1
|
Walters U, Pidgeon T, Yap T, Takhar M, Gresty H, Bertoncelli Tanaka M, Dusoye A, Eyskens P, Junejo M, Bell K, Sahota K, Crawford R, Kanthabalan A, Bedi N, Hosking-Jervis F, Oliver R, Rashid T. Early surgical outcomes following 400 feminising genital reconstructive surgeries performed by a single urological surgeon. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01488-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
2
|
Labbé DP, Zadra G, Yang M, Reyes JM, Lin CY, Cacciatore S, Ebot EM, Creech AL, Giunchi F, Fiorentino M, Elfandy H, Syamala S, Karoly ED, Alshalalfa M, Erho N, Ross A, Schaeffer EM, Gibb EA, Takhar M, Den RB, Lehrer J, Karnes RJ, Freedland SJ, Davicioni E, Spratt DE, Ellis L, Jaffe JD, DʼAmico AV, Kantoff PW, Bradner JE, Mucci LA, Chavarro JE, Loda M, Brown M. High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program. Nat Commun 2019; 10:4358. [PMID: 31554818 PMCID: PMC6761092 DOI: 10.1038/s41467-019-12298-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 08/23/2019] [Indexed: 12/16/2022] Open
Abstract
Systemic metabolic alterations associated with increased consumption of saturated fat and obesity are linked with increased risk of prostate cancer progression and mortality, but the molecular underpinnings of this association are poorly understood. Here, we demonstrate in a murine prostate cancer model, that high-fat diet (HFD) enhances the MYC transcriptional program through metabolic alterations that favour histone H4K20 hypomethylation at the promoter regions of MYC regulated genes, leading to increased cellular proliferation and tumour burden. Saturated fat intake (SFI) is also associated with an enhanced MYC transcriptional signature in prostate cancer patients. The SFI-induced MYC signature independently predicts prostate cancer progression and death. Finally, switching from a high-fat to a low-fat diet, attenuates the MYC transcriptional program in mice. Our findings suggest that in primary prostate cancer, dietary SFI contributes to tumour progression by mimicking MYC over expression, setting the stage for therapeutic approaches involving changes to the diet.
Collapse
Affiliation(s)
- David P Labbé
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Urology, Department of Surgery, McGill University and Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Giorgia Zadra
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Meng Yang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stefano Cacciatore
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amanda L Creech
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Francesca Giunchi
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, IT, Italy
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, IT, Italy
| | - Habiba Elfandy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudeepa Syamala
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Ashley Ross
- James Buchanan Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | | | | | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | | | - R Jeffrey Karnes
- Department of Urology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Stephen J Freedland
- Department of Surgery, Division of Urology, Center for Integrated Research on Cancer and Lifestyle, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Surgery Section, Durham Veteran Affairs Medical Center, Durham, NC, USA
| | | | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Leigh Ellis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jacob D Jaffe
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Anthony V DʼAmico
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Philip W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge E Chavarro
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA.
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY, USA.
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
3
|
Lee EC, Valencia T, Allerson C, Schairer A, Flaten A, Yheskel M, Kersjes K, Li J, Gatto S, Takhar M, Lockton S, Pavlicek A, Kim M, Chu T, Soriano R, Davis S, Androsavich JR, Sarwary S, Owen T, Kaplan J, Liu K, Jang G, Neben S, Bentley P, Wright T, Patel V. Discovery and preclinical evaluation of anti-miR-17 oligonucleotide RGLS4326 for the treatment of polycystic kidney disease. Nat Commun 2019; 10:4148. [PMID: 31515477 PMCID: PMC6742637 DOI: 10.1038/s41467-019-11918-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/09/2019] [Indexed: 12/17/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), caused by mutations in either PKD1 or PKD2 genes, is one of the most common human monogenetic disorders and the leading genetic cause of end-stage renal disease. Unfortunately, treatment options for ADPKD are limited. Here we report the discovery and characterization of RGLS4326, a first-in-class, short oligonucleotide inhibitor of microRNA-17 (miR-17), as a potential treatment for ADPKD. RGLS4326 is discovered by screening a chemically diverse and rationally designed library of anti-miR-17 oligonucleotides for optimal pharmaceutical properties. RGLS4326 preferentially distributes to kidney and collecting duct-derived cysts, displaces miR-17 from translationally active polysomes, and de-represses multiple miR-17 mRNA targets including Pkd1 and Pkd2. Importantly, RGLS4326 demonstrates a favorable preclinical safety profile and attenuates cyst growth in human in vitro ADPKD models and multiple PKD mouse models after subcutaneous administration. The preclinical characteristics of RGLS4326 support its clinical development as a disease-modifying treatment for ADPKD. Autosomal dominant polycystic kidney disease (ADPKD) is a leading genetic cause of end-stage renal disease with limited treatment options. Here the authors discover and characterize a microRNA inhibitor as a potential treatment for ADPKD.
Collapse
Affiliation(s)
- Edmund C Lee
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA.
| | | | | | | | - Andrea Flaten
- Department of Internal Medicine and Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Matanel Yheskel
- Department of Internal Medicine and Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kara Kersjes
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Jian Li
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Sole Gatto
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | | | | | - Adam Pavlicek
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Michael Kim
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Tiffany Chu
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Randy Soriano
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Scott Davis
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | | | - Salma Sarwary
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Tate Owen
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Julia Kaplan
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Kai Liu
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Graham Jang
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Steven Neben
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | | | | | - Vishal Patel
- Department of Internal Medicine and Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
4
|
Boufaied N, Takhar M, Nash C, Erho N, Bismar TA, Davicioni E, Thomson AA. Development of a predictive model for stromal content in prostate cancer samples to improve signature performance. J Pathol 2019; 249:411-424. [PMID: 31206668 PMCID: PMC6900085 DOI: 10.1002/path.5315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/27/2019] [Accepted: 06/13/2019] [Indexed: 01/23/2023]
Abstract
Prostate cancer is heterogeneous in both cellular composition and patient outcome, and development of biomarker signatures to distinguish indolent from aggressive tumours is a high priority. Stroma plays an important role during prostate cancer progression and undergoes histological and transcriptional changes associated with disease. However, identification and validation of stromal markers is limited by a lack of datasets with defined stromal/tumour ratio. We have developed a prostate‐selective signature to estimate the stromal content in cancer samples of mixed cellular composition. We identified stromal‐specific markers from transcriptomic datasets of developmental prostate mesenchyme and prostate cancer stroma. These were experimentally validated in cell lines, datasets of known stromal content, and by immunohistochemistry in tissue samples to verify stromal‐specific expression. Linear models based upon six transcripts were able to infer the stromal content and estimate stromal composition in mixed tissues. The best model had a coefficient of determination R2 of 0.67. Application of our stromal content estimation model in various prostate cancer datasets led to improved performance of stromal predictive signatures for disease progression and metastasis. The stromal content of prostate tumours varies considerably; consequently, deconvolution of stromal proportion may yield better results than tumour cell deconvolution. We suggest that adjusting expression data for cell composition will improve stromal signature performance and lead to better prognosis and stratification of men with prostate cancer. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Nadia Boufaied
- Division of Urology and Cancer Research Program, McGill University Health Centre Research Institute, Quebec, Canada
| | - Mandeep Takhar
- Research and Development, GenomeDx Biosciences, Vancouver, Canada
| | - Claire Nash
- Division of Urology and Cancer Research Program, McGill University Health Centre Research Institute, Quebec, Canada
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, Canada
| | - Tarek A Bismar
- Department of Pathology and Laboratory Medicine, University of Calgary Cumming School of Medicine, Calgary, Canada.,Department of Oncology, Biochemistry and Molecular Biology, University of Calgary Cumming School of Medicine, Calgary, Canada
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, Canada
| | - Axel A Thomson
- Division of Urology and Cancer Research Program, McGill University Health Centre Research Institute, Quebec, Canada
| |
Collapse
|
5
|
Salami SS, Kaplan JB, Nallandhighal S, Takhar M, Tosoian JJ, Lee M, Yoon J, Hovelson DH, Plouffe KR, Kaffenberger SD, Schaeffer EM, Karnes RJ, Lotan TL, Morgan TM, George AK, Montgomery JS, Davenport MS, You S, Tomlins SA, Curci NE, Kim HL, Spratt DE, Udager AM, Palapattu GS. Biologic Significance of Magnetic Resonance Imaging Invisibility in Localized Prostate Cancer. JCO Precis Oncol 2019; 3:1900054. [PMID: 32914029 DOI: 10.1200/po.19.00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2019] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Multiparametric magnetic resonance imaging (mpMRI) is used widely for prostate cancer (PCa) evaluation. Approximately 35% of aggressive tumors, however, are not visible on mpMRI. We sought to identify the molecular alterations associated with mpMRI-invisible tumors and determine whether mpMRI visibility is associated with PCa prognosis. METHODS Discovery and validation cohorts included patients who underwent mpMRI before radical prostatectomy and were found to harbor both mpMRI-visible (Prostate Imaging and Reporting Data System 3 to 5) and -invisible (Prostate Imaging and Reporting Data System 1 or 2) foci on surgical pathology. Next-generation sequencing was performed to determine differential gene expression between mpMRI-visible and -invisible foci. A genetic signature for tumor mpMRI visibility was derived in the discovery cohort and assessed in an independent validation cohort. Its association with long-term oncologic outcomes was evaluated in a separate testing cohort. RESULTS The discovery cohort included 10 patients with 26 distinct PCa foci on surgical pathology, of which 12 (46%) were visible and 14 (54%) were invisible on preoperative mpMRI. Next-generation sequencing detected prioritized genetic mutations in 14 (54%) tumor foci (n = 8 mpMRI visible, n = 6 mpMRI invisible). A nine-gene signature (composed largely of cell organization/structure genes) associated with mpMRI visibility was derived (area under the curve = 0.89), and the signature predicted MRI visibility with 75% sensitivity and 100% specificity (area under the curve = 0.88) in the validation cohort. In the testing cohort (n = 375, median follow-up 8 years) there was no significant difference in biochemical recurrence, distant metastasis, or cancer-specific mortality in patients with predicted mpMRI-visible versus -invisible tumors (all P > .05). CONCLUSION Compared with mpMRI-invisible disease, mpMRI-visible tumors are associated with underexpression of cellular organization genes. mpMRI visibility does not seem to be predictive of long-term cancer outcomes, highlighting the need for biopsy strategies that detect mpMRI-invisible tumors.
Collapse
Affiliation(s)
- Simpa S Salami
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | | | | | | | | | - Junhee Yoon
- Cedars-Sinai Medical Center, Los Angeles, CA
| | | | | | - Samuel D Kaffenberger
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | | | | | - Todd M Morgan
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Arvin K George
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jeffrey S Montgomery
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | | | - Scott A Tomlins
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | - Hyung L Kim
- Cedars-Sinai Medical Center, Los Angeles, CA
| | - Daniel E Spratt
- University of Michigan Rogel Cancer Center, Ann Arbor, MI.,Michigan Medicine, Ann Arbor, MI
| | - Aaron M Udager
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Ganesh S Palapattu
- Michigan Medicine, Ann Arbor, MI.,University of Michigan Rogel Cancer Center, Ann Arbor, MI.,Medical University of Vienna, Vienna, Austria
| |
Collapse
|
6
|
Alshalalfa M, Liu Y, Wyatt AW, Gibb EA, Tsai HK, Erho N, Lehrer J, Takhar M, Ramnarine VR, Collins CC, Den RB, Schaeffer EM, Davicioni E, Lotan TL, Bismar TA. Characterization of transcriptomic signature of primary prostate cancer analogous to prostatic small cell neuroendocrine carcinoma. Int J Cancer 2019; 145:3453-3461. [PMID: 31125117 PMCID: PMC6852174 DOI: 10.1002/ijc.32430] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/09/2019] [Accepted: 04/23/2019] [Indexed: 01/27/2023]
Abstract
Prostatic small cell neuroendocrine carcinoma (SC/NE) is well studied in metastatic castration‐resistant prostate cancer; however, it is not well characterized in the primary setting. Herein, we used gene expression profiling of SC/NE prostate cancer (PCa) to develop a 212 gene signature to identify treatment‐naïve primary prostatic tumors that are molecularly analogous to SC/NE (SC/NE‐like PCa). The 212 gene signature was tested in several cohorts confirming similar molecular profile between prostatic SC/NE and small cell lung carcinoma. The signature was then translated into a genomic score (SCGScore) using modularized logistic regression modeling and validated in four independent cohorts achieving an average AUC >0.95. The signature was evaluated in more than 25,000 primary adenocarcinomas to characterize the biology, prognosis and potential therapeutic response of predicted SC/NE‐like tumors. Assessing SCGScore in a prospective cohort of 17,967 RP and 6,697 biopsy treatment‐naïve primary tumors from the Decipher Genomic Resource Information Database registry, approximately 1% of the patients were found to have a SC/NE‐like transcriptional profile, whereas 0.5 and 3% of GG1 and GG5 patients respectively showed to be SC/NE‐like. More than 80% of these patients are genomically high‐risk based on Decipher score. Interrogating in vitro drug sensitivity analyses, SC/NE‐like prostatic tumors showed higher response to PARP and HDAC inhibitors. What's new? While genomic/transcriptomic data analysis has revolutionized cancer biology, this analysis is frequently only available late in the cancer history, often after years of therapy. Here the authors built a single sample genomic classifier to predict primary prostate cancer tumors with early small cell neuroendocrine differentiation. They show in three independent cohorts that small cell neuroendocrine tumors of the prostate are similar to small cell tumors of the lung and predict the specific prostate tumors to be responsive to inhibitors of poly ADP ribose polymerase and histone deacetylases, underscoring the use of these drugs in this subtype of prostate cancer.
