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Azzalini E, Bonin S. Molecular diagnostics of prostate cancer: impact of molecular tests. Asian J Androl 2024:00129336-990000000-00185. [PMID: 38738960 DOI: 10.4103/aja202411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/29/2024] [Indexed: 05/14/2024] Open
Abstract
ABSTRACT Prostate cancer (PCa) is the second leading cause of cancer-related death among men. Prostate-specific antigen (PSA) testing is used in screening programs for early detection with a consequent reduction of PCa-specific mortality at the cost of overdiagnosis and overtreatment of the nonaggressive PCa. Recently, several assays have been commercially developed to implement PCa diagnosis, but they have not been included in both screening and diagnosis of PCa. This review aims to describe the actual and novel commercially available molecular biomarkers that can be used in PCa management to implement and tailor the screening and diagnosis of PCa.
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Affiliation(s)
- Eros Azzalini
- DSM, Department of Medical Sciences, University of Trieste, Trieste 34149, Italy
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2
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Laajala TD, Sreekanth V, Soupir AC, Creed JH, Halkola AS, Calboli FCF, Singaravelu K, Orman MV, Colin-Leitzinger C, Gerke T, Fridley BL, Tyekucheva S, Costello JC. A harmonized resource of integrated prostate cancer clinical, -omic, and signature features. Sci Data 2023; 10:430. [PMID: 37407670 PMCID: PMC10322899 DOI: 10.1038/s41597-023-02335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical outcomes and to test hypotheses across multiple, independent patient cohorts. In addition, derived features, such as estimates of cell composition, risk scores, and androgen receptor (AR) scores, can be used to develop novel hypotheses leveraging existing multi-omic datasets. The full potential of such data is yet to be realized as independent datasets exist in different repositories, have been processed using different pipelines, and derived and clinical features are often not provided or not standardized. Here, we present the curatedPCaData R package, a harmonized data resource representing >2900 primary tumor, >200 normal tissue, and >500 metastatic PCa samples across 19 datasets processed using standardized pipelines with updated gene annotations. We show that meta-analysis across harmonized studies has great potential for robust and clinically meaningful insights. curatedPCaData is an open and accessible community resource with code made available for reproducibility.
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Affiliation(s)
- Teemu D Laajala
- Department of Mathematics and Statistics, University of Turku, Turku, Finland.
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alex C Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jordan H Creed
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Anni S Halkola
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Federico C F Calboli
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Natural Resources Institute Finland (Luke), F-31600, Jokioinen, Finland
| | | | - Michael V Orman
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Travis Gerke
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Svitlana Tyekucheva
- Department of Data Science, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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3
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Laajala TD, Sreekanth V, Soupir A, Creed J, Calboli FCF, Singaravelu K, Orman M, Colin-Leitzinger C, Gerke T, Fidley BL, Tyekucheva S, Costello JC. curatedPCaData: Integration of clinical, genomic, and signature features in a curated and harmonized prostate cancer data resource. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524403. [PMID: 36711769 PMCID: PMC9882125 DOI: 10.1101/2023.01.17.524403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical outcomes and to test hypotheses across multiple, independent patient cohorts. In addition, derived features, such as estimates of cell composition, risk scores, and androgen receptor (AR) scores, can be used to develop novel hypotheses leveraging existing multi-omic datasets. The full potential of such data is yet to be realized as independent datasets exist in different repositories, have been processed using different pipelines, and derived and clinical features are often not provided or unstandardized. Here, we present the curatedPCaData R package, a harmonized data resource representing >2900 primary tumor, >200 normal tissue, and >500 metastatic PCa samples across 19 datasets processed using standardized pipelines with updated gene annotations. We show that meta-analysis across harmonized studies has great potential for robust and clinically meaningful insights. curatedPCaData is an open and accessible community resource with code made available for reproducibility.
