Identifying epigenomic and transcriptomic placental signatures in fetuses with congenital heart disease

Study objectives. To identify cell type-specific molecular signatures in term placentas from fetuses with congenital heart disease (CHD) compared to case-matched controls. Hypothesis. Cells at the maternal-fetal interface harbor distinct epigenomic signatures and transcriptomic profiles in fetuses with CHD. Methods. Term placental tissues from fetuses with CHD (N=14) and without CHD (N=13) were matched for gestational age, maternal age, and ethnicity; samples with chromosomal abnormalities were excluded. Chromatin accessibility and gene expression were jointly profiled in 59,739 nuclei using ATAC- and RNA-sequencing, respectively. DNA from matched maternal peripheral blood and umbilical cord blood was used for genotype-based demultiplexing to assign nuclei as maternal or fetal. For secondary analysis, CHD cases were categorized into one of four groups: (1) conotruncal defects, (2) septal defects, (3) single ventricle lesions, or (4) small left-side. Differential gene expression and pathway analyses were used to identify cell-type specific molecular signatures. Data and Results. We identified fourteen cell clusters, including trophoblast, immune, and stromal populations across maternal and fetal compartments. Three clusters were maternal-specific; four clusters were fetal-specific, and seven were a mix of maternal and fetal cells. Immune cells were the most abundant and consisted primarily of maternal macrophages and T cells. Placentas from CHD cases showed an increased proportion of fetal immune cells, including T cells, macrophages, B cells, and natural killer cells and a decreased proportion of extravillous trophoblast cells. Cell proportions did not differ by fetal sex; however, fibroblast proportions were lower in caesarian section deliveries compared to vaginal deliveries. Differential expression analysis within individual cell clusters revealed distinct molecular signatures in CHD placentas, primarily in fetal cells. Differentially expressed genes included structural extracellular matrix components such as collagens (COL1A1, COL6A3) and proteoglycans (DCN, LUM), as well as extracellular matrix-interacting and remodeling factors (ADAMTS2, TIMP3, LGALS1). Conclusions. CHD alters cell composition at the maternal-fetal interface, predominantly within the fetal compartment. Extracellular matrix-associated signatures rank among the top differential pathways, representing a promising direction for future studies. Overall, we mapped 14 distinct cell clusters in term placentas, including five of fetal origin that are impacted by fetal CHD. Identifying placental signatures dysregulated in CHD may provide novel insight into the etiology of this complex developmental condition. Funding Sources. This work was supported by the Children’s Mercy Research Institute (K.M.V. and E.G.), the Sosland Foundation (Children’s Mercy Perinatal Research Biorepository), and the Madison and Lila Self Graduate Fellowship (A.S.H.). This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.