Collapse
Affiliation(s)
| | - Yang Liu
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ewan A Gibb
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | | | | | | | - Varune R Ramnarine
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Robert B Den
- Sidney Kimmel Cancer Centre, Thomas Jefferson University, Philadelphia, PA
| | - Edward M Schaeffer
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Tamara L Lotan
- Department of Pathology and Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Tarek A Bismar
- Department of Pathology & Laboratory Medicine, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
7
|
Salami SS, Kaplan JB, Nallandhighal S, Takhar M, Tosoian JJ, Lee M, Yoon J, Hovelson DH, Plouffe KR, Kaffenberger SD, George AK, Montgomery JS, Davenport M, You S, Tomlins SA, Curci NE, Kim HL, Spratt DE, Udager AM, Palapattu GS. Radiogenomic characterization of multifocal prostate cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.7_suppl.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
126 Background: Up to 20% of patients with negative multiparametric magnetic resonance imaging (MRI) harbor Gleason score ≥7 prostate cancer (PCa). We sought to elucidate the molecular basis of and determine the prognostic significance of PCa visibility on MRI. Methods: We identified a retrospective cohort of patients who underwent MRI prior to prostatectomy with both MRI visible (PIRADS 3 – 5) and invisible PCa. MRI for each patient was re-reviewed and co-registered with whole-mount histopathology. DNA and RNA were co-isolated from all tumor foci pre-identified on FFPE specimens. High depth, targeted DNA and RNA next generation sequencing was performed to characterize the molecular profile of each tumor focus using the Oncomine Comprehensive Panel (DNA) and a custom targeted RNAseq panel assessing PCa relevant alterations. A multigene RNAseq model was developed and validated in two independent cohorts to predict MRI visible PCa and to determine the prognostic significance of MRI visibility. Results: A total of 26 primary tumor foci from 10 patients were analyzed. Of the 14 (54%) invisible lesions on MRI, 5 (36%) were Gleason 3+4 = 7 and the remainder were Gleason 6. We detected high-confidence prioritized PCa relevant mutations in 54% (14/26) of tumor foci, 43% (6/14) of which were in MRI invisible lesions. Notable point mutations were in APC, AR, ARID1B, ATM, ATRX, BRCA2, FAT1, MAP3K1, NF1, SPEN, SPOP, and TP53. A 9-gene RNA signature, the majority of which were under-expressed cellular organization and structure genes, was developed to predict MRI visibility with an AUC of 0.89. Validation of this signature in an independent data set (n = 16) yielded an AUC of 0.88 with a specificity of 100% for predicting MRI visible tumors. Using this signature in a cohort of 375 patients with clinical follow up, we found that predicted MRI visibility status was not an independent predictor of biochemical recurrence, metastasis-free survival, or PCa specific mortality (all p > 0.05). Conclusions: We observed under-expression of cellular organization and structural genes in MRI visible tumors compared to MRI invisible cancer foci. Using our validated signature to predict MRI visibility status, we found that MRI visibility is not a significant predictor of oncological outcomes.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Junhee Yoon
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | | | | | | | | | | | - Sungyong You
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | | | | | | | | | | |
Collapse
|
8
|
Ramnarine VR, Alshalalfa M, Mo F, Nabavi N, Erho N, Takhar M, Shukin R, Brahmbhatt S, Gawronski A, Kobelev M, Nouri M, Lin D, Tsai H, Lotan TL, Karnes RJ, Rubin MA, Zoubeidi A, Gleave ME, Sahinalp C, Wyatt AW, Volik SV, Beltran H, Davicioni E, Wang Y, Collins CC. The long noncoding RNA landscape of neuroendocrine prostate cancer and its clinical implications. Gigascience 2018; 7:4994835. [PMID: 29757368 PMCID: PMC6007253 DOI: 10.1093/gigascience/giy050] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/01/2018] [Indexed: 01/29/2023] Open
Abstract
Background Treatment-induced neuroendocrine prostate cancer (tNEPC) is an aggressive variant of late-stage metastatic castrate-resistant prostate cancer that commonly arises through neuroendocrine transdifferentiation (NEtD). Treatment options are limited, ineffective, and, for most patients, result in death in less than a year. We previously developed a first-in-field patient-derived xenograft (PDX) model of NEtD. Longitudinal deep transcriptome profiling of this model enabled monitoring of dynamic transcriptional changes during NEtD and in the context of androgen deprivation. Long non-coding RNA (lncRNA) are implicated in cancer where they can control gene regulation. Until now, the expression of lncRNAs during NEtD and their clinical associations were unexplored. Results We implemented a next-generation sequence analysis pipeline that can detect transcripts at low expression levels and built a genome-wide catalogue (n = 37,749) of lncRNAs. We applied this pipeline to 927 clinical samples and our high-fidelity NEtD model LTL331 and identified 821 lncRNAs in NEPC. Among these are 122 lncRNAs that robustly distinguish NEPC from prostate adenocarcinoma (AD) patient tumours. The highest expressed lncRNAs within this signature are H19, LINC00617, and SSTR5-AS1. Another 742 are associated with the NEtD process and fall into four distinct patterns of expression (NEtD lncRNA Class I, II, III, and IV) in our PDX model and clinical samples. Each class has significant (z-scores >2) and unique enrichment for transcription factor binding site (TFBS) motifs in their sequences. Enriched TFBS include (1) TP53 and BRN1 in Class I, (2) ELF5, SPIC, and HOXD1 in Class II, (3) SPDEF in Class III, (4) HSF1 and FOXA1 in Class IV, and (5) TWIST1 when merging Class III with IV. Common TFBS in all NEtD lncRNA were also identified and include E2F, REST, PAX5, PAX9, and STAF. Interrogation of the top deregulated candidates (n = 100) in radical prostatectomy adenocarcinoma samples with long-term follow-up (median 18 years) revealed significant clinicopathological associations. Specifically, we identified 25 that are associated with rapid metastasis following androgen deprivation therapy (ADT). Two of these lncRNAs (SSTR5-AS1 and LINC00514) stratified patients undergoing ADT based on patient outcome. Discussion To date, a comprehensive characterization of the dynamic landscape of lncRNAs during the NEtD process has not been performed. A temporal analysis of the PDX-based NEtD model has for the first time provided this dynamic landscape. TFBS analysis identified NEPC-related TF motifs present within the NEtD lncRNA sequences, suggesting functional roles for these lncRNAs in NEPC pathogenesis. Furthermore, select NEtD lncRNAs appear to be associated with metastasis and patients receiving ADT. Treatment-related metastasis is a clinical consequence of NEPC tumours. Top candidate lncRNAs FENDRR, H19, LINC00514, LINC00617, and SSTR5-AS1 identified in this study are implicated in the development of NEPC. We present here for the first time a genome-wide catalogue of NEtD lncRNAs that characterize the transdifferentiation process and a robust NEPC lncRNA patient expression signature. To accomplish this, we carried out the largest integrative study that applied a PDX NEtD model to clinical samples. These NEtD and NEPC lncRNAs are strong candidates for clinical biomarkers and therapeutic targets and warrant further investigation.
Collapse
Affiliation(s)
- Varune Rohan Ramnarine
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Fan Mo
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Noushin Nabavi
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Robert Shukin
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sonal Brahmbhatt
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alexander Gawronski
- Department of Computer Science, Simon Fraser University, Burnaby, BC, Canada
| | - Maxim Kobelev
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Mannan Nouri
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Dong Lin
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Harrison Tsai
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - R Jefferey Karnes
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Amina Zoubeidi
- 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
| | - Cenk Sahinalp
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stanislav V Volik
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Himisha Beltran
- Department of Medicine, Weill Cornell Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | | | - Yuzhuo Wang
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
9
|
Berglund AE, Rounbehler RJ, Gerke T, Awasthi S, Cheng CH, Takhar M, Davicioni E, Alshalalfa M, Erho N, Klein EA, Freedland SJ, Ross AE, Schaeffer EM, Trock BJ, Den RB, Cleveland JL, Park JY, Dhillon J, Yamoah K. Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer. Prostate Cancer Prostatic Dis 2018; 22:292-302. [PMID: 30367117 PMCID: PMC6760558 DOI: 10.1038/s41391-018-0103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/27/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Background Prostate cancer (PCa) tumors harboring translocations of ETS family genes with the androgen responsive TMPRSS2 gene (ETS+ tumors) provide a robust biomarker for detecting PCa in approximately 70% of patients. ETS+ PCa express high levels of the androgen receptor (AR), yet PCa tumors lacking ETS fusions (ETS−) also express AR and demonstrate androgen-regulated growth. In this study, we evaluate the differences in the AR-regulated transcriptomes between ETS+ and ETS− PCa tumors. Methods 10,608 patient tumors from three independent PCa datasets classified as ETS+ (samples overexpressing ERG or other ETS family members) or ETS− (all other PCa) were analyzed for differential gene expression using false-discovery-rate adjusted methods and gene-set enrichment analysis (GSEA). Results Based on the expression of AR-dependent genes and an unsupervised Principal Component Analysis (PCA) model, AR-regulated gene expression alone was able to separate PCa samples into groups based on ETS status in all PCa databases. ETS status distinguished several differentially expressed genes in both TCGA (6.9%) and GRID (6.6%) databases, with 413 genes overlapping in both databases. Importantly, GSEA showed enrichment of distinct androgen-responsive genes in both ETS− and ETS+ tumors, and AR ChIP-seq data identified 131 direct AR-target genes that are regulated in an ETS-specific fashion. Notably, dysregulation of ETS-dependent AR-target genes within the metabolic and non-canonical WNT pathways was associated with clinical outcomes. Conclusions ETS status influences the transcriptional repertoire of the AR, and ETS− PCa tumors appear to rely on distinctly different AR-dependent transcriptional programs to drive and sustain tumorigenesis.
Collapse
Affiliation(s)
- Anders E Berglund
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Robert J Rounbehler
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.,Department of Oncological Sciences, University of South Florida, Tampa, FL, USA
| | - Travis Gerke
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Chia-Ho Cheng
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | | | | | | | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Stephen J Freedland
- Department of Surgery, Division of Urology, Center for Integrated Research on Cancer and Lifestyle, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Bruce J Trock
- Department of Urology, Johns Hopkins, Baltimore, MD, USA
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - John L Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jasreman Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. .,Department of Radiation Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| |
Collapse
|
10
|
Den R, Lehrer J, Takhar M, Alshalalfa M, Erho N, Davicioni E, Feng F. Abstract B069: Drug response variability between luminal and basal prostate cancer tumors. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-b069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Prostate cancer (PCa) is a genomically heterogeneous disease that has been subtyped into molecularly distinct subtypes. Over the past several years, multiple drugs have demonstrated improvements in overall survival in men with advanced prostate cancer, prompting further investigations of these drugs. However, characterizing drug response in the localized disease setting and in the context of PCa molecular subtypes needs further investigation. Here in a large prospective cohort of men with adverse pathology we explore the heterogeneity of patient drug response between basal, luminal, and neuroendocrine prostate cancer subtypes.
Methods: Whole-transcriptome RNA expression profiles of 9,640 radical prostatectomy (RP) samples from prospective use of the Decipher test were obtained from the GRID registry database. Patients were subtyped into basal, luminal A, luminal B, and neuroendocrine subtypes using the PAM50 and small cell gene expression signatures. Drug response scores (DRS) predicting patient sensitivity for 89 oncology drugs were determined using in vitro drug sensitivity and microarray data from the NCI-60 panel. Pearson’s chi squared test was used to determine significant differences in drug sensitivity among PCa subtypes.
Results: Applying the subtype signatures to the cohort, we classified 43% of samples as basal, 26% as luminal A, 30% as luminal B, and 2% as neuroendocrine. DRS was highly variable across the subtypes. Basal tumors showed a distinct drug response profile where basal tumors were more sensitive to kinase inhibitors (e.g., cabozantanib, dasatnib, erlotinib), mTOR inhibitors (e.g., everolimus, temsirolumus), DNA repair inhibitors (e.g., olaparib, mitoxantrone), and alkylating (e.g., cisplatin, carboplatin) chemotherapy. Luminal A and B were more sensitive to steroid inhibition (e.g., abiraterone, tamoxifen) and anti-microtuble (e.g., docetaxel, paclitaxel, vinorelbine) chemotherapy, whereas neuroendocrine had highest DRS for antiproliferative agents (e.g., mitomycin, cytabarine, carmustine, topotecan), Significant differences in average DRS scores in subtypes were observed for all 89 drugs (p<0.001).
Conclusion: Prostate cancer subtypes in the localized disease setting have distinct drug response profiles, suggesting that subtyping and DRS scores may be useful for selecting candidates for systemic therapy trials.
Citation Format: Robert Den, Jonathan Lehrer, Mandeep Takhar, Mohammed Alshalalfa, Nicholas Erho, Elai Davicioni, Felix Feng. Drug response variability between luminal and basal prostate cancer tumors [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr B069.
