TLSB-25 SINGLE-CELL CHARACTERIZATION OF RENAL CELL CARCINOMA BRAIN METASTASIS

Abstract

Abstract Background Brain metastasis (BM) in renal cell carcinoma (RCC) remains a major clinical challenge and is frequently resistant to immune checkpoint inhibitor (ICI) therapy. The metabolic and immunological adaptations enabling tumor survival within the brain microenvironment remain poorly defined. A comprehensive, brain-specific characterization of the tumor–microenvironment is needed to understand immune dysfunction and therapeutic resistance in RCC BM. Methods We generated a large single-nucleus RNA sequencing dataset comprising 184,037 nuclei from 14 RCC BM patients, including matched primary kidney tumors (n = 8) and extracranial metastases (n = 5). Cell populations were identified across tumor, immune, and stromal compartments. Comparative analyses identified BM-specific transcriptional, metabolic, and immune programs. Spatial transcriptomic profiling was conducted on 12 BM samples (13,128 cells) to validate cellular localization and interactions. Ligand–receptor inference was applied to reconstruct intercellular communication. Results RCC BM is associated with extensive immune remodeling of the brain microenvironment and stromal involvement. Tumor cells show neural-like features with evidence of neuroglial cells infiltration, while stromal populations display immunomodulatory phenotypes beyond structural roles. This landscape includes expansion of immunosuppressive myeloid populations, depletion of dendritic cells, absence of tertiary lymphoid structures, and CD8+ T cells exhibiting terminal exhaustion. Across compartments, we observed coordinated metabolic shifts, including enhanced OXPHOS and MYC-associated programs. Spatial and ligand–receptor analyses confirmed interactions providing mechanistic insight and informing therapeutic targeting. Conclusion RCC BM represents a biologically distinct tumor entity shaped by neural adaptation, metabolic reprogramming, and immune dysfunction. Immunosuppressive myeloid signaling, T cell exhaustion, and impaired antigen presentation establish a brain-specific microenvironment limiting immune checkpoint efficacy. These findings highlight context-dependent resistance mechanisms and identify actionable pathways to guide brain-tailored immunotherapy. Importantly, this work supported clinical trials approval testing lenvatinib plus pembrolizumab and zanzalitinib in RCC BM patients.