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Affiliation(s)
- Teemu D Laajala
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alex Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jordan Creed
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Federico CF Calboli
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Natural Resources Institute Finland (Luke), F-31600, Jokioinen, Finland
| | | | - Michael Orman
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Travis Gerke
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L. Fidley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Svitlana Tyekucheva
- Department of Data Science, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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4
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Spohn SKB, Draulans C, Kishan AU, Spratt D, Ross A, Maurer T, Tilki D, Berlin A, Blanchard P, Collins S, Bronsert P, Chen R, Pra AD, de Meerleer G, Eade T, Haustermans K, Hölscher T, Höcht S, Ghadjar P, Davicioni E, Heck M, Kerkmeijer LGW, Kirste S, Tselis N, Tran PT, Pinkawa M, Pommier P, Deltas C, Schmidt-Hegemann NS, Wiegel T, Zilli T, Tree AC, Qiu X, Murthy V, Epstein JI, Graztke C, Gao X, Grosu AL, Kamran SC, Zamboglou C. Genomic Classifiers in Personalized Prostate Cancer Radiation Therapy Approaches: A Systematic Review and Future Perspectives Based on International Consensus. Int J Radiat Oncol Biol Phys 2022:S0360-3016(22)03691-4. [PMID: 36596346 DOI: 10.1016/j.ijrobp.2022.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/09/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023]
Abstract
Current risk-stratification systems for prostate cancer (PCa) do not sufficiently reflect the disease heterogeneity. Genomic classifiers (GC) enable improved risk stratification after surgery, but less data exist for patients treated with definitive radiation therapy (RT) or RT in oligo-/metastatic disease stages. To guide future perspectives of GCs for RT, we conducted (1) a systematic review on the evidence of GCs for patients treated with RT and (2) a survey of experts using the Delphi method, addressing the role of GCs in personalized treatments to identify relevant fields of future clinical and translational research. We performed a systematic review and screened ongoing clinical trials on ClinicalTrials.gov. Based on these results, a multidisciplinary international team of experts received an adapted Delphi method survey. Thirty-one and 30 experts answered round 1 and round 2, respectively. Questions with ≥75% agreement were considered relevant and included in the qualitative synthesis. Evidence for GCs as predictive biomarkers is mainly available to the postoperative RT setting. Validation of GCs as prognostic markers in the definitive RT setting is emerging. Experts used GCs in patients with PCa with extensive metastases (30%), in postoperative settings (27%), and in newly diagnosed PCa (23%). Forty-seven percent of experts do not currently use GCs in clinical practice. Expert consensus demonstrates that GCs are promising tools to improve risk-stratification in primary and oligo-/metastatic patients in addition to existing classifications. Experts were convinced that GCs might guide treatment decisions in terms of RT-field definition and intensification/deintensification in various disease stages. This work confirms the value of GCs and the promising evidence of GC utility in the setting of RT. Additional studies of GCs as prognostic biomarkers are anticipated and form the basis for future studies addressing predictive capabilities of GCs to optimize RT and systemic therapy. The expert consensus points out future directions for GC research in the management of PCa.
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Affiliation(s)
- Simon K B Spohn
- Department of Radiation Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Cédric Draulans
- Department of Radiation Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU Leuven, Belgium
| | - Amar U Kishan
- Departments of Radiation Oncology and Urology, University of California, Los Angeles, California
| | - Daniel Spratt
- Department of Radiation Oncology, UH Seidman Cancer Center, Case Western Reserve University
| | - Ashley Ross
- Department of Urology, Northwestern Feinberg School of Medicine, Chicago, Illinois
| | - Tobias Maurer
- Martini-Klinik Prostate Cancer Center, Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Derya Tilki
- Martini-Klinik Prostate Cancer Center, Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany; Department of Urology, Koc University Hospital, Istanbul, Turkey
| | - Alejandro Berlin
- Department of Radiation Oncology, Temerty Faculty of Medicine, University of Toronto, and Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network. Toronto, Canada
| | - Pierre Blanchard
- Department of Radiation Oncology, Gustave Roussy, Oncostat U1018, Inserm, Paris-Saclay University, Villejuif, France
| | - Sean Collins
- Department of Radiation Medicine, Medstar Georgetown University Hospital, Washington, DC
| | - Peter Bronsert
- Institute for Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ronald Chen
- Department of Radiation Oncology, University of Kansas Cancer Center, Kansas City, Kansas
| | - Alan Dal Pra
- Department of Radiation Oncology, University of Miami, Miller School of Medicine
| | - Gert de Meerleer
- Department of Radiation Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU Leuven, Belgium
| | - Thomas Eade
