An integrative placental gene signature identified via M2 macrophage–guided co-expression analysis reflects multi-pathway dysregulation in preeclampsia

Abstract Background Preeclampsia (PE) involves complex placental microenvironment alterations, with immune dysregulation playing a central role. While M2 macrophages have been implicated, specific co-expression modules to M2 enrichment and their differential expression in PE remain poorly defined. Methods We conducted a computational study to identify genes transcriptionally correlated with inferred M2 macrophage enrichment in PE. Using the xCell algorithm, we inferred relative immune cell enrichment scores from bulk placental transcriptomes. Weighted gene co-expression network analysis was applied to identify M2-correlated modules; module genes were intersected with PE-associated differentially expressed genes. The overlap underwent feature selection via three machine learning approaches in a discovery cohort. A logistic regression model based on the consensus genes was evaluated in an independent validation cohort. Results PE placentas showed significant differences in inferred immune cell enrichment. From the intersection of M2-correlated module genes and differentially expressed genes, we identified a robust three-gene placental signature (FLT1, LEP, HTRA4). The signature achieved area under the curve of 0.869 (discovery) and 0.865 (validation). Functional annotation associated each gene to core pathologies: FLT1 (VEGF signaling antagonism and impaired angiogenesis), LEP (metabolic-inflammatory dysregulation), and HTRA4 (extravillous trophoblast function and remodeling). Literature suggests these genes operate within an M2-enriched microenvironment and may participate in immune–trophoblast crosstalk, collectively reflecting multi-pathway dysregulation. Conclusions We identify and validate a three-gene placental expression signature for PE within an M2-correlated transcriptional context, linking angiogenic, metabolic, and trophoblast-immune axes. This integrative placental expression framework advances understanding of microenvironment-level immune dysregulation and serves as a foundation for future mechanistic studies, though single-cell or spatial resolution is required to confirm cellular origins and causal relationships.