Evidence map›Paper›PMID 28074387›Full record

ArticleCellular oncology (Dordrecht, Netherlands)2017

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

Christophe Van Neste, Alexander Laird, Fiach O'Mahony, Wim Van Criekinge, Dieter Deforce, Filip Van Nieuwerburgh, Thomas Powles, David J Harrison, Grant D Stewart, Tim De Meyer

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cellular oncology (Dordrecht, Netherlands), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact, top 100% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 4 citations in OpenAlex.

  1. Review
  2. Resolvin D1 Suppresses HAntioxidants (Basel, Switzerland) · 2021
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 5 institutions in 2 countries.

Christophe Van NesteLaboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.ORCID http://orcid.org/0000-0002-5958-5731
Alexander LairdEdinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
Fiach O'MahonyEdinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
Wim Van CriekingeBiobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
Dieter DeforceLaboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
Filip Van NieuwerburghLaboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
Thomas PowlesRenal Cancer Unit, The Royal Free Hospital, London, NW3 2QG, UK.
David J HarrisonEdinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. david.harrison@st-andrews.ac.uk.
Grant D StewartEdinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
Tim De MeyerBiobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioninformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
Ghent University · BEEdinburgh Cancer Research · GBGhent University Hospital · BEQueen Mary University of London · GBUniversity of St Andrews · GB

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

NephrectomyTranslational Research, BiomedicalCarcinoma, Renal CellDNA MethylationEpigenomicsHumansIschemiaKidney NeoplasmsLigationRenal ArteryTranscriptomeCancer epigeneticsDNA methylationHypoxiaSampling effects

Identifiers

PMID28074387
PMCPMC13001542
OpenAlexW2570104364

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.