Sex-influenced DNA methylation differs by placental cell type

Sex differences in the function and morphology of the human placenta can lead to sex differences in pregnancy outcomes. X chromosome inactivation (XCI) is the primary mechanism for dosage compensation between the sexes, and is strongly associated with X-chromosome promoter DNA methylation (DNAme) in somatic cells. However, in the placenta, low X-chromosome promoter DNAme has been reported. The placenta is a complex organ consisting of cells of different developmental origins, but the sex differences in DNAme by specific cell types have not been investigated.

We examined sex-influenced DNAme from 18 to 19 samples each of endothelial, stromal, cytotrophoblast and Hofbauer cells, sorted from term placentas, as well as matched whole chorionic villi. We also compared these profiles with data from 65 endothelial cell samples from placental chorionic plate arteries and veins (XX = 16, XY = 13) and umbilical cord veins (XX = 22, XY = 14). All data were derived from Illumina Infinium HumanMethylation450 or EPIC DNAme arrays. Sex-stratified analyses of the X/Y and autosomal DNAme were undertaken to identify DNAme differences associated with sex chromosome complement.

The DNAme distribution on both the X and Y chromosomes differed by cell type. These differences clustered according to the differing developmental origins from extraembryonic mesoderm (endothelial/stromal), trophectoderm (cytotrophoblast) and epiblast (Hofbauer cells), with Hofbauer cells sharing a similar distribution with blood and umbilical endothelial cells. Interestingly, the typical XCI-associated DNAme at promoter CpG islands (CGI) on the X-chromosome of XX cells was absent for endothelial/stromal cells and present only at low levels in trophoblasts, suggesting that de novo establishment of promoter-CGI DNAme on the X-chromosome may differ by cell type.

The lack of X-linked promoter DNAme in extraembryonic mesoderm-derived cells (endothelial/stromal) is consistent with a distinct developmental origin of these populations relative to the other placental and umbilical cell types. Autosomal DNAme also showed cell-type differences in alignment with cellular relationships observed for sex chromosomes. This work suggests the effects of sex chromosome complement on pregnancy outcomes may differ by placental cell type.