Collapse
Affiliation(s)
- Robert Den
- 1Thomas Jefferson University, Philadelphia, PA,
| | | | | | | | | | | | - Felix Feng
- 3University of California at San Francisco, San Francisco, CA
| |
Collapse
|
11
|
Liu D, Takhar M, Alshalalfa M, Erho N, Shoag J, Jenkins RB, Karnes RJ, Ross AE, Schaeffer EM, Rubin MA, Trock B, Klein EA, Den RB, Tomlins SA, Spratt DE, Davicioni E, Sboner A, Barbieri CE. Impact of the SPOP Mutant Subtype on the Interpretation of Clinical Parameters in Prostate Cancer. JCO Precis Oncol 2018; 2018. [PMID: 30761387 PMCID: PMC6370327 DOI: 10.1200/po.18.00036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose Molecular characterization of prostate cancer, including The Cancer Genome Atlas, has revealed distinct subtypes with underlying genomic alterations. One of these core subtypes, SPOP (speckle-type POZ protein) mutant prostate cancer, has previously only been identifiable via DNA sequencing, which has made the impact on prognosis and routinely used risk stratification parameters unclear. Methods We have developed a novel gene expression signature, classifier (Subclass Predictor Based on Transcriptional Data), and decision tree to predict the SPOP mutant subclass from RNA gene expression data and classify common prostate cancer molecular subtypes. We then validated and further interrogated the association of prostate cancer molecular subtypes with pathologic and clinical outcomes in retrospective and prospective cohorts of 8,158 patients. Results The subclass predictor based on transcriptional data model showed high sensitivity and specificity in multiple cohorts across both RNA sequencing and microarray gene expression platforms. We predicted approximately 8% to 9% of cases to be SPOP mutant from both retrospective and prospective cohorts. We found that the SPOP mutant subclass was associated with lower frequency of positive margins, extraprostatic extension, and seminal vesicle invasion at prostatectomy; however, SPOP mutant cancers were associated with higher pretreatment serum prostate-specific antigen (PSA). The association between SPOP mutant status and higher PSA level was validated in three independent cohorts. Despite high pretreatment PSA, the SPOP mutant subtype was associated with a favorable prognosis with improved metastasis-free survival, particularly in patients with high-risk preoperative PSA levels. Conclusion Using a novel gene expression model and a decision tree algorithm to define prostate cancer molecular subclasses, we found that the SPOP mutant subclass is associated with higher preoperative PSA, less adverse pathologic features, and favorable prognosis. These findings suggest a paradigm in which the interpretation of common risk stratification parameters, particularly PSA, may be influenced by the underlying molecular subtype of prostate cancer.
Collapse
Affiliation(s)
| | - Mandeep Takhar
- GenomeDx Bioscience, Vancouver, British Columbia, Canada
| | | | - Nicholas Erho
- GenomeDx Bioscience, Vancouver, British Columbia, Canada
| | | | | | | | | | | | - Mark A Rubin
- Weill Cornell Medicine, NewYork-Presbyterian Hospital, New York, NY
| | | | | | - Robert B Den
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA
| | | | | | - Elai Davicioni
- GenomeDx Bioscience, Vancouver, British Columbia, Canada
| | - Andrea Sboner
- Weill Cornell Medicine, NewYork-Presbyterian Hospital, New York, NY
| | | |
Collapse
|
12
|
Radtke JP, Takhar M, Bonekamp D, Kesch C, Erho N, du Plessis M, Buerki C, Ong K, Davicioni E, Hohenfellner M, Hadaschik BA. Transcriptome Wide Analysis of Magnetic Resonance Imaging-targeted Biopsy and Matching Surgical Specimens from High-risk Prostate Cancer Patients Treated with Radical Prostatectomy: The Target Must Be Hit. Eur Urol Focus 2018; 4:540-546. [DOI: 10.1016/j.euf.2017.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/29/2016] [Accepted: 01/11/2017] [Indexed: 01/14/2023]
|
13
|
Karnes RJ, Sharma V, Choeurng V, Ashab HAD, Erho N, Alshalalfa M, Trock B, Ross A, Yousefi K, Tsai H, Zhao SG, Tosoian JJ, Haddad Z, Takhar M, Chang SL, Spratt DE, Abdollah F, Jenkins RB, Klein EA, Nguyen PL, Dicker AP, Den RB, Davicioni E, Feng FY, Lotan TL, Schaeffer EM. Development and Validation of a Prostate Cancer Genomic Signature that Predicts Early ADT Treatment Response Following Radical Prostatectomy. Clin Cancer Res 2018; 24:3908-3916. [PMID: 29760221 DOI: 10.1158/1078-0432.ccr-17-2745] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/29/2018] [Accepted: 05/08/2018] [Indexed: 12/19/2022]
Abstract
Purpose: Currently, no genomic signature exists to distinguish men most likely to progress on adjuvant androgen deprivation therapy (ADT) after radical prostatectomy for high-risk prostate cancer. Here we develop and validate a gene expression signature to predict response to postoperative ADT.Experimental Design: A training set consisting of 284 radical prostatectomy patients was established after 1:1 propensity score matching metastasis between adjuvant-ADT (a-ADT)-treated and no ADT-treated groups. An ADT Response Signature (ADT-RS) was identified from neuroendocrine and AR signaling-related genes. Two independent cohorts were used to form three separate data sets for validation (set I, n = 232; set II, n = 435; set III, n = 612). The primary endpoint of the analysis was postoperative metastasis.Results: Increases in ADT-RS score were associated with a reduction in risk of metastasis only in a-ADT patients. On multivariable analysis, ADT-RS by ADT treatment interaction term remained associated with metastasis in both validation sets (set I: HR = 0.18, Pinteraction = 0.009; set II: HR = 0.25, Pinteraction = 0.019). In a matched validation set III, patients with Low ADT-RS scores had similar 10-year metastasis rates in the a-ADT and no-ADT groups (30.1% vs. 31.0%, P = 0.989). Among High ADT-RS patients, 10-year metastasis rates were significantly lower for a-ADT versus no-ADT patients (9.4% vs. 29.2%, P = 0.021). The marginal ADT-RS by ADT interaction remained significant in the matched dataset (Pinteraction = 0.035).Conclusions: Patients with High ADT-RS benefited from a-ADT. In combination with prognostic risk factors, use of ADT-RS may thus allow for identification of ADT-responsive tumors that may benefit most from early androgen blockade after radical prostatectomy. We discovered a gene signature that when present in primary prostate tumors may be useful to predict patients who may respond to early ADT after surgery. Clin Cancer Res; 24(16); 3908-16. ©2018 AACR.
Collapse
Affiliation(s)
| | - Vidit Sharma
- Department of Urology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - Bruce Trock
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley Ross
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Harrison Tsai
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey J Tosoian
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zaid Haddad
- GenomeDx Biosciences Inc., Vancouver, Canada
| | | | - S Laura Chang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Firas Abdollah
- Vattikuti Urology Institute, Henry Ford Hospital, Detroit, Michigan
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | - Paul L Nguyen
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Adam P Dicker
- Department of Radiation Oncology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Tamara L Lotan
- Department of Pathology, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Edward M Schaeffer
- Department of Urology, Feinberg School of Medicine, Northwestern University, Evanston, Illinois
| |
Collapse
|
14
|
Yang L, Roberts D, Takhar M, Erho N, Bibby BAS, Thiruthaneeswaran N, Bhandari V, Cheng WC, Haider S, McCorry AMB, McArt D, Jain S, Alshalalfa M, Ross A, Schaffer E, Den RB, Jeffrey Karnes R, Klein E, Hoskin PJ, Freedland SJ, Lamb AD, Neal DE, Buffa FM, Bristow RG, Boutros PC, Davicioni E, Choudhury A, West CML. Development and Validation of a 28-gene Hypoxia-related Prognostic Signature for Localized Prostate Cancer. EBioMedicine 2018; 31:182-189. [PMID: 29729848 PMCID: PMC6014579 DOI: 10.1016/j.ebiom.2018.04.019] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Hypoxia is associated with a poor prognosis in prostate cancer. This work aimed to derive and validate a hypoxia-related mRNA signature for localized prostate cancer. METHOD Hypoxia genes were identified in vitro via RNA-sequencing and combined with in vivo gene co-expression analysis to generate a signature. The signature was independently validated in eleven prostate cancer cohorts and a bladder cancer phase III randomized trial of radiotherapy alone or with carbogen and nicotinamide (CON). RESULTS A 28-gene signature was derived. Patients with high signature scores had poorer biochemical recurrence free survivals in six of eight independent cohorts of prostatectomy-treated patients (Log rank test P < .05), with borderline significances achieved in the other two (P < .1). The signature also predicted biochemical recurrence in patients receiving post-prostatectomy radiotherapy (n = 130, P = .007) or definitive radiotherapy alone (n = 248, P = .035). Lastly, the signature predicted metastasis events in a pooled cohort (n = 631, P = .002). Prognostic significance remained after adjusting for clinic-pathological factors and commercially available prognostic signatures. The signature predicted benefit from hypoxia-modifying therapy in bladder cancer patients (intervention-by-signature interaction test P = .0026), where carbogen and nicotinamide was associated with improved survival only in hypoxic tumours. CONCLUSION A 28-gene hypoxia signature has strong and independent prognostic value for prostate cancer patients.
Collapse
Affiliation(s)
- Lingjian Yang
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester M20 4BX, UK
| | - Darren Roberts
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester M20 4BX, UK
| | | | | | - Becky A S Bibby
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester M20 4BX, UK
| | - Niluja Thiruthaneeswaran
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester M20 4BX, UK; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Vinayak Bhandari
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada; Sydney Medical School, University of Sydney, Sydney, Australia
| | - Wei-Chen Cheng
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Syed Haider
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Amy M B McCorry
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Darragh McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Suneil Jain
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | | | - Ashley Ross
- James Buchanan Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | | | - Eric Klein
- Glickman Urological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter J Hoskin
- Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, Middlesex HA6 2RN, UK
| | - Stephen J Freedland
- Department of Surgery, Division of Urology, Center for Integrated Research on Cancer and Lifestyle, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK
| | - Francesca M Buffa
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester M20 4BX, UK
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester M20 4BX, UK; NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, UK.
| |
Collapse
|
15
|
Itkonen HM, Brown M, Urbanucci A, Tredwell G, Ho Lau C, Barfeld S, Hart C, Guldvik IJ, Takhar M, Heemers HV, Erho N, Bloch K, Davicioni E, Derua R, Waelkens E, Mohler JL, Clarke N, Swinnen JV, Keun HC, Rekvig OP, Mills IG. Lipid degradation promotes prostate cancer cell survival. Oncotarget 2018; 8:38264-38275. [PMID: 28415728 PMCID: PMC5503531 DOI: 10.18632/oncotarget.16123] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/01/2017] [Indexed: 01/07/2023] Open
Abstract
Prostate cancer is the most common male cancer and androgen receptor (AR) is the major driver of the disease. Here we show that Enoyl-CoA delta isomerase 2 (ECI2) is a novel AR-target that promotes prostate cancer cell survival. Increased ECI2 expression predicts mortality in prostate cancer patients (p = 0.0086). ECI2 encodes for an enzyme involved in lipid metabolism, and we use multiple metabolite profiling platforms and RNA-seq to show that inhibition of ECI2 expression leads to decreased glucose utilization, accumulation of fatty acids and down-regulation of cell cycle related genes. In normal cells, decrease in fatty acid degradation is compensated by increased consumption of glucose, and here we demonstrate that prostate cancer cells are not able to respond to decreased fatty acid degradation. Instead, prostate cancer cells activate incomplete autophagy, which is followed by activation of the cell death response. Finally, we identified a clinically approved compound, perhexiline, which inhibits fatty acid degradation, and replicates the major findings for ECI2 knockdown. This work shows that prostate cancer cells require lipid degradation for survival and identifies a small molecule inhibitor with therapeutic potential.
Collapse
Affiliation(s)
- Harri M Itkonen
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Michael Brown
- Genito Urinary Cancer Research Group, Institute of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Alfonso Urbanucci
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.,Department of Molecular Oncology, Institute for Cancer Research and Oslo University Hospital, Oslo, Norway
| | - Gregory Tredwell
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chung Ho Lau
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Stefan Barfeld
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Claire Hart
- Genito Urinary Cancer Research Group, Institute of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Ingrid J Guldvik
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Mandeep Takhar
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Hannelore V Heemers
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Hematology/Medical Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nicholas Erho
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Katarzyna Bloch
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, LKI Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Elai Davicioni
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Rita Derua
- Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - James L Mohler
- Department of Urology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Noel Clarke
- Genito Urinary Cancer Research Group, Institute of Cancer Sciences, University of Manchester, Manchester, United Kingdom.,PCUK/Movember Centre of Excellence for Prostate Cancer Research, CRUK Manchester Institute for Cancer Research, University of Manchester, Manchester, UK.,Department of Urology, The Christie NHS Foundation Trust, Manchester, UK
| | - Johan V Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, LKI Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Ole P Rekvig
- Department of Medical Biology, University of Tromso, Tromso Norway
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.,Department of Molecular Oncology, Institute for Cancer Research and Oslo University Hospital, Oslo, Norway.,PCUK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| |
Collapse
|
16
|
Seiler R, Gibb EA, Wang NQ, Oo HZ, Lam HM, Takhar M, Erho N, van Kessel KE, Winters B, Douglas J, Lopez FV, Crabb SJ, van Rhijn BW, Franzen van de Putte EE, Zwarthoff EC, Thalmann GN, Davicioni E, Boormans JL, Dall'Era M, van der Heijden MS, Wright JL, Black PC. MP54-05 PLASTICITY IN THE BIOLOGICAL RESPONSE TO NEOADJUVANT CHEMOTHERAPY IN MUSCLE-INVASIVE BLADDER CANCER. J Urol 2018. [DOI: 10.1016/j.juro.2018.02.1696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
17
|
Urbanucci A, Barfeld SJ, Kytölä V, Itkonen HM, Coleman IM, Vodák D, Sjöblom L, Sheng X, Tolonen T, Minner S, Burdelski C, Kivinummi KK, Kohvakka A, Kregel S, Takhar M, Alshalalfa M, Davicioni E, Erho N, Lloyd P, Karnes RJ, Ross AE, Schaeffer EM, Vander Griend DJ, Knapp S, Corey E, Feng FY, Nelson PS, Saatcioglu F, Knudsen KE, Tammela TLJ, Sauter G, Schlomm T, Nykter M, Visakorpi T, Mills IG. Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer. Cell Rep 2018; 19:2045-2059. [PMID: 28591577 DOI: 10.1016/j.celrep.2017.05.049] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 04/01/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022] Open
Abstract
Global changes in chromatin accessibility may drive cancer progression by reprogramming transcription factor (TF) binding. In addition, histone acetylation readers such as bromodomain-containing protein 4 (BRD4) have been shown to associate with these TFs and contribute to aggressive cancers including prostate cancer (PC). Here, we show that chromatin accessibility defines castration-resistant prostate cancer (CRPC). We show that the deregulation of androgen receptor (AR) expression is a driver of chromatin relaxation and that AR/androgen-regulated bromodomain-containing proteins (BRDs) mediate this effect. We also report that BRDs are overexpressed in CRPCs and that ATAD2 and BRD2 have prognostic value. Finally, we developed gene stratification signature (BROMO-10) for bromodomain response and PC prognostication, to inform current and future trials with drugs targeting these processes. Our findings provide a compelling rational for combination therapy targeting bromodomains in selected patients in which BRD-mediated TF binding is enhanced or modified as cancer progresses.
