Genome-wide DNA methylation and gene expression in human placentas derived from assisted reproductive technology

Abstract

Assisted reproductive technology (ART) has been associated with increased risks for growth disturbance, disrupted imprinting as well as cardiovascular and metabolic disorders. However, the molecular mechanisms and whether they are a result of the ART procedures or the underlying subfertility are unknown. We performed genome-wide DNA methylation (EPIC Illumina microarrays) and gene expression (mRNA sequencing) analyses for a total of 80 ART and 77 control placentas. The separate analyses for placentas from different ART procedures and sexes were performed. To separate the effects of ART procedures and subfertility, 11 placentas from natural conception of subfertile couples and 12 from intrauterine insemination treatments were included. Here we show that ART-associated changes in the placenta enriche in the pathways of hormonal regulation, insulin secretion, neuronal development, and vascularization. Observed decreased number of stromal cells as well as downregulated TRIM28 and NOTCH3 expressions in ART placentas indicate impaired angiogenesis and growth. DNA methylation changes in the imprinted regions and downregulation of TRIM28 suggest defective stabilization of the imprinting. Furthermore, downregulated expression of imprinted endocrine signaling molecule DLK1 associates with both ART and subfertility. Decreased expressions of TRIM28, NOTCH3, and DLK1 bring forth potential mechanisms for several phenotypic features associated with ART. Our results support previous procedure specific findings: the changes associated with growth and metabolism link more prominently to the fresh embryo transfer with smaller placentas and newborns, than to the frozen embryo transfer with larger placentas and newborns. Furthermore, since the observed changes associate also with subfertility, they offer a precious insight to the molecular background of infertility. For those that struggle with conception, medical and scientific methods called Assisted Reproductive Technology (ART) may help. However, ART have been associated with increased risks for negative medical outcomes for babies. Whether these risks are caused by ART use or the underlying condition of subfertility (less than ideal natural conception outcomes) are not known. Here we looked at the effects of ART and subfertility by studying specific genetics in placenta and newborn’s characteristics. We show that changes in genetics in the placenta from ART use are linked to hormonal control, insulin secretion, and brain and blood vessel development. Although the observed changes are subtle, they can contribute to risks for metabolic and heart disorders as well as growth disturbances in newborns. Our results provide important evidence for the effect of medical outcomes associated with both ART and subfertility. Auvinen et al. examine genome-wide DNA methylation, imprinting, and gene expression in human placentas. Placentas from assisted reproductive technologies experience a variety of altered signaling pathways with variability based on method providing insight into subfertility.