(852) What Can cfDNA Tell Us About Normal Pregnancy? Insights from cfChIP-seq

Objective:
Placental cell-free DNA (cfDNA) circulating in maternal blood is widely used for non-invasive prenatal testing. Recent evidence shows that most cfDNA exists as cell-free chromatin, retaining epigenetic marks from the source cells. Analyzing these fragments via cfChIP-seq allows identification of active genes and regulatory pathways in the tissue of origin. The release of placental cell-free chromatin into maternal blood offers a non-invasive window into placental molecular states. We hypothesized that physiologic and molecular changes during normal pregnancy are reflected in maternal cfChIP-seq profiles, even early in gestation.

Study Design:
This is a prospective longitudinal study. Sampling began as early as gestational week 9 and included all three trimesters, the peripartum period, and the immediate postpartum. For each participant, last menstrual period and clinical course were documented. cfChIP-seq was used to profile promoter-associated chromatin in plasma cfDNA, reflecting gene activity in contributing tissues.

Results:
A total of 96 blood samples were collected from 36 pregnant women across gestation, with 2 to 7 samples per participant (mean 2.6). Genes were filtered for low signal in non-pregnant controls and for correlation with gestational age (Kendall tau > 0.5). We identified 126 genes with low expression in non-pregnant controls that showed increasing cfChIP signal across gestation. Ontology analysis (TISSUES Curated 2025) revealed enrichment in placenta, embryonic structures, and organism morphogenesis. Cell-type enrichment (CellMarker 2024) confirmed placental cell predominance, supporting the placental origin of the signal and its relation to normal gestational physiology
 

Conclusion:
cfChIP-seq enables non-invasive monitoring of transcriptional regulation during pregnancy and reveals dynamic gene expression patterns reflective of normal placental and embryonic physiology. These findings provide a foundational physiological reference for future studies exploring cfChIP in pregnancy complications such as IUGR, preeclampsia, gestational diabetes, and placenta accreta spectrum