Genomic analysis of BCG unresponsive non-muscle-invasive bladder cancer identifies drivers of sensitivity to intravesical Gemcitabine/Docetaxel

Yim, K.; Vergara, M.; Lee, J.; Reardon, B.; Park, J.; Melnick, K.; Clinton, T. N.; Matthew, M.; Steele, G. S.; Bolduc, J.; Hirsch, M. S.; Rizzo, N.; Wu, C.-L.; Wszolek, M. F.; Salari, K.; Feldman, A. S.; Kibel, A. S.; Mouw, K. W.; Van Allen, E. M.; Preston, M. A.; Carvalho, F. L.

doi:10.64898/2026.05.10.724123

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bioRxiv · 10.64898/2026.05.10.724123

Genomic analysis of BCG unresponsive non-muscle-invasive bladder cancer identifies drivers of sensitivity to intravesical Gemcitabine/Docetaxel

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Abstract

Background and ObjectivesIntravesical gemcitabine/docetaxel (Gem/Doce) is an effective therapy for Bacillus Calmette- Guerin (BCG)-unresponsive non-muscle-invasive bladder cancer (NMIBC), achieving 50% complete responses at 2 years. However, the genomic determinants underlying response and resistance to Gem/Doce remain poorly defined. Our objective was to define the mutational landscape of BCG-unresponsive NMIBC and nominate genomic features associated with response or resistance Gem/Doce. MethodsPatients with BCG-unresponsive NMIBC treated with Gem/Doce were classified as responders (recurrence-free survival [RFS] >12 months) or non-responders (RFS <12 months). Whole-exome sequencing was performed on tumors prior to Gem/Doce treatment (n=23). Single nucleotide variants were identified and annotated using a Cancer Genome Analysis pipeline. Copy number alterations were inferred with ABSOLUTE, and clonal architecture was reconstructed using PhylogicNDT. Key Findings and LimitationsResponders demonstrated significantly prolonged time to high-grade recurrence (3.5 vs 42 months, p<0.001) and cystectomy compared with non-responders (9.5 months vs not reached; p<0.001). Non-responders exhibited higher tumor mutational burden (13.66 vs 8.71; p=0.02) and more frequent whole-genome doubling (2/2 non-responders vs 0/1 responders; p=0.33). Phylogenetic analyses revealed clonal BAP1 and subclonal BRCA2 mutations in responders, whereas non-responders harbored clonal FGFR3 mutations. Limitations include small sample size and retrospective design. Conclusions and Clinical ImplicationsDistinct genomic features underlie differential response to Gem/Doce in BCG-unresponsive NMIBC. In responders, alterations in DNA repair pathways (e.g., BRCA2) may sensitize tumors to chemotherapy, while non-responders with FGFR3 mutations may benefit from alternative targeted strategies. These findings warrant validation in larger cohorts and support the development of biomarker-driven clinical trials. Patient summaryIn this report we analyzed bladder tumors and found that some tumors respond well to treatment because they have defects in repairing DNA, making them more vulnerable to chemotherapy. In contrast, tumors that do not respond to chemotherapy harbor different genetic changes that help them survive and grow. These findings may help physicians choose more effective and personalized treatments in the future.

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Yim, K., Vergara, M., Lee, J., Reardon, B., Park, J., Melnick, K., Clinton, T. N., Matthew, M., Steele, G. S., Bolduc, J., Hirsch, M. S., Rizzo, N., Wu, C.-L., Wszolek, M. F., Salari, K., Feldman, A. S., Kibel, A. S., Mouw, K. W., Van Allen, E. M., Preston, M. A., Carvalho, F. L.. 2026-05-18. Genomic analysis of BCG unresponsive non-muscle-invasive bladder cancer identifies drivers of sensitivity to intravesical Gemcitabine/Docetaxel. https://doi.org/10.64898/2026.05.10.724123

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