- Northern Sydney Cancer Centre, Radiation Oncology Unit, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Karin Haustermans
- Department of Radiation Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU Leuven, Belgium
| | - Tobias Hölscher
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stefan Höcht
- Xcare Practices Dept. Radiotherapy, Saarlouis, Germany
| | - Pirus Ghadjar
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin
| | | | - Matthias Heck
- Department of Urology, Rechts der Isar Medical Center, Technical University of Munich, Germany
| | - Linda G W Kerkmeijer
- Department of Radiation Oncology, Radboud University Medical Center, The Netherlands
| | - Simon Kirste
- Department of Radiation Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Nikolaos Tselis
- Department of Radiation Oncology, University Hospital Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland
| | - Michael Pinkawa
- Department of Radiation Oncology, MediClin Robert Janker Klinik Bonn, Germany
| | - Pascal Pommier
- Department of Radiation Oncology, Centre Léon Bérard, Lyon, France
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Thomas Wiegel
- Department of Radiation Oncology, University Hospital Ulm, Ulm, Germany
| | - Thomas Zilli
- Department of Radiation Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Alison C Tree
- Department of Radiotherapy, Royal Marsden Hospital and the Institute of Cancer Research, London, United Kingdom
| | - Xuefeng Qiu
- Department of Urology, Medical School of Nanjing University, Affiliated Drum Tower Hospital, Nanjing, China
| | - Vedang Murthy
- Department of Radiation Oncology, ACTREC, Tata Memorial Centre, Homi Bhabha National University, India
| | - Jonathan I Epstein
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christian Graztke
- Department of Urology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xin Gao
- Department of Internal Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Anca L Grosu
- Department of Radiation Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Constantinos Zamboglou
- Department of Radiation Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Oncology Center, European University of Cyprus, Limassol, Cyprus
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Fernandez N, Chavarriaga J, Ayala P, Pedraza A, Bolivar J, Prada JG, Cataño JG, García-Perdomo HA, Villanueva J, Varela D, Zarante I. MicroRNAs as Potential Liquid Biopsy Biomarker for Patients with Castration-Resistant Prostate Cancer. Res Rep Urol 2022; 14:63-70. [PMID: 35257006 PMCID: PMC8898099 DOI: 10.2147/rru.s332578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Patients and Methods Results Conclusion
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Affiliation(s)
- Nicolas Fernandez
- Division of Urology Seattle Children’s Hospital, University of Washington, Seattle, WA, USA
- Correspondence: Nicolas Fernandez, Division of Urology, Seattle Children’s Hospital, University of Washington, 5801 Sand Point Way NE, Seattle, WA, 98105, USA, Tel +1 206 351 2618, Email
| | | | - Paola Ayala
- Human Genetics Institute, Pontificia Universidad Javeriana, Bogota, Colombia
| | | | - John Bolivar
- Division of Urology, Department of Surgery, Hospital Universitario San Ignacio, Bogota, Colombia
| | - Juan Guillermo Prada
- Division of Urology, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Juan Guillermo Cataño
- Division of Urology, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogota, Colombia
| | | | - Juliana Villanueva
- Division of Urology, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Daniela Varela
- Division of Urology, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Ignacio Zarante
- Human Genetics Institute, Pontificia Universidad Javeriana, Bogota, Colombia
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Thiemeyer H, Taher L, Schille JT, Packeiser EM, Harder LK, Hewicker-Trautwein M, Brenig B, Schütz E, Beck J, Nolte I, Murua Escobar H. An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes. Int J Mol Sci 2021; 22:11481. [PMID: 34768937 PMCID: PMC8584104 DOI: 10.3390/ijms222111481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 01/01/2023] Open
Abstract
Prostate cancer (PCa) in dogs is a highly malignant disease akin to its human counterpart. In contrast to the situation in humans, multi-gene approaches facilitating risk stratification of canine PCa are barely established. The aims of this study were the characterization of the transcriptional landscape of canine PCa and the identification of diagnostic, prognostic and/or therapeutic biomarkers through a multi-step screening approach. RNA-Sequencing of ten malignant tissues and fine-needle aspirations (FNA), and 14 nonmalignant tissues and FNAs was performed to find differentially expressed genes (DEGs) and deregulated pathways. The 4098 observed DEGs were involved in 49 pathways. These 49 pathways could be grouped into five superpathways summarizing the hallmarks of canine PCa: (i) inflammatory response and cytokines; (ii) regulation of the immune system and cell death; (iii) cell surface and PI3K signaling; (iv) cell cycle; and (v) phagosome and autophagy. Among the highly deregulated, moderately to strongly expressed DEGs that were members of one or more superpathways, 169 DEGs were listed in relevant databases and/or the literature and included members of the PCa pathway, oncogenes, prostate-specific genes, and druggable genes. These genes are novel and promising candidate diagnostic, prognostic and/or therapeutic canine PCa biomarkers.
