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Kumar A, Coleman I, Morrissey C, Zhang X, True LD, Gulati R, Etzioni R, Bolouri H, Montgomery B, White T, Lucas JM, Brown LG, Dumpit RF, DeSarkar N, Higano C, Yu EY, Coleman R, Schultz N, Fang M, Lange PH, Shendure J, Vessella RL, Nelson PS. Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nat Med 2016; 22:369-78. [PMID: 26928463 PMCID: PMC5045679 DOI: 10.1038/nm.4053] [Citation(s) in RCA: 536] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/01/2016] [Indexed: 12/17/2022]
Abstract
Tumor heterogeneity may reduce the efficacy of molecularly guided systemic therapy for cancers that have metastasized. To determine whether the genomic alterations in a single metastasis provide a reasonable assessment of the major oncogenic drivers of other dispersed metastases in an individual, we analyzed multiple tumors from men with disseminated prostate cancer through whole-exome sequencing, array comparative genomic hybridization (CGH) and RNA transcript profiling, and we compared the genomic diversity within and between individuals. In contrast to the substantial heterogeneity between men, there was limited diversity among metastases within an individual. The number of somatic mutations, the burden of genomic copy number alterations and aberrations in known oncogenic drivers were all highly concordant, as were metrics of androgen receptor (AR) activity and cell cycle activity. AR activity was inversely associated with cell proliferation, whereas the expression of Fanconi anemia (FA)-complex genes was correlated with elevated cell cycle progression, expression of the E2F transcription factor 1 (E2F1) and loss of retinoblastoma 1 (RB1). Men with somatic aberrations in FA-complex genes or in ATM serine/threonine kinase (ATM) exhibited significantly longer treatment-response durations to carboplatin than did men without defects in genes encoding DNA-repair proteins. Collectively, these data indicate that although exceptions exist, evaluating a single metastasis provides a reasonable assessment of the major oncogenic driver alterations that are present in disseminated tumors within an individual, and thus may be useful for selecting treatments on the basis of predicted molecular vulnerabilities.
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Affiliation(s)
- Akash Kumar
- Department of Genome Sciences, University of Washington, 3720 15 Ave. NE, Seattle, WA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Colm Morrissey
- Department of Urology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Xiaotun Zhang
- Department of Urology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Lawrence D. True
- Department of Pathology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Ruth Etzioni
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Hamid Bolouri
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Thomas White
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Lisha G. Brown
- Department of Urology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Ruth F. Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Navonil DeSarkar
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Celestia Higano
- Department of Medicine, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Evan Y. Yu
- Department of Medicine, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Roger Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Min Fang
- Department of Pathology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
| | - Paul H. Lange
- Department of Urology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, 3720 15 Ave. NE, Seattle, WA
| | - Robert L. Vessella
- Department of Urology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
| | - Peter S. Nelson
- Department of Genome Sciences, University of Washington, 3720 15 Ave. NE, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
- Department of Urology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
- Department of Pathology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
- Department of Medicine, University of Washington, 1959 Northeast Pacific Street, Seattle, WA
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA
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202
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Yang Q, Laknaur A, Elam L, Ismail N, Gavrilova-Jordan L, Lue J, Diamond MP, Al-Hendy A. Identification of Polycomb Group Protein EZH2-Mediated DNA Mismatch Repair Gene MSH2 in Human Uterine Fibroids. Reprod Sci 2016; 23:1314-25. [PMID: 27036951 DOI: 10.1177/1933719116638186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Uterine fibroids (UFs) are benign smooth muscle neoplasms affecting up to 70% of reproductive age women. Treatment of symptomatic UFs places a significant economic burden on the US health-care system. Several specific genetic abnormalities have been described as etiologic factors of UFs, suggesting that a low DNA damage repair capacity may be involved in the formation of UF. In this study, we used human fibroid and adjacent myometrial tissues, as well as an in vitro cell culture model, to evaluate the expression of MutS homolog 2 (MSH2), which encodes a protein belongs to the mismatch repair system. In addition, we deciphered the mechanism by which polycomb repressive complex 2 protein, EZH2, deregulates MSH2 in UFs. The RNA expression analysis demonstrated the deregulation of MSH2 expression in UF tissues in comparison to its adjacent myometrium. Notably, protein levels of MSH2 were upregulated in 90% of fibroid tissues (9 of 10) as compared to matched adjacent myometrial tissues. Human fibroid primary cells treated with 3-deazaneplanocin A (DZNep), chemical inhibitor of EZH2, exhibited a significant increase in MSH2 expression (P < .05). Overexpression of EZH2 using an adenoviral vector approach significantly downregulated the expression of MSH2 (P < .05). Chromatin immunoprecipitation assay demonstrated that enrichment of H3K27me3 in promoter regions of MSH2 was significantly decreased in DZNep-treated fibroid cells as compared to vehicle control. These data suggest that EZH2-H3K27me3 regulatory mechanism dynamically changes the expression levels of DNA mismatch repair gene MSH2, through epigenetic mark H3K27me3. MSH2 may be considered as a marker for early detection of UFs.
