Divergent clonal evolution of castration resistant neuroendocrine prostate cancer

An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, in which tumor cells demonstrate low to absent AR expression and often have neuroendocrine features. The etiology and molecular basis for this 'alternative' treatment-resistant cell state remain incompletely understood. Here, by analyzing whole-exome sequencing data of metastatic biopsies from patients, we observed substantial genomic overlap between castration-resistant tumors that were histologically characterized as prostate adenocarcinomas (CRPC-Adeno) and neuroendocrine prostate cancer (CRPC-NE); analysis of biopsy samples from the same individuals over time points to a model most consistent with divergent clonal evolution. Genome-wide DNA methylation analysis revealed marked epigenetic differences between CRPC-NE tumors and CRPC-Adeno, and also designated samples of CRPC-Adeno with clinical features of AR independence as CRPC-NE, suggesting that epigenetic modifiers may play a role in the induction and/or maintenance of this treatment-resistant state. This study supports the emergence of an alternative, 'AR-indifferent' cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer.

[1]  Ximing J. Yang,et al.  Small Cell Carcinoma of the Prostate: An Immunohistochemical Study , 2006, The American journal of surgical pathology.

[2]  M. Rubin,et al.  Proposed Morphologic Classification of Prostate Cancer With Neuroendocrine Differentiation , 2014, The American journal of surgical pathology.

[3]  C. Bieberich,et al.  Shared TP53 gene mutation in morphologically and phenotypically distinct concurrent primary small cell neuroendocrine carcinoma and adenocarcinoma of the prostate , 2009, The Prostate.

[4]  Jun Yu,et al.  EZH2-mediated concordant repression of Wnt antagonists promotes β-catenin-dependent hepatocarcinogenesis. , 2011, Cancer research.

[5]  Levi Garraway,et al.  SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines , 2008, Nucleic acids research.

[6]  Benjamin J. Raphael,et al.  The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer , 2012, Nature.

[7]  R. Vessella,et al.  Molecular determinants of resistance to antiandrogen therapy , 2004, Nature Medicine.

[8]  Alessandro Romanel,et al.  Unraveling the clonal hierarchy of somatic genomic aberrations , 2014, Genome Biology.

[9]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

[10]  Mark Gerstein,et al.  RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries , 2010, Bioinform..

[11]  Vladimir Vacic,et al.  Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. , 2015, JAMA oncology.

[12]  A. Sivachenko,et al.  Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer , 2012, Nature Genetics.

[13]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[14]  S. Varambally,et al.  Antibody-based detection of ERG rearrangement-positive prostate cancer. , 2010, Neoplasia.

[15]  A. Ashworth,et al.  The cylindromatosis gene product, CYLD, interacts with MIB2 to regulate Notch signalling , 2014, Oncotarget.

[16]  P. Bourne,et al.  CYLD negatively regulates transforming growth factor-β-signalling via deubiquitinating Akt , 2012, Nature Communications.

[17]  Eugenia G. Giannopoulou,et al.  The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer , 2014, Nature Communications.

[18]  Steven J. M. Jones,et al.  The Molecular Taxonomy of Primary Prostate Cancer , 2015, Cell.

[19]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of human colon and rectal cancer , 2012, Nature.

[20]  F. Demichelis,et al.  Tumor clone dynamics in lethal prostate cancer , 2014, Science Translational Medicine.

[21]  Bernhard O. Palsson,et al.  Cancer cell lines , 1999 .

[22]  M. Nykter,et al.  The Evolutionary History of Lethal Metastatic Prostate Cancer , 2015, Nature.

[23]  C. Huggins,et al.  Studies on prostatic cancer: I. The effect of castration, of estrogen and of androgen injection on serum phosphatases in metastatic carcinoma of the prostate , 1941, CA: a cancer journal for clinicians.

[24]  M. Rubin,et al.  Next-generation Prostate Cancer Biobanking: Toward a Processing Protocol Amenable for the International Cancer Genome Consortium , 2012, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[25]  W. Lam,et al.  Polycomb-mediated silencing in neuroendocrine prostate cancer , 2015, Clinical Epigenetics.

[26]  Jiao Zhang,et al.  Neuroendocrine Prostate Cancer (NEPC) progressing from conventional prostatic adenocarcinoma: factors associated with time to development of NEPC and survival from NEPC diagnosis-a systematic review and pooled analysis. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[27]  David C. Smith,et al.  Integrative Clinical Genomics of Advanced Prostate Cancer , 2015, Cell.

[28]  Kristian Cibulskis,et al.  ContEst: estimating cross-contamination of human samples in next-generation sequencing data , 2011, Bioinform..

[29]  C. Logothetis,et al.  Molecular classification of prostate cancer progression: foundation for marker-driven treatment of prostate cancer. , 2013, Cancer discovery.

[30]  Marc Ladanyi,et al.  Bringing the genomic landscape of small-cell lung cancer into focus , 2012, Nature Genetics.

[31]  Arturo Molina,et al.  Abiraterone and increased survival in metastatic prostate cancer. , 2011, The New England journal of medicine.

[32]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[33]  A. Berruti,et al.  Abiraterone and increased survival in metastatic prostate cancer. , 2011, The New England journal of medicine.

[34]  R. Vessella,et al.  Ligand-independent androgen receptor variants derived from splicing of cryptic exons signify hormone-refractory prostate cancer. , 2009, Cancer research.

