Comparison of DNA methylation patterns of parentally imprinted genes in placenta derived from IVF conceptions in two different culture media

• Published in: Human reproduction (Oxford) 2020-03, Vol.35 (3), p.516-528
• Main Authors: Mulder, Callista L, Wattimury, Tess M, Jongejan, Aldo, de Winter-Korver, Cindy M, van Daalen, Saskia K M, Struijk, Robert B, Borgman, Susanne C M, Wurth, Yvonne, Consten, Dimitri, van Echten-Arends, Jannie, Mastenbroek, Sebastiaan, Dumoulin, John C M, Repping, Sjoerd, van Pelt, Ans M M, van Montfoort, Aafke P A
• Format: Article
• Language: English
• Subjects: Culture Media - metabolism; DNA Methylation; Female; Fertilization in Vitro; Humans; Netherlands; Original; Placenta - metabolism; Pregnancy
• ISSN: 0268-1161; 1460-2350
• DOI: 10.1093/humrep/deaa004

Abstract Study question Is there a difference in DNA methylation status of imprinted genes in placentas derived from IVF conceptions where embryo culture was performed in human tubal fluid (HTF) versus G5 culture medium? Summary answer We found no statistically significant differences in the mean DNA methylation status of differentially methylated regions (DMRs) associated with parentally imprinted genes in placentas derived from IVF conceptions cultured in HTF versus G5 culture medium. What is known already Animal studies indicate that the embryo culture environment affects the DNA methylation status of the embryo. In humans, birthweight is known to be affected by the type of embryo culture medium used. The effect of embryo culture media on pregnancy, birth and child development may thus be mediated by differential methylation of parentally imprinted genes in the placenta. Study design, size, duration To identify differential DNA methylation of imprinted genes in human placenta derived from IVF conceptions exposed to HTF or G5 embryo culture medium, placenta samples (n = 43 for HTF, n = 54 for G5) were collected between 2010 and 2012 s as part of a multi-center randomized controlled trial in the Netherlands comparing these embryo culture media. Placenta samples from 69 naturally conceived (NC) live births were collected during 2008–2013 in the Netherlands as reference material. Participants/materials, setting, methods To identify differential DNA methylation of imprinted genes, we opted for an amplicon-based sequencing strategy on an Illumina MiSeq sequencing platform. DNA was isolated and 34 DMRs associated with well-defined parentally imprinted genes were amplified in a two-step PCR before sequencing using MiSeq technology. Sequencing data were analyzed in a multivariate fashion to eliminate possible confounding effects. Main results and the role of chance We found no statistically significant differences in the mean DNA methylation status of any of the imprinted DMRs in placentas derived from IVF conceptions cultured in HTF or G5 culture medium. We also did not observe any differences in the mean methylation status per amplicon nor in the variance in methylation per amplicon between the two culture medium groups. A separate surrogate variable analysis also demonstrated that the IVF culture medium was not associated with the DNA methylation status of these DMRs. The mean methylation level and variance per CpG was equal between HTF and G5 placenta. Addit