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Affiliation(s)
- Qiwei Yang
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Archana Laknaur
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Lelyand Elam
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Nahed Ismail
- Clinical Microbiology Division, Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Larisa Gavrilova-Jordan
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - John Lue
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Michael P Diamond
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Ayman Al-Hendy
- Division of Translational Research, Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, USA
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203
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Dominguez-Valentin M, Joost P, Therkildsen C, Jonsson M, Rambech E, Nilbert M. Frequent mismatch-repair defects link prostate cancer to Lynch syndrome. BMC Urol 2016; 16:15. [PMID: 27013479 PMCID: PMC4806412 DOI: 10.1186/s12894-016-0130-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A possible role for prostate cancer in Lynch syndrome has been debated based on observations of mismatch-repair defective tumors and reports of an increased risk of prostate cancer in mutation carriers. Potential inclusion of prostate cancer in the Lynch syndrome tumor spectrum is relevant for family classification, risk estimates and surveillance recommendations in mutation carriers. METHODS We used the population-based Danish HNPCC-register to identify all prostate cancers that developed in mutation carriers and in their first-degree relatives from 288 Lynch syndrome families. The tumors were evaluated for clinicopathologic features and mismatch-repair status, and the cumulative risk of prostate cancer was determined. RESULTS In total, 28 prostate cancers developed in 16 mutation carriers and in 12 first-degree relatives at a median age of 63 years. The majority of the tumors were high-grade tumors with Gleason scores 8-10. Prostate cancer was associated with mutations in MSH2, MLH1 and MSH6 with loss of the respective mismatch repair protein in 69 % of the tumors, though a MSI-high phenotype was restricted to 13 % of the tumors. The cumulative risk of prostate cancer at age 70 was 3.7 % (95 % CI: 2.3-4.9). CONCLUSION We provide evidence to link prostate cancer to Lynch syndrome through demonstration of MMR defective tumors and an increased risk of the disease, which suggests that prostate cancer should be considered in the diagnostic work-up of Lynch syndrome.
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Affiliation(s)
- Mev Dominguez-Valentin
- Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, SE-22381, Lund, Sweden
| | - Patrick Joost
- Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, SE-22381, Lund, Sweden
| | - Christina Therkildsen
- HNPCC-Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Mats Jonsson
- Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, SE-22381, Lund, Sweden
| | - Eva Rambech
- Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, SE-22381, Lund, Sweden
| | - Mef Nilbert
- Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, SE-22381, Lund, Sweden. .,HNPCC-Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark.
