Bridging phenotype and function in bladder cancer using immuno-competent organoids and ex vivo drug screening

Bladder cancer (BLC) remains a clinically challenging malignancy due to its pronounced inter- and intra-patient heterogeneity, which contributes to therapeutic resistance and poor clinical outcomes. Capturing and modeling this complexity is essential for the development of effective, personalized therapeutic strategies. To investigate molecularly and functionally BLC heterogeneity, this study employed three-dimensional patient-derived organoids (PDOs) and ex vivo tissue slice culture as advanced preclinical models. PDOs were established from a patient’s cohort enrolled at Regina Elena National Cancer Institute in Rome using spatially distinct tumor samples from central (TC) and peripheral (TP) tumor regions to preserve intratumoral heterogeneity. Genomic and transcriptomic fidelity between PDOs and their parental tumors was assessed through multi-omics analyses. Functional assays were conducted to evaluate therapeutic responses. A second patient cohort from the University of Bern, was used to further characterize cellular and microenvironmental features of BLC samples combining ex vivo tissue culture and multiparametric-Flow Cytometry (FACS) to address treatment-induced cancer cell plasticity and epithelial-marker expression dynamics. PDOs recapitulated the genomic and transcriptomic landscapes of the original tumors. Early passage PDOs retained components of the tumor microenvironment, including immune cell subsets, suggesting their relevance for ex vivo modeling of tumor-immune interactions. Functional assays revealed spatial heterogeneous responses to both chemotherapy and EGFR/FGFR-targeted therapies. A corresponding reduction of the EGFR-high basal-like population was observed in ex vivo tissue cultures. In contrast, treatment with a PD-1 immune checkpoint inhibitor showed consistent responses across PDOs regions but correlated with the degree of immune infiltration observed in the parental tumors. This integrated dual-cohort approach demonstrates that both BLC PDOs and ex vivo tissue cultures offer a versatile and faithful platform for dissecting BLC heterogeneity and advancing functional precision medicine recapitulating patient-specific immune-tumor interactions observed in native tissues.