Abstract 5931: Characterizing tumor heterogeneity through bulk and single cell analysis of patient derived bladder cancer models
Authors: Chen Ziyu , Tang Xinran , Havasov Eliyahu , Mcpherson Andrew , Chu Carissa , Christin John R. , Berger Michael F. , Schultz Nikolaus D. , de Stanchina Elisa , Shen Michael M. , Al-Ahmadie Hikmat , Kim Kwanghee , Iyer Gopa , Solit David B. 
Published: April 2023

Abstract
Background: A major hurdle to the development of novel targeted therapies for bladder cancer is the lack of preclinical models that reflect the genomic and biological heterogeneity of this human disease. To address this deficiency, we generated and characterized a new collection of patient-derived organoid (PDO) and xenograft (PDX) models and then used these models to study the role of mutated kinases in bladder cancer pathogenesis and the potential clinical utility of HER2-targeted antibody-drug conjugates (ADC).
Material and Methods: To define the landscape of HER2 and FGFR3 alterations in bladder cancer patients, we leveraged data generated by The Cancer Genome Atlas and multiple cohort subsets of the first 50,000 cancer patients enrolled in the MSK-IMPACT prospectively sequencing cohort. We successfully generated 19 PDOs and 34 PDXs that genetically and phenotypically reflect the molecular heterogeneity of human bladder cancers. A subset of these models was further characterized using a multiplatform approach, including bulk and single-cell DNA and RNA sequencing; and employed to study HER2 oncogenic dependence and sensitivity to multiple anti-HER2 targeted agents.
Results: 16% and 24% of the patients in the prospective MSK bladder cancer cohort had oncogenic HER2 and FGFR3 alterations, respectively. HER2 alteration frequency varied significantly as a function of histology, while FGFR3 alteration were less common in all variant histologies as compared to UC, NOS. Analysis of 119 patients with paired primary/metastatic tumors noted HER2 and FGFR3 mutational discordance in over 35% and 10% respectively. Single-cell RNA seq and DNA seq analysis of 4 PDOs demonstrated high interpatient and intratumoral heterogeneity of HER2 expression and ERBB2 copy number. Our bladder cancer PDX models also demonstrated greater sensitivity to the HER2-targeted ADC trastuzumab deruxtecan (T-DXd) than to the kinase inhibitor neratinib, consistent with clinical data in bladder cancer patients.
Conclusion: FGFR3 and HER2 are both commonly mutated in bladder cancer patients. We observed frequent discordance in HER2 mutational status between primary/metastatic pairs suggesting that the analysis of archival primary tumor tissue may fail to detect actionable genomic alterations when present in a subset of bladder cancer patients. Multi-omic single-cell analysis demonstrated significant interpatient and intratumor heterogeneity of HER2 expression and ERBB2 copy number gain. Preclinical evaluation of HER2-altered PDO/PDXs indicated significantly greater sensitivity to the HER2-directed ADC T-DXd compared to the HER kinase inhibitor neratinib, providing rationale for future clinical trials of HER2 ADCs in bladder cancer patients.
Citation Format: Ziyu Chen, Xinran Tang, Eliyahu Havasov, Andrew Mcpherson, Carissa Chu, John R. Christin, Michael F. Berger, Nikolaus D. Schultz, Elisa de Stanchina, Michael M. Shen, Hikmat Al-Ahmadie, Kwanghee Kim, Gopa Iyer, David B. Solit. Characterizing tumor heterogeneity through bulk and single cell analysis of patient derived bladder cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5931.