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Monteiro AVO, Dos Santos NNDC, da Silva JPR, Brasileiro SA, Botelho JC, Sobreira LER, Leal ALAB, Pereira AL, de Oliveira ACA, Monteiro JRS, da Silva FRP. Genetic variations related to the prostate cancer risk: A field synopsis and revaluation by Bayesian approaches of genome-wide association studies. Urol Oncol 2025; 43:270.e19-270.e28. [PMID: 39603876 DOI: 10.1016/j.urolonc.2024.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 10/14/2024] [Accepted: 10/17/2024] [Indexed: 11/29/2024]
Abstract
Prostate cancer (PCa) is a complex disease influenced by many factors, with the genetic contribution for this neoplasia having a great role in its risk. The literature brings an increased number of Genome-Wide Association Studies (GWAS's) that attempt to elucidate the genetic associations with PCa. However, these genome studies have a considerable rate of false-positive data whose results may be biased. Therefore, we aimed to apply Bayesian approaches on significant associations among polymorphisms and PCa from GWAS's data. A literature search was performed for data published before April 20, 2024, whereby two investigators used a specific combination of keywords and Boolean operators in the search ("prostate carcinoma or prostate cancer or PCa" and "polymorphism or genetic variation" and "Genome-Wide Association Study or GWAS"). The records were retrieved, and the data were extracted with further application of two different Bayesian approaches: The False Positive Report Probability (FPRP) and the Bayesian False-Discovery Probability (BFDP), both at the prior probabilities of 10-3 and 10-6. The data were considered as noteworthy at the level of FPRP <0.2 and BFDP <0.8. Besides, in-silico analyses by gene-gene network and gene enrichment were performed to evaluate the role of the noteworthy genes in PCa. As results, 13 GWAS's were included, with 2,520 values for FPRP and 1,368 values for BFDP being obtained. Our study showed an extensive number of gene variations as noteworthy candidate biomarkers for PCa risk, with highlighting for those occurred in the 8q24 locus and in the MSMB, ITGA6, SUN2, FGF10, INCENP, MLPH, and KLK3 genes.
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Affiliation(s)
- André Victor Oliveira Monteiro
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - Naum Neves da Costa Dos Santos
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | | | - Samuel Arcebispo Brasileiro
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - Juliana Campos Botelho
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | | | - Alessandro Luiz Araújo Bentes Leal
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - Adenilson Leão Pereira
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - Ana Carolina Alves de Oliveira
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - José Rogério Souza Monteiro
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - Felipe Rodolfo Pereira da Silva
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil; Laboratory of Genetics and Medicine-Based Evidence, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil.
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2
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Srinivasan S, Kryza T, Bock N, Tse BWC, Sokolowski KA, Janaththani P, Fernando A, Moya L, Stephens C, Dong Y, Röhl J, Alinezhad S, Vela I, Perry-Keene JL, Buzacott K, Nica R, Gago-Dominguez M, Schleutker J, Maier C, Muir K, Tangen CM, Gronberg H, Pashayan N, Albanes D, Wolk A, Stanford JL, Berndt SI, Mucci LA, Koutros S, Cussenot O, Sorensen KD, Grindedal EM, Travis RC, Haiman CA, MacInnis RJ, Vega A, Wiklund F, Neal DE, Kogevinas M, Penney KL, Nordestgaard BG, Brenner H, John EM, Gamulin M, Claessens F, Melander O, Dahlin A, Stattin P, Hallmans G, Häggström C, Johansson R, Thysell E, Rönn AC, Li W, Brown N, Dimeski G, Shepherd B, Dadaev T, Brook MN, Spurdle AB, Stenman UH, Koistinen H, Kote-Jarai Z, Klein RJ, Lilja H, Ecker RC, Eeles R, Clements J, Batra J. A PSA SNP associates with cellular function and clinical outcome in men with prostate cancer. Nat Commun 2024; 15:9587. [PMID: 39505858 PMCID: PMC11541583 DOI: 10.1038/s41467-024-52472-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/05/2024] [Indexed: 11/08/2024] Open
Abstract
Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility in men. The non-synonymous KLK3 single nucleotide polymorphism (SNP), rs17632542 (c.536 T > C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity mediates prostate cancer pathogenesis. The 'Thr' PSA variant leads to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displays higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterisation of this PSA variant demonstrates markedly reduced proteolytic activity that correlates with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele have reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.