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204
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Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med 2016; 22:298-305. [PMID: 26855148 PMCID: PMC4777652 DOI: 10.1038/nm.4045] [Citation(s) in RCA: 1134] [Impact Index Per Article: 141.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/11/2016] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
| | - Davide Prandi
- Centre for Integrative Biology, University of Trento. Trento, Italy
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Department of Pathology and Laboratory Medicine. Weill Cornell Medicine. New York, NY
| | - Matteo Benelli
- Centre for Integrative Biology, University of Trento. Trento, Italy
| | - Loredana Puca
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
| | - Joanna Cyrta
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
| | - Clarisse Marotz
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
| | | | | | | | | | - David M. Nanus
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
| | - Scott T. Tagawa
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- The Broad Institute of MIT and Harvard, Boston, MA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Department of Physiology and Biophysics. Weill Cornell Medicine. New York, NY
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine. New York, NY
| | - Levi A. Garraway
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- The Broad Institute of MIT and Harvard, Boston, MA
| | - Mark A. Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
- Department of Pathology and Laboratory Medicine. Weill Cornell Medicine. New York, NY
| | - Francesca Demichelis
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Centre for Integrative Biology, University of Trento. Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medicine. New York, NY
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205
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Mathias PC, Turner EH, Scroggins SM, Salipante SJ, Hoffman NG, Pritchard CC, Shirts BH. Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing. Am J Clin Pathol 2016; 145:308-15. [PMID: 27124912 DOI: 10.1093/ajcp/aqv098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To apply techniques for ancestry and sex computation from next-generation sequencing (NGS) data as an approach to confirm sample identity and detect sample processing errors. METHODS We combined a principal component analysis method with k-nearest neighbors classification to compute the ancestry of patients undergoing NGS testing. By combining this calculation with X chromosome copy number data, we determined the sex and ancestry of patients for comparison with self-report. We also modeled the sensitivity of this technique in detecting sample processing errors. RESULTS We applied this technique to 859 patient samples with reliable self-report data. Our k-nearest neighbors ancestry screen had an accuracy of 98.7% for patients reporting a single ancestry. Visual inspection of principal component plots was consistent with self-report in 99.6% of single-ancestry and mixed-ancestry patients. Our model demonstrates that approximately two-thirds of potential sample swaps could be detected in our patient population using this technique. CONCLUSIONS Patient ancestry can be estimated from NGS data incidentally sequenced in targeted panels, enabling an inexpensive quality control method when coupled with patient self-report.
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Affiliation(s)
- Patrick C Mathias
- From the Department of Laboratory Medicine, University of Washington, Seattle.
| | - Emily H Turner
- From the Department of Laboratory Medicine, University of Washington, Seattle
| | - Sheena M Scroggins
- From the Department of Laboratory Medicine, University of Washington, Seattle
| | - Stephen J Salipante
- From the Department of Laboratory Medicine, University of Washington, Seattle
| | - Noah G Hoffman
- From the Department of Laboratory Medicine, University of Washington, Seattle
| | - Colin C Pritchard
- From the Department of Laboratory Medicine, University of Washington, Seattle
| | - Brian H Shirts
- From the Department of Laboratory Medicine, University of Washington, Seattle
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206
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Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma. Proc Natl Acad Sci U S A 2016; 113:2170-5. [PMID: 26864202 DOI: 10.1073/pnas.1525735113] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The presence of sarcomatoid features in clear cell renal cell carcinoma (ccRCC) confers a poor prognosis and is of unknown pathogenesis. We performed exome sequencing of matched normal-carcinomatous-sarcomatoid specimens from 21 subjects. Two tumors had hypermutation consistent with mismatch repair deficiency. In the remainder, sarcomatoid and carcinomatous elements shared 42% of somatic single-nucleotide variants (SSNVs). Sarcomatoid elements had a higher overall SSNV burden (mean 90 vs. 63 SSNVs, P = 4.0 × 10(-4)), increased frequency of nonsynonymous SSNVs in Pan-Cancer genes (mean 1.4 vs. 0.26, P = 0.002), and increased frequency of loss of heterozygosity (LOH) across the genome (median 913 vs. 460 Mb in LOH, P < 0.05), with significant recurrent LOH on chromosomes 1p, 9, 10, 14, 17p, 18, and 22. The most frequent SSNVs shared by carcinomatous and sarcomatoid elements were in known ccRCC genes including von Hippel-Lindau tumor suppressor (VHL), polybromo 1 (PBRM1), SET domain containing 2 (SETD2), phosphatase and tensin homolog (PTEN). Most interestingly, sarcomatoid elements acquired biallelic tumor protein p53 (TP53) mutations in 32% of tumors (P = 5.47 × 10(-17)); TP53 mutations were absent in carcinomatous elements in nonhypermutated tumors and rare in previously studied ccRCCs. Mutations in known cancer drivers AT-rich interaction domain 1A (ARID1A) and BRCA1 associated protein 1 (BAP1) were significantly mutated in sarcomatoid elements and were mutually exclusive with TP53 and each other. These findings provide evidence that sarcomatoid elements arise from dedifferentiation of carcinomatous ccRCCs and implicate specific genes in this process. These findings have implications for the treatment of patients with these poor-prognosis cancers.
