4543 Background: Clear cell renal cell carcinoma (ccRCC) is commonly driven by VHL loss, resulting in HIF-2α stabilization and upregulation of targets such as carbonic anhydrase IX (CA9). Clarifying the relationship between CA9 and HIF-2α expression is critical to guide rational therapeutic strategies. Methods: DNA (592-gene panel or whole exome) and RNA (whole transcriptome) sequencing was performed on ccRCC and RCC–not otherwise specified, (NOS) tumors with VHL alterations via Caris Life Sciences for integrated genomic and transcriptomic profiling. The primary objective was to characterize the expression patterns of HIF-2α and CA9 across RCC tumors and co-occurring genomic alterations. Overall survival (OS) as measured from initial diagnosis. Results: A total of 1,935 RCC tumors were analyzed, including 967 (50%) ccRCC and the remainder RCC–NOS with VHL alterations; 49% were derived from the primary site. Expression of HIF-2α and CA9 were similar across racial and ethnic subgroups. Compared to primary kidney tumors, lower HIF-2α expression was observed in lymph node and liver metastases (both p <0.0001) and lower CA9 expressions were observed in CNS and bone metastases (both p <0.0001). Increased either HIF-2α or CA9 expressions were associated with high angiogenic and T-effector gene signatures as defined in IMmotion150 (all p < 0.001). HIF-2α expression positively correlated with CA9 expression (r=0.43, p <0.001). Tumors with highest quartile HIF-2α expression (Q4) had increased PBRM1 and decreased BAP1, TP53, and TERT mutation frequencies (Table). High CA9 expression (Q4) had increased PBRM1 and decreased TP53 mutations. High HIF-2α (Q4) and CA9 (Q4) expressions were associated with improved OS compared with Q1 (HIF-2α: median OS 97 vs 64.7 months, HR 0.56, p < 0.0001; CA9: median OS 90 vs 49 months, HR 0.63, p = 0.002). Conclusions: High expression of HIF-2α and CA9 identifies a canonical VHL/HIF-driven RCC subtype marked by enrichment of PBRM1 mutations, depletion of aggressive genomic alterations ( BAP1 , TP53 , TERT ), and improved OS. Strong associations with angiogenic and immune-related gene signatures further support a coherent HIF-dependent phenotype. Key gene mutation frequency by HIF-2 α/CA9 expression. HIF-2α (Q1) HIF-2α (Q4) P value CA9 (Q1) CA9 (Q4) P value PBRM1 33% 48% <0.001 22% 46% <0.001 BAP1 29% 8% <0.001 22% 19% 0.43 TP53 13% 7% 0.012 16% 8% 0.04 TERT 13% 6% 0.005 12% 8% 0.37
Chen et al. (2026) studied this question.