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Bang BR, Zhong J, Oh TJ, Lee JY, Seo Y, Woo MA, Lim JS, Na YG, Song KH, Shin JH, Lee JJ, Im CS, Kim S, Beqaj S, Shirk JD, Ke KW, Vallone J, An S. EarlyTect BCD, a Streamlined PENK Methylation Test in Urine DNA, Effectively Detects Bladder Cancer in Patients with Hematuria. J Mol Diagn 2024; 26:613-623. [PMID: 38677548 DOI: 10.1016/j.jmoldx.2024.04.001] [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: 09/27/2023] [Revised: 02/08/2024] [Accepted: 04/03/2024] [Indexed: 04/29/2024] Open
Abstract
The current noninvasive diagnostic approaches for detecting bladder cancer (BC) often exhibit limited clinical performance, especially for the initial diagnosis. This study aims to evaluate the validity of a streamlined urine-based PENK methylation test called EarlyTect BCD in detecting BC in patients with hematuria scheduled for cystoscopy in Korean and American populations. The test seamlessly integrates two steps, linear target enrichment and quantitative methylation-specific PCR within a single closed tube. The detection limitation of the test was approximately two genome copies of methylated PENK per milliliter of urine. In the retrospective training set (n = 105), an optimal cutoff value was determined to distinguish BC from non-BC, resulting in a sensitivity of 87.3% and a specificity of 95.2%. In the prospective validation set (n = 210, 122 Korean and 88 American patients), the overall sensitivity for detecting all stages of BC was 81.0%, with a specificity of 91.5% and an area under the curve value of 0.889. There was no significant difference between the two groups. The test achieved a sensitivity of 100% in detecting high-grade Ta and higher stages of BC. The negative predictive value of the test was 97.7%, and the positive predictive value was 51.5%. The findings of this study demonstrate that EarlyTect BCD is a highly effective noninvasive diagnostic tool for identifying BC among patients with hematuria.
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Affiliation(s)
| | - Jin Zhong
- Pathology and Laboratory Medicine Service, VA Greater Los Angeles Medical Center, Los Angeles, California
| | | | - Ji Yong Lee
- Department of Urology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Yangyei Seo
- Genomictree, Inc., Daejeon, Republic of Korea
| | - Min A Woo
- Genomictree, Inc., Daejeon, Republic of Korea
| | - Jae Sung Lim
- Department of Urology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Yong Gil Na
- Department of Urology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Ki Hak Song
- Department of Urology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Ju Hyun Shin
- Department of Urology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | | | - Chan Su Im
- Promis Diagnostics Inc., Irvine, California
| | | | | | - Joseph D Shirk
- Department of Urology, VA Greater Los Angeles Medical Center, Los Angeles, California; Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Katelyn W Ke
- Pathology and Laboratory Medicine Service, VA Greater Los Angeles Medical Center, Los Angeles, California
| | - John Vallone
- Pathology and Laboratory Medicine Service, VA Greater Los Angeles Medical Center, Los Angeles, California
| | - Sungwhan An
- Promis Diagnostics Inc., Irvine, California; Genomictree, Inc., Daejeon, Republic of Korea.
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Schmitz-Dräger C, Goebell PJ, Paxinos E, Bismarck E, Chen J, Balakrishnan P, Bates M, Ebert T, Schmitz-Dräger BJ, Benderska-Söder N. Potential of an mRNA-Based Urine Assay (Xpert ® Bladder Cancer Detection 1) in Hematuria Patients - Results from a Cohort Study. Bladder Cancer 2024; 10:25-33. [PMID: 38993527 PMCID: PMC11181824 DOI: 10.3233/blc-230089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/04/2023] [Indexed: 07/13/2024]
Abstract
BACKGROUND AND OBJECTIVE Assessment of patients with hematuria (aH) remains a challenge in urological practice, balancing the benefits of diagnosing a potentially underlying bladder cancer (UCa) against the risks of possibly unnecessary diagnostic interventions. This study analyzes the potential of an mRNA-based urine assay, the Xpert® Bladder Cancer Detection- CE-IVD (Xpert BC-D), in patients with hematuria. MATERIALS AND METHODS Overall, 368 patients with newly observed painless hematuria and no history of UCa were included in this observational study. Patients received urological workup, including urethrocystoscopy (WLC), upper tract imaging, urine cytology and Xpert BC-D. Patients with positive WLC were recommended to undergo tumor resection (TUR-B). RESULTS After excluding non-assessable cases, 324 patients were considered for analysis (188 males, 136 females; median age: 61 years). Eight of twenty-eight patients with a positive TUR-B had Ta low grade (LG) tumors; the others were diagnosed with high grade (HG) lesions (Ta: 4, CIS: 2, T1:11, > T1:3). The Xpert BC-D was more sensitive than urine cytology (96% vs. 61%) (p = 0.002). Increased risk ratios (RR) were observed for gross hematuria, gender, urine cytology, and positive Xpert BC-D (all p < 0.05). Age and positive Xpert BC-D remained independent predictors of UCa in multivariate analysis. Simulating a triage with WLC restricted to patients with positive Xpert BC-D could have saved 240 (74.1%) assessments at the cost of missing one pTa LG tumor. CONCLUSIONS The results suggest a potential role for Xpert BC-D in preselecting patients with hematuria for either further invasive diagnosis or an alternate diagnostic procedure.
