Super-Enhancer Network in Metastatic Prostate Cancer: A Bioinformatics and Experimental Approach

Prostate cancer (PC) metastasis poses a critical therapeutic challenge, driven in part by dysregulated transcriptional landscapes governed by super-enhancers (SEs). This study combines integrative bioinformatics and experimental validation to uncover SE-associated hub genes implicated in metastatic PC. RNA-seq datasets from metastatic PC cell lines (PC3 and DU-145) treated with the BET inhibitor JQ1 (GSE126779) and untreated controls (GSE118435) were comparatively analyzed. Differential expression analysis identified 4,197 significantly altered genes (|logFC| > 3, adjusted p < 0.001), revealing broad transcriptional reprogramming upon BET inhibition. Functional enrichment analyses indicated predominant enrichment in neuroactive ligand–receptor interaction, calcium signaling, vascular smooth muscle contraction, and drug metabolism pathways. Construction of protein–protein interaction (PPI) networks highlighted central hub genes including AGT , AGTR1 , and EDN1 . Cross-referencing with SE databases (SEA v3.0 and SEdb 2.0) identified 257 SE-associated differentially expressed genes (SE-DEGs), predominantly enriched in pathways related to vascular regulation, renin secretion, and xenobiotic metabolism. Network prioritization revealed CALML3 as a top-ranking hub gene, while experimental validation confirmed the significant upregulation of EDN1 and CALML3 in PC3 cells. Collectively, these findings elucidate key SE-driven regulatory hubs underlying metastatic PC and underscore the therapeutic potential of targeting SE-associated oncogenic networks in advanced disease management.