Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis

Kristen M Kocher; Julius Ngwa; Kushal J Kapse; Surajit Bhattacharya; Christopher Rossi; Emmanuele Delot; Adre duPlessis; Catherine Limperopoulos; Nickie Andescavage

doi:10.1186/s13148-024-01741-8

Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis

Clin Epigenetics. 2024 Sep 16;16(1):128. doi: 10.1186/s13148-024-01741-8.

Authors

Kristen M Kocher^{1

2}, Julius Ngwa¹, Kushal J Kapse¹, Surajit Bhattacharya³, Christopher Rossi⁴, Emmanuele Delot^{3

2}, Adre duPlessis^{2

5}, Catherine Limperopoulos^{1

2}, Nickie Andescavage^{1

2

6}

Affiliations

¹ Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
² Department of Pediatrics, The George Washington University, Washington, DC, USA.
³ Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
⁴ Department of Pathology and Laboratory Medicine, Children's National Hospital, Washington, DC, USA.
⁵ Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
⁶ Division of Neonatology, Children's National Hospital, Washington, DC, USA.

Abstract

To assess the impact of postnatal processing on placental DNA methylation, array data from flash-frozen placental tissue was compared to perfluorocarbon-immersed and formalin-fixed paraffin-embedded placental tissue. We observed that tissue exposed to perfluorocarbon showed no significant DNA methylation differences when compared to unprocessed tissue, while formalin processing altered the quality and reliability of the data produced on the DNA methylation array platform. Placental DNA methylation allows for the study of gene-environment interactions that influence the fetal environment and development. Our study highlights that placental post-processing techniques must be considered in the evaluation and interpretation of epigenetic studies.

Keywords: DNA methylation; Epigenetic aging; FFPE; Placenta.

MeSH terms

DNA Methylation* / genetics
Epigenesis, Genetic / genetics
Epigenomics / methods
Female
Humans
Paraffin Embedding / methods
Placenta* / metabolism
Pregnancy

Abstract

MeSH terms

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