Single-cell and spatial transcriptomic analysis reveal cellular heterogeneity and cancer cell-intrinsic major histocompatibility complex II expression in urothelial carcinoma

Muscle-invasive (MI) urothelial carcinoma (UC) is a clinically challenging malignancy with a poor prognosis. Understanding the cellular dynamics that drive UC progression is critical for the development of optimized therapeutic strategies. Through integrative analysis of large-scale single-cell transcriptomic datasets from non-muscle-invasive (NMI) and MI tumours and validation with spatial transcriptomic datasets, we systematically characterized immune cell dynamics and cancer cell plasticity during UC progression. Our analysis revealed an immunosuppressive tumour microenvironment and a subset of cancer cells with upregulated major histocompatibility complex II (MHC-II) expression in MI tumours. Notably, MHC-II⁺ cancer cells were induced by interferon-γ signalling, as confirmed through in vitro experiments, and exhibited phenotypic alterations characterized by enhanced proliferative and migratory capacities. Furthermore, MHC-II⁺ cancer cells spatially colocalized with CD8⁺ T cells, regulatory T cells, and SPP1⁺ macrophages, where they engaged with inhibitory receptors on these immune cells, promoted CD8⁺ T cell exhaustion and facilitated immune evasion.