The role of DNA methylation in human trophoblast differentiation

Abstract

The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate placental function. Trophoblasts transform the maternal vasculature to allow efficient blood flow to the placenta and facilitate adequate nutrient uptake. Placental development is in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes to human trophoblast differentiation is limited. To better understand how genome-wide methylation differences affect trophoblast differentiation, reduced representation bisulfite sequencing (RRBS) was conducted on four matched sets of trophoblasts; side-population trophoblasts (a candidate human trophoblast stem cell population), cytotrophoblasts (an intermediate progenitor population), and extravillous trophoblasts (EVT, a terminally differentiated population) each isolated from the same first trimester placenta. Each trophoblast population had a distinct methylome. In line with their close differentiation relationship, the methylation profile of side-population trophoblasts was most similar to cytotrophoblasts, whilst EVT had the most distinct methylome. In comparison to mature trophoblast populations, side-population trophoblasts exhibited differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation, and regulation of pluripotency. A combined methylomic and transcriptomic approach was taken to better understand cytotrophoblast differentiation to EVT. This revealed methylation of 41 genes involved in epithelial to mesenchymal transition and metastatic cancer pathways, which likely contributes to the acquisition of an invasive EVT phenotype. However, the methylation status of a gene did not always predict gene expression. Therefore, while CpG methylation plays a role in trophoblast differentiation, it is likely not the only regulatory mechanism involved in this process.

The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia

“…A recent study has addressed this question using a side-population trophoblasts, a candidate human TSC [55], isolated from first trimester placenta. The comparison of the methylomes of this side-population trophoblasts and the methylomes of vCTs and EVTs all isolated from the same first trimester placenta, showed that each population had a distinctive methylome [56]. In comparison to mature vCTs, side-population trophoblasts, showed differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation and regulation of pluripotency.…”

“…This has also been analyzed by genome-scale DNA methylation analysis. Gamage and coworkers have analyzed by RRBS side population trophoblasts, CTs and EVTs from human first trimester placentas [56]. Forty-one genes involved in EMT and metastatic cancer pathways were found methylated between CT and EVTs, possibly contributing to the invasive phenotype of these cells.…”

“…Table S1. High-throughput studies analyzing methylation profiles of different relevant tissues in the context of preeclampsia [42,43,47,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73].…”

Cell-specific Characterization of the Placental Methylome

“…We performed a comprehensive analysis of DNAm for human placental cell types using the Illumina EPIC methylation array. Previous placental cell DNAm studies have focused on a lesser number of cell types (41), used lower resolution approaches (42), or focused on a narrow gestational age range (e.g. only rst trimester, or only term).…”

“…The relationships we found for repetitive elements and global DNAm between cell types and CV were also largely consistent in our rst trimester samples (Additional File 7: Table S8, Additional File 1: Figure S11B). To determine genome-wide repetitive element DNAm, we used the random forest -based 'REMP' algorithm (41) to predict 438,664 Alu CpGs and 39,136 LINE1 CpGs that are not covered by the EPIC array. Relationships between cell types and CV for predicted and non-predicted repetitive elements were mostly the same, except TB DNAm in predicted Alu and LINE1 CpGs was not signi cantly different compared to CV (Additional File 7: Table S8, Additional File 1: Figure S11C).…”