Collapse
Affiliation(s)
- Alfonso Urbanucci
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway.
| | - Stefan J Barfeld
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway
| | - Ville Kytölä
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Tampere University of Technology, 33520 Tampere, Finland
| | - Harri M Itkonen
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway
| | - Ilsa M Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel Vodák
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway
| | - Liisa Sjöblom
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Xia Sheng
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Teemu Tolonen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Sarah Minner
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Christoph Burdelski
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kati K Kivinummi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Tampere University of Technology, 33520 Tampere, Finland
| | - Annika Kohvakka
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Steven Kregel
- Department of Surgery - Section of Urology, University of Chicago, Chicago, IL 60637, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109-0940, USA
| | - Mandeep Takhar
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Mohammed Alshalalfa
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Paul Lloyd
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143-0410, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94143-0981, USA
| | | | - Ashley E Ross
- Brady Urological Institute, Johns Hopkins Medical Institute, Baltimore, MD 21287, USA
| | - Edward M Schaeffer
- Department of Urology, Northwestern University, Feinberg School of Medicine, 303 East Chicago Avenue, Tarry 16-703, Chicago, IL 60611-3008, USA
| | - Donald J Vander Griend
- Department of Surgery - Section of Urology, University of Chicago, Chicago, IL 60637, USA
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK; Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, Campus Riedberg, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Felix Y Feng
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143-0410, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94143-0981, USA; Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Urology, University of Washington, Seattle, WA 98195, USA; Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Fahri Saatcioglu
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway; Institute for Cancer Genetics and Informatics, Oslo University Hospital, 0424 Oslo, Norway
| | - Karen E Knudsen
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Teuvo L J Tammela
- Prostate Cancer Research Center and Department of Urology, University of Tampere and Tampere University Hospital, 33014 Tampere, Finland
| | - Guido Sauter
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg 20095, Germany
| | - Matti Nykter
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Tampere University of Technology, 33520 Tampere, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Ian G Mills
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; PCUK Movember Centre of Excellence, CCRCB, Queen's University, Belfast BT7 1NN, Northern Ireland, UK.
| |
Collapse
|
18
|
Walter R, Jordan J, Takhar M, Alshalalfa M, Dai D, Erho N, Greenberger M, Bradley R, Davicioni E. Genomic variations associated with prostate cancer in large cohort of African American men. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.6_suppl.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
20 Background: Racial disparities in prostate cancer (PCa) incidence and mortality are well known. PCa is known to be more aggressive in African American men (AAM) in terms of higher incidence and mortality rates. Here we validate a tumor gene expression pan-cancer race model in men with PCa and further characterize genomic differences that may contribute to disparate clinical outcomes Methods: We obtained de-identified genome-wide expression profiles from clinical use of the Decipher RP test in 9,953 men from the GRID registry database. A subset of men (n = 313) had known race status. A pan-cancer race model, developed to predict patient AAM race from analysis of gene expression patterns in 4,162 tumors from retrospective cohorts with known race status was applied to the prospective cohort for race prediction. Gene expression data was used to define genomic differences. Results: The race model has an AUC of 0.98 discriminating EAM from AAM in independent PCa cohort. The model was then applied to the 9,640 GRID patients with unknown race status and classified 6,831 as EAM, 1,058 as AAM with 1,751 as having indeterminate race. Characterizing the molecular subtypes, we found known and predicted AAM to be enriched with SPINK1+ tumors (21% and 24%, respectively) compared to predicted EAM (8%). In contrast, while ERG+ was found 22% and 19% in known and predicted AAM, respectively compared to 46% in predicted EAM. Based on PAM50 prostate cancer classifier, 61% of AAM were classified as basal-like tumors, whereas 41% were basal-like in EAM. Similarly, 28% of AAM had low AR-A while only 11% of EAM had low AR-A. AAM tumors had higher levels of immune infiltration signatures as well as higher scores for inflammatory and interferon gamma responses, and Interleukin 6 (IL6) signaling activity scores. AAM had lower DNA repair and glycolysis pathway activity compared to EAM Conclusions: Known and predicted AAM, were enriched with SPINK1+ tumors, higher immune infiltration and activation but lower ERG+, DNA repair and AR activity tumors. Using such large GRID data with known race, we will further understand the underlying causes associated with prostate cancer racial disparities which could lead to personalized diagnosis and treatment.
Collapse
Affiliation(s)
| | | | | | | | - Darlene Dai
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | | | | | | | | |
Collapse
|
19
|
Seiler R, Gibb E, Wang NQ, Oo HZ, Lam HM, van Kessel KE, Takhar M, Erho N, Winters B, Douglas J, Van Rhijn BW, Sjödahl G, Zwarthoff EC, Thalmann GN, Davicioni E, Boormans JL, Dall'era M, Van Der Heijden MS, Wright JL, Black PC. Apparent plasticity in the biological response to neoadjuvant chemotherapy in muscle-invasive bladder cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.6_suppl.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
433 Background: After cisplatin-based neoadjuvant chemotherapy (NAC) almost two thirds of patients have residual muscle-invasive bladder cancer (MIBC) present at radical cystectomy (RC). The alterations induced by NAC in these cisplatin-resistant tumors remain largely unstudied. Here, we aim to investigate the characteristics of cisplatin-resistant tumors. Methods: RC samples were available for gene expression analysis from 133 patients with residual invasive disease after cisplatin-based NAC, of whom 116 had matched pre-NAC samples. In addition, the tumor bed (scar tissue) of 21 post-NAC RC specimens with no residual tumor was profiled. Unsupervised consensus clustering (CC) was performed and the CC were investigated for their biological and clinical characteristics. H&E and immunohistochemistry (KRT5/6, GATA3, KI67 and CD8) were used to confirm tissue sampling and gene expression analysis. Results: Unsupervised consensus clustering yielded four distinct consensus clusters (CC). Consistent basal-(CC1) and luminal-like (CC2) phenotype similar to pre-NAC subtyping was observed in 42% of cases. One third of cases became immune-infiltrated (CC3) in the post-NAC setting but lacked basal and luminal markers. These tumors expressed a strong T-cell signature, chemokine signaling and checkpoint molecules. Conversely, CC4 was associated with healing/scarring. This ‘scar-like’ character of CC4 was consistent with the scar samples. Despite being pathological non-responders, the relative risk of death for CC4 was 2.8 and 3 times less than CC2-Luminal (p = 0.038) and CC3-Infiltrated (p = 0.018), respectively. Luminal-like pre-NAC samples were more likely to adopt a scar-like character (CC4) in the post-NAC setting, while the basal-like tumors were more likely to develop luminal features (CC2). Conclusions: This study expands our knowledge of cisplatin-resistant MIBC by suggesting molecular subtypes to understand the biology of these tumors. Clinical trials are necessary to test the impact of these molecular subtypes with respect to selection of adjuvant and salvage treatments. Post-NAC immune infiltration could have implications for subsequent immunotherapy.
Collapse
Affiliation(s)
| | - Ewan Gibb
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | | | - Htoo Zarni Oo
- University of British Columbia, Vancouver, BC, Canada
| | | | | | | | | | - Brian Winters
- University of Washington School of Medicine, Seattle, WA
| | - James Douglas
- University of Southampton, Southampton, United Kingdom
| | - Bas W.G. Van Rhijn
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Badhoevedorp, Netherlands
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Malmo, Sweden
| | | | | | | | - Joost L Boormans
- Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marc Dall'era
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
| | | | | | | |
Collapse
|
20
|
Choudhury A, Yang L, Roberts D, Takhar M, Vinayak B, Bibby B, Cheng WC, Haider S, Thiruthaneeswaran N, Hoskin P, McArt D, Jain S, Buffa FM, Erho N, Bristow RG, Boutros PC, Davicioni E, West C. Hypoxia related mRNA biomarker to predict biochemical failure and metastasis for prostate cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.6_suppl.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5 Background: Hypoxia is an important regulatory factor in tumorigenesis and is associated with a poor prognosis. Patients with high risk locally advanced disease account for 13-21% of prostate cancer cases and the ten year cancer specific survival rate for these patients is 62%. Patients with hypoxic tumours could benefit from hypoxia modifying therapeutics in addition to radiotherapy. Clinical companion biomarkers are needed to stratify patients who would benefit from hypoxia modifying therapy in addition to radiotherapy. Methods: RNA-seq analysis was performed on prostate cell lines (PNT2-C2, PC-3, LNCaP and DU145) exposed to 1% hypoxia for 24 hrs. A prostate cancer hypoxia gene signature was derived in silico using publicly available prostate gene expression data sets and the RNA-seq data. The biomarker was then independently validated in multiple cohorts of prostate cancer patients with localized diseases receiving prostatectomy alone, prostatectomy plus adjuvant radiotherapy, prostatectomy plus salvage radiotherapy, or definitive radiotherapy alone. Results: In vitro the hypoxia inducible expression of the hypoxia gene signature was tested at 1% and 0.1% oxygen of which 21 of the 28 genes were regulated by hypoxia. Patients stratified as high hypoxia were associated with significantly poorer 5-year biochemical recurrence free survival in patients undergoing prostatectomy alone, prostatectomy plus adjuvant radiotherapy and definitive radiotherapy alone. In multivariable analysis, the biomarker retained significance after correcting for confounding factors including Gleason group, PSA, a molecular classifier, etc. In another cohort of prostatectomy and salvage radiotherapy treated patients, the mRNA signature predicts metastasis free survival in both univariable and multivariable analyses. Conclusions: We derived a de novo mRNA signature based on hypoxia-regulated genes. The biomarker consistently predicts biochemical failure and metastasis for prostate cancer patients with localized disease.
Collapse
Affiliation(s)
- Ananya Choudhury
- Christie NHS Foundation Trust and University of Manchester, Manchester, United Kingdom
| | - Lingjian Yang
- University of Manchester, Manchester, United Kingdom
| | | | | | | | | | - Wei-chen Cheng
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Syed Haider
- University of Oxford, Oxford, United Kingdom
| | | | - Peter Hoskin
- Mount Vernon Cancer Centre, London, United Kingdom
| | - Darragh McArt
- Queen's University Belfast Center for Cancer Research and Cell Biology, Belfast, United Kingdom
| | - Suneil Jain
- Queen's University Belfast, Belfast, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
21
|
Stoyanova R, Pollack A, Takhar M, Lynne C, Parra N, Lam LLC, Alshalalfa M, Buerki C, Castillo R, Jorda M, Ashab HAD, Kryvenko ON, Punnen S, Parekh DJ, Abramowitz MC, Gillies RJ, Davicioni E, Erho N, Ishkanian A. Association of multiparametric MRI quantitative imaging features with prostate cancer gene expression in MRI-targeted prostate biopsies. Oncotarget 2018; 7:53362-53376. [PMID: 27438142 PMCID: PMC5288193 DOI: 10.18632/oncotarget.10523] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/30/2016] [Indexed: 01/06/2023] Open
Abstract
Standard clinicopathological variables are inadequate for optimal management of prostate cancer patients. While genomic classifiers have improved patient risk classification, the multifocality and heterogeneity of prostate cancer can confound pre-treatment assessment. The objective was to investigate the association of multiparametric (mp)MRI quantitative features with prostate cancer risk gene expression profiles in mpMRI-guided biopsies tissues.Global gene expression profiles were generated from 17 mpMRI-directed diagnostic prostate biopsies using an Affimetrix platform. Spatially distinct imaging areas ('habitats') were identified on MRI/3D-Ultrasound fusion. Radiomic features were extracted from biopsy regions and normal appearing tissues. We correlated 49 radiomic features with three clinically available gene signatures associated with adverse outcome. The signatures contain genes that are over-expressed in aggressive prostate cancers and genes that are under-expressed in aggressive prostate cancers. There were significant correlations between these genes and quantitative imaging features, indicating the presence of prostate cancer prognostic signal in the radiomic features. Strong associations were also found between the radiomic features and significantly expressed genes. Gene ontology analysis identified specific radiomic features associated with immune/inflammatory response, metabolism, cell and biological adhesion. To our knowledge, this is the first study to correlate radiogenomic parameters with prostate cancer in men with MRI-guided biopsy.
