Distinct genomic and microenvironmental profiles of brain metastases in renal cell carcinoma: Insights into hypoxia-driven adaptation and therapeutic vulnerabilities.

Abstract

2033 Background: Brain metastases (BM) in renal cell carcinoma (RCC) are associated with poor prognosis and may exhibit unique genomic alterations influenced by the tumor microenvironment (TME), differing from primary tumors or extracranial metastases (ECM). This study aimed to characterize these differences to identify potential therapeutic targets. Methods: 3,913 RCC samples underwent NGS of DNA and RNA at Caris Life Sciences (Phoenix, AZ) and were linked to corresponding insurance claims data. Real-world overall survival (rwOS) was calculated from the date of sample collection to last contact using Cox PH model and log-rank testing. Genomic alterations were compared at an adjusted significance level of 0.05 using Fisher’s exact test. TME differences between the primary RCC, BM and ECM were assessed by therapeutic target gene expression using Mann-Whitney U test, gene set enrichment analysis (GSEA) by normalized enrichment scores (NES) and false discovery rates (FDR), and a gene expression-based score reflecting HIF1-associated metabolic and stress-response pathways. Results: The cohort consisted of 1,775 primary, 138 BM, and 2,000 ECM. Median age was different in BM vs ECM vs primary (64 vs 66 vs 63 y, p<0.0001). Approximately 75% of BM patients had not received any systemic or radiation therapy prior to tissue collection. The rwOS was 49.4 months for primary, and 30.3 months for both BM and ECM (BM vs. ECM: HR=0.96, 95%CI: 0.76-1.22, p=0.796). Genomic profiling revealed, in BM compared with primary tumors, CDKN2B deletions (41% vs. 18.1%, p<0.0001), as well as PTEN (22.5% vs 6.7%, p<0.0001), and TP53 mutations (22.7% vs 11%, p=0.0088). Gene expression analysis demonstrated no significant differences in the expression of RCC novel therapeutic targets, including CD70 , ENPP3 , CA9 , HLA-G , CDH6 and FOLH1 , between BM and primary (p>0.05). Compared to primary, GSEA revealed BM were enriched in pathways including epithelial-mesenchymal transition (NES=3.41, FDR<0.001), mTORC1 signaling (NES=3.05, FDR=0.002), hypoxia (NES=2.68, FDR=0.009), and others. Compared to ECM, BM showed hypoxia enrichment (NES=2.90, FDR=0.023), while ECM was enriched in mitotic spindle (NES=-3.84, FDR<0.0001) and G2M checkpoints (NES=-3.32, FDR<0.0001). The HIF1-associated hypoxia score was significantly higher in BM vs primary (p<0.01). Conclusions: Conserved expression of multiple actionable RCC therapeutic targets across primary and BM sites supports the biological feasibility of emerging targeted and immune-based therapies in CNS disease. The findings provide a biologic framework for understanding RCC BM and highlight hypoxia-associated pathways. Key limitations include the use of tissue-based rather than clinically adjudicated BM definitions, and the lack of cancer stage information.