Comprehensive analysis of RNA sequencing reveals DNA damage response and immune-associated alternative splicing and RBP regulators contributing to preeclampsia

Abstract Background Preeclampsia (PE), a life-threatening hypertensive disorder of pregnancy, remains poorly characterized at the post-transcriptional regulation level. While alternative splicing (AS) perturbations drive pathological processes in numerous diseases, their systematic investigation in PE pathogenesis is lacking. Results Through integrative analysis of placental RNA-seq data (n = 18; 9 early-onset severe PE vs. 9 controls) using SUVA-based splicing quantification and RBP interactome mapping, we identified 276 conserved regulated splicing events (PE-RAS) with dominant isoform usage (pSAR ≥ 50%, pvalue ≤ 0.05). These events disproportionately affected DNA damage response (DDR) pathways, particularly in DYRK2 (Δsplicing ratio = 0.33, p = 2.8e-3) and FZR1 (Δsplicing ratio = 0.23, p = 2.2e-4), whose aberrant splicing correlated with DNA repair function. Co-expression network analysis revealed 11 upregulated RNA-binding proteins (RBPs) (e.g., DUSP1, FLNB; FC > 2, FDR < 0.05) orchestrating DDR-associated splicing through sequence-specific interactions (|r| >0.6, p < 0.01). Strikingly, these RBP-AS axes coincided with immune microenvironment remodeling, manifesting as resting NK cells, resting memory CD4 + T-cell and Neutrophils cells depletion, potentially linking splicing dysregulation to maternal-fetal interface inflammation. Experimental validation confirmed RBPs overexpression (qRT–PCR) in PE placentas. Conclusions Our study establishes RBP-mediated splicing coordination as a novel regulatory layer connecting genomic instability and immune dyshomeostasis in PE, providing a framework for splicing-targeted therapeutic development.