[35]  P. Nowell.  The clonal evolution of tumor cell populations. , 1976, Science.

[36]  S. Varambally,et al.  Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer , 2008, Science.

[37]  Joshua M. Stuart,et al.  A basal stem cell signature identifies aggressive prostate cancer phenotypes , 2015, Proceedings of the National Academy of Sciences.

[38]  Wennuan Liu,et al.  Rb Loss Is Characteristic of Prostatic Small Cell Neuroendocrine Carcinoma , 2013, Clinical Cancer Research.

[39]  M. Rubin,et al.  Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer. , 2013, Neoplasia.

[40]  M. Rubin,et al.  Challenges in recognizing treatment-related neuroendocrine prostate cancer. , 2012, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[41]  D. Ghosh,et al.  A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. , 2007, Cancer research.

[42]  E. Wieben,et al.  The genomic landscape of small intestine neuroendocrine tumors. , 2013, The Journal of clinical investigation.

[43]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[44]  A. Jemal,et al.  Cancer statistics, 2015 , 2015, CA: a cancer journal for clinicians.

[45]  David C. Corney,et al.  Synergy of p53 and Rb deficiency in a conditional mouse model for metastatic prostate cancer. , 2006, Cancer research.

[46]  M. Rubin,et al.  Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation. , 2012, Cancer discovery.

[47]  Alessandro Romanel,et al.  ASEQ: fast allele-specific studies from next-generation sequencing data , 2015, BMC Medical Genomics.

[48]  Lawrence D. True,et al.  Integrative Clinical Genomics of Advanced Prostate Cancer , 2015, Cell.

[49]  M. Rubin,et al.  High fidelity patient-derived xenografts for accelerating prostate cancer discovery and drug development. , 2014, Cancer research.

[50]  Michael R Hamblin,et al.  CA : A Cancer Journal for Clinicians , 2011 .

[51]  David Z. Chen,et al.  METHOD Open Access , 2014 .

[52]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[53]  Kurt Miller,et al.  Increased survival with enzalutamide in prostate cancer after chemotherapy. , 2012, The New England journal of medicine.

[54]  M. Fraga,et al.  The Polycomb group protein EZH2 directly controls DNA methylation , 2006, Nature.

[55]  C. Liang,et al.  Pathogenesis of prostatic small cell carcinoma involves the inactivation of the P53 pathway. , 2012, Endocrine-related cancer.

[56]  S. Carr,et al.  Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer , 2014, Science.

[57]  Ming Yu,et al.  Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer , 2014, Nature Communications.

[58]  Jing Chen,et al.  ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..

[59]  T. Golub,et al.  Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. , 2006, Cancer cell.

[60]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[61]  H. Scher,et al.  Starving the Addiction: New Opportunities for Durable Suppression of AR Signaling in Prostate Cancer , 2009, Clinical Cancer Research.

[62]  M. Rubin,et al.  Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. , 2013, European urology.

[63]  Joshua J. Steffan,et al.  The Transcription Factor SPDEF Suppresses Prostate Tumor Metastasis* , 2012, The Journal of Biological Chemistry.

[64]  Brent S. Pedersen,et al.  Pybedtools: a flexible Python library for manipulating genomic datasets and annotations , 2011, Bioinform..

[65]  A. Aparicio,et al.  Neuroendocrine (small-cell) carcinomas: why they teach us essential lessons about prostate cancer. , 2014, Oncology.

[66]  M. Gerstein,et al.  Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. , 2011, Cancer discovery.

[67]  Trevor J Pugh,et al.  Oncotator: Cancer Variant Annotation Tool , 2015, Human mutation.

[68]  B. Sander,et al.  A key role for EZH2 in epigenetic silencing of HOX genes in mantle cell lymphoma , 2013, Epigenetics.

[69]  V. Arora,et al.  Emerging mechanisms of resistance to androgen receptor inhibitors in prostate cancer , 2015, Nature Reviews Cancer.

[70]  W. Isaacs,et al.  AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer. , 2014, The New England journal of medicine.

[71]  Kyung Park,et al.  Epigenomic alterations in localized and advanced prostate cancer. , 2013, Neoplasia.

[72]  Yibing Ma,et al.  Mechanisms Underlying Cancer Growth and Apoptosis by DEK Overexpression in Colorectal Cancer , 2014, PloS one.

[73]  Carissa A. Sanchez,et al.  Genetic clonal diversity predicts progression to esophageal adenocarcinoma , 2006, Nature Genetics.

[74]  A. Sivachenko,et al.  Punctuated Evolution of Prostate Cancer Genomes , 2013, Cell.

[75]  Dennis C. Friedrich,et al.  Whole-exome sequencing and clinical interpretation of formalin-fixed , paraffin-embedded tumor samples to guide precision cancer medicine , 2014 .

[76]  S. Tagawa.  Neuroendocrine prostate cancer after hormonal therapy: knowing is half the battle. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[77]  Lily Wu,et al.  Comprehensive evaluation of the role of EZH2 in the growth, invasion, and aggression of a panel of prostate cancer cell lines , 2010, The Prostate.

[78]  Robert H. Bell,et al.  The Placental Gene PEG10 Promotes Progression of Neuroendocrine Prostate Cancer. , 2015, Cell reports.