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Affiliation(s)
- Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
- Centre for Genomic and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thomas Kryza
- Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Nathalie Bock
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
| | - Brian W C Tse
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Kamil A Sokolowski
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Panchadsaram Janaththani
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Achala Fernando
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
- Centre for Genomic and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Leire Moya
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
| | - Carson Stephens
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
| | - Ying Dong
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
| | - Joan Röhl
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Faculty of Health Sciences and Medicine, Bond University, 14 University Drive, Robina, QLD, 4226, Australia
| | - Saeid Alinezhad
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
| | - Ian Vela
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Department of Urology, Princess Alexandra Hospital, Brisbane, Woolloongabba, Brisbane, QLD, Australia
| | - Joanna L Perry-Keene
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - Katie Buzacott
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | | | - Manuela Gago-Dominguez
- Health Research Institute of Santiago de Compostela (IDIS), Galicia Public Foundation IDIS, SERGAS, Cancer Genetics and Epidemiology Group, Genomic Medicine Group, Santiago de Compostela, Spain
| | - Johanna Schleutker
- Institute of Biomedicine, Kiinamyllynkatu 10, FI-20014 University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521, Turku, Finland
| | - Christiane Maier
- Humangenetik Tuebingen, Paul-Ehrlich-Str 23, D-72076, Tuebingen, Germany
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, M13 9PL, UK
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, 177 77, Stockholm, Sweden
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Olivier Cussenot
- CeRePP, Tenon Hospital, F-75020, Paris, France
- Sorbonne Universite, GRC n°5, AP-HP, Tenon Hospital, 4 rue de la Chine, F-75020, Paris, France
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensen Boulevard 99, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, DK-8200, Aarhus N., Denmark
| | - Eli Marie Grindedal
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, 15706, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, 15706, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- University of Cambridge, Department of Oncology, Box 279, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02115, USA
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Marija Gamulin
- School of Medicine, University of Zagreb, Salata 3, 10 000, Zagreb, Croatia
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, BE-3000, Belgium
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Anders Dahlin
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Pär Stattin
- Institute of Environmental Medicine, Karolinska Institutet, 177 77, Stockholm, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, Umeå, Sweden
| | | | | | - Elin Thysell
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Ann-Charlotte Rönn
- Translational Analysis in Molecular Medicine, Karolinska University Hospital, Huddinge, Sweden
| | - Weiqiang Li
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nigel Brown
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Goce Dimeski
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Benjamin Shepherd
- Department of Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Mark N Brook
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry and Haematology, University of Helsinki, Helsinki, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry and Haematology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Robert J Klein
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans Lilja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery (Urology Service) and Medicine (Genitourinary Oncology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Rupert C Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
- TissueGnostics GmbH, Vienna, Austria
| | - Rosalind Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland (QLD), Australia.
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, QLD, Australia.
- Centre for Genomic and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia.
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3
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Koistinen H, Kovanen RM, Hollenberg MD, Dufour A, Radisky ES, Stenman UH, Batra J, Clements J, Hooper JD, Diamandis E, Schilling O, Rannikko A, Mirtti T. The roles of proteases in prostate cancer. IUBMB Life 2023; 75:493-513. [PMID: 36598826 PMCID: PMC10159896 DOI: 10.1002/iub.2700] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 01/05/2023]
Abstract
Since the proposition of the pro-invasive activity of proteolytic enzymes over 70 years ago, several roles for proteases in cancer progression have been established. About half of the 473 active human proteases are expressed in the prostate and many of the most well-characterized members of this enzyme family are regulated by androgens, hormones essential for development of prostate cancer. Most notably, several kallikrein-related peptidases, including KLK3 (prostate-specific antigen, PSA), the most well-known prostate cancer marker, and type II transmembrane serine proteases, such as TMPRSS2 and matriptase, have been extensively studied and found to promote prostate cancer progression. Recent findings also suggest a critical role for proteases in the development of advanced and aggressive castration-resistant prostate cancer (CRPC). Perhaps the most intriguing evidence for this role comes from studies showing that the protease-activated transmembrane proteins, Notch and CDCP1, are associated with the development of CRPC. Here, we review the roles of proteases in prostate cancer, with a special focus on their regulation by androgens.
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Affiliation(s)
- Hannu Koistinen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
| | - Ruusu-Maaria Kovanen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland
| | - Morley D Hollenberg
- Department of Physiology & Pharmacology and Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology and Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, U.S.A
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - John D. Hooper
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Eleftherios Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland
- Department of Urology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Mirtti
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland
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4
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Srinivasan S, Kryza T, Bock N, Tse BWC, Sokolowski KA, Panchadsaram J, Moya L, Stephens C, Dong Y, Röhl J, Alinezhad S, Vela I, Perry-Keene JL, Buzacott K, The IMPACT Study, Gago-Dominguez M, The PROFILE Study Steering Committee, Schleutker J, Maier C, Muir K, Tangen CM, Gronberg H, Pashayan N, Albanes D, Wolk A, Stanford JL, Berndt SI, Mucci LA, Koutros S, Cussenot O, Sorensen KD, Grindedal EM, Key TJ, Haiman CA, Giles GG, Vega A, Wiklund F, Neal DE, Kogevinas M, Stampfer MJ, Nordestgaard BG, Brenner H, Gamulin M, Claessens F, Melander O, Dahlin A, Stattin P, Hallmans G, Häggström C, Johansson R, Thysell E, Rönn AC, Li W, Brown N, Dimeski G, Shepherd B, Dadaev T, Brook MN, Spurdle AB, Stenman UH, Koistinen H, Kote-Jarai Z, Klein RJ, Lilja H, Ecker RC, Eeles R, The Practical Consortium, The Australian Prostate Cancer BioResource, Clements J, Batra J. Biochemical activity induced by a germline variation in KLK3 (PSA) associates with cellular function and clinical outcome in prostate cancer. RESEARCH SQUARE 2023:rs.3.rs-2650312. [PMID: 37034758 PMCID: PMC10081352 DOI: 10.21203/rs.3.rs-2650312/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility. The non-synonymous KLK3 SNP, rs17632542 (c.536T>C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity as a previously undescribed function mediating prostate cancer pathogenesis. The 'Thr' PSA variant led to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displayed higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterization of this PSA variant demonstrated markedly reduced proteolytic activity that correlated with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele had reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.
