Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome
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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.
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.
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.
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.
KeywordsHypoxia Cancer epigenetics DNA methylation Sampling effects
Conception and design: DJH, AL, GDS, TDM, TP. Development of methodology: CVN, GDS, DJH, TP, TDM. Acquisition of data (acquired and managed patients, provided facilities, etc.): GDS, FOM, AL, DJH, TP. Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis): CVN, TDM, GDS, DJH. Writing, review, and/or revision of the manuscript: CVN, AL, FOM, WVC, DD, FVN, TP, DJH, GDS, TDM. Study supervision: GDS, DJH, TDM, WVC.
Compliance with ethical standards
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Permission to use tissue was obtained from local research ethics committees.
This work was supported by the Chief Scientist Office, Scotland (ETM37; GDS, DJH), Cancer Research UK (Experimental Cancer Medicine Centre; TP, London, DJH, Edinburgh), Medical Research Council (AL, DJH), Royal College of Surgeons of Edinburgh Robertson Trust (AL), Melville Trust AL), Renal Cancer Research Fund (GDS, DJH), Kidney Cancer Scotland (GDS) and an educational grant from Pfizer (TP). CVN and TDM were funded by Ghent University Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’.
Conflict of interest
The authors declare that they have no conflict of interest.
Informed consent was obtained from all participants included in the study.
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