Proliferation- and cytotoxic immune signatures identify chemotherapy-responsive bladder tumors in a molecular subtype dependent manner.

Neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC) has been the standard care for muscle-invasive bladder cancer (MIBC) for two decades. One third of NAC-treated patients achieve pathologic complete response (pT0N0), a proxy for improved survival after RC. Predicting response already at transurethral resection of bladder tumor (TUR-BT) would enable selective use of NAC, minimizing exposure to ineffective therapy. We aimed to identify tumor mRNAs associated with response across multiple transcriptomic studies, prioritizing subsequent biomarkers for validation. Three NAC-treated cohort with tumor transcriptomic profiles were included. Differential mRNA-expression analysis and subtype classification according to the Lund Taxonomy were performed. Within each cohort and subtype, genes were ranked by differential expression, and integrated into a meta rank-score. Survival associations of top genes in the NAC-cohorts were used to select candidate biomarkers for protein validation. Proliferation/late cell-cycle gene predicted response in Urothelial-like subtype and cytotoxic T- and NK-cell-related genes predicted response in Basal/Squamous tumors. These findings were validated by immunostainings for CCNB1 and NKG7, respectively. This integrative framework suggests a complex picture in which two NAC-predictive signals identify responders in a subtype dependent manner. The framework can be updated as new datasets become available, providing dynamic exploration of NAC-predictive biomarkers in MIBC.