Resistance to AR Signaling Inhibition Does Not Necessitate Prostate Neuroendocrine Differentiation

Resistance to 2nd generation androgen receptor (AR) signaling inhibitors (ARSi) occurs in a subset of metastatic castration-resistant prostate cancer (mCRPC) patients with the emergence of a neuroendocrine (NE) phenotype. This NE phenotype is typically accompanied by loss of AR expression coupled with mutations/deletions in PTEN, TP53, and/or RB1, in addition to overexpression of DNMTs, EZH2, and/or SOX2. A combination of cell and molecular biology analyses of 29 prostate cancer patient-derived xenografts (PDXs) recapitulating the full spectrum of proposed genetic alterations driving NE differentiation, in addition to CRISPR-Cas9 AR-knockout cells were utilized. These analyses document that: 1) ARSi-resistance in mCRPC cells that lack AR expression in the context of a TP53 mutation and PTEN deletion does not necessitate acquiring a NE phenotype, but alternatively can occur via emergence of an AR-/NE- double negative (DN) cancer; 2) NE cancers lack AR expression due to transcriptional silencing via promoter hypermethylation; and 3) in contrast, the lack of AR expression in DN cancers is not due to promoter hypermethylation-dependent silencing. Regardless of their cell of origin, the prevalence of both AR-/NE- DN and AR-/NE+ ARSi-resistant cancers is increasing clinically, highlighting the urgent need to develop therapies that target vulnerabilities beyond AR pathway inhibition. RNA sequencing of patient-derived xenograft (PDX) models using Illumina TruSeq Library prep and sequenced on Illumina HiSeq 2500 and NovaSeq