Spatial and single-cell transcriptomics identify a CD276-rich vascular matrix-associated CAF state linked to adverse outcomes under targeted therapy–immunotherapy combinations in clear cell renal cell carcinoma

Background Targeted therapy–immunotherapy combinations have improved treatment outcomes in advanced clear cell renal cell carcinoma (ccRCC), but primary non-response and post-treatment residual progression remain common. Cancer-associated fibroblasts (CAFs) exhibit marked heterogeneity and are closely associated with tumor treatment tolerance; however, specific stromal states associated with treatment non-response, post-treatment residual disease, and immune exclusion remain insufficiently characterized. Methods This study integrated ccRCC single-cell RNA sequencing, bulk transcriptomic cohorts annotated with clinical outcomes, CosMx and Visium spatial transcriptomic data, and multiplex immunofluorescence results. We re-clustered stromal cells to define vascular matrix-associated CAF (vMat-CAF) and construct the corresponding signature, followed by survival, treatment-response, correlation, pseudotime, CellChat, NicheNet, and spatial neighborhood analyses. Results We identified a vascular matrix-associated CAF (vMat-CAF) state in the single-cell stromal atlas of ccRCC, characterized by CD276 enrichment and perivascular localization. Single-cell transcriptomic analysis showed that vMat-CAF was enriched in tumor tissues and relatively enriched in non-responders; bulk clinical cohorts further showed that it was associated with adverse outcomes under targeted therapy–immunotherapy combinations. Further analyses suggested that predicted vMat-CAF-derived LAMA4/COL4A1–CD44 communication was associated with tumor EMT-like programs; meanwhile, vMat-CAF exhibited high CD276 expression, and the association between CD276 and adverse clinical outcomes was more evident in the vMat-CAF-high context. Moreover, spatial transcriptomics and immunofluorescence showed that CD276-high vMat-CAF was enriched in perivascular regions and was associated with a spatial distribution pattern characterized by insufficient infiltration of CD8 + T cells into the tumor center. Conclusions vMat-CAF is a CD276-enriched perivascular stromal state associated with adverse outcomes under targeted therapy–immunotherapy combinations in ccRCC. Further analyses connected this state with tumor EMT-like programs, the context-dependent clinical significance of CD276, and restricted CD8 + T-cell infiltration into the tumor center, supporting a candidate perivascular stromal–immune gating model.