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Bach S, Wever BMM, van de Wiel MA, Veltman JD, Hashemi SMS, Kazemier G, Bahce I, Steenbergen RDM. Dynamics of methylated cell-free DNA in the urine of non-small cell lung cancer patients. Epigenetics 2021; 17:1057-1069. [PMID: 34605346 PMCID: PMC9542718 DOI: 10.1080/15592294.2021.1982511] [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] [Indexed: 01/19/2023] Open
Abstract
High levels of methylated DNA in urine represent an emerging biomarker for non-small cell lung cancer (NSCLC) detection and are the subject of ongoing research. This study aimed to investigate the circadian variation of urinary cell-free DNA (cfDNA) abundance and methylation levels of cancer-associated genes in NSCLC patients. In this prospective study of 23 metastatic NSCLC patients with active disease, patients were asked to collect six urine samples during the morning, afternoon, and evening of two subsequent days. Urinary cfDNA concentrations and methylation levels of CDO1, SOX17, and TAC1 were measured at each time point. Circadian variation and between- and within-subject variability were assessed using linear mixed models. Variability was estimated using the Intraclass Correlation Coefficient (ICC), representing reproducibility. No clear circadian patterns could be recognized for cfDNA concentrations or methylation levels across the different sampling time points. Significantly lower cfDNA concentrations were found in males (p=0.034). For cfDNA levels, the between- and within-subject variability were comparable, rendering an ICC of 0.49. For the methylation markers, ICCs varied considerably, ranging from 0.14 to 0.74. Test reproducibility could be improved by collecting multiple samples per patient. In conclusion, there is no preferred collection time for NSCLC detection in urine using methylation markers, but single measurements should be interpreted carefully, and serial sampling may increase test performance. This study contributes to the limited understanding of cfDNA dynamics in urine and the continued interest in urine-based liquid biopsies for cancer diagnostics.
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Affiliation(s)
- Sander Bach
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Birgit M M Wever
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Mark A van de Wiel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Joris D Veltman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sayed M S Hashemi
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Geert Kazemier
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Idris Bahce
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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Chiarella P, Capone P, Carbonari D, Sisto R. A Predictive Model Assessing Genetic Susceptibility Risk at Workplace. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16112012. [PMID: 31195756 PMCID: PMC6603935 DOI: 10.3390/ijerph16112012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 01/08/2023]
Abstract
(1) Background: The study of susceptibility biomarkers in the immigrant workforce integrated into the social tissue of European host countries is always a challenge, due to high individual heterogeneity and the admixing of different ethnicities in the same workplace. These workers having distinct cultural backgrounds, beliefs, diets, and habits, as well as a poor knowledge of the foreign language, may feel reluctant to donate their biological specimens for the biomonitoring research studies. (2) Methods: A model predicting ethnicity-specific susceptibility based on principal component analysis has been conceived, using the genotype frequency of the investigated populations available in publicly accessible databases. (3) Results: Correlations among ethnicities and between ethnic and polymorphic genes have been found, and low/high-risk profiles have been identified as valuable susceptibility biomarkers. (4) Conclusions: In the absence of workers’ consent or access to blood genotyping, ethnicity represents a good indicator of the subject’s genotype. This model, associating ethnicity-specific genotype frequency with the susceptibility biomarkers involved in the metabolism of toxicants, may replace genotyping, ensuring the necessary safety and health conditions of workers assigned to hazardous jobs.
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Affiliation(s)
- Pieranna Chiarella
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL Research, Via Fontana Candida 1, 00078 Monteporzio Catone, Rome, Italy.
| | - Pasquale Capone
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL Research, Via Fontana Candida 1, 00078 Monteporzio Catone, Rome, Italy.
| | - Damiano Carbonari
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL Research, Via Fontana Candida 1, 00078 Monteporzio Catone, Rome, Italy.
| | - Renata Sisto
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL Research, Via Fontana Candida 1, 00078 Monteporzio Catone, Rome, Italy.
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4
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Streleckiene G, Reid HM, Arnold N, Bauerschlag D, Forster M. Quantifying cell free DNA in urine: comparison between commercial kits, impact of gender and inter-individual variation. Biotechniques 2019; 64:225-230. [PMID: 29793362 DOI: 10.2144/btn-2018-0003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA can enter the blood circulation from living cells by extracellular vesicles or at cell death, and pass into urine through the kidney barrier. Urine can be collected non-invasively, making it an interesting source of cell-free DNA (cfDNA) for research studies and ultimately for clinical diagnostics. However, there is currently a lack of data on the quantity and variability of cfDNA in urine. Here, we benchmark two commercial urine cfDNA isolation kits with respect to the quantity of DNA, the labor time, and cost. The results show distinctive differences between each kit. Furthermore, the cfDNA amount from the same probands varied strongly from day to day and may be higher in female samples than in male samples (p = 0.003).
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Affiliation(s)
- Greta Streleckiene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Eiveniu Str. 2, LT-50009 Kaunas, Lithuania.,Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Hayley M Reid
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany.,Department of Gynecology & Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts-Universität zu Kiel, D-24105 Kiel, Germany
| | - Dirk Bauerschlag
- Department of Gynecology & Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts-Universität zu Kiel, D-24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
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Confronting two biomolecular techniques to detect NRF2 gene polymorphism biomarkers. Future Sci OA 2019; 5:FSO361. [PMID: 30820344 PMCID: PMC6391633 DOI: 10.4155/fsoa-2018-0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
Aim: Gene polymorphism biomarkers identify individual susceptibility to environmental and occupational hazards. The conventional approach considers polymerase chain reaction (PCR) followed by restriction fragment length polymorphism analysis (RFLP), a reliable but expensive and time-consuming two-step procedure. Therefore we evaluated the simpler method confronting two-pair primers (CTPP)–PCR for its robustness and applicability to epidemiologic studies. Materials & methods: We compared CTPP–PCR and PCR–RFLP techniques to detect two NRF2 polymorphisms in a set of biological samples. Results: CTPP–PCR produced contradictory results and required the orthogonal technique for confirming the data. Conclusion: In contrast to PCR-RFLP, CTPP–PCR of NRF2 polymorphisms resulted in ambiguous genotyping which strongly jeopardized heterozygosis classification. The necessity of long optimization and control procedures nullified the potential advantages of CTPP–PCR in terms of costs and time. Confronting two-pair primers-polymerase chain reaction (CTPP–PCR) is potentially a fast, simple and cost-efficient method for the detection of gene polymorphism biomarkers. This technique was used to genotype two SNPs of NRF2 gene in a set of biological samples but resulted in ambiguous results. Therefore, it was necessary to validate the CTPP–PCR genotyping data with the orthogonal technique PCR-RFLP. Since reproducibility is a critical issue in both biomedical research and diagnostics, we advise pairing CTPP–PCR with control methods and evaluating whether the overall package is still convenient for massive genetic screening.
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