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207
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Wei XX, Fong L, Small EJ. Prospects for the use of ipilimumab in treating advanced prostate cancer. Expert Opin Biol Ther 2016; 16:421-32. [PMID: 26698365 DOI: 10.1517/14712598.2016.1136284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Ipilimumab is a fully human monoclonal antibody that blocks Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) to potentiate antitumor T cell response. Ipilimumab is approved for the treatment of advanced melanoma based on improved overall survival. Clinical trials of ipilimumab in patients with metastatic castrate-resistant prostate cancer (mCRPC) have demonstrated some clinical activity, but have largely been disappointing to date. AREAS COVERED Results of key clinical studies of ipilimumab in the treatment of prostate cancer, including clinical efficacy and toxicities, are summarized. EXPERT OPINION There is likely a clinical benefit to ipilimumab in a subset of mCRPC patients. The development of biomarkers for enrichment treatment strategies that select for patients most likely to benefit from ipilimumab is a top priority. Similarly, an understanding of the factors predictive of toxicity will be important in the development of future treatment approaches.
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Affiliation(s)
- Xiao X Wei
- a Division of Hematology and Oncology, UCSF Helen Diller Family Comprehensive Cancer Center , University of California, San Francisco , San Francisco , CA , USA
| | - Lawrence Fong
- a Division of Hematology and Oncology, UCSF Helen Diller Family Comprehensive Cancer Center , University of California, San Francisco , San Francisco , CA , USA
| | - Eric J Small
- a Division of Hematology and Oncology, UCSF Helen Diller Family Comprehensive Cancer Center , University of California, San Francisco , San Francisco , CA , USA
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208
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Nicolas E, Arora S, Zhou Y, Serebriiskii IG, Andrake MD, Handorf ED, Bodian DL, Vockley JG, Dunbrack RL, Ross EA, Egleston BL, Hall MJ, Golemis EA, Giri VN, Daly MB. Systematic evaluation of underlying defects in DNA repair as an approach to case-only assessment of familial prostate cancer. Oncotarget 2015; 6:39614-33. [PMID: 26485759 PMCID: PMC4741850 DOI: 10.18632/oncotarget.5554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/02/2015] [Indexed: 01/03/2023] Open
Abstract
Risk assessment for prostate cancer is challenging due to its genetic heterogeneity. In this study, our goal was to develop an operational framework to select and evaluate gene variants that may contribute to familial prostate cancer risk. Drawing on orthogonal sources, we developed a candidate list of genes relevant to prostate cancer, then analyzed germline exomes from 12 case-only prostate cancer patients from high-risk families to identify patterns of protein-damaging gene variants. We described an average of 5 potentially disruptive variants in each individual and annotated them in the context of public databases representing human variation. Novel damaging variants were found in several genes of relevance to prostate cancer. Almost all patients had variants associated with defects in DNA damage response. Many also had variants linked to androgen signaling. Treatment of primary T-lymphocytes from these prostate cancer patients versus controls with DNA damaging agents showed elevated levels of the DNA double strand break (DSB) marker γH2AX (p < 0.05), supporting the idea of an underlying defect in DNA repair. This work suggests the value of focusing on underlying defects in DNA damage in familial prostate cancer risk assessment and demonstrates an operational framework for exome sequencing in case-only prostate cancer genetic evaluation.