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Affiliation(s)
- Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Thomas Kryza
- Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Nathalie Bock
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Brian WC Tse
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Kamil A. Sokolowski
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Janaththani Panchadsaram
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Leire Moya
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Carson Stephens
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Ying Dong
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
| | - Joan Röhl
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
| | - Saeid Alinezhad
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Ian Vela
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Department of Urology, Princess Alexandra Hospital, Brisbane, Woolloongabba, Brisbane, QLD, Australia
| | - Joanna L. Perry-Keene
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - Katie Buzacott
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - The IMPACT Study
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, IDIS, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - The PROFILE Study Steering Committee
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
- Ronald and Rita McAulay Foundation, London, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- University of Oxford, Oxford, UK
- Queen Mary University of London, London, UK
| | - Johanna Schleutker
- Institute of Biomedicine, Kiinamyllynkatu 10, FI-20014 University of Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521 Turku, Finland
| | - Christiane Maier
- Humangenetik Tuebingen, Paul-Ehrlich-Str 23, D-72076 Tuebingen, Germany
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Catherine M. Tangen
- SWOG Statistical Center, Division of Public Health Sciences
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Lorelei A. Mucci
- Department of Epidemiology,Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Olivier Cussenot
- CeRePP and Sorbonne Universite, GRC N°5 AP-HP, Tenon Hospital, Paris, France
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University & Department of Molecular Medicine (MOMA), Aarhus University Hospital, DK-8200 Aarhus N., Denmark
| | | | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, USA
| | - Graham G. Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
- Biomedical Network on Rare Diseases (CIBERER), Santiago de Compostela, Spain
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, England
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Meir J. Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Børge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Anders Dahlin
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Pär Stattin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, Umeå, Sweden
| | - Christel Häggström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | | | - Elin Thysell
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Ann-Charlotte Rönn
- Clinical Research Center, Karolinska University Hospital, Huddinge, Sweden
| | - Weiqiang Li
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nigel Brown
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Goce Dimeski
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Benjamin Shepherd
- Department of Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Mark N. Brook
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Robert J. Klein
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans Lilja
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- Departments of Laboratory Medicine, Surgery (Urology Service) and Medicine (Genitourinary Oncology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
- TissueGnostics GmbH, Vienna, Austria
| | - Rosalind Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | - The Australian Prostate Cancer BioResource
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
- Centre for Genomic and Personalised Health, Queensland University of Technology, Brisbane, QLD
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Raina P, Guinea R, Chatsirisupachai K, Lopes I, Farooq Z, Guinea C, Solyom CA, de Magalhães JP. GeneFriends: gene co-expression databases and tools for humans and model organisms. Nucleic Acids Res 2022; 51:D145-D158. [PMID: 36454018 PMCID: PMC9825523 DOI: 10.1093/nar/gkac1031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022] Open
Abstract
Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring the relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have now updated the GeneFriends database and website. Here, we present the new version of GeneFriends, which includes gene and transcript co-expression networks based on RNA-seq data from 46 475 human and 34 322 mouse samples. The new database also encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on TCGA and GTEx projects and gene co-expression networks for additional seven model organisms (fruit fly, zebrafish, worm, rat, yeast, cow and chicken). GeneFriends is freely available at http://www.genefriends.org/.
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Affiliation(s)
- Priyanka Raina
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Rodrigo Guinea
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Zoya Farooq
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Cristina Guinea
- UCAL - Universidad de Ciencias y Artes de América Latina, Faculty of Design, Lima 15026, Perú
| | - Csaba-Attila Solyom
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
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6
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Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study. Cancers (Basel) 2022; 14:cancers14082001. [PMID: 35454907 PMCID: PMC9031064 DOI: 10.3390/cancers14082001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is one of the most common cancers. Due to the limited and invasive approaches for PCa diagnosis, it is crucial to identify more accurate and non-invasive biomarkers for its detection. The aim of our study was to non-invasively uncover new protein targets for detecting PCa using a proteomics and proteogenomics approach. This work identified several dysregulated mutant protein isoforms in urine from PCa patients, some of them predicted to have a protective or an adverse role in these patients. These results are promising given urine’s non-invasive nature and offers an auspicious opportunity for research and development of PCa biomarkers. Abstract To identify new protein targets for PCa detection, first, a shotgun discovery experiment was performed to characterize the urinary proteome of PCa patients. This revealed 18 differentially abundant urinary proteins in PCa patients. Second, selected targets were clinically tested by immunoblot, and the soluble E-cadherin fragment was detected for the first time in the urine of PCa patients. Third, the proteogenome landscape of these PCa patients was characterized, revealing 1665 mutant protein isoforms. Statistical analysis revealed 6 differentially abundant mutant protein isoforms in PCa patients. Analysis of the likely effects of mutations on protein function and PPIs involving the dysregulated mutant protein isoforms suggests a protective role of mutations HSPG2*Q1062H and VASN*R161Q and an adverse role of AMBP*A286G and CD55*S162L in PCa patients. This work originally characterized the urinary proteome, focusing on the proteogenome profile of PCa patients, which is usually overlooked in the analysis of PCa and body fluids. Combined analysis of mass spectrometry data using two different software packages was performed for the first time in the context of PCa, which increased the robustness of the data analysis. The application of proteogenomics to urine proteomic analysis can be very enriching in mutation-related diseases such as cancer.
