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

ABSTRACT: 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.

SUBMITTER: Baca SC

PROVIDER: S-EPMC8010057 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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

Baca Sylvan C SC Takeda David Y DY Seo Ji-Heui JH Hwang Justin J Ku Sheng Yu SY Arafeh Rand R Arnoff Taylor T Agarwal Supreet S Bell Connor C O'Connor Edward E Qiu Xintao X Alaiwi Sarah Abou SA Corona Rosario I RI Fonseca Marcos A S MAS Giambartolomei Claudia C Cejas Paloma P Lim Klothilda K He Monica M Sheahan Anjali A Nassar Amin A Berchuck Jacob E JE Brown Lisha L Nguyen Holly M HM Coleman Ilsa M IM Kaipainen Arja A De Sarkar Navonil N Nelson Peter S PS Morrissey Colm C Korthauer Keegan K Pomerantz Mark M MM Ellis Leigh L Pasaniuc Bogdan B Lawrenson Kate K Kelly Kathleen K Zoubeidi Amina A Hahn William C WC Beltran Himisha H Long Henry W HW Brown Myles M Corey Eva E Freedman Matthew L ML

Nature communications 20210330 1

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 in ...[more]

PMID: 33785741

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Project description:Purpose The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)-targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Methods Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. Metastatic biopsy specimens underwent independent, blinded pathology review along with RNA/DNA sequencing. Results A total of 202 consecutive patients were enrolled. One hundred forty-eight (73%) had prior disease progression on abiraterone and/or enzalutamide. The biopsy evaluable rate was 79%. The overall incidence of t-SCNC detection was 17%. AR amplification and protein expression were present in 67% and 75%, respectively, of t-SCNC biopsy specimens. t-SCNC was detected at similar proportions in bone, node, and visceral organ biopsy specimens. Genomic alterations in the DNA repair pathway were nearly mutually exclusive with t-SCNC differentiation ( P = .035). Detection of t-SCNC was associated with shortened overall survival among patients with prior AR-targeting therapy for mCRPC (hazard ratio, 2.02; 95% CI, 1.07 to 3.82). Unsupervised hierarchical clustering of the transcriptome identified a small-cell-like cluster that further enriched for adverse survival outcomes (hazard ratio, 3.00; 95% CI, 1.25 to 7.19). A t-SCNC transcriptional signature was developed and validated in multiple external data sets with > 90% accuracy. Multiple transcriptional regulators of t-SCNC were identified, including the pancreatic neuroendocrine marker PDX1. Conclusion t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival. The near-mutual exclusivity with DNA repair alterations suggests t-SCNC may be a distinct subset of mCRPC. Transcriptional profiling facilitates the identification of t-SCNC and novel therapeutic targets.

Dataset Information

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

Publications

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

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