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Affiliation(s)
| | - Peter J. Goebell
- Department of Urology and Pediatric Urology, Friedrich-Alexander University, Erlangen, Germany
| | - Ellen Paxinos
- Medical and Scientific Affairs and Strategy, Oncology, Cepheid, Sunnyvale, CA, USA
| | | | - Jack Chen
- Department of Clinical Research and Biostatistics, Cepheid, Sunnyvale, CA, USA
| | - Priya Balakrishnan
- Department of Clinical Research and Biostatistics, Cepheid, Sunnyvale, CA, USA
| | - Michael Bates
- Medical and Scientific Affairs and Strategy, Oncology, Cepheid, Sunnyvale, CA, USA
| | - Thomas Ebert
- Urologie 24, St. Theresienkrankenhaus, Nuremberg, Germany
| | - Bernd J. Schmitz-Dräger
- Urologie 24, St. Theresienkrankenhaus, Nuremberg, Germany
- Department of Urology and Pediatric Urology, Friedrich-Alexander University, Erlangen, Germany
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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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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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Kuckuck EC, Hennenlotter J, Todenhöfer T, Brünn LA, Rass GC, Stenzl A, Hakenberg OW, Roghmann F, Goebell PJ, Grimm MO, Pycha A, Bolenz C, Burger M, Benderska-Söder N, Schmitz-Dräger BJ. Discriminative capacity of guideline recommendations in the assessment of patients with asymptomatic microhematuria. Urol Oncol 2023; 41:254.e1-254.e8. [PMID: 36274029 DOI: 10.1016/j.urolonc.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/20/2022] [Accepted: 08/26/2022] [Indexed: 03/29/2023]
Abstract
BACKGROUND & OBJECTIVE Asymptomatic microhematuria (aMh) remains a diagnostic challenge in urological practice: while aMh is a risk factor of urothelial carcinoma (UC), prevalence of aMh is high. Guidelines were developed to permit risk stratification and reduce diagnostic workload. This study investigates the efficacy of several recommendations. MATERIAL & METHODS Sixty hundred eight patients with newly diagnosed aMh without previous UC from an academic referral center (A; n = 320) and a private outpatient clinic (B; n = 288) were included. All patients underwent clinical workup including medical history, urine cytology, upper tract imaging and cystoscopy. Eleven former and current guidelines were applied to each patient individually; every patient was classified as either low risk (no further workup recommended) or high risk. Furthermore, a recently developed nomogram for hematuria assessment was included. RESULTS The cohort comprised 142 females and 466 males (mean age 62 [range 18-92] years). Sixty-one patients (10.0%) were diagnosed with UC. Excluding the Swedish and recent NICE guideline generally advising against urologic workup, application of 9 other recommendations would have diagnosed all UCs and saved 1.6% to 16.1% of patients from workup. For the 2020 US guideline, solely applied to cohort B, 10.6% of patients were classified as low risk. The use of the nomogram would have saved 17.1% to 25% of patients from workup. CONCLUSIONS Practical relevance of current guidelines is limited as they do not sufficiently identify patients not requiring clinical work up. Thus, guideline adherence may trigger overdiagnosis and even overtreatment. New ways of risk stratification are needed to improve aMh assessment.
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Affiliation(s)
| | | | - Tilman Todenhöfer
- Department of Urology, Eberhard-Karl University, Tuebingen, Germany; Studienpraxis Urologie, Nürtingen, Germany
| | | | | | - Arnulf Stenzl
- Department of Urology, Eberhard-Karl University, Tuebingen, Germany
| | | | | | | | | | - Armin Pycha
- General Hospital of Bolzano, Department of Urology, Bolzano, Italy; Sigmund Freud University Vienna, Medical School Vienna, Austria
| | | | - Maximilian Burger
- Department of Urology, St. Josefs Hospital, University of Regensburg, Germany
| | | | - Bernd J Schmitz-Dräger
- Urologie 24, Nuremberg, Germany; Department of Urology, University Clinic, Erlangen, Germany.
