Abstract 1421: Targeting cell-adaptive mechanisms of drug resistance in lethal prostate cancer

Precision oncology therapies are significantly hindered by the emergence of genetically or epigenetically-distinct cellular sub-populations, presenting either pre-existing or acquired drug resistance. For example, patients affected by advanced prostate cancer (PC), which is initially driven by aberrant activation of androgen receptor (AR) signals, often respond to Androgen Deprivation Therapy (ADT). Unfortunately, long-term treatment leads to the emergence of ADT-resistant tumors, termed Castration Resistant Prostate Cancer (CRPC), and poor outcome. Next-generation AR inhibitors extend CRPC patient survival, but frequently lead to the emergence of an even more aggressive Neuroendocrine PC (NEPC) phenotype, with exceedingly poor prognosis. Progression to NEPC is often determined by epigenetic-mediated reprogramming, rather than genomic alterations, resulting in cell-adaptive resistance, driven by aberrant activation of a handful of Master Regulator (MR) proteins. Consequently, better and more mechanistic understanding of cell-adaptive resistance is necessary to develop effective therapeutic strategies for CRPC. To address this challenge, we devised an RNA-based, high-throughput methodology, to systematically elucidate drug resistance mechanisms with single-cell resolution, and we applied it to study diverse, clonal populations that emerge following long-term treatment of PC LnCAP cells with next-generation AR inhibitors. Specifically, we identified Master Regulator (MR) proteins leading to the emergence of drug resistance, as well as clinically-available inhibitors able to reversing their activity, which were experimentally validated. We used PLATE-Seq, a low-cost, high-throughput RNA-Seq technology to profile more than 80 clonal, ADT-resistant populations, with single-cell resolution, and the VIPER algorithm to elucidate the MR proteins that mechanistically regulate their cell-adaptation programs. Our analysis revealed distinct cell-adaptive responses, associated with profound epigenetic reprogramming of prostate cancer cells. We used OncoTreat to prioritize a list of more than 400 FDA-approved and late-stage investigational drugs. Sensitivity to predicted drugs was confirmed in vitro and in vivo studies, in xenograft models derived from ADT- resistant clones are underway. We propose that this framework may represent a relevant advance to the study of cell-adaptive mechanism of drug resistance. Critically, this methodology is not limited to prostate cancer and can be applied to study arbitrary drug-resistance phenotypes. Citation Format: Prem Subramaniam, Alessandro Vasciaveo, Juan Arriaga, Jordan Kesner, Cory Abate-Shen, Andrea Califano. Targeting cell-adaptive mechanisms of drug resistance in lethal prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1421.