Transcriptomics and metabolomics analysis reveal cell subpopulations of trophoblast cells associated with preeclampsia

Placental abnormalities are central to preeclampsia (PE), yet the cellular and molecular mechanisms underlying this dysfunction remain unclear. We applied a multi-layered, integrative approach to investigate placental tissue from patients with PE and matched controls. Single-cell RNA sequencing (scRNA-seq; GSE173193) and bulk RNA sequencing (bulk RNA-seq; GSE203507) datasets were obtained from the Gene Expression Omnibus. The scRNA-seq dataset included two PE and two control samples, whereas the bulk RNA-seq dataset focused on eight early-onset PE and five uncomplicated term births. Trophoblast subpopulations were identified via scRNA-seq, and pseudotime analysis was used to trace differentiation trajectories. Differential expression and pathway enrichment analyses were performed to elucidate molecular alterations. For metabolomic profiling, plasma samples from six patients with PE and six controls (3 replicates each) were analyzed. Transcriptomic and metabolomic data were integrated to investigate gene-metabolite interactions and their relevance to PE pathogenesis. Villous cytotrophoblasts (VCTs) and syncytiotrophoblasts (SCTs) were more abundant in PE placentas, whereas extravillous trophoblasts (EVTs) were reduced compared with controls. Five trophoblast subpopulations-SCT-VCT, Mix, EVT, VCT, and SCT-were characterized by distinct marker genes. Pseudotime analysis indicated differentiation from mixed states toward specific trophoblast lineages. Immune-related pathways were significantly enriched in PE. Integrated analysis highlighted key connections between metabolites, gene expression, and PE-related pathways, implicating oxidative stress, inflammation, metabolic dysregulation, and vascular dysfunction. Our study provides novel insights into placental dysfunction in PE, highlighting alterations in trophoblast subpopulations and immune pathways. These findings may inform strategies for early diagnosis, prevention, and therapeutic intervention in PE.<b>NEW & NOTEWORTHY</b> Our integrative multi-omics approach, spanning single-cell, bulk transcriptomic, and targeted metabolomic data, demonstrates convergent cellular and metabolic abnormalities in preeclampsia. We find disrupted trophoblast composition, altered differentiation patterns, and metabolic pathway shifts that jointly distinguish preeclamptic placentas from controls. These results advance understanding of placental dysfunction and underscore the value of multi-omics strategies for dissecting complex pregnancy disorders.