Co-evolution of AR gene copy number and structural complexity in castration-resistant prostate cancer

Abstract

Prostate cancer is the second leading cause of cancer death in males. Management of metastatic prostate cancer involves the therapeutic targeting of the androgen receptor (AR). AR is vital for normal prostate development and homeostasis, and prostate cells remain dependent on continued AR signaling for growth and survival. While initially efficacious, AR-targeted therapies will eventually fail during the emergence of castration-resistant prostate cancer (CRPC). CRPC is the lethal from of prostate cancer, and represents a major clinical challenge to managing this disease. The majority of CRPC remains dependent on AR, demonstrating continued reliance on AR signaling. The AR gene undergoes alterations during chronic AR-targeted therapy as prostate cancer cells adapt to castrate conditions. These alterations include mutations, structural rearrangement and amplification of the AR gene, and are involved in reactivating AR signaling under castrate conditions. These AR alterations often co-occur in CRPC tumors, but it is unclear whether this reflects intra-tumor heterogeneity or clonality. The goals of the studies performed in this dissertation were to characterize complex AR alterations and their clonality, and investigate their functional implications in conferring a selective advantage during androgen deprivation. We analyzed 41 CRPC tumors and 6 patient-derived xenografts (PDXs) using linked-read DNA-sequencing. We discovered that 7 samples harbored complex, phased AR rearrangements that occurred in a high AR copy number context. The mechanism behind these complex alterations in AR was found to be AR extrachromosomal DNA. Additionally, we investigated the clonal dynamics of two patient-derived xenografts (PDX) models of prostate cancer, which we propagated under hormone-replete and hormone-depleted conditions in vivo and in vitro. We measured the clonal dynamics by assessing a tandem duplication with a breakpoint transecting the AR gene in LuCaP 77 PDXs and double minute chromosomes harboring the AR gene in the LuCaP 105CR PDXs. We found that both of these AR alterations were clonally stable in these PDX models under different hormonal conditions in vitro and in vivo. We describe two different mechanisms of AR amplification found in LuCaP 105CR and VCaP-EnzR cells that have emerged with chronic selection pressure from AR inhibition. Our findings show that certain AR alterations remain clonally stable during acute androgen depletion, while others display clonal evolution during chronic androgen depletion or pharmacological inhibition of AR.