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

Authors

Kristen M. Kocher, Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Julius Ngwa, Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Kushal J. Kapse, Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Surajit Bhattacharya, Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Christopher Rossi, Department of Pathology and Laboratory Medicine, Children's National Hospital, Washington, DC, USA.
Emmanuele Delot, Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Adre duPlessis, Department of Pediatrics, The George Washington University, Washington, DC, USA.
Catherine Limperopoulos, Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Nickie Andescavage, Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.

Document Type

Journal Article

Publication Date

9-16-2024

Journal

Clinical epigenetics

Volume

16

Issue

1

DOI

10.1186/s13148-024-01741-8

Keywords

DNA methylation; Epigenetic aging; FFPE; Placenta

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.

APA Citation

Kocher, Kristen M.; Ngwa, Julius; Kapse, Kushal J.; Bhattacharya, Surajit; Rossi, Christopher; Delot, Emmanuele; duPlessis, Adre; Limperopoulos, Catherine; and Andescavage, Nickie, "Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis" (2024). GW Authored Works. Paper 5634.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/5634

Department

Pediatrics