Collapse
Affiliation(s)
- Radka Stoyanova
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alan Pollack
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mandeep Takhar
- Reserach and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Charles Lynne
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nestor Parra
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lucia L C Lam
- Reserach and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | | | - Christine Buerki
- Reserach and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Rosa Castillo
- Department of Radiology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Merce Jorda
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Oleksandr N Kryvenko
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sanoj Punnen
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dipen J Parekh
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Matthew C Abramowitz
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Robert J Gillies
- Cancer Imaging and Metabolism, Moffitt Cancer Center, Tampa, FL, USA
| | - Elai Davicioni
- Reserach and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Nicholas Erho
- Reserach and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Adrian Ishkanian
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
22
|
Liang Y, Ahmed M, Guo H, Soares F, Hua JT, Gao S, Lu C, Poon C, Han W, Langstein J, Ekram MB, Li B, Davicioni E, Takhar M, Erho N, Karnes RJ, Chadwick D, van der Kwast T, Boutros PC, Arrowsmith CH, Feng FY, Joshua AM, Zoubeidi A, Cai C, He HH. LSD1-Mediated Epigenetic Reprogramming Drives CENPE Expression and Prostate Cancer Progression. Cancer Res 2017; 77:5479-5490. [PMID: 28916652 DOI: 10.1158/0008-5472.can-17-0496] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 06/28/2017] [Accepted: 08/17/2017] [Indexed: 12/31/2022]
Abstract
Androgen receptor (AR) signaling is a key driver of prostate cancer, and androgen-deprivation therapy (ADT) is a standard treatment for patients with advanced and metastatic disease. However, patients receiving ADT eventually develop incurable castration-resistant prostate cancer (CRPC). Here, we report that the chromatin modifier LSD1, an important regulator of AR transcriptional activity, undergoes epigenetic reprogramming in CRPC. LSD1 reprogramming in this setting activated a subset of cell-cycle genes, including CENPE, a centromere binding protein and mitotic kinesin. CENPE was regulated by the co-binding of LSD1 and AR to its promoter, which was associated with loss of RB1 in CRPC. Notably, genetic deletion or pharmacological inhibition of CENPE significantly decreases tumor growth. Our findings show how LSD1-mediated epigenetic reprogramming drives CRPC, and they offer a mechanistic rationale for its therapeutic targeting in this disease. Cancer Res; 77(20); 5479-90. ©2017 AACR.
Collapse
Affiliation(s)
- Yi Liang
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Haiyang Guo
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Junjie T Hua
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shuai Gao
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Catherine Lu
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Christine Poon
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Wanting Han
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Jens Langstein
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Muhammad B Ekram
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Brian Li
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Elai Davicioni
- Research & Development, GenomeDx Biosciences Inc., Vancouver BC, Canada
| | - Mandeep Takhar
- Research & Development, GenomeDx Biosciences Inc., Vancouver BC, Canada
| | - Nicholas Erho
- Research & Development, GenomeDx Biosciences Inc., Vancouver BC, Canada
| | | | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital/University Health Network, Toronto, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, California
- Department of Urology, University of California at San Francisco, San Francisco, California
- Department of Medicine, University of California at San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Anthony M Joshua
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, Australia
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Housheng H He
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
23
|
Yamoah K, Rounbehler R, Takhar M, Gerke T, Park J, Awasthi S, Erho N, Davicioni E, Cleveland J, Berglund A. Distinct AR-Dependent Transcriptional Program in TMPRSS2-ERG Fusion Negative Tumors in African-American Men With Prostate Cancer. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
24
|
Yang L, Roberts D, Takhar M, Bibby B, Cheng W, Haider S, Buffa F, Erho N, Hoskin P, West C, Choudhury A. Hypoxia Gene Expression Signature Independently Predicts Prognosis for Prostate Cancer Patients. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
25
|
Seiler R, Gibb EA, Takhar M, Kessel KV, van Rhijn BW, Winters B, Douglas J, Wang Q, Choeurng V, Erho N, Buerki C, Davicioni E, Sjödahl G, Thalmann GN, Zwarthoff EC, Boormans JL, Dall’Era M, van der Heijden MS, Wright J, Black PC. Plasticity in muscle-invasive bladder cancer before and after cisplatin-based neoadjuvant chemotherapy. Urol Oncol 2017. [DOI: 10.1016/j.urolonc.2017.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
Nouri M, Caradec J, Lubik AA, Li N, Hollier BG, Takhar M, Altimirano-Dimas M, Chen M, Roshan-Moniri M, Butler M, Lehman M, Bishop J, Truong S, Huang SC, Cochrane D, Cox M, Collins C, Gleave M, Erho N, Alshalafa M, Davicioni E, Nelson C, Gregory-Evans S, Karnes RJ, Jenkins RB, Klein EA, Buttyan R. Therapy-induced developmental reprogramming of prostate cancer cells and acquired therapy resistance. Oncotarget 2017; 8:18949-18967. [PMID: 28145883 PMCID: PMC5386661 DOI: 10.18632/oncotarget.14850] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/16/2017] [Indexed: 01/01/2023] Open
Abstract
Treatment-induced neuroendocrine transdifferentiation (NEtD) complicates therapies for metastatic prostate cancer (PCa). Based on evidence that PCa cells can transdifferentiate to other neuroectodermally-derived cell lineages in vitro, we proposed that NEtD requires first an intermediary reprogramming to metastable cancer stem-like cells (CSCs) of a neural class and we demonstrate that several different AR+/PSA+ PCa cell lines were efficiently reprogrammed to, maintained and propagated as CSCs by growth in androgen-free neural/neural crest (N/NC) stem medium. Such reprogrammed cells lost features of prostate differentiation; gained features of N/NC stem cells and tumor-initiating potential; were resistant to androgen signaling inhibition; and acquired an invasive phenotype in vitro and in vivo. When placed back into serum-containing mediums, reprogrammed cells could be re-differentiated to N-/NC-derived cell lineages or return back to an AR+ prostate-like state. Once returned, the AR+ cells were resistant to androgen signaling inhibition. Acute androgen deprivation or anti-androgen treatment in serum-containing medium led to the transient appearance of a sub-population of cells with similar characteristics. Finally, a 132 gene signature derived from reprogrammed PCa cell lines distinguished tumors from PCa patients with adverse outcomes. This model may explain neural manifestations of PCa associated with lethal disease. The metastable nature of the reprogrammed stem-like PCa cells suggests that cycles of PCa cell reprogramming followed by re-differentiation may support disease progression and therapeutic resistance. The ability of a gene signature from reprogrammed PCa cells to identify tumors from patients with metastasis or PCa-specific mortality implies that developmental reprogramming is linked to aggressive tumor behaviors.
Collapse
Affiliation(s)
- Mannan Nouri
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Josselin Caradec
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Amy Anne Lubik
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Na Li
- Vancouver Prostate Centre, Vancouver, Canada
| | - Brett G Hollier
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | | | | | - Mengqian Chen
- Drug Discovery & Biomedical Sciences, South Carolina College of Pharmacy, Columbia, South Carolina, USA
| | | | | | - Melanie Lehman
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | | | | | | | - Dawn Cochrane
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Michael Cox
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Colin Collins
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Nicholas Erho
- GenomeDX Biosciences, Vancouver, Canada.,GenomeDX Biosciences, San Diego, California, USA
| | | | - Elai Davicioni
- GenomeDX Biosciences, Vancouver, Canada.,GenomeDX Biosciences, San Diego, California, USA
| | - Colleen Nelson
- Vancouver Prostate Centre, Vancouver, Canada.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Sheryl Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, Canada
| | | | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Ralph Buttyan
- Vancouver Prostate Centre, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| |
Collapse
|
27
|
Volpert M, Tse B, Ratther E, Stylianou N, Nouri M, Lehman M, McPherson S, Roshan-Moniri M, Takhar M, Erho N, Alshalafa M, Davicioni E, Jenkins R, Ross A, Karnes J, Den R, Fazli L, Gleave M, Williams E, Rennie P, Buttyan R, Russell P, Nelson C, Hollier B. Abstract 4908: Neuropilin-1 is up-regulated in the adaptive response of prostate tumors to androgen targeted therapies and is prognostic of metastatic progression and patient mortality. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aims: Androgen-targeted therapies (ATTs) are the mainstay treatment for metastatic prostate cancer (PCa). However, ATTs promote adaptation of tumour cells and lead to castration resistant disease (CRPC). We have recently identified the cell surface receptor, Neuropilin-1 (NRP1) as increased during EMT and in CRPC. However, the role of NRP1 in the prostate epithelium is poorly understood. This study aims to determine whether the inhibition of NRP1 will be a feasible therapeutic strategy for blocking PCa metastasis and therapy resistance.
Methods: qPCR and western blotting were used to assess NRP1 expression in PCa cell lines. NRP1 expression in CRPC was assessed using a murine LNCaP xenograft model of castration. NRP1 was knocked down with shRNA sequences from the pLKO.1 lentiviral construct. For metastasis assays, PC3 cells were microinjected into the zebrafish yolk sac and metastatic dissemination imaged 5 days later. NRP1 expression in radical prostatectomy (RP) samples from Mayo Clinic (545 patients) and Johns Hopkins Medical Institutions (JHMI; 188 patients) cohorts was quantified by Affymetrix exon arrays and multivariable analysis performed. Wound scratch migration and invasion assays were performed with the WoundMaker™ tool and IncuCyte™ FLR imaging systems.
Results: NRP1 levels were elevated in humanCRPC xenografts, metastatic and castrate resistant clinical PCa samples (p <0.0001), and PCa cell lines. NRP1 suppression significantly reduced metastasis of human xenografts in zebrafish and the migratory and invasive behaviour of metastatic PCa cells (p=0.0002). Multivariable analysis identified NRP1 as a significant independent prognostic indicator of metastasis and prostate cancer specific mortality in two large clinical cohorts (Mayo Clinic and JHMI; p=0.008/0.048 and 0.013/0,034 respectively). We show that NRP1 knockdown promotes E-Cadherin expression and loss of vimentin in mesenchymal PCa cells.
Conclusion: These results will provide the preclinical data necessary to rationalise the use of anti-NRP1 directed adjuvant therapies for clinical use in PCa patients receiving ATTs, and will pave the way for larger scale preclinical and clinical trials in the PCa setting.
Citation Format: Marianna Volpert, Brian Tse, Ellca Ratther, Nataly Stylianou, Mannan Nouri, Melanie Lehman, Stephen McPherson, Mani Roshan-Moniri, Mandeep Takhar, Nicholas Erho, Mohamed Alshalafa, Elai Davicioni, Robert Jenkins, Ashley Ross, Jeffrey Karnes, Robert Den, Ladan Fazli, Martin Gleave, Elizabeth Williams, Paul Rennie, Ralph Buttyan, Pamela Russell, Colleen Nelson, Brett Hollier. Neuropilin-1 is up-regulated in the adaptive response of prostate tumors to androgen targeted therapies and is prognostic of metastatic progression and patient mortality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4908. doi:10.1158/1538-7445.AM2017-4908
Collapse
Affiliation(s)
| | - Brian Tse
- 2Translational Research Institute, Brisbane, Australia
| | - Ellca Ratther
- 1Queensland University of Technology, Brisbane, Australia
| | | | - Mannan Nouri
- 3University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Lehman
- 1Queensland University of Technology, Brisbane, Australia
| | | | | | - Mandeep Takhar
- 4GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Nicholas Erho
- 4GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | | | - Elai Davicioni
- 4GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | | | - Ashley Ross
- 6Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Robert Den
- 7Thomas Jefferson University, Philadelphia, PA
| | - Ladan Fazli
- 3University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Gleave
- 3University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Paul Rennie
- 3University of British Columbia, Vancouver, British Columbia, Canada
| | - Ralph Buttyan
- 3University of British Columbia, Vancouver, British Columbia, Canada
| | - Pamela Russell
- 1Queensland University of Technology, Brisbane, Australia
| | - Colleen Nelson
- 1Queensland University of Technology, Brisbane, Australia
| | - Brett Hollier
- 1Queensland University of Technology, Brisbane, Australia
| |
Collapse
|
28
|
Kepplinger D, Takhar M, Sasaki M, Hollander Z, Smith D, McManus B, McMaster WR, Ng RT, Cohen Freue GV. PGCA: An algorithm to link protein groups created from MS/MS data. PLoS One 2017; 12:e0177569. [PMID: 28562641 PMCID: PMC5451011 DOI: 10.1371/journal.pone.0177569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra. To address this identification problem, many MS/MS data processing software tools combine all plausible protein identifiers matching a common set of peptides into a protein group. However, this solution introduces new challenges in studies with multiple experimental runs, which can be characterized by three main factors: i) protein groups' identifiers are local, i.e., they vary run to run, ii) the composition of each group may change across runs, and iii) the supporting evidence of proteins within each group may also change across runs. Since in general there is no conclusive evidence about the absence of proteins in the groups, protein groups need to be linked across different runs in subsequent statistical analyses. We propose an algorithm, called Protein Group Code Algorithm (PGCA), to link groups from multiple experimental runs by forming global protein groups from connected local groups. The algorithm is computationally inexpensive and enables the connection and analysis of lists of protein groups across runs needed in biomarkers studies. We illustrate the identification problem and the stability of the PGCA mapping using 65 iTRAQ experimental runs. Further, we use two biomarker studies to show how PGCA enables the discovery of relevant candidate protein group markers with similar but non-identical compositions in different runs.