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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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7
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Oh TJ, Lim E, Bang BR, Lee JJ, Na YG, Shin JH, Lim JS, Song KH, An S. Identification and validation of methylated PENK gene for early detection of bladder cancer using urine DNA. BMC Cancer 2022; 22:1195. [PMID: 36403035 PMCID: PMC9675278 DOI: 10.1186/s12885-022-10275-2] [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: 10/03/2021] [Accepted: 11/02/2022] [Indexed: 11/21/2022] Open
Abstract
Background Early detection of bladder cancer (BCa) offers patients a favorable outcome and avoids the need for cystectomy. Development of an accurate and sensitive noninvasive BCa diagnostic test is imperative. DNA methylation is an early epigenetic event in the development of BCa. Certain specific aberrant methylations could serve as useful biomarkers. The aim of this study was to identify methylation biomarkers for early detection of BCa. Methods CpG methylation microarray analysis was conducted on primary tumors with varying stages (T1—T4) and paired nontumor tissues from nine BCa patients. Bisulfite-pyrosequencing was performed to confirm the methylation status of candidate genes in tissues and urine sediments (n = 51). Among them, PENK was selected as a potential candidate and validated using an independent set of 169 urine sediments (55 BCa, 25 benign urologic diseases, 8 other urologic cancers, and 81 healthy controls) with a quantitative methylation-specific real time PCR (mePENK-qMSP). All statistical analyses were performed using MedCalc software version 9.3.2.0. Results CpG methylation microarray analysis and stepwise validation by bisulfite-pyrosequencing for tissues and urine sediments supported aberrant methylation sites of the PENK gene as potential biomarkers for early detection of BCa. Clinical validation of the mePENK-qMSP test using urine sediment-DNA showed a sensitivity of 86.5% (95% CI: 71.2 – 95.5%), a specificity of 92.5% (95% CI: 85.7 – 96.7%), and an area under ROC of 0.920 (95% CI: 0.863 – 0.959) in detecting Ta high-grade and advanced tumor stages (T1-T4) of BCa patients. Sensitivities for Ta low-grade, Ta high-grade, T1 and T2-T4 were 55.6, 83.3, 88.5, and 100%, respectively. Methylation status of PENK was not correlated with sex, age or stage, while it was associated with the tumor grade of BCa. Conclusions In this study, we analyzed the comprehensive patterns of DNA methylation identified that PENK methylation possesses a high potential as a biomarker for urine-based early detection of BCa. Validation of PENK methylation confirms that it could significantly improve the noninvasive detection of BCa. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10275-2.
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Affiliation(s)
- Tae Jeong Oh
- Genomictree, Inc., 44-6 Techno 10-Ro Yuseong-Gu, Daejeon, 34027 Republic of Korea
| | - Eunkyung Lim
- Genomictree, Inc., 44-6 Techno 10-Ro Yuseong-Gu, Daejeon, 34027 Republic of Korea
| | - Bo-Ram Bang
- Promis Diagnostics Inc., 1 Post, Irvine, CA 92618 USA
| | | | - Yong Gil Na
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Ju Hyun Shin
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Jae Sung Lim
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Ki Hak Song
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Sungwhan An
- Genomictree, Inc., 44-6 Techno 10-Ro Yuseong-Gu, Daejeon, 34027 Republic of Korea ,Promis Diagnostics Inc., 1 Post, Irvine, CA 92618 USA
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8
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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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9
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Rai BP, Luis Dominguez Escrig J, Vale L, Kuusk T, Capoun O, Soukup V, Bruins HM, Yuan Y, Violette PD, Santesso N, van Rhijn BWG, Hugh Mostafid A, Imran Omar M. Systematic Review of the Incidence of and Risk Factors for Urothelial Cancers and Renal Cell Carcinoma Among Patients with Haematuria. Eur Urol 2022; 82:182-192. [PMID: 35393159 DOI: 10.1016/j.eururo.2022.03.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/12/2022] [Accepted: 03/17/2022] [Indexed: 12/21/2022]
Abstract
CONTEXT The current impact of haematuria investigations on health care organisations is significant. There is currently no consensus on how to investigate patients with haematuria. OBJECTIVE To evaluate the incidence of bladder cancer, upper tract urothelial carcinoma (UTUC), and renal cell carcinoma (RCC) among patients undergoing investigation for haematuria and identify any risk factors for bladder cancer, UTUC, and RCC (BUR). EVIDENCE ACQUISITION Medline, Embase, and Cochrane controlled trials databases and ClinicalTrials.gov were searched for all relevant publications from January 1, 2000 to June 2021 according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Prospective, retrospective, and cross-sectional studies with a minimum population of 50 patients with haematuria were considered for the review. EVIDENCE SYNTHESIS A total of 44 studies were included. The total number of participants was 229701. The pooled incidence rate for urothelial bladder cancer was 17% (95% confidence interval [CI] 14-20%) for visible haematuria (VH) and 3.3% (95% CI 2.45-4.3%) for nonvisible haematuria (NVH). The pooled incidence rate for RCC was 2% (95% CI 1-2%) for VH and 0.58% (95% CI 0.42-0.77%) for NVH. The pooled incidence rate for UTUC was 0.75% (95% CI 0.4-1.2%) for VH and 0.17% (95% CI 0.081-0.299%) for NVH. On sensitivity analysis, the proportions of males (risk ratio [RR] 1.14, 95% CI 1.10-1.17 for VH; 1.54, 95% CI 1.34-1.78 for NVH; p < 0.00001; moderate certainty evidence) and individuals with a smoking history (RR 1.41, 95% CI 1.24-1.61 for VH; 1.53, 95% CI 1.36-1.72 for NVH; p < 0.00001; moderate certainty evidence) appeared to be higher in BUR than in non-BUR groups. CONCLUSIONS Male gender and smoking history are risk factors for BUR cancer in haematuria, with bladder cancer being the commonest cancer. The incidence of RCC and UTUC in NVH is low. The review serves as a reference standard for future policy-making on investigation of haematuria by global organisations. PATIENT SUMMARY Our review shows that male gender and smoking history are risk factors for cancers of the bladder, kidney, and ureter. The review also provides information on the proportion of patients who have cancer when they have blood in their urine (haematuria) and will allow policy-makers to decide on the most appropriate method for investigating haematuria in patients.
