Association of PON2 and Its S311C Substitution with Tumor Progression and Its Significance as an Immune-Associated Prognostic Indicator in Clear Cell Renal Cell Carcinoma

Background: Clear cell renal cell carcinoma (ccRCC), the predominant histological subtype of kidney malignancies, is characterized by metabolic dysregulation and therapeutic resistance. Although the intracellular antioxidant paraoxonase 2 (PON2) is frequently dysregulated across multiple cancers, its biological role in ccRCC—particularly the contribution of its enzymatic activity and interplay with the tumor immune microenvironment—remains poorly defined. Methods: Multi-cohort analysis integrating TCGA, ICGC, GEO, and CPTAC datasets was combined with single-cell transcriptomic profiling, survival and Cox regression modeling, immune infiltration estimation, and in vitro loss- and gain-of-function experiments in ccRCC cell lines. Results: PON2 was markedly elevated in ccRCC tissues, predominantly localizing to malignant epithelial and endothelial cells as determined by single-cell transcriptomic profiling. High PON2 expression correlated with advanced T/M stages and independently predicted poor prognosis. Functional experiments showed that PON2 silencing was associated with reduced tumor cell proliferation, invasion, and glycolysis, while rescue experiments using wild-type—but not S311C mutant—PON2 partially restored these phenotypes. PON2 expression was associated with glycolysis-related metabolic changes and CEBPB-related expression of downstream glycolytic targets, including LDHA and PGK1. Furthermore, PON2-high tumors showed transcriptomic features consistent with an immunosuppressive microenvironment, with higher computational estimates of CD8+ T-cell infiltration accompanied by elevated immune checkpoint expression (PD-L1, CTLA4) and higher estimated abundance of immunosuppressive populations (Tregs, MDSCs). Conclusions: Collectively, our findings identify PON2 as a candidate biomarker associated with ccRCC progression and CEBPB-related glycolysis and features consistent with an immunosuppressive microenvironment.