Integrated Multi-Omics Analysis Identifies ATAD5 as a Mediator of Tumor Plasticity and Immunosuppressive Microenvironmental Remodeling in Castration-Resistant Prostate Cancer

Abstract Purpose Castration-resistant prostate cancer (CRPC) is a lethal malignancy with limited therapeutic options. This study aimed to identify clinically relevant molecular markers linking tumor plasticity and microenvironmental remodeling in CRPC through integrated multi-omics analysis. Methods Transcriptomic data from three GEO cohorts (GSE32269, GSE35988, GSE80609; 68 CRPC, 87 LPCa) were analyzed by differential expression analysis and weighted gene co-expression network analysis (WGCNA). Hub genes were prioritized by stemness-like (SCL) association scoring and validated across TCGA-PRAD, SU2C/PCF, DKFZ, and ICGC cohorts. Immune infiltration was estimated using xCell. Single-cell RNA-seq (GSE137829) and spatial transcriptomics (GSE308486) resolved cellular and tissue-level expression patterns. Immunohistochemistry (IHC) was performed on 10 LPCa and 10 CRPC specimens, and ATAD5 function was assessed by siRNA knockdown in C4-2 and 22Rv1 cells via Transwell invasion and colony formation assays. Results WGCNA identified the MEblack module as most strongly correlated with CRPC status (r = 0.72), enriched in stemness and DNA replication programs. ATAD5 ranked highest by SCL score (0.89) among hub genes. High ATAD5 expression consistently associated with shorter OS, PFS, DSS, and relapse-free survival across all four independent cohorts, and with advanced T stage, nodal involvement, higher Gleason score, and elevated PSA. ATAD5-high tumors exhibited reduced cytotoxic T-cell signatures, increased cancer-associated fibroblast enrichment, and upregulation of immune checkpoint genes (IDO1, CTLA4, CD274, LAG3, TIGIT). Single-cell analysis revealed ATAD5 predominantly in malignant epithelial cells with higher SCL scores, late pseudotime enrichment, and stronger predicted interactions with CAFs and myeloid cells. IHC confirmed elevated ATAD5, CD44, FAP, and CD8A protein in CRPC. ATAD5 knockdown significantly reduced invasion and colony formation in both cell lines (p < 0.05). Conclusion ATAD5 marks an aggressive, plasticity-associated malignant epithelial state in CRPC, linked to immunosuppressive microenvironmental features and adverse clinical outcomes, warranting further investigation of its therapeutic potential.