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KLK3 germline mutation I179T complements DNA repair genes for predicting prostate cancer progression. Prostate Cancer Prostatic Dis 2022; 25:749-754. [PMID: 35149774 DOI: 10.1038/s41391-021-00466-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Germline mutations in DNA repair genes and KLK3 have been associated with adverse prostate cancer (PCa) outcomes in separate studies but never jointly. The objective of this study is to simultaneously assess these two types of germline mutations. METHODS Germline rare pathogenic mutations (RPMs) in 9 commonly tested DNA repair genes and KLK3 variants were tested for their associations with PCa progression in two PCa cohorts: (1) hospital-based PCa patients treated with radical surgery at the Johns Hopkins Hospital (JHH, N = 1943), and (2) population-based PCa patients in the UK Biobank (UKB, N = 10,224). Progression was defined as metastasis and/or PCa-specific death (JHH) and PCa-specific death (UKB). RPMs of DNA repair genes were annotated using the American College of Medical Genetics recommendations. Known KLK3 variants were genotyped. Associations were tested using a logistic regression model adjusting for genetic background (top ten principal components). RESULTS In the JHH, 3.2% (59/1,843) of patients had RPMs in 9 DNA repair genes; odds ratio (OR, 95% confidence interval) for progression was 2.99 (1.6-5.34), P < 0.001. In comparison, KLK3 I179T mutation was more common; 9.7% (189/1,943) carried the mutation, OR = 1.6 (1.05-2.37), P = 0.02. Similar results were found in the UKB. Both types of mutations remained statistically significant in multivariable analyses. In the combined cohort, compared to patients without any mutations (RPMs-/KLK3-), RPMs-/KLK3+ patients had modestly increased risk for progression [OR = 1.54 (1.15-2.02), P = 0.003], and RPMs+/KLK3+ patients had greatly increased risk for progression [OR = 5.41 (2.04-12.99), P < 0.001]. Importantly, associations of mutations with PCa progression were found in patients with clinically defined low- or intermediate risk for disease progression. CONCLUSIONS Two different cohorts consistently demonstrate that KLK3 I179T and RPMs of nine commonly tested DNA repair genes are complementary for predicting PCa progression. These results are highly relevant to PCa germline testing and provide critical information for KLK3 I179T to be considered in guidelines.
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8
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Tian P, Zhong M, Wei GH. Mechanistic insights into genetic susceptibility to prostate cancer. Cancer Lett 2021; 522:155-163. [PMID: 34560228 DOI: 10.1016/j.canlet.2021.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is the second most common cancer in men and is a highly heritable disease that affects millions of individuals worldwide. Genome-wide association studies have to date discovered nearly 270 genetic loci harboring hundreds of single nucleotide polymorphisms (SNPs) that are associated with PCa susceptibility. In contrast, the functional characterization of the mechanisms underlying PCa risk association is still growing. Given that PCa risk-associated SNPs are highly enriched in noncoding cis-regulatory genomic regions, accumulating evidence suggests a widespread modulation of transcription factor chromatin binding and allelic enhancer activity by these noncoding SNPs, thereby dysregulating gene expression. Emerging studies have shown that a proportion of noncoding variants can modulate the formation of transcription factor complexes at enhancers and CTCF-mediated 3D genome architecture. Interestingly, DNA methylation-regulated CTCF binding could orchestrate a long-range chromatin interaction between PCa risk enhancer and causative genes. Additionally, one-causal-variant-two-risk genes or multiple-risk-variant-multiple-genes are prevalent in some PCa risk-associated loci. In this review, we will discuss the current understanding of the general principles of SNP-mediated gene regulation, experimental advances, and functional evidence supporting the mechanistic roles of several PCa genetic loci with potential clinical impact on disease prevention and treatment.
