Abstract 2107: Integrative molecular and functional genomic analysis of chemotherapy resistant bladder cancer cell lines identifies novel mediators of therapeutic response
Authors: Jones Robert T. , Zuiverloon Tahlita C. , Vekony Hedvig , Goodspeed Andrew , Laajala Teemu D. , Joshi Molishree , Sempeck Colin , Tu Megan , Costello James C. , Theodorescu Dan 
Published: August 2019

Abstract
Gemcitabine and cisplatin (GC) combination neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC) is the standard of care for treating muscle-invasive bladder cancer (MIBC). Approximately 25% of patients experience complete pathologic response (pT0), while the remaining ~75% have residual disease and poorer prognosis. Therefore, defining mechanisms that enable bladder cancer cells to survive NAC will allow us to I) identify predictive biomarkers of response to NAC and improve MIBC patient stratification for NAC, and II) define novel genetic dependencies in GC-resistant bladder cancers for future drug development. We have performed RNA sequencing on a panel of six genetically diverse urothelial cancer cell lines, each with matched derivatives possessing acquired resistance to single agent gemcitabine, cisplatin, and combination GC. Initial analyses of RNA sequencing data has revealed hundreds of differentially expressed genes and associated pathways as potential drivers of resistance to these agents. Examples of significantly dysregulated pathways seen in gene set enrichment analyses implicate a range of pathways known to be associated with many diverse cellular processes such as: extracellular matrix organization, invasion and migration, interferon signaling, lipid and cholesterol metabolism and cellular differentiation status, among others. Importantly, these candidates include both shared and context-specific resistance phenotypes, which vary based on the genetic and molecular alterations found in the parental cell line. To complement these transcriptomic profiling experiments and to better understand how these changes in gene expression relate to mutation status and pathway activation status on the protein level, we have performed whole-exome sequencing, and are currently conducting phospho-proteomic profiling with reverse-phase protein microarray to enable more integrative analyses. Together the complement of transcriptomic, genomic and proteomic analyses will facilitate a more comprehensive assessment of which molecular patterns are drivers of resistance in our resistant cell lines. Finally, we have taken a more systematic approach to define functional genetic dependencies acquired in these NAC-resistant cells. To accomplish this we have performed whole-genome CRISPR knockout screening on the combined GC-resistant cells to identify vulnerabilities associated with GC-resistance. Taken together, our data provide a deep look into the context-specific and shared molecular mechanisms driving resistance to GC chemotherapy and provide a rational basis for the future development of molecularly guided therapies for NAC resistant bladder cancers.
Citation Format: Robert T. Jones, Tahlita C. Zuiverloon, Hedvig Vekony, Andrew Goodspeed, Teemu D. Laajala, Molishree Joshi, Colin Sempeck, Megan Tu, James C. Costello, Dan Theodorescu. Integrative molecular and functional genomic analysis of chemotherapy resistant bladder cancer cell lines identifies novel mediators of therapeutic response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2107.