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Affiliation(s)
| | - Sanjeevani Arora
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yan Zhou
- Programs in Biostatistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ilya G. Serebriiskii
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
- Kazan Federal University, Kazan, Russia
| | - Mark D. Andrake
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Dale L. Bodian
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Joseph G. Vockley
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Roland L. Dunbrack
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Eric A. Ross
- Programs in Biostatistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Brian L. Egleston
- Programs in Biostatistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael J. Hall
- Cancer Prevention and Control, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Erica A. Golemis
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Veda N. Giri
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA, USA
| | - Mary B. Daly
- Cancer Prevention and Control, Fox Chase Cancer Center, Philadelphia, PA, USA
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209
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The Molecular Taxonomy of Primary Prostate Cancer. Cell 2015; 163:1011-25. [PMID: 26544944 PMCID: PMC4695400 DOI: 10.1016/j.cell.2015.10.025] [Citation(s) in RCA: 2164] [Impact Index Per Article: 240.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/14/2015] [Accepted: 10/06/2015] [Indexed: 12/12/2022]
Abstract
There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary prostate carcinomas. Our results revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, and FLI1) or mutations (SPOP, FOXA1, and IDH1). Epigenetic profiles showed substantial heterogeneity, including an IDH1 mutant subset with a methylator phenotype. Androgen receptor (AR) activity varied widely and in a subtype-specific manner, with SPOP and FOXA1 mutant tumors having the highest levels of AR-induced transcripts. 25% of the prostate cancers had a presumed actionable lesion in the PI3K or MAPK signaling pathways, and DNA repair genes were inactivated in 19%. Our analysis reveals molecular heterogeneity among primary prostate cancers, as well as potentially actionable molecular defects.
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210
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Wyatt AW, Gleave ME. Targeting the adaptive molecular landscape of castration-resistant prostate cancer. EMBO Mol Med 2015; 7:878-94. [PMID: 25896606 PMCID: PMC4520654 DOI: 10.15252/emmm.201303701] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 03/12/2015] [Accepted: 03/26/2015] [Indexed: 12/19/2022] Open
Abstract
Castration and androgen receptor (AR) pathway inhibitors induce profound and sustained responses in advanced prostate cancer. However, the inevitable recurrence is associated with reactivation of the AR and progression to a more aggressive phenotype termed castration-resistant prostate cancer (CRPC). AR reactivation can occur directly through genomic modification of the AR gene, or indirectly via co-factor and co-chaperone deregulation. This mechanistic heterogeneity is further complicated by the stress-driven induction of a myriad of overlapping cellular survival pathways. In this review, we describe the heterogeneous and evolvable molecular landscape of CRPC and explore recent successes and failures of therapeutic strategies designed to target AR reactivation and adaptive survival pathways. We also discuss exciting areas of burgeoning anti-tumour research, and their potential to improve the survival and management of patients with CRPC.
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Affiliation(s)
- Alexander W Wyatt
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM. Integrative clinical genomics of advanced prostate cancer. Cell 2015; 161:1215-1228. [PMID: 26000489 PMCID: PMC4484602 DOI: 10.1016/j.cell.2015.05.001] [Citation(s) in RCA: 2332] [Impact Index Per Article: 259.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/06/2015] [Accepted: 04/27/2015] [Indexed: 12/15/2022]
Abstract
Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole-exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53, and PTEN were frequent (40%-60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF. Moreover, aberrations of BRCA2, BRCA1, and ATM were observed at substantially higher frequencies (19.3% overall) compared to those in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration, including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides clinically actionable information that could impact treatment decisions for these affected individuals.
