Molecular signatures of preeclampsia subtypes determined through integrated weighted gene co-expression network analysis and differential gene expression analysis of placental transcriptomics

Background Preeclampsia (PE) is a multisystemic pregnancy syndrome that presents in different clinical subtypes. While placental dysfunction is a critical feature of PE, its contribution to different PE subtypes remains unclear. This study aims to use integrated bioinformatics analysis of placental transcriptomics to investigate subtype-specific molecular mechanisms associated with PE. Methods A systematic search of the Gene Expression Omnibus (GEO) repository identified two datasets (GSE234729, n = 123; GSE75010, n = 157) for integrated Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis. We constructed co-expression networks and identified gene modules correlated with three PE subtypes (severe, early-onset and late-onset). Differential gene expression analysis was conducted using the “limma” R package. Differentially expressed genes (DEGs) overlapping with PE subtype-correlated WGCNA modules underwent Gene Ontology (GO) enrichment analysis. Consistently dysregulated genes were validated in an additional external dataset (GSE25906) and RT-PCR analysis of placental samples from 21 PE cases and 21 uncomplicated controls. Results We identified distinct molecular signatures associated with each PE subtype. The green gene module was positively correlated with severe PE (r = 0.63, p = 4e-15), containing 179 DEGs primarily involved in lipid metabolism and hypoxia response processes. Early-onset PE had two highly significant gene modules: the yellow module (r = 0.73, p = 4e-15) with 112 DEGs enriched in biological processes related to gonadotrophin secretion and lipid storage, and the black module (r = −0.55, p = 5e-08) with 47 DEGs significantly enriched in chronic inflammation responses. Late-onset PE showed moderate correlation with the ivory module (r = 0.46, p = 5e-05), containing 23 DEGs enriched in p38MAPK stress-response signalling. Cross-subtype analysis identified 20 consistently dysregulated genes across three PE subtypes, with four upregulated genes ( LEP , FSTL3 , HTRA4 , and HK2 ) confirmed in the external dataset GSE25906. However, RT-PCR validation showed only moderate upregulation without statistical significance. Conclusion Though placental dysfunction occurs across all subtypes with a core set of upregulated genes, variation exits in placental gene expression patterns among PE subtypes. Severe and early-onset PE exhibit large molecular perturbations, while late-onset PE presents more subtle alterations. Aberrant placental lipid storage may contribute to disease severity and early manifestation.