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Affiliation(s)
- Heike Thiemeyer
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (H.T.); (J.T.S.); (E.-M.P.); (L.K.H.); (I.N.)
- Department of Hematology/Oncology/Palliative Care, Rostock University Medical Centre, 18057 Rostock, Germany
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, 8010 Graz, Austria;
| | - Jan Torben Schille
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (H.T.); (J.T.S.); (E.-M.P.); (L.K.H.); (I.N.)
- Department of Hematology/Oncology/Palliative Care, Rostock University Medical Centre, 18057 Rostock, Germany
| | - Eva-Maria Packeiser
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (H.T.); (J.T.S.); (E.-M.P.); (L.K.H.); (I.N.)
- Department of Hematology/Oncology/Palliative Care, Rostock University Medical Centre, 18057 Rostock, Germany
| | - Lisa K. Harder
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (H.T.); (J.T.S.); (E.-M.P.); (L.K.H.); (I.N.)
| | - Marion Hewicker-Trautwein
- Institute of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany;
| | - Ekkehard Schütz
- Chronix Biomedical GmbH, 37079 Göttingen, Germany; (E.S.); (J.B.)
| | - Julia Beck
- Chronix Biomedical GmbH, 37079 Göttingen, Germany; (E.S.); (J.B.)
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (H.T.); (J.T.S.); (E.-M.P.); (L.K.H.); (I.N.)
| | - Hugo Murua Escobar
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (H.T.); (J.T.S.); (E.-M.P.); (L.K.H.); (I.N.)
- Department of Hematology/Oncology/Palliative Care, Rostock University Medical Centre, 18057 Rostock, Germany
- Comprehensive Cancer Center Mecklenburg-Vorpommern (CCC-MV), Campus Rostock, University of Rostock, 18057 Rostock, Germany
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7
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Cangiano M, Grudniewska M, Salji MJ, Nykter M, Jenster G, Urbanucci A, Granchi Z, Janssen B, Hamilton G, Leung HY, Beumer IJ. Gene Regulation Network Analysis on Human Prostate Orthografts Highlights a Potential Role for the JMJD6 Regulon in Clinical Prostate Cancer. Cancers (Basel) 2021; 13:cancers13092094. [PMID: 33925994 PMCID: PMC8123677 DOI: 10.3390/cancers13092094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Prostate cancer is a very common malignancy worldwide. Treatment resistant prostate cancer poses a big challenge to clinicians and is the second most common cause of premature death in men with cancer. Gene expression analysis has been performed on clinical tumours but to date none of the gene expression-based biomarkers for prostate cancer have been successfully integrated to into clinical practice to improve patient management and treatment choice. We applied a novel laboratory prostate cancer model to mimic clinical hormone responsive and resistant prostate cancer and tested whether a network of genes similarly regulated by transcription factors (gene products that control the expression of target genes) are associated with patient outcome. We identified regulons (networks of genes similarly regulated) from our preclinical prostate cancer models and further evaluated the top ranked JMJD6 gene related regulated network in three independent clinical patient cohorts. Abstract Background: Prostate cancer (PCa) is the second most common tumour diagnosed in men. Tumoral heterogeneity in PCa creates a significant challenge to develop robust prognostic markers and novel targets for therapy. An analysis of gene regulatory networks (GRNs) in PCa may provide insight into progressive PCa. Herein, we exploited a graph-based enrichment score to integrate data from GRNs identified in preclinical prostate orthografts and differentially expressed genes in clinical resected PCa. We identified active regulons (transcriptional regulators and their targeted genes) associated with PCa recurrence following radical prostatectomy. Methods: The expression of known transcription factors and co-factors was analysed in a panel of prostate orthografts (n = 18). We searched for genes (as part of individual GRNs) predicted to be regulated by the highest number of transcriptional factors. Using differentially expressed gene analysis (on a per sample basis) coupled with gene graph enrichment analysis, we identified candidate genes and associated GRNs in PCa within the UTA cohort, with the most enriched regulon being JMJD6, which was further validated in two additional cohorts, namely EMC and ICGC cohorts. Cox regression analysis was performed to evaluate the association of the