CYP51A1 acts as a metabolic immune coupling node in clear cell renal cell carcinoma investigating expression, epigenetic regulation, prognosis and immune microenvironment characterization

Clear cell renal cell carcinoma (ccRCC) is an immunogenic malignancy in which immune checkpoint inhibitors have become a cornerstone of therapy; however, biomarkers that robustly inform immunotherapy-oriented stratification remain limited. CYP51A1 encodes a key enzyme in sterol biosynthesis and may represent a metabolic–immune coupling node in ccRCC. Using an integrative multi-database framework (TIMER3, TCGA, HPA, UALCAN and CPTAC), we systematically profiled CYP51A1 expression at the transcript and protein levels, examined promoter methylation, evaluated prognostic significance, and explored immune-microenvironment associations and immunotherapy-relevant signatures. CYP51A1 was markedly downregulated in ccRCC compared with normal kidney tissue, and low CYP51A1 expression was consistently associated with unfavorable clinicopathological features and poorer overall and progression-free survival. Promoter methylation analyses indicated increased CYP51A1 methylation in tumors with a stepwise elevation across older age and higher stage/grade subgroups, suggesting an epigenetic contribution to CYP51A1 suppression. Functional analyses of CYP51A1-associated transcriptional changes implicated coordinated alterations in immune-related pathways and metabolic programs. Immune profiling further showed that CYP51A1-low tumors exhibited an inflamed immune contexture, characterized by higher infiltration of regulatory T cells, CD8 + T cells and activated NK cells, together with increased ImmuneScore and ESTIMATE score. Importantly, multiple immune checkpoint molecules, including CTLA4 and PDCD1, were upregulated in the CYP51A1-low group. Consistent with these findings, immunophenoscore (IPS) analyses demonstrated significantly higher IPS in CYP51A1-low tumors across PD-1/CTLA4 combinational settings, indicating a potentially greater likelihood of benefit from checkpoint blockade. Collectively, CYP51A1 downregulation in ccRCC, potentially driven by promoter hypermethylation, is linked to immune activation and enhanced checkpoint/IPS signatures, supporting CYP51A1 as a candidate biomarker for prognostic assessment and immunotherapy-oriented patient stratification pending validation in independent immunotherapy-treated cohorts.