developing a broad-acting anti-tumor gene therapy.
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Affiliation(s)
- Tongyi Lu
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
| | - Ligang Zhang
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
| | - Wenhui Zhu
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
| | - Yinmei Zhang
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
| | - Simin Zhang
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
| | - Binhua Wu
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
| | - Ning Deng
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Department of Biology, Jinan University, Guangzhou, China
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de Oliveira MC, Caires HR, Oliveira MJ, Fraga A, Vasconcelos MH, Ribeiro R. Urinary Biomarkers in Bladder Cancer: Where Do We Stand and Potential Role of Extracellular Vesicles. Cancers (Basel) 2020; 12:E1400. [PMID: 32485907 PMCID: PMC7352974 DOI: 10.3390/cancers12061400] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022] Open
Abstract
Extracellular vesicles (EVs) are small membrane vesicles released by all cells and involved in intercellular communication. Importantly, EVs cargo includes nucleic acids, lipids, and proteins constantly transferred between different cell types, contributing to autocrine and paracrine signaling. In recent years, they have been shown to play vital roles, not only in normal biological functions, but also in pathological conditions, such as cancer. In the multistep process of cancer progression, EVs act at different levels, from stimulation of neoplastic transformation, proliferation, promotion of angiogenesis, migration, invasion, and formation of metastatic niches in distant organs, to immune escape and therapy resistance. Moreover, as products of their parental cells, reflecting their genetic signatures and phenotypes, EVs hold great promise as diagnostic and prognostic biomarkers. Importantly, their potential to overcome the current limitations or the present diagnostic procedures has created interest in bladder cancer (BCa). Indeed, cystoscopy is an invasive and costly technique, whereas cytology has poor sensitivity for early staged and low-grade disease. Several urine-based biomarkers for BCa were found to overcome these limitations. Here, we review their potential advantages and downfalls. In addition, recent literature on the potential of EVs to improve BCa management was reviewed and discussed.
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Affiliation(s)
- Manuel Castanheira de Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (H.R.C.); (M.J.O.); (A.F.); (M.H.V.)
- Tumor & Microenvironment Interactions Group, INEB - Institute of Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
- Department of Urology, Centro Hospitalar e Universitário do Porto, 4099-001 Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Hugo R. Caires
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (H.R.C.); (M.J.O.); (A.F.); (M.H.V.)
- Cancer Drug Resistance Group, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Maria J. Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (H.R.C.); (M.J.O.); (A.F.); (M.H.V.)
- Tumor & Microenvironment Interactions Group, INEB - Institute of Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | - Avelino Fraga
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (H.R.C.); (M.J.O.); (A.F.); (M.H.V.)
- Tumor & Microenvironment Interactions Group, INEB - Institute of Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
- Department of Urology, Centro Hospitalar e Universitário do Porto, 4099-001 Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - M. Helena Vasconcelos
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (H.R.C.); (M.J.O.); (A.F.); (M.H.V.)
- Cancer Drug Resistance Group, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Department of Biological Sciences, FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ricardo Ribeiro
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (H.R.C.); (M.J.O.); (A.F.); (M.H.V.)
- Tumor & Microenvironment Interactions Group, INEB - Institute of Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
- Laboratory of Genetics and Instituto de Saúde Ambiental, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Department of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
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miR-6086 inhibits ovarian cancer angiogenesis by downregulating the OC2/VEGFA/EGFL6 axis. Cell Death Dis 2020; 11:345. [PMID: 32393810 PMCID: PMC7214437 DOI: 10.1038/s41419-020-2501-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
miRNAs have emerged as a pivotal component of gene regulatory networks, mediating cytokines secretion, cell cycle, and differentiation regulation. However, how miRNAs collaborate with transcription factors and downstream effector proteins that determine the fate of ovarian cancer cells remains to be understood, especially regarding to mechanism of tumor angiogenesis regulation. Based on the qRT-PCR and IHC analysis, we found that miR-6086 was maintained a very low level both in ovarian cancer cell lines and tissues. Further, we identified OC2 and EGFL6 as the direct targets of miR-6086 by luciferase assay and we observed an inverse relationship between the expression of miR-6086 and the OC2/VEGFA/EGFL6 axis. The Western blotting analysis suggested that OC2 could directly upregulate VEGFA and indirectly up-regulate EGFL6 through VEGFA. Moreover, miR-6086 could indirectly downregulate VEGFA through OC2. In addition, miR-6086, siOC2 and siEGFL6 could negatively regulate the tumor growth and angiogenesis of ovarian cancer (Skov3) in the animal studies, with the inhibition rates of 77.07%, 69.89%, and 73.62%, respectively (**p < 0.01). Moreover, the tumor cell proliferation, migration, and invasion of ovarian cancer cell lines (Caov3 and Skov3) and vascular formation (HUVECs) were significantly suppressed in vitro, by decreasing the AKT/MAPK pathways (*p < 0.05). Taken together, our results reveal that miR-6086 can suppress the angiogenesis networks in ovarian cancer by down-regulating the OC2/VEGFA/EGFL6 axis, directly or indirectly, which may provide potential targets for tumor therapeutics.