JMJD6 regulon activity with disease-free survival time in the three clinical cohorts as well as compared to three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). Results: 1308 regulons were correlated to transcriptomic data from the three clinical prostatectomy cohorts. The JMJD6 regulon was identified as the top enriched regulon in the UTA cohort and again validated in the EMC cohort as the top-ranking regulon. In both UTA and EMC cohorts, the JMJD6 regulon was significantly associated with cancer recurrence. Active JMJD6 regulon also correlated with disease recurrence in the ICGC cohort. Furthermore, Kaplan–Meier analysis confirmed shorter time to recurrence in patients with active JMJD6 regulon for all three clinical cohorts (UTA, EMC and ICGC), which was not the case for three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). In multivariate analysis, the JMJD6 regulon status significantly predicted disease recurrence in the UTA and EMC, but not ICGC datasets, while none of the three published signatures significantly prognosticate for cancer recurrence. Conclusions: We have characterised gene regulatory networks from preclinical prostate orthografts and applied transcriptomic data from three clinical cohorts to evaluate the prognostic potential of the JMJD6 regulon.
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Affiliation(s)
- Mario Cangiano
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Magda Grudniewska
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Mark J. Salji
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK;
- CRUK Beatson Institute, Glasgow G61 1BD, UK
| | - Matti Nykter
- Laboratory of Computational Biology, Institute of Biomedical Technology, Arvo Ylpön katu 34, 33520 Tampere, Finland;
| | - Guido Jenster
- Department of Urology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands;
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway;
| | - Zoraide Granchi
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Bart Janssen
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, UK;
| | - Hing Y. Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK;
- CRUK Beatson Institute, Glasgow G61 1BD, UK
- Correspondence: (H.Y.L.); (I.J.B.)
| | - Inès J. Beumer
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
- Correspondence: (H.Y.L.); (I.J.B.)
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8
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Pudova EA, Krasnov GS, Nyushko KM, Kobelyatskaya AA, Savvateeva MV, Poloznikov AA, Dolotkazin DR, Klimina KM, Guvatova ZG, Simanovsky SA, Gladysh NS, Tokarev AT, Melnikova NV, Dmitriev AA, Alekseev BY, Kaprin AD, Kiseleva MV, Snezhkina AV, Kudryavtseva AV. miRNAs expression signature potentially associated with lymphatic dissemination in locally advanced prostate cancer. BMC Med Genomics 2020; 13:129. [PMID: 32948204 PMCID: PMC7500008 DOI: 10.1186/s12920-020-00788-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background Prostate cancer is one of the most common and socially significant cancers among men. The aim of our study was to reveal changes in miRNA expression profiles associated with lymphatic dissemination in prostate cancer and to identify the most prominent miRNAs as potential prognostic markers for future studies. Methods High-throughput miRNA sequencing was performed for 44 prostate cancer specimens taken from Russian patients, with and without lymphatic dissemination (N1 – 20 samples; N0 – 24 samples). Results We found at least 18 microRNAs with differential expression between N0 and N1 sample groups: miR-182-5p, miR-183-5p, miR-96-5p, miR-25-3p, miR-93-5p, miR-7-5p, miR-615-3p, miR-10b, miR-1248 (N1-miRs; elevated expression in N1 cohort; p < 0.05); miR-1271-5p, miR-184, miR-222-3p, miR-221-5p, miR-221-3p, miR-455-3p, miR-143-5p, miR-181c-3p and miR-455-5p (N0-miRs; elevated expression in N0; p < 0.05). The expression levels of N1-miRs were highly correlated between each other (the same is applied for N0-miRs) and the expression levels of N0-miRs and N1-miRs were anti-correlated. The tumor samples can be divided into two groups depending on the expression ratio between N0-miRs and N1-miRs. Conclusions We found the miRNA expression signature associated with lymphatic dissemination, in particular on the Russian patient cohort. Many of these miRNAs are well-known players in either oncogenic transformation or tumor suppression. Further experimental studies with extended sampling are required to validate these results.