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Affiliation(s)
- Pan Tian
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Mengjie Zhong
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Gong-Hong Wei
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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Huang D, Ruan X, Wu Y, Lin X, Huang J, Ye D, Gao Y, Ding Q, Xu D, Na R. Genetic polymorphisms at 19q13.33 are associated with [-2]proPSA (p2PSA) levels and provide additional predictive value to prostate health index for prostate cancer. Prostate 2021; 81:971-982. [PMID: 34254325 PMCID: PMC8456816 DOI: 10.1002/pros.24192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/29/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Prostate health index (phi), a derivative of [-2]proPSA (p2PSA), has shown better accuracy than prostate-specific antigen (PSA) in prostate cancer (PCa) detection. The present study was to investigate whether previously identified PSA-associated single nucleotide polymorphisms (SNPs) influence p2PSA or phi levels and lead to potential clinical utility. METHODS We conducted an observational prospective study with 2268 consecutive patients who underwent prostate biopsy in three tertiary medical centers from August 2013 to March 2019. Genotyping data of the 46 candidate genes with a ± 100 kb window were tested for association with p2PSA and phi levels using linear regression. Multivariable logistic regression models were performed and internally validated using repeated tenfold cross-validation. We further calculated personalized phi cutoff values based on the significant genotypes. Discriminative performance was assessed using decision curve analysis and net reclassification improvement (NRI) index. RESULTS We detected 11 significant variants at 19q13.33 which were p2PSA-associated independent of PCa. The most significant SNP, rs198978 in KLK2 (Pcombined = 5.73 × 10-9 ), was also associated with phi values (Pcombined = 3.20 × 10-6 ). Compared to the two commonly used phi cutoffs of 27.0 and 36.0, the personalized phi cutoffs had a significant NRI for PCa ranged from 5.23% to 9.70% among men carrying variant types (all p < .01). CONCLUSION Rs198978, is independently associated with p2PSA values, and can improve the diagnostic ability of phi for PCa using personalized cutoff values.
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Affiliation(s)
- Da Huang
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaohao Ruan
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yishuo Wu
- Department of Urology, Huashan HospitalFudan UniversityShanghaiChina
| | - Xiaoling Lin
- Department of Urology, Huashan HospitalFudan UniversityShanghaiChina
| | - Jingyi Huang
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Dingwei Ye
- Department of Urology, Shanghai Cancer CenterFudan UniversityShanghaiChina
| | - Yi Gao
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Qiang Ding
- Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Danfeng Xu
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Rong Na
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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Saunders EJ, Kote-Jarai Z, Eeles RA. Identification of Germline Genetic Variants that Increase Prostate Cancer Risk and Influence Development of Aggressive Disease. Cancers (Basel) 2021; 13:760. [PMID: 33673083 PMCID: PMC7917798 DOI: 10.3390/cancers13040760] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PrCa) is a heterogeneous disease, which presents in individual patients across a diverse phenotypic spectrum ranging from indolent to fatal forms. No robust biomarkers are currently available to enable routine screening for PrCa or to distinguish clinically significant forms, therefore late stage identification of advanced disease and overdiagnosis plus overtreatment of insignificant disease both remain areas of concern in healthcare provision. PrCa has a substantial heritable component, and technological advances since the completion of the Human Genome Project have facilitated improved identification of inherited genetic factors influencing susceptibility to development of the disease within families and populations. These genetic markers hold promise to enable improved understanding of the biological mechanisms underpinning PrCa development, facilitate genetically informed PrCa screening programmes and guide appropriate treatment provision. However, insight remains largely lacking regarding many aspects of their manifestation; especially in relation to genes associated with aggressive phenotypes, risk factors in non-European populations and appropriate approaches to enable accurate stratification of higher and lower risk individuals. This review discusses the methodology used in the elucidation of genetic loci, genes and individual causal variants responsible for modulating PrCa susceptibility; the current state of understanding of the allelic spectrum contributing to PrCa risk; and prospective future translational applications of these discoveries in the developing eras of genomics and personalised medicine.
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Affiliation(s)
- Edward J. Saunders
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
- Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
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11
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Pan CW, Wen S, Chen L, Wei Y, Niu Y, Zhao Y. Functional roles of antisense enhancer RNA for promoting prostate cancer progression. Am J Cancer Res 2021; 11:1780-1794. [PMID: 33408781 PMCID: PMC7778597 DOI: 10.7150/thno.51931] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Rationale: Enhancer RNA (eRNA) bi-directionally expresses from enhancer region and sense eRNA regulates adjacent mRNA in cis and in trans. However, it has remained unclear whether antisense eRNAs in different direction are functional or merely a reflection of enhancer activation. Methods: Strand-specific, ribosome-minus RNA sequencing (RNA-seq) were performed in AR positive prostate cancer cells. RNA-seq, GRO-seq, ChIP-seq, 4C-seq and DNA-methylation-seq that published in our and other labs were re-analyzed to define bi-directional enhancer RNA and DNA methylation regions. Molecular mechanisms were demonstrated by 3C, ChIP, ChIRP, CLIP, RT-PCR and western blot assays. The biological functions of antisense-eRNA were assessed using mice xenograft model and RT-PCR analysis in human tissues. Results: In this study, we identified that antisense eRNA was regulated by androgen receptor (AR) activity in prostate cancer cells. Antisense eRNA negatively regulated antisense ncRNA in AR-related target genes' loci, through recruiting DNMT1 on the antisense enhancer in the gene-ending regions and elevating DNA methylation. Importantly, the chromatin exhibited a double looping manner that facilitated sense-eRNA to promoter and antisense-eRNA to gene-ending region in cis. Depletion of antisense eRNA impaired its neighbor mRNA expression, cancer growth and invasion. The expressions of antisense eRNA were correlated with biochemical recurrence and clinical marker PSA's levels in patients' tissues. Conclusions: The findings indicated that antisense eRNA was a functional RNA and may be a novel target that when suppressed improved prostate cancer therapy and diagnosis. New chromatin interaction among enhancer, promoter and gene-ending region might provide new insight into the spatiotemporal mechanism of the gene transcription and acting of bi-directional eRNAs.