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Affiliation(s)
- Bhavan P Rai
- Department of Urology, Freeman Hospital, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | | | - Luís Vale
- Department of Urology, Centro Hospital Universitário S. João, Porto, University of Porto, Porto, Portugal
| | - Teele Kuusk
- Department of Urology, Darent Valley Hospital, Dartford and Gravesham NHS Trust, Dartford, UK
| | - Otakar Capoun
- Department of Urology, General University Hospital, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Viktor Soukup
- Department of Urology, General University Hospital, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Harman M Bruins
- Department of Urology, Zuyderland Medical Center, Sittard-Geleen-Heerlen, The Netherlands
| | - Yuhong Yuan
- Department of Medicine, Health Science Centre, McMaster University, Hamilton, ON, Canada
| | - Philippe D Violette
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada; Department of Surgery, Division of Urology, McMaster University, Hamilton, ON, Canada
| | - Nancy Santesso
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Cochrane Canada Centre, McMaster University, Hamilton, ON, Canada
| | - Bas W G van Rhijn
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - A Hugh Mostafid
- Department of Urology, Royal Surrey County Hospital, Guildford, UK
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10
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Harrison H, Usher-Smith JA, Li L, Roberts L, Lin Z, Thompson RE, Rossi SH, Stewart GD, Walter FM, Griffin S, Zhou Y. Risk prediction models for symptomatic patients with bladder and kidney cancer: a systematic review. Br J Gen Pract 2022; 72:e11-e18. [PMID: 34844922 PMCID: PMC8714528 DOI: 10.3399/bjgp.2021.0319] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/25/2021] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Timely diagnosis of bladder and kidney cancer is key to improving clinical outcomes. Given the challenges of early diagnosis, models incorporating clinical symptoms and signs may be helpful to primary care clinicians when triaging at-risk patients. AIM To identify and compare published models that use clinical signs and symptoms to predict the risk of undiagnosed prevalent bladder or kidney cancer. DESIGN AND SETTING Systematic review. METHOD A search identified primary research reporting or validating models predicting the risk of bladder or kidney cancer in MEDLINE and EMBASE. After screening identified studies for inclusion, data were extracted onto a standardised form. The risk models were classified using TRIPOD guidelines and evaluated using the PROBAST assessment tool. RESULTS The search identified 20 661 articles. Twenty studies (29 models) were identified through screening. All the models included haematuria (visible, non-visible, or unspecified), and seven included additional signs and symptoms (such as abdominal pain). The models combined clinical features with other factors (including demographic factors and urinary biomarkers) to predict the risk of undiagnosed prevalent cancer. Several models (n = 13) with good discrimination (area under the receiver operating curve >0.8) were identified; however, only eight had been externally validated. All of the studies had either high or unclear risk of bias. CONCLUSION Models were identified that could be used in primary care to guide referrals, with potential to identify lower-risk patients with visible haematuria and to stratify individuals who present with non-visible haematuria. However, before application in general practice, external validations in appropriate populations are required.
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Affiliation(s)
- Hannah Harrison
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge
| | - Juliet A Usher-Smith
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge
| | - Lanxin Li
- University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge
| | - Lydia Roberts
- University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge
| | - Zhiyuan Lin
- University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge
| | - Rachel E Thompson
- University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge
| | - Sabrina H Rossi
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge
| | - Grant D Stewart
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge
| | - Fiona M Walter
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, and director, Wolfson Institute of Population Health, Queen Mary University of London, London
| | - Simon Griffin
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge
| | - Yin Zhou
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge
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11
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Budaya TN, Permatasari HK, Widodo W, Prawiro SR. Novel Insight of Cytokeratin 14 as a Biomarker in Diagnosing Bladder Cancer. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.7258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Bladder cancer is the ninth most common type of cancer occurring in men. Screening for bladder cancer is often difficult due to limited proper modality and symptoms that is mild and unspecific. Leaving it untreated leads to greater morbidity and mortality. Therefore, finding a simple biomarker for screening purpose is necessary. Cytokeratin (CK) has been studied extensively as cancer biomarker. Detectable soluble CK was found in body fluid, including urine, and histological specimen using immunoassays. The level of its expression is mainly affected by cell proliferation, apoptosis, and cellular stress. CK 14, which is type I CK, was detected in the basal layer of epithelial cells and specific for squamous type of epithelial cell. CK 14 analysis in bladder cancer has revealed numerous functions such as predicting the development of bladder cancer, differentiating cancer origins, stratifying bladder cancer patients based on disease severity, and predicting bladder cancer recurrence. Its potential to become excellent biomarker makes it subject of interest in research development.
