Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
29 09 2023
29 09 2023
Historique:
received:
09
08
2023
accepted:
28
09
2023
medline:
5
10
2023
pubmed:
29
9
2023
entrez:
29
9
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37773256
doi: 10.1038/s41598-023-43788-2
pii: 10.1038/s41598-023-43788-2
pmc: PMC10541404
doi:
Substances chimiques
Formaldehyde
1HG84L3525
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
16381Informations de copyright
© 2023. Springer Nature Limited.
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