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

(2017) CELLULAR ONCOLOGY. 40(3). p.293-297
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Abstract
Purpose: 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. Conclusion: 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.
Keywords
Hypoxia, Cancer epigenetics, DNA methylation, Sampling effects, GENE-EXPRESSION, UP-REGULATION, CARCINOMA, ACTIVATION, INHIBITOR, HYPOXIA

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Chicago
Van Neste, Christophe, Alexander Laird, Fiach O’Mahony, Wim Van Criekinge, Dieter Deforce, Filip Van Nieuwerburgh, Thomas Powles, David J Harrison, Grant D Stewart, and Tim De Meyer. 2017. “Epigenetic Sampling Effects : Nephrectomy Modifies the Clear Cell Renal Cell Cancer Methylome.” Cellular Oncology 40 (3): 293–297.
APA
Van Neste, C., Laird, A., O’Mahony, F., Van Criekinge, W., Deforce, D., Van Nieuwerburgh, F., Powles, T., et al. (2017). Epigenetic sampling effects : nephrectomy modifies the clear cell renal cell cancer methylome. CELLULAR ONCOLOGY, 40(3), 293–297.
Vancouver
1.
Van Neste C, Laird A, O’Mahony F, Van Criekinge W, Deforce D, Van Nieuwerburgh F, et al. Epigenetic sampling effects : nephrectomy modifies the clear cell renal cell cancer methylome. CELLULAR ONCOLOGY. 2017;40(3):293–7.
MLA
Van Neste, Christophe, Alexander Laird, Fiach O’Mahony, et al. “Epigenetic Sampling Effects : Nephrectomy Modifies the Clear Cell Renal Cell Cancer Methylome.” CELLULAR ONCOLOGY 40.3 (2017): 293–297. Print.
@article{8509330,
  abstract     = {Purpose: 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. 
Conclusion: 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.},
  author       = {Van Neste, Christophe and Laird, Alexander and O{\textquoteright}Mahony, Fiach and Van Criekinge, Wim and Deforce, Dieter and Van Nieuwerburgh, Filip and Powles, Thomas and Harrison, David J and Stewart, Grant D and De Meyer, Tim},
  issn         = {2211-3428},
  journal      = {CELLULAR ONCOLOGY},
  language     = {eng},
  number       = {3},
  pages        = {293--297},
  title        = {Epigenetic sampling effects : nephrectomy modifies the clear cell renal cell cancer methylome},
  url          = {http://dx.doi.org/10.1007/s13402-016-0313-5},
  volume       = {40},
  year         = {2017},
}

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