Proteogenomic characterization of the non-muscle-invasive bladder cancer response to BCG reveals potential therapeutic strategies

Background: Intravesical bacillus Calmette-Guérin (BCG) is the standard therapy for adjuvant treatment in patients with intermediate- and high-risk superficial bladder cancer. However, the molecular properties associated with BCG therapy have not been fully characterized. Methods We reported a comprehensive proteogenomic analysis, including whole-genome sequencing, proteomics, and phosphoproteomics profiling, of 160 non-invasive-muscle bladder cancer (NMIBC) patients treated with BCG. Results Proteogenomic integration analysis indicted that tumor mutational burden (TMB), associated with STAT1 activity, was relevant to drug sensitivity. Additionally, our analysis of copy number alterations (CNAs) showed that TLR3 deletion was negatively correlated with response to BCG therapy. TLR3 was validated to regulate the cytokine secretion, and enhance sensitivity to BCG in BC cell lines and organoids. High TMB levels were also associated with improved BCG efficacy across different TLR3 expression subgroups, which holds significant implications. Through proteomic analysis, we identified three subtypes in patients with BCG, reflecting distinct clinical prognosis and biological characteristics. Furthermore, we developed prognostic models with high accuracy to predict the therapeutic response and PFS of NMIBC. Conclusions This study provides a rich resource for investigating the mechanisms and indicators of BCG therapy in NMIBC, which can be basis for further improvement of therapeutic response.