Abstract 4091: Functional genomic screening in gemcitabine and cisplatin resistant bladder cancer cell lines identifies DNA repair pathways as mediators of chemosensitivity

Abstract

Abstract Gemcitabine and cisplatin (GC) combination neoadjuvant chemotherapy (NAC) is standard of care for patients with muscle-invasive bladder cancer (MIBC). This combination is preferred due to its favorable toxicity profile. Approximately 25% of NAC treated patients will experience complete pathological response (pT0) at time of radical cystectomy (RC). NAC-treated patients with residual disease at RC have poorer prognosis compared to those who achieved pT0. Here we systematically defined the in vitro functional determinants of resistance to gemcitabine and cisplatin in bladder cancer. To accomplish this, we performed molecular profiling and functional genomic screening on a panel of bladder cancer cell lines (KU-19-19, T24, TCCSUP, 253J and 5637), each having the parental cell line with matched gemcitabine-, cisplatin-, and dual GC-resistant derivatives. We performed whole exome sequencing, RNA sequencing, and phospho-proteomic profiling on these 20 cell lines. To identify chemogenetic interactions that govern sensitivity or resistance to these agents, we performed whole genome CRISPR knockout screening in the GC-resistant cells both in the presence and absence of GC. We identified several novel genes that when inactivated are capable of sensitizing GC resistant cell lines to the two agents. The majority of shared chemosensitizing genes fall into several DNA damage response pathways. This is consistent with the established mechanism of action of GC chemotherapy and observations that have been made from clinical cohorts, where loss-of-function mutations in these pathways correlate with response to platinum-based chemotherapy. Notably, our work has identified several druggable candidates that could serve as potential targets for enhancing responses rates to GC. Interestingly, comparing these candidate genes and pathways with those differentially expressed in the RNA sequencing and proteomic profiling showed limited overlap. This work provides a comprehensive view of the functional determinants of GC sensitivity in bladder cancer. In support of and expanding on previous studies, we identified additional DNA damage response genes that when lost enhance sensitivity to GC. These genes should be further explored for their utility as predictive biomarkers of response to GC-based therapy in clinical cohorts. Importantly, a number of these could be targeted in combination with GC-based NAC to potentially improve response. Citation Format: Robert T. Jones, Tahlita C. 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. Functional genomic screening in gemcitabine and cisplatin resistant bladder cancer cell lines identifies DNA repair pathways as mediators of chemosensitivity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4091.