Single-cell and spatial atlas unveil tumor-specific microenvironment convergence and a prognosis-associated PLXDC1+ myofibroblast population in metastatic bladder cancer.

BACKGROUND: While single-cell technologies have advanced bladder cancer research, the microenvironment of lymph node metastases and its role in progression remain unclear. We aimed to elucidate dynamic tumor-microenvironment interactions across metastatic and primary sites, identify poor-prognosis features, and uncover novel therapeutic targets. METHODS: We profiled matched single-cell and spatial transcriptomic samples from lymph node-metastasized bladder cancer to construct a high-resolution atlas. Bioinformatic analyses were used to inferred ligand-receptor interactions, regulatory networks, and spatial co-localization. Integration with multiple prognostic cohorts revealed key cell subpopulations linked to tumor biology and poor outcomes. RESULTS: Our atlas included 32 samples, 61 cell subtypes, key ligand signals (e.g., TGFB1, OSM, IFNG), 343 transcription factors, 188 co-localization events, over 1,000 spatially validated interactions, and 21 cell niches. Tumor-driven convergence was observed across distinct microenvironments. Notably, a pericyte-like myofibroblast subtype, myoCAF_PLXDC1, was enriched in malignant tissues, associated with poor prognosis, and exhibited enhanced angiogenic but reduced chemotactic activity compared to myoCAF_CCL21. Its phenotype was linked to intracellular regulators (PRRX1 and MXD4) and extracellular signals (IFNG and TGFB1). Spatially, myoCAF_PLXDC1 co-localized with ITGA8+ endothelial cells and enriched in tumor regions. CONCLUSIONS: This study offers a comprehensive resource for lymph node-metastasized bladder cancer and identifies PLXDC1+ fibroblasts co-localized with ITGA8+ ECs as potential components of a tumor-specific vascular niche and therapeutic target. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07534-8.