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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

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 st...

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Autores principales: Dupont, Mikkel Eriksen, Jacobsen, Stine Bøttcher, Christiansen, Steffan Noe Niikanoff, Tfelt-Hansen, Jacob, Smerup, Morten Holdgaard, Andersen, Jeppe Dyrberg, Morling, Niels
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541404/
https://www.ncbi.nlm.nih.gov/pubmed/37773256
http://dx.doi.org/10.1038/s41598-023-43788-2
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author Dupont, Mikkel Eriksen
Jacobsen, Stine Bøttcher
Christiansen, Steffan Noe Niikanoff
Tfelt-Hansen, Jacob
Smerup, Morten Holdgaard
Andersen, Jeppe Dyrberg
Morling, Niels
author_facet Dupont, Mikkel Eriksen
Jacobsen, Stine Bøttcher
Christiansen, Steffan Noe Niikanoff
Tfelt-Hansen, Jacob
Smerup, Morten Holdgaard
Andersen, Jeppe Dyrberg
Morling, Niels
author_sort Dupont, Mikkel Eriksen
collection PubMed
description 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.
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spelling pubmed-105414042023-10-01 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 Noe Niikanoff Tfelt-Hansen, Jacob Smerup, Morten Holdgaard Andersen, Jeppe Dyrberg Morling, Niels Sci Rep Article 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. Nature Publishing Group UK 2023-09-29 /pmc/articles/PMC10541404/ /pubmed/37773256 http://dx.doi.org/10.1038/s41598-023-43788-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Dupont, Mikkel Eriksen
Jacobsen, Stine Bøttcher
Christiansen, Steffan Noe Niikanoff
Tfelt-Hansen, Jacob
Smerup, Morten Holdgaard
Andersen, Jeppe Dyrberg
Morling, Niels
Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
title Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
title_full Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
title_fullStr Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
title_full_unstemmed Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
title_short Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
title_sort fresh and frozen cardiac tissue are comparable in dna methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate dna methylation levels
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541404/
https://www.ncbi.nlm.nih.gov/pubmed/37773256
http://dx.doi.org/10.1038/s41598-023-43788-2
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