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12
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Liss MA, Leach RJ, Sanda MG, Semmes OJ. Prostate Cancer Biomarker Development: National Cancer Institute's Early Detection Research Network Prostate Cancer Collaborative Group Review. Cancer Epidemiol Biomarkers Prev 2020; 29:2454-2462. [PMID: 33093161 PMCID: PMC7710596 DOI: 10.1158/1055-9965.epi-20-1104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Prostate cancer remains the most common non-skin cancer and second leading cause of death among men in the United States. Although progress has been made in diagnosis and risk assessment, many clinical questions remain regarding early identification of prostate cancer and management. The early detection of aggressive disease continues to provide high curative rates if diagnosed in a localized state. Unfortunately, prostate cancer displays significant heterogeneity within the prostate organ and between individual patients making detection and treatment strategies complex. Although prostate cancer is common among men, the majority will not die from prostate cancer, introducing the issue of overtreatment as a major concern in clinical management of the disease. The focus of the future is to identify those at highest risk for aggressive prostate cancer and to develop prevention and screening strategies, as well as discerning the difference in malignant potential of diagnosed tumors. The Prostate Cancer Research Group of the National Cancer Institute's Early Detection Research Network has contributed to the progress in addressing these concerns. This summary is an overview of the activities of the group.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Michael A Liss
- Department of Urology, University of Texas Health San Antonio, San Antonio, Texas
| | - Robin J Leach
- Department of Urology, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Martin G Sanda
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia
| | - Oliver J Semmes
- The Leroy T. Canoles Jr. Cancer Research Center, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia.
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13
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Otto JJ, Correll VL, Engstroem HA, Hitefield NL, Main BP, Albracht B, Johnson‐Pais T, Yang LF, Liss M, Boutros PC, Kislinger T, Leach RJ, Semmes OJ, Nyalwidhe JO. Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype Determination. Proteomics Clin Appl 2020; 14:e2000012. [PMID: 32614141 PMCID: PMC7674190 DOI: 10.1002/prca.202000012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 06/08/2020] [Indexed: 01/03/2023]
Abstract
PURPOSE The rs17632542 single nucleotide polymorphism (SNP) results in lower serum prostate specific antigen (PSA) levels which may further mitigate against its clinical utility as a prostate cancer biomarker. Post-digital rectal exam (post-DRE) urine is a minimally invasive fluid that is currently utilized in prostate cancer diagnosis. To detect and quantitate the variant protein in urine. EXPERIMENTAL DESIGN Fifty-three post-DRE urines from rs17632542 genotyped individuals processed and analyzed by liquid chromatography/mass spectrometry (LC-MS) in a double-blinded randomized study. The ability to distinguish between homozygous wild-type, heterozygous, or homozygous variant is examined before unblinding. RESULTS Stable-isotope labeled peptides are used in the detection and quantitation of three peptides of interest in each sample using parallel reaction monitoring (PRM). Using these data, groupings are predicted using hierarchical clustering in R. Accuracy of the predictions show 100% concordance across the 53 samples, including individuals homozygous and heterozygous for the SNP. CONCLUSIONS AND CLINICAL RELEVANCE The study demonstrates that MS based peptide variant quantitation in urine could be useful in determining patient genotype expression. This assay provides a tool to evaluate the utility of PSA variant (rs17632542) in parallel with current and forthcoming urine biomarker panels.
