Spatial transcriptomics of urothelial carcinoma with basal/squamous differentiation identifies Galectin-7 as a specific marker of squamous lineage commitment

Urothelial carcinoma (UC) with basal/squamous (Ba/Sq) differentiation is an aggressive subtype associated with chemoresistance and poor prognosis. However, reliable biomarkers for its diagnosis remain limited, and current evaluation largely relies on morphology and p63 immunostaining, which lacks specificity. Using high-resolution spatial transcriptomics, we characterized the molecular continuum underlying Ba/Sq differentiation within UC and validated the findings by immunohistochemistry (IHC) in independent Ba/Sq UC and pure UC cohorts. Functional assays were performed in squamous carcinoma cell lines to assess the role of Galectin-7, a transcriptional target of p63, in cellular proliferation. Spatial analysis revealed a stromal–epithelial signaling axis driving Ba/Sq differentiation within UC, with NGFR-positive basal-like cells inducing Galectin-7 expression during early squamous commitment. Galectin-7 was absent in UC regions but strongly expressed in Ba/Sq-differentiated tumor nests. Its knockdown suppressed squamous carcinoma cell proliferation, supporting a functional role in tumor survival. Immunohistochemical analysis confirmed markedly higher specificity of Galectin-7 (92.2%) compared with p63 (12.5%), while maintaining high sensitivity (89.3% vs. 100%). Galectin-7 positivity was also associated with poorer progression-free survival, indicating its dual diagnostic and prognostic value. This study proposes a molecular and spatial framework for Ba/Sq differentiation within UC and identifies Galectin-7 as a specific diagnostic and prognostic marker, offering potential as a therapeutic target in Ba/Sq UC.