Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
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Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. / Dupont, Mikkel Eriksen; Jacobsen, Stine Bøttcher; Christiansen, Steffan; Tfelt-Hansen, Jacob; Smerup, Morten Holdgaard; Andersen, Jeppe Dyrberg; Morling, Niels.
In: Scientific Reports, Vol. 13, 16381, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
AU - Dupont, Mikkel Eriksen
AU - Jacobsen, Stine Bøttcher
AU - Christiansen, Steffan
AU - Tfelt-Hansen, Jacob
AU - Smerup, Morten Holdgaard
AU - Andersen, Jeppe Dyrberg
AU - Morling, Niels
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - Faculty of Health and Medical Sciences
KW - DNA methylation
KW - Epigenetic
KW - Cardiac Catheterization/methods
U2 - 10.1038/s41598-023-43788-2
DO - 10.1038/s41598-023-43788-2
M3 - Journal article
C2 - 37773256
VL - 13
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
M1 - 16381
ER -
ID: 369394931