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Affiliation(s)
- Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Juan-Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Bruce Montgomery
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA; Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Gerhardt Attard
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Himisha Beltran
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Wassim Abida
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA
| | - Jake Vinson
- Prostate Cancer Clinical Trials Consortium, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maha Hussain
- Department of Internal Medicine, Division of Hematology Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kathleen A Cooney
- Department of Internal Medicine, Division of Hematology Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David C Smith
- Department of Internal Medicine, Division of Hematology Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christine Brennan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Chen
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana E Rathkopf
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael J Morris
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephen B Solomon
- Interventional Radiology, Department of Radiology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeremy C Durack
- Interventional Radiology, Department of Radiology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Massimo Loda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Rosina T Lis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Stephen P Balk
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Glenn Gaviola
- Department of Musculoskeletal Radiology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Carrie Sougnez
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Manaswi Gupta
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Evan Y Yu
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Elahe A Mostaghel
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA; Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Heather H Cheng
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA; Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Hyojeong Mulcahy
- Department of Radiology, University of Washington, Seattle, WA 98109, USA
| | - Lawrence D True
- Department of Pathology, University of Washington Medical Center, Seattle, WA 98109, USA
| | - Stephen R Plymate
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Heidi Dvinge
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA
| | - Roberta Ferraldeschi
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Penny Flohr
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Susana Miranda
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Zafeiris Zafeiriou
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Nina Tunariu
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Joaquin Mateo
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Raquel Perez-Lopez
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Francesca Demichelis
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, 38123 Mattarello TN, Italy
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Marc Schiffman
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Division of Interventional Radiology, Department of Radiology, New York-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - David M Nanus
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Scott T Tagawa
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Alexandros Sigaras
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA; Department of Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Kenneth W Eng
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA; Department of Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Elisabeth I Heath
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Howard I Scher
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Philip Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Johann S de Bono
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Peter S Nelson
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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212
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Hong MK, Macintyre G, Wedge DC, Van Loo P, Patel K, Lunke S, Alexandrov LB, Sloggett C, Cmero M, Marass F, Tsui D, Mangiola S, Lonie A, Naeem H, Sapre N, Phal PM, Kurganovs N, Chin X, Kerger M, Warren AY, Neal D, Gnanapragasam V, Rosenfeld N, Pedersen JS, Ryan A, Haviv I, Costello AJ, Corcoran NM, Hovens CM. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nat Commun 2015; 6:6605. [PMID: 25827447 PMCID: PMC4396364 DOI: 10.1038/ncomms7605] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/11/2015] [Indexed: 12/29/2022] Open
Abstract
Tumour heterogeneity in primary prostate cancer is a well-established phenomenon. However, how the subclonal diversity of tumours changes during metastasis and progression to lethality is poorly understood. Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic tumours. We find one case of metastatic spread to the surgical bed causing local recurrence, and another case of cross-metastatic site seeding combining with dynamic remoulding of subclonal mixtures in response to therapy. By ultra-deep sequencing end-stage blood, we detect both metastatic and primary tumour clones, even years after removal of the prostate. Analysis of mutations associated with metastasis reveals an enrichment of TP53 mutations, and additional sequencing of metastases from 19 patients demonstrates that acquisition of TP53 mutations is linked with the expansion of subclones with metastatic potential which we can detect in the blood.
