title: Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.|Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.
authors.forename: Christophe
authors.identifier: http://orcid.org/0000-0002-5958-5731
authors.initials: C
authors.lastname: Van Neste
authors.affiliation: 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.
authors.forename: Alexander
authors.initials: A
authors.lastname: Laird
authors.affiliation: 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.
authors.forename: Fiach
authors.initials: F
authors.lastname: O'Mahony
authors.affiliation: Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Van Criekinge
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
authors.affiliation: 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.
authors.forename: Thomas
authors.initials: T
authors.lastname: Powles
authors.affiliation: Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. david.harrison@st-andrews.ac.uk.|Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Edinburgh, UK. david.harrison@st-andrews.ac.uk.|School of Medicine, University of St Andrews, Edinburgh, St Andrews, KY16 9TF, UK. david.harrison@st-andrews.ac.uk.
authors.forename: David J
authors.initials: DJ
authors.lastname: Harrison
authors.affiliation: 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.
authors.forename: Grant D
authors.initials: GD
authors.lastname: Stewart
authors.affiliation: Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
authors.forename: Tim
authors.initials: T
authors.lastname: De Meyer
mesh_terms: D002292:Carcinoma, Renal Cell / Q000601:surgery*; D019175:DNA Methylation; D057890:Epigenomics; D006801:Humans; D007511:Ischemia / Q000235:genetics*; D007680:Kidney Neoplasms / Q000601:surgery*; D008026:Ligation; D009392:Nephrectomy; D012077:Renal Artery / Q000601:surgery; D059467:Transcriptome; D057170:Translational Research, Biomedical
keywords: Cancer epigenetics; DNA methylation; Hypoxia; Sampling effects