Immunosuppressed patients with non-melanoma skin cancer experience worse clinical outcomes, yet the tumor immune microenvironment associated with systemic immunosuppression remains incompletely defined. Using integrated single-cell, spatial transcriptomic, multiplex immunofluorescence, and spatial epigenomic profiling across immunocompetent and immunosuppressed tumors, we found that overall immune-cell composition was largely preserved despite differences in immune-cell distribution, spatial organization, and T cell clonality. Immunosuppressed tumors demonstrated reduced intratumoral macrophage densities, decreased T cell clonal diversity, altered antigen-presenting cell and T cell spatial interactions, and distinct fibroblast- and macrophage-associated spatial niches. Multi-cohort validation across complementary spatial and single-cell platforms identified consistent alterations in innate-adaptive immune organization in immunosuppressed tumors. Together, these findings define spatial and functional remodeling of the tumor immune microenvironment under systemic immunosuppression and provide a framework for future therapeutic investigation in high-risk patients.
Shorook Naara, V. Kochat, Xiayu Rao et al.· Cell· 0 citations
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.
M. I. Ali, Z. Akpinar, Jose A. Ovando-Ricardez et al.· Neuro-Oncology Advances· 0 citations
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