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Affiliation(s)
- Joseph J. Otto
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Vanessa L. Correll
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Hampus A. Engstroem
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Naomi L. Hitefield
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Brian P. Main
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Brenna Albracht
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
| | - Teresa Johnson‐Pais
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
| | - Li Fang Yang
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Michael Liss
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
- Mays Cancer Center at UT Health San Antonio/MD AndersonSan AntonioTX78229USA
| | - Paul C. Boutros
- Departments of Human Genetics and UrologyJonsson Comprehensive Cancer CenterInstitute for Precision Health University of California Los AngelesLos AngelesCA90095USA
- University of TorontoDepartment of Medical BiophysicsTorontoON M5G 1L7Canada
| | - Thomas Kislinger
- University of TorontoDepartment of Medical BiophysicsTorontoON M5G 1L7Canada
| | - Robin J. Leach
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
- Department of Cell Systems and AnatomyThe University of Texas Health San AntonioSan AntonioTX78229USA
| | - Oliver J. Semmes
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Julius O. Nyalwidhe
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
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14
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Identification of key genes and pathways in castrate-resistant prostate cancer by integrated bioinformatics analysis. Pathol Res Pract 2020; 216:153109. [DOI: 10.1016/j.prp.2020.153109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
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15
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Rashkin SR, Graff RE, Kachuri L, Thai KK, Alexeeff SE, Blatchins MA, Cavazos TB, Corley DA, Emami NC, Hoffman JD, Jorgenson E, Kushi LH, Meyers TJ, Van Den Eeden SK, Ziv E, Habel LA, Hoffmann TJ, Sakoda LC, Witte JS. Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts. Nat Commun 2020; 11:4423. [PMID: 32887889 PMCID: PMC7473862 DOI: 10.1038/s41467-020-18246-6] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Deciphering the shared genetic basis of distinct cancers has the potential to elucidate carcinogenic mechanisms and inform broadly applicable risk assessment efforts. Here, we undertake genome-wide association studies (GWAS) and comprehensive evaluations of heritability and pleiotropy across 18 cancer types in two large, population-based cohorts: the UK Biobank (408,786 European ancestry individuals; 48,961 cancer cases) and the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging cohorts (66,526 European ancestry individuals; 16,001 cancer cases). The GWAS detect 21 genome-wide significant associations independent of previously reported results. Investigations of pleiotropy identify 12 cancer pairs exhibiting either positive or negative genetic correlations; 25 pleiotropic loci; and 100 independent pleiotropic variants, many of which are regulatory elements and/or influence cross-tissue gene expression. Our findings demonstrate widespread pleiotropy and offer further insight into the complex genetic architecture of cross-cancer susceptibility.
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Affiliation(s)
- Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta A Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Taylor B Cavazos
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California, San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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16
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Hamdy FC, Donovan JL, Lane JA, Mason M, Metcalfe C, Holding P, Wade J, Noble S, Garfield K, Young G, Davis M, Peters TJ, Turner EL, Martin RM, Oxley J, Robinson M, Staffurth J, Walsh E, Blazeby J, Bryant R, Bollina P, Catto J, Doble A, Doherty A, Gillatt D, Gnanapragasam V, Hughes O, Kockelbergh R, Kynaston H, Paul A, Paez E, Powell P, Prescott S, Rosario D, Rowe E, Neal D. Active monitoring, radical prostatectomy and radical radiotherapy in PSA-detected clinically localised prostate cancer: the ProtecT three-arm RCT. Health Technol Assess 2020; 24:1-176. [PMID: 32773013 PMCID: PMC7443739 DOI: 10.3310/hta24370] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Prostate cancer is the most common cancer among men in the UK. Prostate-specific antigen testing followed by biopsy leads to overdetection, overtreatment as well as undertreatment of the disease. Evidence of treatment effectiveness has lacked because of the paucity of randomised controlled trials comparing conventional treatments. OBJECTIVES To evaluate the effectiveness of conventional treatments for localised prostate cancer (active monitoring, radical prostatectomy and radical radiotherapy) in men aged 50-69 years. DESIGN A prospective, multicentre prostate-specific antigen testing programme followed by a randomised trial of treatment, with a comprehensive cohort follow-up. SETTING Prostate-specific antigen testing in primary care and treatment in nine urology departments in the UK. PARTICIPANTS Between 2001 and 2009, 228,966 men aged 50-69 years received an invitation to attend an appointment for information about the Prostate testing for cancer and Treatment (ProtecT) study and a prostate-specific antigen test; 82,429 men were tested, 2664 were diagnosed with localised prostate cancer, 1643 agreed to randomisation to active monitoring (n = 545), radical prostatectomy (n = 553) or radical radiotherapy (n = 545) and 997 chose a treatment. INTERVENTIONS The interventions were active monitoring, radical prostatectomy and radical radiotherapy. TRIAL PRIMARY OUTCOME MEASURE Definite or probable disease-specific mortality at the 10-year median follow-up in randomised participants. SECONDARY OUTCOME MEASURES Overall mortality, metastases, disease progression, treatment complications, resource utilisation and patient-reported outcomes. RESULTS There were no statistically significant differences between the groups for 17 prostate cancer-specific (p = 0.48) and 169 all-cause (p = 0.87) deaths. Eight men died of prostate cancer in the active monitoring group (1.5 per 1000 person-years, 95% confidence interval 0.7 to 3.0); five died of prostate cancer in the radical prostatectomy group (0.9 per 1000 person-years, 95% confidence interval 0.4 to 2.2 per 1000 person years) and four died of prostate cancer in the radical radiotherapy group (0.7 per 1000 person-years, 95% confidence interval 0.3 to 2.0 per 1000 person years). More men developed metastases in the active monitoring group than in the