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Affiliation(s)
- Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kirill M Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Maria V Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Daniyar R Dolotkazin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Kseniya M Klimina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Simanovsky
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Boris Y Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Marina V Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Greenland NY, Cowan JE, Zhang L, Carroll PR, Chan E, Stohr BA, Simko JP. Expansile cribriform Gleason pattern 4 has histopathologic and molecular features of aggressiveness and greater risk of biochemical failure compared to glomerulation Gleason pattern 4. Prostate 2020; 80:653-659. [PMID: 32220141 DOI: 10.1002/pros.23977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND Molecular testing of prostate cancer biopsies with Gleason pattern 4 suggests the expansile cribriform pattern is more aggressive than the glomerulation pattern. These two extreme patterns have not been compared at prostatectomy. We hypothesized that at prostatectomy the expansile cribriform pattern would be associated with histopathologic and molecular features of aggressiveness and with greater risk of biochemical recurrence (BCR) than the glomerulation pattern. METHODS In a retrospective cohort study, radical prostatectomy reports with expansile cribriform pattern or glomerulation pattern were analyzed for percentage of total pattern 4, extraprostatic extension (EPE), positive lymph nodes, seminal vesicle invasion (SVI), and intraductal carcinoma (IDC). Cases with pattern 5 or with both expansile cribriform and glomerulations patterns present were excluded. The electronic medical record was reviewed for BCR-free survival and for Decipher test results. RESULTS Of 1020 radical prostatectomies from July 2015 to July 2018, 110 (11%) had either expansile cribriform or glomerulation pattern present. The expansile cribriform group was associated with more histopathologic features of aggressiveness, with higher average total percentage pattern 4 (43.7 vs 27.0, P = .002), a trend of greater extensive EPE (32.7% vs 17.2%, P = .06), a trend toward statistical significance of higher rate of SVI (11.5% vs 3.4%, P = .1), greater positive lymph nodes (9.6% vs 0%, P = .02), and a higher percentage of cases with or suspicious for IDC (23.1% vs 8.6%, P = .04). The risk of BCR was 4.4 (1.3-15.4) fold greater for the expansile cribriform group vs the glomerulations group (P = .02). For the 38 patients who underwent Decipher testing, the expansile cribriform group had a high-risk assay category mean score whereas the glomerulations group had an average risk assay category mean score (0.61 vs 0.47, P = .02). CONCLUSIONS In a comparison of prostatectomy cases with expansile cribriform pattern to those with glomerulation pattern, the expansile cribriform pattern was associated with more histopathologic features of aggressiveness, greater risk of biochemical failure, and higher scores with a molecular classifier (Decipher) test. These findings underscore the importance of reporting the types of pattern 4 and supports the argument that men with expansile cribriform likely require more aggressive management.