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12
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Jiang L, Zuo Z, Lin J, Yang C. Orthodenticle homeobox OTX1 is a potential prognostic biomarker for bladder cancer. Bioengineered 2021; 12:6559-6571. [PMID: 34559577 PMCID: PMC8806575 DOI: 10.1080/21655979.2021.1974646] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Bladder cancer (BC) is one of the most aggressive tumors worldwide. OTX1 (orthodenticle homeobox 1) is an important transcription factor involved in various diseases, such as cancers. The aim of this study was to further investigate the role of OTX1 in BC. In this study, differentially expressed genes (DEGs) were screened from tumor tissues and para-cancerous tissues by bioinformatics. The expression of protein and RNA was separately detected by western blotting and immunohistochemistry (IHC), and quantitative polymerase chain reaction (qPCR); cell viability and cell growth were determined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and clone formation assays, respectively; cell motility was measured by transwell and wound healing assays; cell cycle was measured by flow cytometry. In this study, 9 DEGs were screened out, and OTX1 was employed as a candidate gene for subsequent study. Results found that OTX1 was highly expressed in BC cells and BC tissues, which was significantly associated with poor prognosis of patients. In addition, OTX1 silencing significantly reduced cell viability, and inhibited cell growth and motility, while OTX1 overexpression got opposite results. Moreover, OTX1 co-expressed genes were enriched in cell cycle-related pathways, suggesting that the role of OTX1 in BC may be related to cell cycle, which was confirmed by flow cytometry analysis. Furthermore, in vivo experiments showed that OTX1 silencing significantly inhibited tumor growth in tumor-bearing mice. Taken together, our findings suggested that OTX1 may play a promotional role in BC progression.
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Affiliation(s)
- Lei Jiang
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
| | - Zhongqiang Zuo
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
| | - Jie Lin
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
| | - Chuanfeng Yang
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
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13
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Hayashi Y, Fujita K. Toward urinary cell-free DNA-based treatment of urothelial carcinoma: a narrative review. Transl Androl Urol 2021; 10:1865-1877. [PMID: 33968675 PMCID: PMC8100839 DOI: 10.21037/tau-20-1259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsy technique targeting urinary cell-free DNA (cfDNA) is getting a lot of attention to overcome limitations of the present treatment strategy for urothelial carcinoma, including urothelial bladder carcinoma (UBC) and upper tract urothelial carcinoma (UTUC). Analysis of tumor-derived DNA in urine focusing either on genomic or epigenomic alterations, holds great potential as a noninvasive method for the detection of urothelial carcinoma with high accuracy. It is also predictive of prognosis and response to drugs, and reveals the underlying characteristics of different stages of urothelial carcinoma. Although cfDNA methylation analyses based on a combination of several methylation profiles have demonstrated high sensitivity for UBC diagnosis, there have been few reports involving epigenomic studies of urinary cfDNA. In mutational analyses, frequent gene mutations (TERT promoter, TP53, FGFR3, PIK3CA, RAS, etc.) have been detected in urine supernatant by using remarkable technological innovations such as next-generation sequencing and droplet digital PCR. These methods allow highly sensitive detection of rare mutation alleles while minimizing artifacts. In this review, we summarize the current insights into the clinical applications of urinary cfDNA from patients with urothelial carcinoma. Although it is necessary to conduct prospective multi-institutional clinical trials, noninvasive urine biopsy is expected to play an important role in the realization of precision medicine in patients with urothelial carcinoma in the near future.
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Affiliation(s)
- Yujiro Hayashi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazutoshi Fujita
- Department of Urology, Kindai University Faculty of Medicine, Osakasayama, Japan
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14
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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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15
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Gİrgİn B, KaradaĞ-Alpaslan M, KocabaŞ F. Oncogenic and tumor suppressor function of MEIS and associated factors. ACTA ACUST UNITED AC 2021; 44:328-355. [PMID: 33402862 PMCID: PMC7759197 DOI: 10.3906/biy-2006-25] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
MEIS proteins are historically associated with tumorigenesis, metastasis, and invasion in cancer. MEIS and associated PBX-HOX proteins may act as tumor suppressors or oncogenes in different cellular settings. Their expressions tend to be misregulated in various cancers. Bioinformatic analyses have suggested their upregulation in leukemia/lymphoma, thymoma, pancreas, glioma, and glioblastoma, and downregulation in cervical, uterine, rectum, and colon cancers. However, every cancer type includes, at least, a subtype with high MEIS expression. In addition, studies have highlighted that MEIS proteins and associated factors may function as diagnostic or therapeutic biomarkers for various diseases. Herein, MEIS proteins and associated factors in tumorigenesis are discussed with recent discoveries in addition to how they could be modulated by noncoding RNAs or newly developed small-molecule MEIS inhibitors.