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Comparative Analysis of Urine Fractions for Optimal Bladder Cancer Detection Using DNA Methylation Markers. Cancers (Basel) 2020; 12:cancers12040859. [PMID: 32252299 PMCID: PMC7226114 DOI: 10.3390/cancers12040859] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methylation analysis of full void urine and urine pellet seems promising for bladder cancer (BC) detection and surveillance. Urinary cell-free DNA from urine supernatant is now gaining interest for other molecular tests in BC. This study aims to evaluate which urine fraction is preferred for BC diagnosis using methylation markers: full void urine, urine pellet or supernatant. Methylation levels of nine markers were determined in the three urine fractions and correlated with their respective tumor tissues in BC patients and compared to controls. For all markers and marker panel GHSR/MAL, diagnostic performance was determined by calculating the area under the curve (AUC) of the respective receiver operating characteristic curves. For most of the markers, there was a significant correlation between the methylation levels in each of the urine fractions and the matched tumor tissues. Urine pellet was the most representative fraction. Generally, AUCs for BC diagnosis were comparable among the fractions. The highest AUC was obtained for GHSR/MAL in urine pellet: AUC 0.87 (95% confidence interval: 0.73-1.00), corresponding to a sensitivity of 78.6% and a specificity of 91.7%. Our results demonstrate that cellular and cell-free DNA in urine can be used for BC diagnosis by urinary methylation analysis. Based on our comparative analysis and for practical reasons, we recommend the use of urine pellet.
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Abstract
PURPOSE OF REVIEW To provide a current comprehensive review of the available urinary biomarkers for the detection and surveillance of bladder cancer. RECENT FINDINGS The limitations of urine cytology and invasive nature of cystoscopic evaluation have led to a growing search for an ideal, cost-effective biomarker with acceptable sensitivity and specificity. Current FDA approved biomarkers such as UroVysion fluorescent in situ hybridization, Immunocyt, and nuclear matrix protein 22 do not have the specificity, and thus positive predictive value to warrant their cost as a routine adjunct or replacement for cystoscopy. Several promising commercially available assays such as Cxbladder, Assure MDx, and Xpert BC may perform better than cytology in select populations. Novel genomic, epigenetic, inflammatory, and metabolomic-based assays are being analyzed as potential urinary biomarkers. SUMMARY Urinary biomarkers with high sensitivity and specificity are an unmet need in bladder cancer. Several new assays may meet these criteria and future research may justify use in clinical practice.
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Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KYC, Ross JP. DNA Methylation Cancer Biomarkers: Translation to the Clinic. Front Genet 2019; 10:1150. [PMID: 31803237 PMCID: PMC6870840 DOI: 10.3389/fgene.2019.01150] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
Carcinogenesis is accompanied by widespread DNA methylation changes within the cell. These changes are characterized by a globally hypomethylated genome with focal hypermethylation of numerous 5’-cytosine-phosphate-guanine-3’ (CpG) islands, often spanning gene promoters and first exons. Many of these epigenetic changes occur early in tumorigenesis and are highly pervasive across a tumor type. This allows DNA methylation cancer biomarkers to be suitable for early detection and also to have utility across a range of areas relevant to cancer detection and treatment. Such tests are also simple in construction, as only one or a few loci need to be targeted for good test coverage. These properties make cancer-associated DNA methylation changes very attractive for development of cancer biomarker tests with substantive clinical utility. Across the patient journey from initial detection, to treatment and then monitoring, there are several points where DNA methylation assays can inform clinical practice. Assays on surgically removed tumor tissue are useful to determine indicators of treatment resistance, prognostication of outcome, or to molecularly characterize, classify, and determine the tissue of origin of a tumor. Cancer-associated DNA methylation changes can also be detected with accuracy in the cell-free DNA present in blood, stool, urine, and other biosamples. Such tests hold great promise for the development of simple, economical, and highly specific cancer detection tests suitable for population-wide screening, with several successfully translated examples already. The ability of circulating tumor DNA liquid biopsy assays to monitor cancer in situ also allows for the ability to monitor response to therapy, to detect minimal residual disease and as an early biomarker for cancer recurrence. This review will summarize existing DNA methylation cancer biomarkers used in clinical practice across the application domains above, discuss what makes a suitable DNA methylation cancer biomarker, and identify barriers to translation. We discuss technical factors such as the analytical performance and product-market fit, factors that contribute to successful downstream investment, including geography, and how this impacts intellectual property, regulatory hurdles, and the future of the marketplace and healthcare system.
