Abstract A14: Next-generation sequencing of Bacille Calmette-Guerin (BCG)-unresponsive tumors identifies actionable alterations for potential targeted therapy in non-muscle invasive bladder cancer
Authors: Walasek Aleksandra , Almassi Nima , McPherson Victor , Dason Shawn , Benfante Nicole , Klein Tanya , Berger Michael F. , Schultz Nikolaus , Dalbagni Guido , Bajorin Dean F. , Rosenberg Jonathan E. , Al-Ahmadie Hikmat , Bochner Bernard H. , Solit David B. , Iyer Gopakumar , Pietzak Eugene J. 
Published: August 2020

Abstract
Introduction and Objective: Intravesical BCG remains standard of care for patients with intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). Although most patients initially respond to therapy, there is a group of patients who will experience recurrence and subsequent progression to invasive disease. There are limited treatment options for patients with BCG-unresponsive bladder cancer and alternative therapeutic strategies are needed. Next-generation sequencing helps identify and prioritize therapeutic opportunities for clinical trial of novel targeted agents.
Methods: All patients with urothelial carcinoma of the bladder who progressed to muscle-invasive disease after at least one course of intravesical BCG were identified within our institutional genomic database and in The Cancer Genome Atlas (TCGA) dataset. DNA from BCG-treated, chemotherapy naive, secondary MIBC tumors and matched normal DNA underwent targeted exome capture sequencing or whole-exome sequencing. Potentially actionable genomic alterations were defined according to OncoKB levels of evidence for each alteration as a predictive biomarker (OncoKB.org).
Results: The cohort comprised 77 secondary MIBC specimens, each from a unique patient. Sixty-six (86%) were male and the median age was 67 years (IQR 61-75). At least one potentially actionable genomic alteration was identified in 85% of the specimens. RTK/MAPK pathway alterations, most commonly FGFR3 (18%) and ERBB2 (15%), were seen in 42% of patients. PIK3CA mutations, seen in 21%, often co-occurred with RTK/MAPK alterations, potentially representing a resistance mechanism to FGFR or ERBB2-directed monotherapy. CDKN2A loss, hypothesized to be a driver of progression in FGFR3-mutated tumors, occurred in 10% of the samples. Alterations in cell cycle regulators were seen in 65% of specimens, of which 40% also had an intact RB gene and could potentially be vulnerable to CDK4/6 inhibitors. MDM2 amplification with “wild-type” TP53 was seen in 13% of specimens that might be sensitive to small-molecule antagonists. Inactivating mutations in histone acetyltransferases, CREBBP or EP300, occurred in 17% of specimens that might confer sensitivity to HDAC inhibitors. Truncating mutations in the SWI/SNF chromatin-modifying complex occurred in 33%, predominately in ARID1A, which we recently reported to be associated with worse recurrence-free survival after BCG. Truncating KDM6A mutations were seen in 19%, which along with ARID1A mutated tumors may be vulnerable to EZH2 inhibitors.
Conclusion: Limited effective treatments beyond radical cystectomy are available for BCG-unresponsive NMIBC. Genomic profiling identified several actionable alterations that offer potential therapeutic strategies for management of BCG-unresponsive disease. Targeted therapy for NMIBC patients warrants further investigation as further advances are made in development of more selective systemic inhibitors and improved intravesical drug delivery.
Citation Format: Aleksandra Walasek, Nima Almassi, Victor McPherson, Shawn Dason, Nicole Benfante, Tanya Klein, Michael F. Berger, Nikolaus Schultz, Guido Dalbagni, Dean F. Bajorin, Jonathan E. Rosenberg, Hikmat Al-Ahmadie, Bernard H. Bochner, David B. Solit, Gopakumar Iyer, Eugene J. Pietzak. Next-generation sequencing of Bacille Calmette-Guerin (BCG)-unresponsive tumors identifies actionable alterations for potential targeted therapy in non-muscle invasive bladder cancer [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 A14.