Cell-specific Characterization of the Placental Methylome

Abstract

<jats:title>Abstract</jats:title> <jats:p>Background DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at &gt; 850,000 CpGs. Results The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare understudied macrophage population thought to derive from fetal monocytes. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation. Conclusions Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from dbGAP (phs002013.v1.p1), through interactive exploration from the web browser (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/), and through the R package <jats:italic>planet</jats:italic>, which allows estimation of cell composition directly from placental DNAm data.</jats:p>

Large-scale placenta DNA methylation mega-analysis reveals fetal sex-specific differentially methylated CpG sites and regions

“…It has been linked to immune cell differentiation 46,47 and tumorigenesis 48,49 , furthering the longstanding narrative noting the similarity in placenta cells and cancer cells with respect to their invasive properties 50 . Along these lines, we found through incorporation of the Yuan et al placenta cell type data 35 that fetal sex differences in ZNF300 promoter DNAm are driven by differences seen in the trophoblast cell type, which is primarily responsible for placental invasion 51 .…”

“…Of the 5,212 differentially methylated sites, 1,285 (24.7%) were identified as distinguishing full term placenta cell types in a recent paper by Yuan et al examining cell type specific DNAm patterns in term and early term placentas 35 .…”

“…Table 1. Cell type specific placenta DNAm data described in Yuan et al 35 were also downloaded from GEO (GSE159526).…”

“…recent dataset described by Yuan et al35 , which profiled DNAm in sorted placenta cell types, allowed for further characterization of these immune pathway findings. While the Yuan et al study found no significant differences in estimated cell type proportions between male and female placentas, it is still possible that individual probes exhibit both sex-specific and cell type specific DNAm patterns.…”

Large-scale placenta DNA methylation mega-analysis reveals fetal sex-specific differentially methylated CpG sites and regions

“…However, these sex-focused analyses are rare, and there have been few studies that have examined sex itself as an "outcome" in analyses, even in normal or non-pathological placentas. Finally, the majority of transcriptomic and DNAm studies of the placenta have not thoroughly accounted for or investigated the role of cell type heterogeneity in phenotypic studies 34 , though a recent study by Yuan et al 35 has helped to address this gap by generating DNAm pro les in the four major placenta cell types. Speci cally, this study pro led endothelial cells, placental macrophages known as Hofbauer cells, mesenchymal stromal cells and trophoblasts, composed of both syncytiotrophoblasts that interact with maternal blood and cytotrophoblasts that invade the uterine spiral arteries 36 .…”