Journal Article

Sex-influenced DNA methylation differs by placental cell type

Yuan, Victor, Peñaherrera, Maria S., Robinson, Wendy P., Han, Jiyoung, Inkster, Amy M.

2026

Overview

Background 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. Methods 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. Results 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. Conclusion 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. Highlights X and Y- chromosome DNA methylation differs by placental cell type. DNA methylation patterns are consistent with the distinct developmental origins of different placental cell types. DNA methylation typically present at X-linked promoters in somatic XX cells was absent in villous endothelial and stromal cells. Endothelial cells in the small vessels of placenta differ strikingly in DNAme from those in umbilical endothelium. Summary The human placenta is a complex organ comprised of diverse cells of different origins, and its function and structure exhibit sex differences associated with pregnancy outcomes. We examined the DNA methylation (DNAme) of placental cells in autosomes and sex chromosomes separately to investigate the impact of sex on the DNAme of placental cells. We used 94 placental cell samples (XX = 50, XY = 44) including 18–19 samples each of endothelial, stromal, Hofbauer cells, cytotrophoblasts and whole chorionic villi, and compared these with public data from 65 endothelial cell samples derived from placental plate artery and vein (XX = 16, XY = 13) and umbilical vein (XX = 22, XY = 14). The DNAme distribution of the X-chromosome differed by cell type in a manner that reflected differing developmental origins. Female (XX) placental endothelial/stromal cells showed distinct DNAme distributions from cytotrophoblast, and both differed from that of Hofbauer cells, which shared a similar DNAme distribution with blood. Interestingly, the typical DNAme associated with X chromosome inactivation was absent or low in endothelial/stromal cells and cytotrophoblasts, suggesting that the DNAme patterns may differ by cell types and their origins. Y-chromosome and autosomal DNAme also showed cell-type differences consistent with a common developmental origin of endothelial and stromal cells distinct from other placental cell types. This work provides insight into the influence of sex and cellular developmental origin on DNAme of mature human placental cell types.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Arteries / Biomedical and Life Sciences / Biomedicine / Cells / Chromosomes / Chromosomes, Human, X - genetics / CpG islands / Data processing / DNA / DNA Methylation / Dosage compensation / Endocrinology / endothelial cell / Endothelial cells / Endothelium / Epigenetics / Female / Flow cytometry / Gender differences / Gene expression / Genetic aspects / Human Physiology / Humans / Male / Mesoderm / Methylation / Placenta / Placenta - cytology / Placenta - metabolism / Pregnancy / Promoter Regions, Genetic / sex / Sex Characteristics / Sex chromosomes / Sex differences / Somatic cells / Somatic chromosomes / Stromal cells / Structure-function relationships / Trophectoderm / Trophoblasts / Tumor necrosis factor-TNF / Umbilical cord / Umbilical vein / X chromosome / X chromosomes / X-chromosome inactivation / Y chromosomes