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Affiliation(s)
- Matthew K.H. Hong
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Geoff Macintyre
- Centre for Neural Engineering, Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Diagnostic Genomics, NICTA, Victoria Research Laboratory, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
- Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000 Leuven, Belgium
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Keval Patel
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Academic Urology Group, Addenbrookes Hospital, Cambridge University, Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Sebastian Lunke
- Centre for Translational Pathology, University of Melbourne, Parkville 3050, Victoria, Australia
| | - Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Clare Sloggett
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville 3050, Victoria, Australia
| | - Marek Cmero
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
- Centre for Neural Engineering, Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
- Diagnostic Genomics, NICTA, Victoria Research Laboratory, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Dana Tsui
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Stefano Mangiola
- Centre for Neural Engineering, Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew Lonie
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville 3050, Victoria, Australia
| | - Haroon Naeem
- Centre for Neural Engineering, Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
- Diagnostic Genomics, NICTA, Victoria Research Laboratory, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nikhil Sapre
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Pramit M. Phal
- Department of Radiology, Royal Melbourne Hospital, Parkville 3050, Victoria, Australia
| | - Natalie Kurganovs
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Xiaowen Chin
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Michael Kerger
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Anne Y. Warren
- Department of Histopathology, University Cambridge Hospitals, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - David Neal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Academic Urology Group, Addenbrookes Hospital, Cambridge University, Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Vincent Gnanapragasam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Academic Urology Group, Addenbrookes Hospital, Cambridge University, Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - John S. Pedersen
- TissuPath Specialist Pathology, Mount Waverley 3149, Victoria, Australia
- Monash University Faculty of Medicine, Clayton 3168, Victoria, Australia
| | - Andrew Ryan
- TissuPath Specialist Pathology, Mount Waverley 3149, Victoria, Australia
| | - Izhak Haviv
- Bar-Ilan University Medical School, Safad 1311502, Israel
| | - Anthony J. Costello
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Niall M. Corcoran
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Christopher M. Hovens
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville 3050, Victoria, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
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213
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Azad AA, Volik SV, Wyatt AW, Haegert A, Le Bihan S, Bell RH, Anderson SA, McConeghy B, Shukin R, Bazov J, Youngren J, Paris P, Thomas G, Small EJ, Wang Y, Gleave ME, Collins CC, Chi KN. Androgen Receptor Gene Aberrations in Circulating Cell-Free DNA: Biomarkers of Therapeutic Resistance in Castration-Resistant Prostate Cancer. Clin Cancer Res 2015; 21:2315-24. [PMID: 25712683 DOI: 10.1158/1078-0432.ccr-14-2666] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/05/2015] [Indexed: 12/13/2022]
Abstract
PURPOSE Although novel agents targeting the androgen-androgen receptor (AR) axis have altered the treatment paradigm of metastatic castration-resistant prostate cancer (mCRPC), development of therapeutic resistance is inevitable. In this study, we examined whether AR gene aberrations detectable in circulating cell-free DNA (cfDNA) are associated with resistance to abiraterone acetate and enzalutamide in mCRPC patients. EXPERIMENTAL DESIGN Plasma was collected from 62 mCRPC patients ceasing abiraterone acetate (n = 29), enzalutamide (n = 19), or other agents (n = 14) due to disease progression. DNA was extracted and subjected to array comparative genomic hybridization (aCGH) for chromosome copy number analysis, and Roche 454 targeted next-generation sequencing of exon 8 in the AR. RESULTS On aCGH, AR amplification was significantly more common in patients progressing on enzalutamide than on abiraterone or other agents (53% vs. 17% vs. 21%, P = 0.02, χ(2)). Missense AR exon 8 mutations were detected in 11 of 62 patients (18%), including the first reported case of an F876L mutation in an enzalutamide-resistant patient and H874Y and T877A mutations in 7 abiraterone-resistant patients. In patients switched onto enzalutamide after cfDNA collection (n = 39), an AR gene aberration (copy number increase and/or an exon 8 mutation) in pretreatment cfDNA was associated with adverse outcomes, including lower rates of PSA decline ≥ 30% (P = 0.013, χ(2)) and shorter time to radiographic/clinical progression (P = 0.010, Cox proportional hazards regression). CONCLUSIONS AR gene aberrations in cfDNA are associated with resistance to enzalutamide and abiraterone in mCRPC. Our data illustrate that genomic analysis of cfDNA is a minimally invasive method for interrogating mechanisms of therapeutic resistance in mCRPC.
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Affiliation(s)
- Arun A Azad
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada. Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Anne Haegert
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Robert H Bell
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Brian McConeghy
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Robert Shukin
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Jenny Bazov
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Jack Youngren
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Pamela Paris
- Department of Urology, UCSF, UCSF Diller Comprehensive Cancer Center, San Francisco, California
| | - George Thomas
- Department of Pathology and Laboratory Medicine, OHSU Knight Cancer Institute, Portland, Oregon
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada. University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada. University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada. University of British Columbia, Vancouver, British Columbia, Canada.
| | - Kim N Chi
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada. Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. University of British Columbia, Vancouver, British Columbia, Canada.
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