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Affiliation(s)
- Nancy Y Greenland
- Department of Anatomic Pathology, University of California, San Francisco, California
- Department of Pathology, Veterans Affairs Health Care System, San Francisco, California
| | - Janet E Cowan
- Department of Urology, University of California, San Francisco, California
| | - Li Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
- UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, California
| | - Peter R Carroll
- Department of Urology, University of California, San Francisco, California
| | - Emily Chan
- Department of Anatomic Pathology, University of California, San Francisco, California
| | - Bradley A Stohr
- Department of Anatomic Pathology, University of California, San Francisco, California
| | - Jeffry P Simko
- Department of Anatomic Pathology, University of California, San Francisco, California
- Department of Urology, University of California, San Francisco, California
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10
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Markers of clinical utility in the differential diagnosis and prognosis of prostate cancer. Mod Pathol 2018; 31:S143-155. [PMID: 29297492 DOI: 10.1038/modpathol.2017.168] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022]
Abstract
Molecular diagnostics is a rapidly evolving area of surgical pathology, that is gradually beginning to transform our diagnostical procedures for a variety of tumors. Next to molecular prognostication that has begun to complement our histological diagnosis in breast cancer, additional testing to detect targets and to predict therapy response has become common practice in breast and lung cancer. Prostate cancer is a bit slower in this respect, as it is still largely diagnosed and classified on morphological grounds. Our diagnostic immunohistochemical armamentarium of basal cell markers and positive markers of malignancy now allows to clarify the majority of lesions, if applied to the appropriate morphological context (and step sections). Prognostic immunohistochemistry remains a problematic and erratic yet tempting research field that provides information on tumor relevance of proteins, but little hard data to integrate into our diagnostic workflow. Main reasons are various issues of standardization that hamper the reproducibility of cut-off values to delineate risk categories. Molecular testing of DNA-methylation or transcript profiling may be much better standardized and this review discusses a couple of commercially available tests: The ConfirmDX test measures DNA-methylation to estimate the likelihood of cancer detection on a repeat biopsy and may help to reduce unnecessary biopsies. The tests Prolaris, OncotypeDX Prostate, and Decipher all are transcript tests that have shown to provide prognostic data independent of clinico-pathological parameters and that may aid in therapy planning. However, further validation and more comparative studies will be needed to clarify the many open questions concerning sampling bias and tumor heterogeneity.
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11
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Egevad L, Delahunt B, Kristiansen G, Samaratunga H, Varma M. Contemporary prognostic indicators for prostate cancer incorporating International Society of Urological Pathology recommendations. Pathology 2018; 50:60-73. [DOI: 10.1016/j.pathol.2017.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 09/28/2017] [Indexed: 12/21/2022]
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12
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Vijayakumar S, Henegan JC, Zhang X, Wang W, Day WA, Vijayakumar V, Moreno CS, Gomez CR. Enriching gene expression profiles will help personalize prostate cancer management for African-Americans: A perspective. Urol Oncol 2017; 35:315-321. [DOI: 10.1016/j.urolonc.2017.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/20/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022]
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13
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Abstract
Unprecedented progress has been made in genomic personalized medicine in the last several years, allowing for more individualized healthcare assessments and recommendations than ever before. However, most of this progress in prostate cancer (PCa) care has focused on developing and selecting therapies for late-stage disease. To address this issue of limited focus, we propose a model for incorporating genomic-based personalized medicine into all levels of PCa care, from prevention and screening to diagnosis, and ultimately to the treatment of both early-stage and late-stage cancers. We have termed this strategy the "Pyramid Model" of personalized cancer care. In this perspective paper, our objective is to demonstrate the potential application of the Pyramid Model to PCa care. This proactive and comprehensive personalized cancer care approach has the potential to achieve three important medical goals: reducing mortality, improving quality of life and decreasing both individual and societal healthcare costs.
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Affiliation(s)
- Carly A Conran
- Program for Personalized Cancer Care, NorthShore University HealthSystem, 1001 University Place, Evanston, IL 60201, USA
| | - Charles B Brendler
- Program for Personalized Cancer Care, NorthShore University HealthSystem, 1001 University Place, Evanston, IL 60201, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, 1001 University Place, Evanston, IL 60201, USA
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14
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Liu W, Xu J. Translation of genomics and epigenomics in prostate cancer: progress and promising directions. Asian J Androl 2016; 18:503-4. [PMID: 27270344 PMCID: PMC4955169 DOI: 10.4103/1008-682x.182820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
During the last several years, exciting discoveries have been made in prostate cancer (PCa) as a result of significant advances in genomic technology and information. For example, using genome-wide association studies, more than 100 inherited genetic variants associated with PCa risk have been identified. Similarly, with the use of next-generation sequencing, various types of recurrent somatic DNA alterations in prostate tumors have been revealed. Some of these discoveries have potential clinical application to supplement existing tools for better decision-making regarding the need for screening, biopsy, and treatment of PCa. However, because of the complexity of these genomic findings and incomplete understanding of the genetics of this multifactorial disease, this potential has not yet been fully realized.
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Affiliation(s)
- Wennuan Liu
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL 60201, USA
| | - Jianfeng Xu
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL 60201, USA
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