A Hierarchy of Luminal Transcription Factors Defines AR Cistrome and Is Lost in Neuroendocrine Prostate Cancer

Androgen receptor (AR) is a hormonal transcription factor (TF) that binds to cis-regulatory elements of prostate lineage-specific genes to govern androgen response and progression of prostate cancer (PCa). This AR cistrome has been reported to be controlled by multiple chromatin-pioneering factors such as FOXA1, HOXB13, and GATA2. However, how these pioneer factors cooperate to regulate the AR cistrome remains unclear. Here, through comparative ChIP-seq analyses, we found that FOXA1 alone was sufficient to recruit AR to its binding sites regardless of H3K4me1. FOXA1 further enlisted HOXB13 and/or GATA2 to augment AR binding and enhancer activation, while HOXB13 and/or GATA2 alone were unable to recruit each other, nor AR. Moreover, HOXB13 knockdown attenuated AR and GATA2 expression and chromatin binding but failed to reprogram their cistromes, suggesting a role as a cofactor rather than a pioneer factor. During the neuroendocrine transformation (NET) of PCa, AR, GATA2, and HOXB13 were lost due to promoter hypermethylation, whereas FOXA1 was down-regulated by transcriptional repression. Lastly, through analyses of tissue microarrays, we confirmed that FOXA1 protein levels were drastically reduced in neuroendocrine PCa, as compared to AR-positive PCa. Therefore, our findings report a hierarchical network of TFs, pioneered by FOXA1 and facilitated by HOXB13 and GATA2, that defines lineage-specific AR cistrome and was lost during NET of PCa.