Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. Here, we investigate the epigenomic basis of this resistance mechanism by profiling histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identify a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying cancer dependencies through epigenomic profiling.


Reporting for specific materials, systems and methods
We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.  (Pomerantz et al., Nature Genetics, 2015;Stelloo et al., EMBO Mol Med, 2015), this sample size is sufficient for identifying cistromic changes in human cancers.
No data were excluded. FOXA1 knock-down experiments were performed twice independently with similar results. ChIP-seq and RNA-seq from cell lines with ASCL1 results were performed across two independent experiments with similar results.
Randomization does not apply for this study because comparisons were across distinct clinical states Immunohistochemistry for FOXA1/FOXA2 was performed in a blinded fashion. All unsupervised analyses described in the study, such as cistrome-wide analyses across states, were blinded as to clinical state of each specimen.

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LNCaP cells were obtained from ATCC. LNCaP 42D and 42F were derived from LNCaP from Dr. Amina Zoubeidi's lab. Available upon request from Dr. Amina Zoubeidi (not commercially available currently).
Cell line identity for LNCaP 42D and 42F was confirmed using short tandem repeat profiling.
Cell lines were not tested for mycoplasma contamination.
No commonly misidentified cell lines were used in the study Two fresh-frozen biopsies from metastatic prostate cancer from adult (" 18 years) males were selected from the Dana-Farber Cancer Institute (DFCI) Gelb Center biobank and database. The subjects were enrolled on DFCI Protocol 01-045, approved by the Dana-Farber Cancer Institute/Harvard Cancer Center IRB. As described in Nguyen et al, Prostate, 2017 (PMID 28156002), production of PDXs, derived from adult male prostate cancer metastases, was approved by the University of Washington Human Subjects Division IRB, which approved all Informed Consents that were used for tissue acquisition (IRB #39053).
LuCaPs were derived from patients (predominantly of European ancestry) who were treated for metastastic prostate cancer at the University of Washington as described in Nguyen et al, Prostate, 2017 (PMID 28156002). The two metastatic biopsy specimens profiled here were from men treated at the Dana-Farber Cancer Institute for metastatic prostate cancer who consented to tissue banking protocols (offered to all patients seen at the center).