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Affiliation(s)
- Birkan Gİrgİn
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
| | - Medine KaradaĞ-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun Turkey
| | - Fatih KocabaŞ
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
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16
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Zeng S, Ying Y, Xing N, Wang B, Qian Z, Zhou Z, Zhang Z, Xu W, Wang H, Dai L, Gao L, Zhou T, Ji J, Xu C. Noninvasive Detection of Urothelial Carcinoma by Cost-effective Low-coverage Whole-genome Sequencing from Urine-Exfoliated Cell DNA. Clin Cancer Res 2020; 26:5646-5654. [PMID: 33037018 DOI: 10.1158/1078-0432.ccr-20-0401] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/28/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Urothelial carcinoma is a malignant cancer with frequent chromosomal aberrations. Here, we investigated the application of a cost-effective, low-coverage whole-genome sequencing technology in detecting all chromosomal aberrations. EXPERIMENTAL DESIGN Patients with urothelial carcinomas and nontumor controls were prospectively recruited in clinical trial NCT03998371. Urine-exfoliated cell DNA was analyzed by Illumina HiSeq XTen, followed by genotyping with a customized bioinformatics workflow named Urine Exfoliated Cells Copy Number Aberration Detector (UroCAD). RESULTS In the discovery phase, urine samples from 126 patients with urothelial carcinomas and 64 nontumor disease samples were analyzed. Frequent chromosome copy-number changes were found in patients with tumor as compared with nontumor controls. A novel diagnosis model, UroCAD, was built by incorporating all the autosomal chromosomal changes. The model reached performance of AUC = 0.92 (95% confidence interval, 89.4%-97.3%). At the optimal cutoff, |Z| ≥ 3.21, the sensitivity, specificity, and accuracy were 82.5%, 96.9%, and 89.0%, respectively. The prediction positivity was found correlated with tumor grade (P = 0.01). In the external validation cohort of 95 participants, the UroCAD assay identified urothelial carcinomas with an overall sensitivity of 80.4%, specificity of 94.9%, and AUC of 0.91. Meanwhile, UroCAD assay outperformed cytology tests with significantly improved sensitivity (80.4% vs. 33.9%; P < 0.001) and comparable specificity (94.9% vs. 100%; P = 0.49). CONCLUSIONS UroCAD could be a robust urothelial carcinoma diagnostic method with improved sensitivity and similar specificity as compared with cytology tests. It may be used as a noninvasive approach for diagnosis and recurrence surveillance in urothelial carcinoma prior to the use of cystoscopy, which would largely reduce the burden on patients.
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Affiliation(s)
- Shuxiong Zeng
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yidie Ying
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Naidong Xing
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Baiyun Wang
- Suzhou Hongyuan Biotech Inc., Biobay, Suzhou, China
| | - Ziliang Qian
- Suzhou Hongyuan Biotech Inc., Biobay, Suzhou, China.,Prophet Genomics Inc., San Jose, California
| | - Zunlin Zhou
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Zhensheng Zhang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Weidong Xu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Huiqing Wang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Lihe Dai
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Li Gao
- Department of Pathology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tie Zhou
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jiatao Ji
- Department of Urology, Shanghai Hudong Hospital, Pudong New Area, Shanghai, China.
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China.
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17
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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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18
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Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T. Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters. Int J Cancer 2019; 145:2861-2872. [PMID: 31008534 DOI: 10.1002/ijc.32356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Urothelial cancer (UCa) is the most predominant cancer of the urinary tract and noninvasive diagnosis using hypermethylation signatures in urinary cells is promising. Here, we assess gender differences in a newly identified set of methylation biomarkers. UCa-associated hypermethylated sites were identified in urine of a male screening cohort (n = 24) applying Infinium-450K-methylation arrays and verified in two separate mixed-gender study groups (n = 617 in total) using mass spectrometry as an independent technique. Additionally, tissue samples (n = 56) of mixed-gender UCa and urological controls (UCt) were analyzed. The hypermethylation signature of UCa in urine was specific and sensitive across all stages and grades of UCa and independent on hematuria. Individual CpG sensitivities reached up to 81.3% at 95% specificity. Albeit similar methylation differences in tissue of both genders, differences were less pronounced in urine from women, most likely due to the frequent presence of squamous epithelial cells and leukocytes. Increased repression of methylation levels was observed at leukocyte counts ≥500/μl urine which was apparent in 30% of female and 7% of male UCa cases, further confirming the significance of the relative amounts of cancerous and noncancerous cells in urine. Our study shows that gender difference is a most relevant issue when evaluating the performance of urinary biomarkers in cancer diagnostics. In case of UCa, the clinical benefits of methylation signatures to male patients may outweigh those in females due to the general composition of women's urine. Accordingly, these markers offer a diagnostic option specifically in males to decrease the number of invasive cystoscopies.
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Affiliation(s)
- Christina U Köhler
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Nadine Bonberg
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Maike Ahrens
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Thomas Behrens
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Jan Hovanec
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | | | - Joachim Noldus
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Thomas Deix
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Katharina Braun
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | | | - Michael Walter
- c.ATG Core Facility for NGS and Microarrays, University of Tübingen, Tübingen, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Yu Tam
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Florian Sommerer
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Charles R Cantor
- Department of Biomedical Engineering, School of Medicine, Boston University, Boston, MA
| | - Heiko U Käfferlein
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
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19
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Abstract
Purpose Use of molecular markers in urine, tissue or blood offers potential opportunities to improve understanding of bladder cancer biology which may help identify disease earlier, risk stratify patients, improve prediction of outcomes or help target therapy. Methods A review of the published literature was performed, without restriction of time. Results Despite the fast-growing literature about the topic and the approval of several urinary biomarkers for use in clinical practice, they have not reached the level of evidence for widespread utilization. Biomarkers could be used in different clinical scenarios, mainly to overcome the limitations of current diagnostic, predictive, and prognostic tools. They have been evaluated to detect bladder cancer in asymptomatic populations or those with hematuria and in surveillance of disease as adjuncts to cystoscopy. There is also a potential role as prognosticators of disease recurrence, progression and survival both in patients with non-invasive cancers and in those with advanced disease. Finally, they promise to be helpful in predicting the response to local and/or systemic chemotherapy and/or immunotherapy. Conclusions To date, due to the lack of high-quality prospective trials, the level of evidence provided by the current literature remains low and, therefore, the potential of biomarkers exceeds utilization in clinical practice.
