Abstract B11: Multi-omic interrogation of gemcitabine and cisplatin-resistant bladder cancer cell lines identifies unique and shared mediators of chemosensitivity and resistance
Authors: Robert T. Jones, Tahlita C. M. Zuiverloon, Hedvig Vekony, Andrew Goodspeed, Teemu D. Laajala, Molishree Joshi, Colin Sempeck, Annie Jean, Megan Tu, Julia D. Wulfkuhle, Emanuel F. Petricoin, James C. Costello, Dan Theodorescu
Journal: Clinical Cancer Research (2020)

Abstract Neoadjuvant platinum-based chemotherapy (NAC) followed by radical cystectomy is the preferred first-line option for treating patients diagnosed with muscle-invasive bladder cancer (MIBC). One of the two most commonly utilized chemotherapy regimens for MIBC consists of combination therapy with gemcitabine and cisplatin (GC). Importantly, cisplatin-based chemotherapy leads to complete response (pT0) in approximately 25% of patients, while the remaining 75% are left with residual disease. For MIBC patients, the presence of residual disease at cystectomy is associated with significantly poorer prognosis. Previous efforts to screen tumor-derived specimens have identified a number of mutational biomarkers associated with NAC response; however, to date these efforts have been limited by the number of patients profiled and the molecular and mutational heterogeneity intrinsic to bladder cancers. Moreover, these efforts have primarily relied on a single technology (e.g., whole-exome sequencing or transcriptome profiling), and were not designed to look at GC-resistance patterns in a way that integrates these data types. Therefore, we sought to systematically define the molecular phenotypes associated with chemoresistant bladder cancer cells, and to functionally interrogate these features to better define essential genes and pathways that govern chemoresponsiveness. To accomplish this, we have extensively characterized a panel of six bladder cancer cell lines (KU-19-19, T24, TCCSUP, 253J, 5637, and RT112), each of which has three derivative cell lines with acquired resistance to gemcitabine, cisplatin, and GC combination. For all of these cell lines we have performed whole-transcriptome mRNA sequencing, whole-exome sequencing, and reverse phase protein microarray. Additionally, we have performed functional genomic screening using whole-genome CRISPR knockout libraries, in the combination GC-resistant derivative cell lines. Using these data we identified multiple important chemoresistance genes and pathways, both previously known and novel. Interestingly, even though we found heterogeneous expression patterns seen across different –omic platforms, the functional genomic screens in GC-resistant cell lines converged on many genes and pathways that are essential to DNA damage response. These data suggest that functional genomic screens are perhaps more likely to identify genes and pathways that are directly linked to each of these drugs' specific mechanisms of action, as opposed to context-specific molecular differences seen across cell lines. Importantly, these results could enable improved prediction and personalization of therapy through identifying biomarkers that predict chemosensitivity and resistance. This study also suggests that identifying more generalizable strategies to overcome chemoresistance could increase the number of bladder cancer patients experiencing deeper and more complete responses to these common chemotherapeutic drugs. Citation Format: Robert T. Jones, Tahlita C. M. Zuiverloon, Hedvig Vekony, Andrew Goodspeed, Teemu D. Laajala, Molishree Joshi, Colin Sempeck, Annie Jean, Megan Tu, Julia D. Wulfkuhle, Emanuel F. Petricoin, James C. Costello, Dan Theodorescu. Multi-omic interrogation of gemcitabine and cisplatin-resistant bladder cancer cell lines identifies unique and shared mediators of chemosensitivity and resistance [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr B11.