Increased chromatin accessibility drives transition to androgen receptor splice variant dependence in castration-resistant prostate cancer [ChIP-Seq]

Androgen receptor (AR) splice variants, of which ARv7 is most common, are increased in prostate cancer (PC) that develops resistance to androgen signaling inhibitor drugs, but the extent to which they drive AR activity, and whether they have novel functions or dependencies, remain to be determined. We generated a subline of VCaP PC cells (VCaP16) that was resistant to the AR inhibitor enzalutamide (ENZ) and found that AR activity was independent of the full length AR (ARfl), despite its continued high level expression, and was instead driven by ARv7. The ARv7 cistrome and transcriptome in these cells mirrored that of the ARfl in VCaP cells, although ARv7 chromatin binding was weaker, and strong ARv7 binding sites correlated with higher affinity ARfl binding sites across multiple models and clinical samples. Notably, although ARv7 expression increased rapidly in response to ENZ, there was a long lag before it gained chromatin binding and transcriptional activity. This lag was associated with an increase in chromatin accessibility, with the AR and nuclear factor I (NFI) motifs being most enriched at these more accessible sites. Moreover, the transcriptional effects of combined NFIB and X knockdown versus ARv7 knockdown were highly correlated. These findings indicate that ARv7 can drive the AR program, but that its activity is dependent on adaptations that increase chromatin accessibility to enhance its intrinsically weak chromatin binding. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ARfl and ARv7 in VCaP and ENZ-resistant VCaP16 cells in response to 10uM ENZ 4hrs or 10nM DHT 4hrs treatment. ChIP-seq for H3K27Ac and H3K4me1 in VCaP and ENZ-resistant VCaP16 cells. ChIP-seq for ARv7 in LNCaP95 cells in responce to 10nM DHT, 100nM dexamethasone (DEX) or DMSO for 2hrs. ChIP-seq for H3K27Ac, BRD4 and p300 in VCaP16 cells in responce to 500nM ARCC-32 or DMSO for 24hrs. ChIP-seq for ARv7 in VCaP16 cells in responce to 500nM ARCC-23 or DMSO for 36hrs.