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Affiliation(s)
- Warwick J Locke
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Dominic Guanzon
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Chenkai Ma
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Yi Jin Liew
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Konsta R Duesing
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Kim Y C Fung
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Jason P Ross
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
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Zhu F, Zhang Y, Shi L, Wu CL, Chen SQ, Zheng H, Song DK. Gene mutation detection of urinary sediment cells for NMIBC early diagnose and prediction of NMIBC relapse after surgery. Medicine (Baltimore) 2019; 98:e16451. [PMID: 31393349 PMCID: PMC6709296 DOI: 10.1097/md.0000000000016451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Early diagnose of bladder cancer could lead to good prognosis and high 5-year-survival rate. Among bladder cancer, about 75% patients with were nonmuscle-invasive bladder cancer (NMIBC). Patients were painful and easily get infected during bladder cancer diagnosis, which mainly depends on invasive cystoscopy and low-sensitivity urine exfoliation cytology. Meanwhile, relapse after surgery was also becoming the major problem for patients. Exploring noninvasive, high-sensitivity, and painless method is very important and meaningful for NMIBC treatment.Firstly, we found potential related gene mutation sites for NMIBC by searching COSMIC database and related study. Urinary sediment cells of patients both in normal group (patients with benign) and NMIMC group were collected before and after operation for potential gene mutation site detecting. Meanwhile, the urinary sediment cells of relapse patients and good prognosis people in NMIBC group after surgery were also collected for further Gene mutation detection and NMIBC relapse after surgery prediction.Fourteen genes (152 mutation sites) were selected between 95 NMIBC patients and 67 control patients, which were FGFR3, TP53, PIK3CA, and others. Compared with control group, mutation ratio of above 14 genes was higher in NMIBC group. NMIBC diagnose model was established by 5 times cross-validation and had a good effects, which included the all mutation site in FGFR3, TP53, PIK3CA, ARID1A, STAG2, and KTM2D. On the contrary, the relapse rate was 30.5% among 95 patients for about 1.5-year follow-up time. Compared with control group, smoking rate and tumor grade were higher in relapse group. Meanwhile, mutation rate of FGFR3, TP53, PIK3CA, ERBB3, and TSC1 in relapse group were higher than that in normal group. According to the mutation sites of FGFR3, TP53, PIK3CA, and ERBB3 and the combination of urinary sediment cells genetic mutation and relapse status, a predicted model for NMIBC relapse was also established, which had 90% accuracy.The diagnosed NMIBC model (based on FGFR3, TP53, PIK3CA, ARID1A, STAG2, and KTM2D gene mutation) and predicted relapse model (based on FGFR3, TP53, PIK3CA, and ERBB3 gene mutation) possess high accuracy and would be applied in early diagnose and early predicting relapse of patients.
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Affiliation(s)
- Feng Zhu
- Fifth Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou City
| | - Yan Zhang
- Department of Neurophysiology, Basic Medical College, Xinxiang Medical College, Xinxiang City
| | - Lei Shi
- Fifth Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou City
| | - Chun-lei Wu
- Department of Urology, First Affiliated Hospital of Xinxiang Medical College, Weihui City
| | - Shuai-qi Chen
- Department of Urology, First Affiliated Hospital of Xinxiang Medical College, Weihui City
| | - Hang Zheng
- Department of Urology, Third Affiliated Hospital of Xinxiang Medical College, Xinxiang City, Henan Province, China
| | - Dong-kui Song
- Fifth Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou City
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Abstract
Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Epigenetic alterations are already being incorporated as valuable candidates in the biomarker field. Furthermore, their reversible nature offers a promising opportunity to ameliorate disease symptoms by using epigenetic-based therapy. Thus, beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.
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Larsen LK, Lind GE, Guldberg P, Dahl C. DNA-Methylation-Based Detection of Urological Cancer in Urine: Overview of Biomarkers and Considerations on Biomarker Design, Source of DNA, and Detection Technologies. Int J Mol Sci 2019; 20:ijms20112657. [PMID: 31151158 PMCID: PMC6600406 DOI: 10.3390/ijms20112657] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Changes in DNA methylation have been causally linked with cancer and provide promising biomarkers for detection in biological fluids such as blood, urine, and saliva. The field has been fueled by genome-wide characterization of DNA methylation across cancer types as well as new technologies for sensitive detection of aberrantly methylated DNA molecules. For urological cancers, urine is in many situations the preferred "liquid biopsy" source because it contains exfoliated tumor cells and cell-free tumor DNA and can be obtained easily, noninvasively, and repeatedly. Here, we review recent advances made in the development of DNA-methylation-based biomarkers for detection of bladder, prostate, renal, and upper urinary tract cancers, with an emphasis on the performance characteristics of biomarkers in urine. For most biomarkers evaluated in independent studies, there was great variability in sensitivity and specificity. We discuss issues that impact the outcome of DNA-methylation-based detection of urological cancer and account for the great variability in performance, including genomic location of biomarkers, source of DNA, and technical issues related to the detection of rare aberrantly methylated DNA molecules. Finally, we discuss issues that remain to be addressed to fully exploit the potential of DNA-methylation-based biomarkers in the clinic, including the need for prospective trials and careful selection of control groups.
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Affiliation(s)
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, NO-0424 Oslo, Norway.
| | - Per Guldberg
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Christina Dahl
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
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