Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels

Mikkel Eriksen Dupont*, Stine Bøttcher Jacobsen, Steffan Noe Niikanoff Christiansen, Jacob Tfelt-Hansen, Morten Holdgaard Smerup, Jeppe Dyrberg Andersen, Niels Morling

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

1 Citation (Scopus)
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Abstract

Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.

Original languageEnglish
Article number16381
JournalScientific Reports
Volume13
Issue number1
Pages (from-to)16381
Number of pages1
ISSN2045-2322
DOIs
Publication statusPublished - 29 Sept 2023

Bibliographical note

© 2023. Springer Nature Limited.

Keywords

  • DNA Methylation
  • Formaldehyde
  • Humans
  • Paraffin Embedding/methods
  • Reproducibility of Results
  • Tissue Fixation/methods

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