Collapse
Affiliation(s)
- David Kepplinger
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mandeep Takhar
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Mayu Sasaki
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | | | - Derek Smith
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Bruce McManus
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - W. Robert McMaster
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond T. Ng
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabriela V. Cohen Freue
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
29
|
Karnes RJ, Choeurng V, Ross AE, Schaeffer EM, Klein EA, Freedland SJ, Erho N, Yousefi K, Takhar M, Davicioni E, Cooperberg MR, Trock BJ. Validation of a Genomic Risk Classifier to Predict Prostate Cancer-specific Mortality in Men with Adverse Pathologic Features. Eur Urol 2017; 73:168-175. [PMID: 28400167 DOI: 10.1016/j.eururo.2017.03.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/24/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Risk of prostate cancer-specific mortality (PCSM) is highly variable for men with adverse pathologic features at radical prostatectomy (RP); a majority will die of other causes. Accurately stratifying PCSM risk can improve therapy decisions. OBJECTIVE Validate the 22 gene Decipher genomic classifier (GC) to predict PCSM in men with adverse pathologic features after RP. DESIGN, SETTING, AND PARTICIPANTS Men with adverse pathologic features: pT3, pN1, positive margins, or Gleason score >7 who underwent RP in 1987-2010 at Johns Hopkins, Cleveland Clinic, Mayo Clinic, and Durham Veteran's Affairs Hospital. We also analyzed subgroups at high risk (prostate-specific antigen >20 ng/ml, RP Gleason score 8-10, or stage >pT3b), or very high risk of PCSM (biochemical recurrence in<2 yr [BCR2], or men who developed metastasis after RP [MET]). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Logistic regression evaluated the association of GC with PCSM within 10 yr of RP (PCSM10), adjusted for the Cancer of the Prostate Risk Assessment Postsurgical Score (CAPRA-S). GC performance was evaluated with area under the receiver operating characteristic curve (AUC) and decision curves. RESULTS AND LIMITATIONS Five hundred and sixty-one men (112 with PCSM10), median follow-up 13.0 yr (patients without PCSM10). For high GC score (> 0.6) versus low-intermediate (≤ 0.6), the odds ratio for PCSM10 adjusted for CAPRA-S was 3.91 (95% confidence interval: 2.43-6.29), with AUC=0.77, an increase of 0.04 compared with CAPRA-S. Subgroup odds ratios were 3.96, 3.06, and 1.95 for high risk, BCR2, or MET, respectively (all p<0.05), with AUCs 0.64-0.72. GC stratified cumulative PCSM10 incidence from 2.8% to 30%. Combined use of case-control and cohort data is a potential limitation. CONCLUSIONS In a large cohort with the longest follow-up to date, Decipher GC demonstrated clinically important prediction of PCSM at 10 yr, independent of CAPRA-S, in men with adverse pathologic features, BCR2, or MET after RP. PATIENT SUMMARY Decipher genomic classifier may improve treatment decision-making for men with adverse or high risk pathology after radical prostatectomy.
Collapse
Affiliation(s)
- R Jeffrey Karnes
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | | | - Ashley E Ross
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Edward M Schaeffer
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Urology, Northwestern University School of Medicine, Chicago, IL, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Stephen J Freedland
- Surgery Section, Durham Veteran Affairs Medical Center, Durham, NC, USA; Department of Surgery, Division of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | | | - Matthew R Cooperberg
- Department of Urology and Epidemiology and Biostatistics, University of California San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Bruce J Trock
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
30
|
Mo F, Lin D, Takhar M, Ramnarine VR, Dong X, Bell RH, Volik SV, Wang K, Xue H, Wang Y, Haegert A, Anderson S, Brahmbhatt S, Erho N, Wang X, Gout PW, Morris J, Karnes RJ, Den RB, Klein EA, Schaeffer EM, Ross A, Ren S, Sahinalp SC, Li Y, Xu X, Wang J, Wang J, Gleave ME, Davicioni E, Sun Y, Wang Y, Collins CC. Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer. Eur Urol 2017; 73:524-532. [PMID: 28330676 DOI: 10.1016/j.eururo.2017.02.038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/28/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Clinical grading systems using clinical features alongside nomograms lack precision in guiding treatment decisions in prostate cancer (PCa). There is a critical need for identification of biomarkers that can more accurately stratify patients with primary PCa. OBJECTIVE To identify a robust prognostic signature to better distinguish indolent from aggressive prostate cancer (PCa). DESIGN, SETTING, AND PARTICIPANTS To develop the signature, whole-genome and whole-transcriptome sequencing was conducted on five PCa patient-derived xenograft (PDX) models collected from independent foci of a single primary tumor and exhibiting variable metastatic phenotypes. Multiple independent clinical cohorts including an intermediate-risk cohort were used to validate the biomarkers. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The outcome measurement defining aggressive PCa was metastasis following radical prostatectomy. A generalized linear model with lasso regularization was used to build a 93-gene stroma-derived metastasis signature (SDMS). The SDMS association with metastasis was assessed using a Wilcoxon rank-sum test. Performance was evaluated using the area under the curve (AUC) for the receiver operating characteristic, and Kaplan-Meier curves. Univariable and multivariable regression models were used to compare the SDMS alongside clinicopathological variables and reported signatures. AUC was assessed to determine if SDMS is additive or synergistic to previously reported signatures. RESULTS AND LIMITATIONS A close association between stromal gene expression and metastatic phenotype was observed. Accordingly, the SDMS was modeled and validated in multiple independent clinical cohorts. Patients with higher SDMS scores were found to have worse prognosis. Furthermore, SDMS was an independent prognostic factor, can stratify risk in intermediate-risk PCa, and can improve the performance of other previously reported signatures. CONCLUSIONS Profiling of stromal gene expression led to development of an SDMS that was validated as independently prognostic for the metastatic potential of prostate tumors. PATIENT SUMMARY Our stroma-derived metastasis signature can predict the metastatic potential of early stage disease and will strengthen decisions regarding selection of active surveillance versus surgery and/or radiation therapy for prostate cancer patients. Furthermore, profiling of stroma cells should be more consistent than profiling of diverse cellular populations of heterogeneous tumors.
Collapse
Affiliation(s)
- Fan Mo
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Dong Lin
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Mandeep Takhar
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Varune Rohan Ramnarine
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xin Dong
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Robert H Bell
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stanislav V Volik
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Kendric Wang
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Hui Xue
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Yuwei Wang
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Anne Haegert
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Shawn Anderson
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sonal Brahmbhatt
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Xinya Wang
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Peter W Gout
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - James Morris
- Department of Radiation Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - R Jeffrey Karnes
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Edward M Schaeffer
- Department of Urology, James Buchanan Brady Urological Institute, Department of Oncology, Johns Hopkins Hospital, Baltimore, MD, USA; Department of Urology, Northwestern University School of Medicine, Chicago, IL, USA
| | - Ashley Ross
- Department of Urology, James Buchanan Brady Urological Institute, Department of Oncology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - S Cenk Sahinalp
- School of Computing Sciences, Simon Fraser University, Burnaby, BC, Canada; School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | | | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Martin E Gleave
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yuzhuo Wang
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada.
| | - Colin C Collins
- Vancouver Prostate Centre & Laboratory for Advanced Genome Analysis, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; School of Computing Sciences, Simon Fraser University, Burnaby, BC, Canada.
| |
Collapse
|
31
|
Pellegrini KL, Sanda MG, Patil D, Long Q, Santiago-Jiménez M, Takhar M, Erho N, Yousefi K, Davicioni E, Klein EA, Jenkins RB, Karnes RJ, Moreno CS. Evaluation of a 24-gene signature for prognosis of metastatic events and prostate cancer-specific mortality. BJU Int 2017; 119:961-967. [PMID: 28107602 DOI: 10.1111/bju.13779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To determine the prognostic potential of a 24-gene signature, Sig24, for identifying patients with prostate cancer who are at risk of developing metastases or of prostate cancer-specific mortality (PCSM) after radical prostatectomy (RP). PATIENTS AND METHODS Sig24 scores were calculated from previously collected gene expression microarray data from the Cleveland Clinic and Mayo Clinic (I and II). The performance of Sig24 was determined using time-dependent c-index analysis, Cox proportional hazards regression and Kaplan-Meier survival analysis. RESULTS Higher Sig24 scores were significantly associated with higher pathological Gleason scores in all three cohorts. Analysis of the Mayo Clinic II cohort, which included time-to-event information, indicated that patients with high Sig24 scores also had a higher risk of developing metastasis (hazard ratio [HR] 3.78, 95% confidence interval [CI]: 1.96-7.29; P < 0.001) or of PCSM (HR 6.54, 95% CI: 2.16-19.83; P < 0.001). CONCLUSIONS The findings of the present study show the applicability of Sig24 for the prognosis of metastasis or PCSM after RP. Future studies investigating the combination of Sig24 with available prognostic tests may provide new approaches to improve risk stratification for patients with prostate cancer.
Collapse
Affiliation(s)
- Kathryn L Pellegrini
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA.,Winship Cancer Institute, Atlanta, GA, USA
| | - Martin G Sanda
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA.,Winship Cancer Institute, Atlanta, GA, USA
| | - Dattatraya Patil
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA.,Winship Cancer Institute, Atlanta, GA, USA
| | - Qi Long
- Winship Cancer Institute, Atlanta, GA, USA.,Department of Biostatistics and Epidemiology and Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | | | | | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Robert B Jenkins
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Carlos S Moreno
- Winship Cancer Institute, Atlanta, GA, USA.,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
32
|
Kim H, Alshalalfa M, Hoffman-Censits J, Lallas CD, Davicioni E, Lin J, Birbe R, Erho N, Lehrer J, Ashab HAD, Takhar M, Olson A, Lam LL, Kelly WK, Knudsen KE, Thangavel C, Seiler R, Feng FY, Schaeffer EM, Trabulsi EJ, Gomella LG, Hurwitz MD, Dicker AP, Den RB. Potential Impact on Clinical Decision Making via a Genome-Wide Expression Profiling: A Case Report. Urol Case Rep 2016; 9:51-54. [PMID: 27713863 PMCID: PMC5050262 DOI: 10.1016/j.eucr.2016.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
Management of men with prostate cancer is fraught with uncertainty as physicians and patients balance efficacy with potential toxicity and diminished quality of life. Utilization of genomics as a prognostic biomarker has improved the informed decision-making process by enabling more rationale treatment choices. Recently investigations have begun to determine whether genomic information from tumor transcriptome data can be used to impact clinical decision-making beyond prognosis. Here we discuss the potential of genomics to alter management of a patient who presented with high-risk prostate adenocarcinoma. We suggest that this information help selecting patients for advanced imaging, chemotherapies, or clinical trial.
Collapse
Affiliation(s)
- Hyun Kim
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | | | | | - Costas D. Lallas
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | | | - Jianqing Lin
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | - Ruth Birbe
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | | | | | | | | | - Anders Olson
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | | | - W. Kevin Kelly
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | - Karen E. Knudsen
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | | | - Roland Seiler
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Felix Y. Feng
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Edward M. Schaeffer
- Department of Urology, Feinberg School of Medicine, Northwestern University, IL, USA
| | | | | | - Mark D. Hurwitz
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | - Adam P. Dicker
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
| | - Robert B. Den
- Sidney Kimmel Cancer Center, Thomas Jefferson University, PA, USA
- Corresponding author. Radiation Oncology, Cancer Biology, and Urology, Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Sidney Kimmel Cancer Center, 111 South 11th St, Philadelphia, PA 19107-5097, USA. Fax: +1 215 955 0412.Radiation Oncology, Cancer Biology, and UrologyDepartment of Radiation OncologySidney Kimmel Medical College at Thomas Jefferson UniversitySidney Kimmel Cancer Center111 South 11th StPhiladelphiaPA19107-5097USA
| |
Collapse
|
33
|
Stoyanova R, Takhar M, Tschudi Y, Ford JC, Solórzano G, Erho N, Balagurunathan Y, Punnen S, Davicioni E, Gillies RJ, Pollack A. Prostate cancer radiomics and the promise of radiogenomics. Transl Cancer Res 2016; 5:432-447. [PMID: 29188191 DOI: 10.21037/tcr.2016.06.20] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prostate cancer exhibits intra-tumoral heterogeneity that we hypothesize to be the leading confounding factor contributing to the underperformance of the current pre-treatment clinical-pathological and genomic assessment. These limitations impose an urgent need to develop better computational tools to identify men with low risk of prostate cancer versus others that may be at risk for developing metastatic cancer. The patient stratification will directly translate to patient treatments, wherein decisions regarding active surveillance or intensified therapy are made. Multiparametric MRI (mpMRI) provides the platform to investigate tumor heterogeneity by mapping the individual tumor habitats. We hypothesize that quantitative assessment (radiomics) of these habitats results in distinct combinations of descriptors that reveal regions with different physiologies and phenotypes. Radiogenomics, a discipline connecting tumor morphology described by radiomic and its genome described by the genomic data, has the potential to derive "radio phenotypes" that both correlate to and complement existing validated genomic risk stratification biomarkers. In this article we first describe the radiomic pipeline, tailored for analysis of prostate mpMRI, and in the process we introduce our particular implementations of radiomics modules. We also summarize the efforts in the radiomics field related to prostate cancer diagnosis and assessment of aggressiveness. Finally, we describe our results from radiogenomic analysis, based on mpMRI-Ultrasound (MRI-US) biopsies and discuss the potential of future applications of this technique. The mpMRI radiomics data indicate that the platform would significantly improve the biopsy targeting of prostate habitats through better recognition of indolent versus aggressive disease, thereby facilitating a more personalized approach to prostate cancer management. The expectation to non-invasively identify habitats with high probability of housing aggressive cancers would result in directed biopsies that are more informative and actionable. Conversely, providing evidence for lack of disease would reduce the incidence of non-informative biopsies. In radiotherapy of prostate cancer, dose escalation has been shown to reduce biochemical failure. Dose escalation only to determinate prostate habitats has the potential to improve tumor control with less toxicity than when the entire prostate is dose escalated.
