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Wever BMM, Steenbergen RDM. Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities. Mol Oncol 2024. [PMID: 38462745 DOI: 10.1002/1878-0261.13628] [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: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/27/2024] [Indexed: 03/12/2024] Open
Abstract
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor-derived cell-free DNA. We also provide future recommendations for technical advancements in urine-based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell-free DNA.
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Affiliation(s)
- Birgit M M Wever
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
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Arhant G, Lachkar S, Thiebaut PA, Marguet F, Lamy A, Thiberville L, Salaün M, Guisier F, Sabourin JC, Piton N. Detection of Tumor DNA in Bronchoscopic Fluids in Peripheral NSCLC: A Proof-of-Concept Study. JTO Clin Res Rep 2024; 5:100596. [PMID: 38328474 PMCID: PMC10847031 DOI: 10.1016/j.jtocrr.2023.100596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction DNA genotyping from plasma is a useful tool for molecular characterization of NSCLC. Nevertheless, the false-negative rate justifies the development of methods with higher sensitivity, especially in difficult-to-reach peripheral lung tumors. Methods We aimed at comparing molecular analysis from the supernatant of guide sheath flush fluid collected during radial-EndoBronchial UltraSound (r-EBUS) bronchoscopy with plasma sampling and tumor biopsies in patients with peripheral NSCLC. The DNA was genotyped using high-throughput sequencing or the COBAS mutation test. There were 65 patients with peripheral lung tumors subjected to concomitant sampling of guide sheath flush supernatant, plasma tumor DNA, and tumor biopsy and cytology using r-EBUS. There were 33 patients (including 24 newly diagnosed with having NSCLC) with an identifiable tumor mutation in the primary lesion selected for the comparative analysis. Results Guide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17 of 24 mutated EGFR, one of two ERBB2, one of one KRAS, one of one MAP2K, one of four MET, and zero of one STK11), compared with 33% in plasma-based genotyping (p = 0.0151). Furthermore, in eight of 34 r-EBUS without tumor cells on microscopic examination, we were able to detect the mutation in four paired guide sheath flush supernatant, compared with only two in paired plasma. Conclusion The detection of tumor DNA in the supernatant of guide sheath flush fluid collected during r-EBUS bronchoscopy represents a sensitive and complementary method for genotyping NSCLC.
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Affiliation(s)
- Gwenaëlle Arhant
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Samy Lachkar
- Department of Pneumology, CHU Rouen, Rouen, France
| | - Pierre-Alain Thiebaut
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Florent Marguet
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Aude Lamy
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Luc Thiberville
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Mathieu Salaün
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Florian Guisier
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Jean-Christophe Sabourin
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Nicolas Piton
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
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Sorber L, Zwaenepoel K, De Winne K, Van Casteren K, Augustus E, Jacobs J, Zhang XH, Galdermans D, De Droogh E, Lefebure A, Morel AM, Saenen E, Bustin F, Demedts I, Himpe U, Pieters T, Germonpré P, Derijcke S, Deschepper K, Van Meerbeeck JP, Rolfo C, Pauwels P. A Multicenter Study to Assess EGFR Mutational Status in Plasma: Focus on an Optimized Workflow for Liquid Biopsy in a Clinical Setting. Cancers (Basel) 2018; 10:E290. [PMID: 30150518 PMCID: PMC6162772 DOI: 10.3390/cancers10090290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 12/02/2022] Open
Abstract
A multicenter study was performed to determine an optimal workflow for liquid biopsy in a clinical setting. In total, 549 plasma samples from 234 non-small cell lung cancer (NSCLC) patients were collected. Epidermal Growth Factor Receptor (EGFR) circulating cell-free tumor DNA (ctDNA) mutational analysis was performed using digital droplet PCR (ddPCR). The influence of (pre-) analytical variables on ctDNA analysis was investigated. Sensitivity of ctDNA analysis was influenced by an interplay between increased plasma volume (p < 0.001) and short transit time (p = 0.018). Multistep, high-speed centrifugation both increased plasma generation (p < 0.001) and reduced genomic DNA (gDNA) contamination. Longer transit time increased the risk of hemolysis (p < 0.001) and low temperatures were shown to have a negative effect. Metastatic sites were found to be strongly associated with ctDNA detection (p < 0.001), as well as allele frequency (p = 0.034). Activating mutations were detected in a higher concentration and allele frequency compared to the T790M mutation (p = 0.003, and p = 0.002, respectively). Optimization of (pre-) analytical variables is key to successful ctDNA analysis. Sufficient plasma volumes without hemolysis or gDNA contamination can be achieved by using multistep, high-speed centrifugation, coupled with short transit time and temperature regulation. Metastatic site location influenced ctDNA detection. Finally, ctDNA levels might have further value in detecting resistance mechanisms.
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Affiliation(s)
- Laure Sorber
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
| | - Karen Zwaenepoel
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
| | - Koen De Winne
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
| | - Kaat Van Casteren
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
- Biomedical Quality Assurance Research Unit, KU Leuven, 3000 Leuven, Belgium.
| | - Elien Augustus
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
| | - Julie Jacobs
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
| | - Xiang Hua Zhang
- Department of Pulmonology & Thoracic Oncology, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
| | - Daniëlla Galdermans
- Pneumology, ZNA Middelheim, 2020 Antwerp, Belgium.
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
| | - Els De Droogh
- Pneumology, ZNA Middelheim, 2020 Antwerp, Belgium.
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
| | - Anneke Lefebure
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
- Pneumology, ZNA STER, 2140 Antwerp, Belgium.
| | - Ann-Marie Morel
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
- Pneumology, AZ Sint-Jozef, 2880 Bornem, Belgium.
| | - Erika Saenen
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
- Lung diseases/Allergology, AZ Heilige Familie, 2840 Reet, Belgium.
| | | | - Ingel Demedts
- Department of Pulmonary diseases, AZ Delta, 8800 Roeselare, Belgium.
| | - Ulrike Himpe
- Department of Pulmonary diseases, AZ Delta, 8800 Roeselare, Belgium.
| | - Thierry Pieters
- Pneumology, Cliniques Universitaires Saint-Luc, 1200 Bruxelles, Belgium.
| | - Paul Germonpré
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
- Pneumology, AZ Maria Middelares, 9000 Gent, Belgium.
| | - Sofie Derijcke
- Pneumology-Thoracic Oncology, AZ Groeninge, 8500 Kortrijk, Belgium.
| | - Koen Deschepper
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
- Pneumology, AZ Nikolaas, 9100 Sint-Niklaas, Belgium.
| | - Jan P Van Meerbeeck
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Department of Pulmonology & Thoracic Oncology, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
| | - Christian Rolfo
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Oncology & Phase I Unit-Early Clinical Trials, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
- Marlene and Steward Greenebaum Comprehensive Cancer Center, Thoracic Medical Oncology & Early Clinical Trials, Baltimore, MD 12116, USA.
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (CORE), University of Antwerp, 2610 Wilrijk, Belgium.
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium.
- Thoracic Oncology Group Antwerp (TOGA), University of Antwerp, 2610 Wilrijk, Belgium.
- Antwerp University Hospital (UZA), Tumor Bank, 2650 Edegem, Belgium.
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