Affordable Access

Access to the full text

Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome

  • Van Neste, Christophe1, 2
  • Laird, Alexander3, 4, 5
  • O’Mahony, Fiach3, 4
  • Van Criekinge, Wim6
  • Deforce, Dieter1
  • Van Nieuwerburgh, Filip1
  • Powles, Thomas7, 8
  • Harrison, David J.3, 4, 9
  • Stewart, Grant D.3, 4
  • De Meyer, Tim6
  • 1 Ghent University, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, Ghent, 9000, Belgium , Ghent (Belgium)
  • 2 Ghent University, Center for Medical Genetics, De Pintelaan 185, Ghent, 9000, Belgium , Ghent (Belgium)
  • 3 University of Edinburgh, Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, Edinburgh, EH4 2XU, UK , Edinburgh (United Kingdom)
  • 4 Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Edinburgh, UK , Edinburgh (United Kingdom)
  • 5 University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, EH4 2XU, UK , Edinburgh (United Kingdom)
  • 6 Ghent University, Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Coupure Links 653, Ghent, 9000, Belgium , Ghent (Belgium)
  • 7 The Royal Free Hospital, Renal Cancer Unit, London, NW3 2QG, UK , London (United Kingdom)
  • 8 Queen Mary University of London, Centre for Experimental Cancer Medicine, Bart’s Cancer Institute, London, EC1A 7BE, UK , London (United Kingdom)
  • 9 University of St Andrews, School of Medicine, Edinburgh, St Andrews, KY16 9TF, UK , Edinburgh (United Kingdom)
Published Article
Cellular Oncology
Publication Date
Jan 10, 2017
DOI: 10.1007/s13402-016-0313-5
Springer Nature


PurposeCurrently, 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.MethodsDNA 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.ResultsWe 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.ConclusionTissue 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.

Report this publication


Seen <100 times