Collapse
Affiliation(s)
- Radka Stoyanova
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mandeep Takhar
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Yohann Tschudi
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - John C Ford
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Gabriel Solórzano
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | | | - Sanoj Punnen
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Robert J Gillies
- Cancer Imaging and Metabolism, Moffitt Cancer Center, Tampa, FL, USA
| | - Alan Pollack
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
34
|
You S, Knudsen B, Erho N, Alshalalfa M, Takhar M, Ashab HAD, Davicioni E, Karnes RJ, Klein EA, Den RB, Ross AE, Schaeffer EM, Garraway IP, Kim J, Freeman MR. Abstract 1502: Three intrinsic subtypes of prostate cancer with distinct pathway activation profiles differ in prognosis and treatment response. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In the era of precision medicine, genomic classifications of prostate cancer (PC) have not broadly impacted patient care. Here we present an integrative transcriptome analysis of 14 disease-related pathways in over 4,600 clinical specimens and 25 PC preclinical models. This approach provides a novel classification scheme, inclusive of 3 PC subtypes (PCS1-3), which predict disease progression and drug resistance. The PCS1 and PCS2 categories possess characteristics of luminal cells, while PCS3 exhibits basal features. Castration-resistant and metastatic cancers are over-represented in PCS1 and PCS3 tumors. All 3 subtypes are represented in commonly used PC cell lines; however, none of the mouse models we analyzed resembles PCS3. PCS classification using RNA expression data appears to be stable across primary and metastatic human tumors, cell lines, xenografts and mouse models. This new subtyping method provides novel opportunities for patient stratification that reflect specific features of tumor biology and may influence therapeutic decisions.
Citation Format: Sungyong You, Beatrice Knudsen, Nicholas Erho, Mohammed Alshalalfa, Mandeep Takhar, Hussam Al-deen Ashab, Elai Davicioni, Robert Jeffrey Karnes, Eric A. Klein, Robert B. Den, Ashley E. Ross, Edward M. Schaeffer, Isla P. Garraway, Jayoung Kim, Michael R. Freeman. Three intrinsic subtypes of prostate cancer with distinct pathway activation profiles differ in prognosis and treatment response. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1502.
Collapse
Affiliation(s)
| | | | - Nicholas Erho
- 2GenomeDx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | - Mandeep Takhar
- 2GenomeDx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | - Elai Davicioni
- 2GenomeDx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | | | | | | | | | | | - Jayoung Kim
- 1Cedars-Sinai Medical Center, Los Angeles, CA
| | | |
Collapse
|
35
|
Labrecque M, Takhar M, Nason RJ, Santacruz S, Tam K, Massah S, Haegert A, Bell R, Altamirano-Dimas M, Collins C, Lee F, Prefontaine G, Cox M, Beischlag T. Abstract 2922: Loss of retinoblastoma protein dysregulates HIF1-mediated genetic programs, and promotes tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Loss of tumour suppressor proteins, such as the retinoblastoma protein (Rb), results in tumour progression and metastasis. Metastasis is facilitated by low oxygen availability within the tumour that is detected by hypoxia inducible factors (HIFs). The HIF1 complex, HIF1α and its dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT), is the master regulator of the hypoxic response. Previously, we demonstrated that Rb represses the transcriptional response to hypoxia by virtue of its association with HIF1. In this report, we further characterized the role of Rb in HIF1-regulated genetic programs by stably ablating Rb expression with retrovirally-introduced short hairpin RNA in LNCaP and 22rV1 human prostate cancer cells. DNA microarray analysis revealed that Rb regulates specific chromosomal gene clusters and loss of Rb in conjunction with hypoxia leads to dysregulation of HIF1-regulated genetic programs that promote cell invasion and neuroendocrine differentiation. Gene ontology analysis of the hypoxia-inducible genes sensitive to loss of Rb revealed that a significant portion of these genes are involved in neuroendocrine differentiation (NED), specifically ENO2, KISS1R and HTR5A. ENO2 is the bonafide marker of neuroendocrine differentiation and it's presence is a signature of late stage castrate resistant prostate cancer. Furthermore, we have functional evidence KISS1R is linked to intracellular calcium mobilization in 22RV1 cells. We have demonstrated that increased expression of HIF-regulated genes in response to loss of Rb activates Akt and ERK signaling pathways and promotes neuroendocrine differentiation and invasion. Inhibition of these signaling pathways significantly decreased actin polymerization in LNCaP cells. For the first time, we have established a direct link between hypoxic tumour environments, Rb inactivation and progression to late stage metastatic neuroendocrine prostate cancer. Understanding the molecular pathways responsible for progression of benign prostate tumours to metastasized and lethal forms will aid in the development of more effective prostate cancer therapies.
Citation Format: Mark Labrecque, Mandeep Takhar, Rebecca J. Nason, Stephanie Santacruz, Kevin Tam, Shabnam Massah, Anne Haegert, Robert Bell, Manuel Altamirano-Dimas, Colin Collins, Frank Lee, Gratien Prefontaine, Michael Cox, Timothy Beischlag. Loss of retinoblastoma protein dysregulates HIF1-mediated genetic programs, and promotes tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2922.
Collapse
Affiliation(s)
- Mark Labrecque
- 1Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mandeep Takhar
- 1Simon Fraser University, Burnaby, British Columbia, Canada
| | | | | | - Kevin Tam
- 3The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Shabnam Massah
- 1Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anne Haegert
- 3The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Robert Bell
- 3The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Colin Collins
- 3The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Frank Lee
- 1Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Michael Cox
- 3The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | |
Collapse
|
36
|
You S, Knudsen BS, Erho N, Alshalalfa M, Takhar M, Al-Deen Ashab H, Davicioni E, Karnes RJ, Klein EA, Den RB, Ross AE, Schaeffer EM, Garraway IP, Kim J, Freeman MR. Integrated Classification of Prostate Cancer Reveals a Novel Luminal Subtype with Poor Outcome. Cancer Res 2016; 76:4948-58. [PMID: 27302169 DOI: 10.1158/0008-5472.can-16-0902] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/25/2016] [Indexed: 01/03/2023]
Abstract
Prostate cancer is a biologically heterogeneous disease with variable molecular alterations underlying cancer initiation and progression. Despite recent advances in understanding prostate cancer heterogeneity, better methods for classification of prostate cancer are still needed to improve prognostic accuracy and therapeutic outcomes. In this study, we computationally assembled a large virtual cohort (n = 1,321) of human prostate cancer transcriptome profiles from 38 distinct cohorts and, using pathway activation signatures of known relevance to prostate cancer, developed a novel classification system consisting of three distinct subtypes (named PCS1-3). We validated this subtyping scheme in 10 independent patient cohorts and 19 laboratory models of prostate cancer, including cell lines and genetically engineered mouse models. Analysis of subtype-specific gene expression patterns in independent datasets derived from luminal and basal cell models provides evidence that PCS1 and PCS2 tumors reflect luminal subtypes, while PCS3 represents a basal subtype. We show that PCS1 tumors progress more rapidly to metastatic disease in comparison with PCS2 or PCS3, including PSC1 tumors of low Gleason grade. To apply this finding clinically, we developed a 37-gene panel that accurately assigns individual tumors to one of the three PCS subtypes. This panel was also applied to circulating tumor cells (CTC) and provided evidence that PCS1 CTCs may reflect enzalutamide resistance. In summary, PCS subtyping may improve accuracy in predicting the likelihood of clinical progression and permit treatment stratification at early and late disease stages. Cancer Res; 76(17); 4948-58. ©2016 AACR.
Collapse
Affiliation(s)
- Sungyong You
- Division of Cancer Biology and Therapeutics, Departments of Surgery & Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Beatrice S Knudsen
- Division of Cancer Biology and Therapeutics, Departments of Surgery & Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nicholas Erho
- GenomeDx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | - Mandeep Takhar
- GenomeDx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | - Elai Davicioni
- GenomeDx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | - Robert B Den
- Department of Radiation Oncology, Jefferson Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ashley E Ross
- Department of Urology, Northwestern University, Chicago, Illinois
| | | | - Isla P Garraway
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jayoung Kim
- Division of Cancer Biology and Therapeutics, Departments of Surgery & Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Michael R Freeman
- Division of Cancer Biology and Therapeutics, Departments of Surgery & Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California.
| |
Collapse
|
37
|
Karnes J, Ross A, Schaeffer EM, Klein EA, Erho N, Yousefi K, Takhar M, Davicioni E, Trock BJ. Validation of a genomic risk classifier to predict prostate cancer-specific mortality (PCSM) in high-risk patients. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.5056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Ashley Ross
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Eric A. Klein
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | | | | | | | | | | |
Collapse
|
38
|
Davicioni E, Erho N, Takhar M, Ashab HAD, Wood PJ, Alshalalfa M. The frequency of druggable targets in localized prostate cancer: Initial analysis from the Decipher GRID. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e16547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
39
|
Seiler R, Lam LL, Erho N, Takhar M, Mitra AP, Buerki C, Davicioni E, Skinner EC, Daneshmand S, Black PC. Prediction of Lymph Node Metastasis in Patients with Bladder Cancer Using Whole Transcriptome Gene Expression Signatures. J Urol 2016; 196:1036-41. [PMID: 27105761 DOI: 10.1016/j.juro.2016.04.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 10/21/2022]
Abstract
PURPOSE Clinical staging in patients with muscle invasive bladder cancer misses up to 25% of lymph node metastasis. These patients are at high risk for disease recurrence and improved clinical staging is critical to guide management. MATERIALS AND METHODS Whole transcriptome expression profiles were generated in 199 patients who underwent radical cystectomy and extended pelvic lymph node dissection. The cohort was divided randomly into a discovery set of 133 patients and a validation set of 66. In the discovery set features were identified and modeled in a KNN51 (K-nearest neighbor classifier 51) to predict pathological lymph node metastases. Two previously described bladder cancer gene signatures, including RF15 (15-gene cancer recurrence signature) and LN20 (20-gene lymph node signature), were also modeled in the discovery set for comparison. The AUC and the OR were used to compare the performance of these signatures. RESULTS In the validation set KNN51 achieved an AUC of 0.82 (range 0.71-0.93) to predict lymph node positive cases. It significantly outperformed RF15 and LN20, which had an AUC of 0.62 (range 0.47-0.76) and 0.46 (range 0.32-0.60), respectively. Only KNN51 showed significant odds of predicting LN metastasis with an OR of 2.65 (range 1.68-4.67) for every 10% increase in score (p <0.001). RF15 and LN20 had a nonsignificant OR of 1.21 (range 0.97-1.54) and 1.39 (range 0.52-3.77), respectively. CONCLUSIONS The new KNN51 signature was superior to previously described gene signatures for predicting lymph node metastasis. If validated prospectively in transurethral resection of bladder tumor samples, KNN51 could be used to guide patients at high risk to early multimodal therapy.