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20
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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21
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Peng M, Chen C, Hulbert A, Brock MV, Yu F. Non-blood circulating tumor DNA detection in cancer. Oncotarget 2017; 8:69162-69173. [PMID: 28978187 PMCID: PMC5620327 DOI: 10.18632/oncotarget.19942] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023] Open
Abstract
Tumor DNA contains specific somatic alterations that are crucial for the diagnosis and treatment of cancer. Due to the spatial and temporal intra-tumor heterogeneity, multi-sampling is needed to adequately characterize the somatic alterations. Tissue biopsy, however, is limited by the restricted access to sample and the challenges to recapitulate the tumor clonal diversity. Non-blood circulating tumor DNA are tumor DNA fragments presents in non-blood body fluids, such as urine, saliva, sputum, stool, pleural fluid, and cerebrospinal fluid (CSF). Recent studies have demonstrated the presence of tumor DNA in these non-blood body fluids and their application to the diagnosis, screening, and monitoring of cancers. Non-blood circulating tumor DNA has an enormous potential for large-scale screening of local neoplasms because of its non-invasive nature, close proximity to the tumors, easiness and it is an economically viable option. It permits longitudinal assessments and allows sequential monitoring of response and progression. Enrichment of tumor DNA of local cancers in non-blood body fluids may help to archive a higher sensitivity than in plasma ctDNA. The direct contact of cancerous cells and body fluid may facilitate the detection of tumor DNA. Furthermore, normal DNA always dilutes the plasma ctDNA, which may be aggravated by inflammation and injury when very high amounts of normal DNA are released into the circulation. Altogether, our review indicate that non-blood circulating tumor DNA presents an option where the disease can be tracked in a simple and less-invasive manner, allowing for serial sampling informing of the tumor heterogeneity and response to treatment.
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Affiliation(s)
- Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Alicia Hulbert
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Malcolm V Brock
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
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22
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An epigenetic biomarker combination of PCDH17 and POU4F2 detects bladder cancer accurately by methylation analyses of urine sediment DNA in Han Chinese. Oncotarget 2016; 7:2754-64. [PMID: 26700620 PMCID: PMC4823069 DOI: 10.18632/oncotarget.6666] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/20/2015] [Indexed: 12/03/2022] Open
Abstract
To develop a routine and effectual procedure of detecting bladder cancer (BlCa), an optimized combination of epigenetic biomarkers that work synergistically with high sensitivity and specificity is necessary. In this study, methylation levels of seven biomarkers (EOMES, GDF15, NID2, PCDH17, POU4F2, TCF21, and ZNF154) in 148 individuals—which including 58 urothelial cell carcinoma (UCC) patients, 20 infected urinary calculi (IUC) patients, 20 kidney cancer (KC) patients,20 prostate cancer (PC) patients, and 30 healthy volunteers (HV)—were quantified by qMSP using the urine sediment DNA. Receiver operating characteristic (ROC) curves were generated for each biomarker. The combining predictors of possible combinations were calculated through logistic regression model. Subsequently, ROC curves of the three best performing combinations were constructed. Then, we validated the three best performing combinations and POU4F2 in another 72 UCC, 21 IUC, 26 KC and 22 PC, and 23 HV urine samples. The combination of POU4F2/PCDH17 has yielded the highest sensitivity and specificity of 90.00% and 93.96% in all the 312 individuals, showing the capability of detecting BlCa effectively among pathologically varied sample groups.
