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dc.contributor.authorVan Neste, Christophe
dc.contributor.authorLaird, Alexander
dc.contributor.authorO'Mahony, Fiach
dc.contributor.authorVan Criekinge, Wim
dc.contributor.authorDeforce, Dieter
dc.contributor.authorVan Nieuwerbugh, Filip
dc.contributor.authorPowles, Thomas
dc.contributor.authorHarrison, David James
dc.contributor.authorStewart, Grant D.
dc.contributor.authorDe Meyer, Tim
dc.identifier.citationVan Neste , C , Laird , A , O'Mahony , F , Van Criekinge , W , Deforce , D , Van Nieuwerbugh , F , Powles , T , Harrison , D J , Stewart , G D & De Meyer , T 2017 , ' Epigenetic sampling effects : nephrectomy modifies the clear cell renal cell cancer methylome ' , Cellular Oncology , vol. 40 , no. 3 , pp. 293-297 .
dc.identifier.otherPURE: 248518466
dc.identifier.otherPURE UUID: a78905eb-3fe2-43fe-b9ed-1d915027e986
dc.identifier.otherScopus: 85009191858
dc.identifier.otherWOS: 000402071800008
dc.identifier.otherORCID: /0000-0001-9041-9988/work/64034205
dc.descriptionThis 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), 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'en
dc.description.abstractBackground: Sample collection for clinical epigenetics research often occurs at the time of surgical excision of a diseased organ. However, this approach may compromise the epigenetic profile under study. The use of different sampling procedures during a study can often not be avoided, but may in theory lead to biased results. The effect of tissue sampling approach on DNA methylation is studied here using clear cell renal cell cancer (ccRCC) as a model. A comparison of the DNA methylation profiles between vascularised tumour biopsy samples and subsequent devascularised nephrectomy samples obtained from the same two individuals (total of 6 samples per individual) was undertaken. Validation of the results was performed using biopsy and nephrectomy samples obtained from 14 patients included in a ccRCC clinical trial (SuMR; identifier: NCT01024205). Findings: Using MBD2 sequencing, the methylome was analysed for all samples and differential methylome regions were retrieved. The results, from the test set, show six differentially methylated genes, of which four were clearly linked to ischaemia or hypoxia (REXO1L1, TLR4, hsa-mir-1299, and ANKRD2). To validate these findings, it was evaluated whether these loci were also featured by differential methylation in the clinical trial cohort with a similar experimental design to the test set. Three of the six genes are again significantly differentially methylated, showing an overall clear impact of renal artery clamping on DNA methylation. Conclusions: Renal artery ligation modulates the ccRCC methylome, impacting methylation of ischaemia and hypoxia associated genes. Results from devascularised surgical resection specimens do not accurately reflect findings from tumour biopsies.
dc.relation.ispartofCellular Oncologyen
dc.rights© 2017, International Society for Cellular Oncology. This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at /
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.subjectRC0254 Neoplasms. Tumors. Oncology (including Cancer)en
dc.titleEpigenetic sampling effects : nephrectomy modifies the clear cell renal cell cancer methylomeen
dc.typeJournal articleen
dc.contributor.institutionUniversity of St Andrews.School of Medicineen
dc.contributor.institutionUniversity of St Andrews.Cellular Medicine Divisionen
dc.description.statusPeer revieweden

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