Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer
Mark P. Labrecque, … , Peter S. Nelson, Colm Morrissey
Mark P. Labrecque, … , Peter S. Nelson, Colm Morrissey
Published July 30, 2019
Citation Information: J Clin Invest. 2019;129(10):4492-4505. https://doi.org/10.1172/JCI128212.
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Research Article Cell biology Oncology Article has an altmetric score of 12

Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer

Abstract

Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease with diverse drivers of disease progression and mechanisms of therapeutic resistance. We conducted deep phenotypic characterization of CRPC metastases and patient-derived xenograft (PDX) lines using whole-genome RNA sequencing, gene set enrichment analysis, and immunohistochemistry. Our analyses revealed 5 mCRPC phenotypes based on the expression of well-characterized androgen receptor (AR) or neuroendocrine (NE) genes: AR-high tumors (ARPC), AR-low tumors (ARLPC), amphicrine tumors composed of cells coexpressing AR and NE genes (AMPC), double-negative tumors (i.e., AR–/NE–; DNPC), and tumors with small cell or NE gene expression without AR activity (SCNPC). RE1 silencing transcription factor (REST) activity, which suppresses NE gene expression, was lost in AMPC and SCNPC PDX models. However, knockdown of REST in cell lines revealed that attenuated REST activity drives the AMPC phenotype but is not sufficient for SCNPC conversion. We also identified a subtype of DNPC tumors with squamous differentiation and generated an encompassing 26-gene transcriptional signature that distinguished the 5 mCRPC phenotypes. Together, our data highlight the central role of AR and REST in classifying treatment-resistant mCRPC phenotypes. These molecular classifications could potentially guide future therapeutic studies and clinical trial design.

Authors

Mark P. Labrecque, Ilsa M. Coleman, Lisha G. Brown, Lawrence D. True, Lori Kollath, Bryce Lakely, Holly M. Nguyen, Yu C. Yang, Rui M. Gil da Costa, Arja Kaipainen, Roger Coleman, Celestia S. Higano, Evan Y. Yu, Heather H. Cheng, Elahe A. Mostaghel, Bruce Montgomery, Michael T. Schweizer, Andrew C. Hsieh, Daniel W. Lin, Eva Corey, Peter S. Nelson, Colm Morrissey

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Figure 3

REST splicing occurs in AMPC and SCNPC phenotypes.

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REST splicing occurs in AMPC and SCNPC phenotypes. (A) Immunofluorescenc...
(A) Immunofluorescence of an AMPC LuCaP 77CR tumor using PSA (green) and SYP (red) antibodies. Sections were counterstained with DAPI (blue) and top panels represent LuCaP 77CR PDX sections stained with secondary antibody only. Scale bars: 20 μM. (B) Immunoblot of LuCaP PDX specimens probing for REST, AR, and SYP. ACTB was used as a loading control. Short, 10-second film exposure; long, 5-minute film exposure. (C) PCR of LuCaP PDX specimens using primers specific to REST shows the REST4 insertion sequence appearing in AMPC (LuCaP 77CR) and SCNPC (LuCaP 93, 145.2, and 173.1) but not in DNPC (LuCaP 173.2) or ARPC (LuCaP 86.2 and 73). (D) RNA-Seq heatmap of VCaP cells displaying NE-associated genes (NEURO I and NEURO II) and AR-associated genes. Results are expressed as log2 FPKM and colored according to scale. (E) Immunoblot of C4-2B, VCaP, and LuCaP 93 whole-cell extracts using antibodies against AR, REST, SYP, and ACTB. ACTB was used as a loading control. (F) PCR of C4-2B, VCaP, and NCIH660 cells using primers specific to REST. The upper band represents the REST4 splice variant.