Unbiased high-throughput approaches provide a global view of the massive genetic and transcriptomic changes that occur in and potentially drive cancer. Such approaches permit the discovery of novel networks that can serve as prognostic markers and therapeutic targets. We performed a systems-biology approach to identify genes linked to the androgen receptor (AR) variant AR-V7 in castration-resistant prostate cancer (CRPC). AR variants are C-terminal truncated, constitutively active, and play key transcriptional regulatory roles resulting in treatment resistance and disease progression. These AR variants lack the C-terminal ligand binding domain, which is the target of all approved drugs against AR, and consequently there is considerable interest in novel therapeutic strategies that are effective against AR variant-expressing prostate tumors. Directly targeting AR variants is challenging, and thus an attractive alternative approach is to identify downstream AR-V7 hub genes that not only drive cancer progression but also feedback to enhance AR-V7 activity. Thus, our goals were to: 1) define clinically relevant gene sets or modules in human PC progression using unbiased gene expression meta-analysis of PC patient samples by Weighted Gene-Co-expression Network Analysis (WGCNA); 2) map the AR-V7 functional interactome using a unique high-throughput synthetic genetic array (SGA) screening in the yeast S. pombe; and 3) identify AR-V7 regulated genes in PC cells. Integration of these approaches resulted in the identification of seven genes that are upregulated in human PC (as determined by WGCNA), functionally interact with AR-V7 (as determined by SGA), and are regulated by AR-V7. This gene set encoded select proteins previously linked to PC, such as members of the cyclin and topoisomerase families, but also proteins with no prior association with AR-V7 or PC. The seven genes comprised a signature that correlated with patient Gleason score and predicted disease free-survival and overall survival in large independent PC patient cohorts. Individual depletion of the expression of these genes decreased ligand-independent AR transcriptional activity concomitant with reduced CRPC cell proliferation. Because CRPC cells were highly dependent on these inter-related genes, combination therapy targeting two of the seven genes led to potent inhibition of CRPC cell proliferation. In contrast, the combination of these agents had little to no effect on nontumorigenic prostate epithelial cells or AR-null PC cells. In summary, we utilized an unbiased and novel gene discovery strategy that combined sophisticated bioinformatics and experimental approaches. This multifaceted approach resulted in the identification of disease-relevant genes that were regulated by AR-V7 and that reciprocally enhanced AR-V7 oncogenic activity. This novel gene set has a prognostic value and provides a rationale for combinatorial CRPC therapy.

Citation Format: Fiorella Magani, Eric Bray, Maria Julia Martinez, Valeria Copello, Ning Zhao, Stephanie Peacock, David Wiley, Gennaro D’urso, Kerry L. Burnstein. Integrated system-level analyses define an androgen receptor variant oncogenic network for advanced prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A050.