Single-cell characterization of renal cell carcinoma brain metastasis.

Abstract

e14013 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 that enable tumor survival within the brain microenvironment remain poorly defined. A comprehensive, brain-specific characterization of tumor–microenvironment is urgently 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 brain metastasis (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 were performed to identify 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 (LR) inference was applied to reconstruct intercellular communications across tumor and microenvironmental cell types. Results: RCC BM is associated with extensive immune remodeling of the brain microenvironment, accompanied by stromal involvement. Tumor cells show neural-like features with evidence of neuronal infiltration, while stromal populations display immunomodulatory phenotypes that shape the immune microenvironment and extend beyond canonical structural roles. This immune landscape is characterized by expansion of immunosuppressive myeloid populations, depletion of antigen-presenting dendritic cells, absence of tertiary lymphoid structures, and CD8⁺ T cells exhibiting terminal exhaustion with impaired proliferative capacity. Across tumor, immune, and stromal compartments, we observed coordinated metabolic shifts including enhanced OXPHOS, and MYC-associated transcriptional programs that are consistent with tumor progression. Spatial profiling and LR analyses confirmed interactions that providing mechanistic insight and informing therapeutic targeting strategies. Conclusions: This study defines RCC BM as biologically distinct tumor entity shaped by neural adaptation, metabolic reprogramming, and profound immune dysfunction. The coordinated emergence of immunosuppressive myeloid signaling, terminal T cell exhaustion, and loss of antigen presentation. This establishes a brain-specific microenvironment that limits the efficacy of immune checkpoint blockade. Together, this work highlights context-dependent therapeutic resistance mechanisms and identifies actionable pathways that may guide the development of effective, brain-tailored immunotherapeutic strategies. Importantly, these findings provided a foundation that directly supported two clinical trials testing lenvatinib plus pembrolizumab, and zanzalitinib in RCC BM patients.