Characterizing placental dysfunction with DNA methylation profiling and placental histopathology

Placental pathology is associated with abnormal fetal growth and development. Altered placental DNA methylation (DNAme) has been associated with preeclampsia and fetal growth restriction but has not been well studied in the context of placental pathology, which likely underlies such changes. Our goal was thus to evaluate the association of DNAme with four major classes of placental pathology.

We utilized data from 484 placentas with both Illumina EPICv1 DNAme data and detailed histopathology information. Placental lesions were grouped as: acute inflammation (AI), chronic inflammation (CI), maternal vascular malperfusion (MVM), and fetal vascular malperfusion (FVM). We evaluated associations with DNAme based estimates of placental cell-types and epigenetic age acceleration, and used linear models to explore changes to autosome-wide DNAme with pathology.

We identified 281 and 56 CpGs that were differentially methylated (FDR<0.05, |Δβ|>0.05) in association with high-grade MVM and high-grade FVM respectively. High-grade MVM and high-grade FVM were associated with increased and decreased estimates of syncytiotrophoblast respectively. There were no CpGs differentially methylated in association with the inflammation pathologies. Epigenetic age acceleration was not associated with any pathology, suggesting the placental epigenetic clocks are robust at estimating gestational age in the presence of pathology.

Changes in DNAme were associated with high-grade vascular pathologies, and DNAme may complement histopathologic placental examination. While changes largely reflected altered cell composition, altered gene regulation at the cellular level may also be present in these pathologies. Differential DNAme in high-grade MVM/FVM may contribute to or be a response to placental pathology.