Collapse
Affiliation(s)
- Roland Seiler
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Lucia L Lam
- GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Nicholas Erho
- GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Mandeep Takhar
- GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Anirban P Mitra
- Institute of Urology and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Elai Davicioni
- GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Eila C Skinner
- Department of Urology and Stanford Cancer Institute, Stanford University, Stanford, California
| | - Siamak Daneshmand
- Institute of Urology and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
40
|
Davicioni E, Erho N, Lam L, Takhar M, Ashab HAD, Olson A, Dillon M, yousefi K, haddad Z, Wood P, alshalalfa M. MP07-10 THE FREQUENCY OF DRUGGABLE TARGETS IN LOCALIZED PROSTATE CANCER: INITIAL ANALYSIS FROM THE DECIPHER GRID. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.2213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
41
|
Karnes RJ, Ashab HAD, J. Trock B, E. Ross A, Tsai H, J. Tosoian J, Erho N, Alshalafa M, Choeurng V, Yousefi K, Takhar M, Haddad Z, Abdollah F, A. Klein E, L. Nguyen P, Y. Feng F, Dicker A, Benjamin Den R, Davicioni E, B. Jenkins R, L. Lotan T, M. Schaeffer E. MP07-20 DEVELOPMENT AND VALIDATION OF GENOMIC SIGNATURE THAT PREDICTS ADT TREATMENT FAILURE. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.2223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
42
|
Benzon B, Zhao G(S, Haffner M, Takhar M, Erho N, Yousefi K, Hurley P, Bishop J, Tosoian J, Ghabili K, Ghabili K, Alshalalfa M, Glavaris S, Simons B, Tran P, Davicioni E, Karnes RJ, Schaeffer E, Drake C, Feng F, Ross A. MP90-08 THE RELATIONSHIP OF B7H3 EXPRESSION TO ANDROGEN AND PROSTATE CANCER OUTCOMES IN A LARGE NATURAL HISTORY COHORT OF MEN UNDERGOING PROSTATECTOMY. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.2552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
43
|
You S, Knudsen B, Erho N, Alshalalfa M, Takhar M, Al-deen Ashab H, Davicioni E, Karnes RJ, Klein E, Den R, Ross A, Schaeffer E, Garraway I, Kim J, Freeman M. LB-S&T-10 THREE INTRINSIC SUBTYPES OF PROSTATE CANCER WITH DISTINCT PATHWAY ACTIVATION PROFILES DIFFER IN PROGNOSIS AND TREATMENT RESPONSE. J Urol 2016. [DOI: 10.1016/j.juro.2016.03.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
44
|
Karnes RJ, Ross A, Schaeffer E, Klein E, Erho N, Yousefi K, Takhar M, Davicioni E, Trock B. MP07-01 VALIDATION OF A GENOMIC RISK CLASSIFIER TO PREDICT PROSTATE CANCER DEATH IN HIGH RISK PATIENTS. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.2204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
45
|
Erho N, Alshalalfa M, Wood PJ, Takhar M, Ashab HAD, Davicioni E. The frequency of druggable targets in localized prostate cancer: Initial analysis from the Decipher GRID. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.2_suppl.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
98 Background: Prostate cancers patient management has been enhanced with commercially available genomic prognostic tests such as the Decipher prostate cancer classifier that are useful for making treatment decision-making. In addition to being the most validated predictor of metastasis in prostate cancer, Decipher is also a genome-wide assay that measures the expression of many druggable targets. Methods: Decipher GRID (Genomic Resource Information Database), was queried to assess the expression patterns of 14 genes from 5 biological pathways (Table) in 1,850 patients from previously published Decipher validation studies. The frequency of high (or low) expression of each gene was ascertained using a standard and more conservative thresholds based on the median absolute deviation (MAD) metric. For the standard threshold, genes whose high expression is of clinical relevance, patients with gene expression above the median + 1.48*MAD were annotated as high expression and for genes whose low expression is of clinical relevance, patients with gene expression below the median - 1.48*MAD were annotated as low expression. For the conservative threshold, median +/- 2*1.48*MAD was used. Results: See Table. Conclusions: Since every patient receiving the Decipher test also has a genome-wide expression profile, the Decipher GRID will allow researchers to evaluate on a systematic population-level the expression of genes that may be targeted with existing therapies. Such information may be useful for selection of optimal systemic therapy and inclusion into clinical trials of novel targeted agents. This rich genomic resource is being made available on a research use only basis to prostate cancer researchers and to clinicians seeking to uncover individualized genomic insights for patients to advance precision medicine. [Table: see text]
Collapse
|
46
|
Ross A, Benzon B, Zhao S, Takhar M, Haffner M, Erho N, Hurley P, Tosoian JJ, Alshalalfa M, Glavaris S, Simons B, Tran PT, Davicioni E, Karnes J, Schaeffer EM, Drake CG, Feng FYC. The relationship of B7H3 expression to androgen and prostate cancer outcomes in a large natural history cohort of men undergoing prostatectomy. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.2_suppl.256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
256 Background: B7-H3 (CD276), part of the B7 superfamily, has been shown to play an immunomodulatory role, however its regulation, receptor and mechanism of action remain unclear. Protein levels of B7-H3 have been previously shown to relate to prostate cancer outcomes and currently, humanized monoclonal antibodies are being developed for clinical use (MGA271, Macrogenics). Here we use genomic expression data to examine the relationship of B7-H3 to prostate cancer outcomes and molecular subtypes. Methods: Prostatectomy tissue from 905 patients were profiled using the Affymetrix HuEx 1.0 ST microarray. Kruskal-Wallis tests were used to identify significant associations of B7-H3 expression with clinico-pathologic variables, and survival analysis were used to evaluate the prognostic value of B7-H3. Pearson’s correlation analyses were also performed to assess the relationship of B7-H3 expression with molecular subtypes and individual transcripts. Androgen receptor (AR) occupancy of promoter regions was derived in silico from chromosomal immune-precipitation (ChIP) data. Results: B7-H3 expression was positively associated with Gleason score (p < 0.01) and tumor stage (p < 0.01). High B7-H3 expression also correlated with the development of metastasis and prostate cancer specific mortality (HR of 3.4 and 2.4 respectively, p < 0.05 for both), but this was not significant on multi-variable analysis. B7-H3 was positively associated with ERG+ disease (n = 670, r = 0.85, p < 0.05) and AR expression (n = 670, r = 0.46, p < 0.001). B7-H3 was found to be one of the most correlated genes with AR (95th percentile) and ChIP analysis revealed AR binding upstream of B7-H3, suggesting potential androgen dependent regulation. Conclusions: B7-H3 expression correlates with high Gleason grade and advanced prostate cancer stage with higher quartiles of expression portending poor oncologic outcomes in two independent prostatectomy cohorts. B7-H3 expression appears to relate to the androgen receptor.
Collapse
Affiliation(s)
- Ashley Ross
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Benjamin Benzon
- The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | | | - Paula Hurley
- The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | - Brian Simons
- The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Phuoc T. Tran
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | - Charles G. Drake
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | | |
Collapse
|
47
|
Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Magee MS, Den RB, Zhu Z, Graham NA, Vashisht AA, Wohlschlegel JA, Graeber TG, Karnes RJ, Takhar M, Davicioni E, Tomlins SA, Sharifi N, Witte ON, Feng FY, Knudsen KE. Abstract 1860: DNA-PK-mediated transcriptional regulation drives tumor progression and metastasis. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Emerging evidence demonstrates that the DNA repair kinase DNA-PK exerts divergent roles in transcriptional regulation of unsolved consequence. Here, in vitro and in vivo interrogation demonstrate that DNA-PK functions as a selective modulator of transcriptional networks that induce cell migration, invasion, and metastasis. Accordingly, suppression of DNA-PK inhibits tumor metastases. Clinical assessment revealed that DNA-PK is significantly elevated in advanced disease, and independently predicts for metastases, recurrence, and reduced overall survival. Further investigation demonstrated that DNA-PK in advanced tumors is highly activated, independently of DNA damage indicators. Combined, these findings put forth new paradigms for DNA-PK function, identify DNA-PK as a potent driver of tumor progression and metastases, and nominate DNA-PK as a therapeutic target for advanced malignancies.
Citation Format: Jonathan F. Goodwin, Vishal Kothari, Justin M. Drake, Shuang Zhao, Emanuela Dylgjeri, Jeffry L. Dean, Matthew J. Schiewer, Christopher McNair, Michael S. Magee, Robert B. Den, Ziqi Zhu, Nicholas A. Graham, Ajay A. Vashisht, James A. Wohlschlegel, Thomas G. Graeber, R Jeffrey Karnes, Mandeep Takhar, Elai Davicioni, Scott A. Tomlins, Nima Sharifi, Owen N. Witte, Felix Y. Feng, Karen E. Knudsen. DNA-PK-mediated transcriptional regulation drives tumor progression and metastasis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1860. doi:10.1158/1538-7445.AM2015-1860
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ziqi Zhu
- 4Cleveland Clinic, Cleveland, OH
| | | | | | | | | | | | - Mandeep Takhar
- 6GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Elai Davicioni
- 6GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | | | | | | | | | | |
Collapse
|
48
|
Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Jones JK, Aytes A, Magee MS, Snook AE, Zhu Z, Den RB, Birbe RC, Gomella LG, Graham NA, Vashisht AA, Wohlschlegel JA, Graeber TG, Karnes RJ, Takhar M, Davicioni E, Tomlins SA, Abate-Shen C, Sharifi N, Witte ON, Feng FY, Knudsen KE. DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis. Cancer Cell 2015; 28:97-113. [PMID: 26175416 PMCID: PMC4531387 DOI: 10.1016/j.ccell.2015.06.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/02/2015] [Accepted: 06/12/2015] [Indexed: 01/06/2023]
Abstract
Emerging evidence demonstrates that the DNA repair kinase DNA-PKcs exerts divergent roles in transcriptional regulation of unsolved consequence. Here, in vitro and in vivo interrogation demonstrate that DNA-PKcs functions as a selective modulator of transcriptional networks that induce cell migration, invasion, and metastasis. Accordingly, suppression of DNA-PKcs inhibits tumor metastases. Clinical assessment revealed that DNA-PKcs is significantly elevated in advanced disease and independently predicts for metastases, recurrence, and reduced overall survival. Further investigation demonstrated that DNA-PKcs in advanced tumors is highly activated, independent of DNA damage indicators. Combined, these findings reveal unexpected DNA-PKcs functions, identify DNA-PKcs as a potent driver of tumor progression and metastases, and nominate DNA-PKcs as a therapeutic target for advanced malignancies.
Collapse
Affiliation(s)
- Jonathan F Goodwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Vishal Kothari
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin M Drake
- Departments of Microbiology, Immunology, & Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Shuang Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jeffry L Dean
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Matthew J Schiewer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Christopher McNair
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jennifer K Jones
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Alvaro Aytes
- Departments of Urology, Pathology & Cell Biology, Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael S Magee
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Adam E Snook
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ziqi Zhu
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Robert B Den
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ruth C Birbe
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Leonard G Gomella
- Department of Urology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Nicholas A Graham
- Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA; Department of Molecular & Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, UCLA, Los Angeles, CA 90095, USA
| | | | - Thomas G Graeber
- Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA; Department of Molecular & Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | | | | | | | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cory Abate-Shen
- Departments of Urology, Pathology & Cell Biology, Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Nima Sharifi
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Urology, Cleveland Clinic, Cleveland, OH 44195, USA; Solid Tumor Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Owen N Witte
- Departments of Microbiology, Immunology, & Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Molecular & Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Urology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| |
Collapse
|
49
|
Cohen Freue GV, Meredith A, Smith D, Bergman A, Sasaki M, Lam KKY, Hollander Z, Opushneva N, Takhar M, Lin D, Wilson-McManus J, Balshaw R, Keown PA, Borchers CH, McManus B, Ng RT, McMaster WR. Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. PLoS Comput Biol 2013; 9:e1002963. [PMID: 23592955 PMCID: PMC3617196 DOI: 10.1371/journal.pcbi.1002963] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 01/16/2013] [Indexed: 11/19/2022] Open
Abstract
Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac rejection may offer a relevant post-transplant monitoring tool to effectively guide clinical care. The proposed computational pipeline is highly applicable to a wide range of biomarker proteomic studies.
Collapse
Affiliation(s)
- Gabriela V. Cohen Freue
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Meredith
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Derek Smith
- University of Victoria Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Axel Bergman
- Immunity and Infection Research Centre, Vancouver, British Columbia, Canada
| | - Mayu Sasaki
- Immunity and Infection Research Centre, Vancouver, British Columbia, Canada
| | - Karen K. Y. Lam
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zsuzsanna Hollander
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nina Opushneva
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Mandeep Takhar
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - David Lin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet Wilson-McManus
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul A. Keown
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Immunology Laboratory, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Christoph H. Borchers
- University of Victoria Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Bruce McManus
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre, Vancouver, British Columbia, Canada
| | - Raymond T. Ng
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - W. Robert McMaster
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Immunity and Infection Research Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | |
Collapse
|
50
|
Günther OP, Chen V, Freue GC, Balshaw RF, Tebbutt SJ, Hollander Z, Takhar M, McMaster WR, McManus BM, Keown PA, Ng RT. A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers. BMC Bioinformatics 2012; 13:326. [PMID: 23216969 PMCID: PMC3575305 DOI: 10.1186/1471-2105-13-326] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/04/2012] [Indexed: 02/08/2023] Open
Abstract
Background Biomarker panels derived separately from genomic and proteomic data and with a variety of computational methods have demonstrated promising classification performance in various diseases. An open question is how to create effective proteo-genomic panels. The framework of ensemble classifiers has been applied successfully in various analytical domains to combine classifiers so that the performance of the ensemble exceeds the performance of individual classifiers. Using blood-based diagnosis of acute renal allograft rejection as a case study, we address the following question in this paper: Can acute rejection classification performance be improved by combining individual genomic and proteomic classifiers in an ensemble? Results The first part of the paper presents a computational biomarker development pipeline for genomic and proteomic data. The pipeline begins with data acquisition (e.g., from bio-samples to microarray data), quality control, statistical analysis and mining of the data, and finally various forms of validation. The pipeline ensures that the various classifiers to be combined later in an ensemble are diverse and adequate for clinical use. Five mRNA genomic and five proteomic classifiers were developed independently using single time-point blood samples from 11 acute-rejection and 22 non-rejection renal transplant patients. The second part of the paper examines five ensembles ranging in size from two to 10 individual classifiers. Performance of ensembles is characterized by area under the curve (AUC), sensitivity, and specificity, as derived from the probability of acute rejection for individual classifiers in the ensemble in combination with one of two aggregation methods: (1) Average Probability or (2) Vote Threshold. One ensemble demonstrated superior performance and was able to improve sensitivity and AUC beyond the best values observed for any of the individual classifiers in the ensemble, while staying within the range of observed specificity. The Vote Threshold aggregation method achieved improved sensitivity for all 5 ensembles, but typically at the cost of decreased specificity. Conclusion Proteo-genomic biomarker ensemble classifiers show promise in the diagnosis of acute renal allograft rejection and can improve classification performance beyond that of individual genomic or proteomic classifiers alone. Validation of our results in an international multicenter study is currently underway.
Collapse
Affiliation(s)
- Oliver P Günther
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, V6Z 1Y6, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|