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23
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Schmitz-Dräger BJ, Kuckuck EC, Zuiverloon TC, Zwarthoff EC, Saltzman A, Srivastava A, Hudson MA, Seiler R, Todenhöfer T, Vlahou A, Grossman HB, Schoenberg MP, Sanchez-Carbayo M, Brünn LA, van Rhijn BW, Goebell PJ, Kamat AM, Roupret M, Shariat SF, Kiemeney LA. Microhematuria assessment an IBCN consensus—Based upon a critical review of current guidelines. Urol Oncol 2016; 34:437-51. [DOI: 10.1016/j.urolonc.2016.05.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/26/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
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24
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Current Status of Urinary Biomarkers for Detection and Surveillance of Bladder Cancer. Urol Clin North Am 2016; 43:47-62. [DOI: 10.1016/j.ucl.2015.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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van Kessel KEM, Van Neste L, Lurkin I, Zwarthoff EC, Van Criekinge W. Evaluation of an Epigenetic Profile for the Detection of Bladder Cancer in Patients with Hematuria. J Urol 2015; 195:601-7. [PMID: 26327355 DOI: 10.1016/j.juro.2015.08.085] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 10/23/2022]
Abstract
PURPOSE Many patients enter the care cycle with gross or microscopic hematuria and undergo cystoscopy to rule out bladder cancer. Sensitivity of this invasive examination is limited, leaving many patients at risk for undetected cancer. To improve current clinical practice more sensitive and noninvasive screening methods should be applied. MATERIALS AND METHODS A total of 154 urine samples were collected from patients with hematuria, including 80 without and 74 with bladder cancer. DNA from cells in the urine was epigenetically profiled using 2 independent assays. Methylation specific polymerase chain reaction was performed on TWIST1. SNaPshot™ methylation analysis was done for different loci of OTX1 and ONECUT2. Additionally all samples were analyzed for mutation status of TERT (telomerase reverse transcriptase), PIK3CA, FGFR3 (fibroblast growth factor receptor 3), HRAS, KRAS and NRAS. RESULTS The combination of TWIST1, ONECUT2 (2 loci) and OTX1 resulted in the best overall performing panel. Logistic regression analysis on these methylation markers, mutation status of FGFR3, TERT and HRAS, and patient age resulted in an accurate model with 97% sensitivity, 83% specificity and an AUC of 0.93 (95% CI 0.88-0.98). Internal validation led to an optimism corrected AUC of 0.92. With an estimated bladder cancer prevalence of 5% to 10% in a hematuria cohort the assay resulted in a 99.6% to 99.9% negative predictive value. CONCLUSIONS Epigenetic profiling using TWIST1, ONECUT2 and OTX1 results in a high sensitivity and specificity. Accurate risk prediction might result in less extensive and invasive examination of patients at low risk, thereby reducing unnecessary patient burden and health care costs.
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Affiliation(s)
- Kim E M van Kessel
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Leander Van Neste
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands; MDxHealth, Inc., Irvine, California
| | - Irene Lurkin
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wim Van Criekinge
- MDxHealth, Inc., Irvine, California; Laboratory of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium.
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26
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Andersson E, Dahmcke CM, Steven K, Larsen LK, Guldberg P. Filtration Device for On-Site Collection, Storage and Shipment of Cells from Urine and Its Application to DNA-Based Detection of Bladder Cancer. PLoS One 2015; 10:e0131889. [PMID: 26151138 PMCID: PMC4495058 DOI: 10.1371/journal.pone.0131889] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 06/08/2015] [Indexed: 02/04/2023] Open
Abstract
Molecular analysis of cells from urine provides a convenient approach to non-invasive detection of bladder cancer. The practical use of urinary cell-based tests is often hampered by difficulties in handling and analyzing large sample volumes, the need for rapid sample processing to avoid degradation of cellular content, and low sensitivity due to a high background of normal cells. We present a filtration device, designed for home or point-of-care use, which enables collection, storage and shipment of urinary cells. A special feature of this device is a removable cartridge housing a membrane filter, which after filtration of urine can be transferred to a storage unit containing an appropriate preserving solution. In spiking experiments, the use of this device provided efficient recovery of bladder cancer cells with elimination of >99% of excess smaller-sized cells. The performance of the device was further evaluated by DNA-based analysis of urinary cells collected from 57 patients subjected to transurethral resection following flexible cystoscopy indicating the presence of a tumor. All samples were tested for FGFR3 mutations and seven DNA methylation markers (BCL2, CCNA1, EOMES, HOXA9, POU4F2, SALL3 and VIM). In the group of patients where a transitional cell tumor was confirmed at histopathological evaluation, urine DNA was positive for one or more markers in 29 out of 31 cases (94%), including 19 with FGFR3 mutation (61%). In the group of patients with benign histopathology, urine DNA was positive for methylation markers in 13 out of 26 cases (50%). Only one patient in this group was positive for a FGFR3 mutation. This patient had a stage Ta tumor resected 6 months later. The ability to easily collect, store and ship diagnostic cells from urine using the presented device may facilitate non-invasive testing for bladder cancer.
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Affiliation(s)
- Elin Andersson
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christina M. Dahmcke
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
| | - Kenneth Steven
- Department of Urology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, Denmark
- * E-mail:
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27
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Wu YC, Lee WC. Alternative performance measures for prediction models. PLoS One 2014; 9:e91249. [PMID: 24608868 PMCID: PMC3946724 DOI: 10.1371/journal.pone.0091249] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/10/2014] [Indexed: 11/19/2022] Open
Abstract
As a performance measure for a prediction model, the area under the receiver operating characteristic curve (AUC) is insensitive to the addition of strong markers. A number of measures sensitive to performance change have recently been proposed; however, these relative-performance measures may lead to self-contradictory conclusions. This paper examines alternative performance measures for prediction models: the Lorenz curve-based Gini and Pietra indices, and a standardized version of the Brier score, the scaled Brier. Computer simulations are performed in order to study the sensitivity of these measures to performance change when a new marker is added to a baseline model. When the discrimination power of the added marker is concentrated in the gray zone of the baseline model, the AUC and the Gini show minimal performance improvements. The Pietra and the scaled Brier show more significant improvements in the same situation, comparatively. The Pietra and the scaled Brier indices are therefore recommended for prediction model performance measurement, in light of their ease of interpretation, clinical relevance and sensitivity to gray-zone resolving markers.
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Affiliation(s)
- Yun-Chun Wu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Wen-Chung Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environment and Human Health, College of Public Health, National Taiwan University, Taipei, Taiwan
- * E-mail:
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