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Van Neste C, Laird A, O'Mahony F, Van Criekinge W, Deforce D, Van Nieuwerburgh F, Powles T, Harrison DJ, Stewart GD, De Meyer T. Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome. Cell Oncol (Dordr) 2017; 40:293-297. [PMID: 28074387 DOI: 10.1007/s13402-016-0313-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2016] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Currently, it is unclear to what extent sampling procedures affect the epigenome. Here, this phenomenon was evaluated by studying the impact of artery ligation on DNA methylation in clear cell renal cancer. METHODS DNA methylation profiles between vascularised tumour biopsy samples and devascularised nephrectomy samples from two individuals were compared. The relevance of significantly altered methylation profiles was validated in an independent clinical trial cohort. RESULTS We found that six genes were differentially methylated in the test samples, of which four were linked to ischaemia or hypoxia (REXO1L1, TLR4, hsa-mir-1299, ANKRD2). Three of these genes were also found to be significantly differentially methylated in the validation cohort, indicating that the observed effects are genuine. CONCLUSION Tissue ischaemia during normal surgical removal of tumour can cause epigenetic changes. Based on these results, we conclude that the impact of sampling procedures in clinical epigenetic studies should be considered and discussed, particularly after inducing hypoxia/ischaemia, which occurs in most oncological surgery procedures through which tissues are collected for translational research.
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Affiliation(s)
- Christophe Van Neste
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Alexander Laird
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Fiach O'Mahony
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Edinburgh, UK
| | - Wim Van Criekinge
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Thomas Powles
- Renal Cancer Unit, The Royal Free Hospital, London, NW3 2QG, UK
- Centre for Experimental Cancer Medicine, Bart's Cancer Institute, Queen Mary University of London, London, EC1A 7BE, UK
| | - David J Harrison
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
- Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Edinburgh, UK.
- School of Medicine, University of St Andrews, Edinburgh, St Andrews, KY16 9TF, UK.
| | - Grant D Stewart
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Edinburgh, UK
| | - Tim De Meyer
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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Barber JCK, Sharp AJ, Hollox EJ, Tyson C. Copy number variation of the REXO1L1 gene cluster; euchromatic deletion variant or susceptibility factor? Eur J Hum Genet 2016; 25:8-9. [PMID: 27485411 DOI: 10.1038/ejhg.2016.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- John C K Barber
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, NY, USA
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | - Christine Tyson
- Department of Pathology, Cytogenetics Laboratory, Royal Columbian Hospital, New Westminster, British Columbia, Canada
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