Single-cell and multi-omics analyses implicate DDX39A as a candidate mediator of the LDHA-lactate-lactylation axis in castration-resistant prostate cancer

Castration-resistant prostate cancer (CRPC) represents the lethal stage of prostate cancer and remains a major clinical challenge, as tumor progression persists despite sustained androgen receptor pathway inhibition. Although metabolic reprogramming and epigenetic remodeling are increasingly recognized as key features of CRPC, the mechanisms linking these processes, particularly those involving lactate-driven lactylation, remain insufficiently defined. Here, we integrated single-cell transcriptomics, bulk RNA sequencing, spatial transcriptomics, and in vitro functional assays to characterize the lactylation-associated landscape of CRPC. Single-cell analysis revealed that lactylation-related transcriptional activity was elevated in CRPC and enriched in a tumor epithelial subpopulation (cluster 6) with enhanced glycolytic features. Through hdWGCNA, prognostic screening, pseudotime analysis, and spatial validation, DDX39A was identified as a hub gene associated with the high-lactylation state, disease progression, and poor clinical outcome. Functional experiments showed that silencing DDX39A in PC3 and 22RV1 cells impaired proliferation, colony formation, migration, and invasion, supporting a tumor-promoting role. DDX39A knockdown reduced LDHA protein levels, intracellular lactate production, and global protein lactylation, suggesting that DDX39A is associated with the LDHA–lactate–lactylation axis. In addition, protein–RNA docking supported a potential interaction between DDX39A and LDHA mRNA, and structure-based screening with molecular dynamics simulation identified Olaparib as a candidate small molecule with favorable binding stability to DDX39A. Collectively, our study implicates DDX39A as a candidate mediator of the LDHA–lactate–lactylation axis in CRPC. These findings link RNA processing, metabolic reprogramming, and lactylation-associated tumor phenotypes, providing a framework for understanding CRPC progression and suggesting DDX39A as a potential therapeutic target.