radical prostatectomy and radical radiotherapy groups: active monitoring, n = 33 (6.3 per 1000 person-years, 95% confidence interval 4.5 to 8.8); radical prostatectomy, n = 13 (2.4 per 1000 person-years, 95% confidence interval 1.4 to 4.2 per 1000 person years); and radical radiotherapy, n = 16 (3.0 per 1000 person-years, 95% confidence interval 1.9 to 4.9 per 1000 person-years; p = 0.004). There were higher rates of disease progression in the active monitoring group than in the radical prostatectomy and radical radiotherapy groups: active monitoring (n = 112; 22.9 per 1000 person-years, 95% confidence interval 19.0 to 27.5 per 1000 person years); radical prostatectomy (n = 46; 8.9 per 1000 person-years, 95% confidence interval 6.7 to 11.9 per 1000 person-years); and radical radiotherapy (n = 46; 9.0 per 1000 person-years, 95% confidence interval 6.7 to 12.0 per 1000 person years; p < 0.001). Radical prostatectomy had the greatest impact on sexual function/urinary continence and remained worse than radical radiotherapy and active monitoring. Radical radiotherapy's impact on sexual function was greatest at 6 months, but recovered somewhat in the majority of participants. Sexual and urinary function gradually declined in the active monitoring group. Bowel function was worse with radical radiotherapy at 6 months, but it recovered with the exception of bloody stools. Urinary voiding and nocturia worsened in the radical radiotherapy group at 6 months but recovered. Condition-specific quality-of-life effects mirrored functional changes. No differences in anxiety/depression or generic or cancer-related quality of life were found. At the National Institute for Health and Care Excellence threshold of £20,000 per quality-adjusted life-year, the probabilities that each arm was the most cost-effective option were 58% (radical radiotherapy), 32% (active monitoring) and 10% (radical prostatectomy). LIMITATIONS A single prostate-specific antigen test and transrectal ultrasound biopsies were used. There were very few non-white men in the trial. The majority of men had low- and intermediate-risk disease. Longer follow-up is needed. CONCLUSIONS At a median follow-up point of 10 years, prostate cancer-specific mortality was low, irrespective of the assigned treatment. Radical prostatectomy and radical radiotherapy reduced disease progression and metastases, but with side effects. Further work is needed to follow up participants at a median of 15 years. TRIAL REGISTRATION Current Controlled Trials ISRCTN20141297. FUNDING This project was funded by the National Institute for Health Research Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 37. See the National Institute for Health Research Journals Library website for further project information.
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Affiliation(s)
- Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - J Athene Lane
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Malcolm Mason
- School of Medicine, University of Cardiff, Cardiff, UK
| | - Chris Metcalfe
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Peter Holding
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Julia Wade
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Sian Noble
- Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Grace Young
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Davis
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Tim J Peters
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Emma L Turner
- Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Jon Oxley
- Department of Cellular Pathology, North Bristol NHS Trust, Bristol, UK
| | - Mary Robinson
- Department of Cellular Pathology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - John Staffurth
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Eleanor Walsh
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Jane Blazeby
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Prasad Bollina
- Department of Urology and Surgery, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - James Catto
- Academic Urology Unit, University of Sheffield, Sheffield, UK
| | - Andrew Doble
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Alan Doherty
- Department of Urology, Queen Elizabeth Hospital, Birmingham, UK
| | - David Gillatt
- Department of Urology, Southmead Hospital and Bristol Urological Institute, Bristol, UK
| | | | - Owen Hughes
- Department of Urology, Cardiff and Vale University Health Board, Cardiff, UK
| | - Roger Kockelbergh
- Department of Urology, University Hospitals of Leicester, Leicester, UK
| | - Howard Kynaston
- Department of Urology, Cardiff and Vale University Health Board, Cardiff, UK
| | - Alan Paul
- Department of Urology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Edgar Paez
- Department of Urology, Freeman Hospital, Newcastle upon Tyne, UK
| | - Philip Powell
- Department of Urology, Freeman Hospital, Newcastle upon Tyne, UK
| | - Stephen Prescott
- Department of Urology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Derek Rosario
- Academic Urology Unit, University of Sheffield, Sheffield, UK
| | - Edward Rowe
- Department of Urology, Southmead Hospital and Bristol Urological Institute, Bristol, UK
| | - David Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Academic Urology Group, University of Cambridge, Cambridge, UK
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17
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Saberian N, Shafi A, Peyvandipour A, Draghici S. MAGPEL: an autoMated pipeline for inferring vAriant-driven Gene PanEls from the full-length biomedical literature. Sci Rep 2020; 10:12365. [PMID: 32703994 PMCID: PMC7378213 DOI: 10.1038/s41598-020-68649-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 06/17/2020] [Indexed: 11/09/2022] Open
Abstract
In spite of the efforts in developing and maintaining accurate variant databases, a large number of disease-associated variants are still hidden in the biomedical literature. Curation of the biomedical literature in an effort to extract this information is a challenging task due to: (i) the complexity of natural language processing, (ii) inconsistent use of standard recommendations for variant description, and (iii) the lack of clarity and consistency in describing the variant-genotype-phenotype associations in the biomedical literature. In this article, we employ text mining and word cloud analysis techniques to address these challenges. The proposed framework extracts the variant-gene-disease associations from the full-length biomedical literature and designs an evidence-based variant-driven gene panel for a given condition. We validate the identified genes by showing their diagnostic abilities to predict the patients' clinical outcome on several independent validation cohorts. As representative examples, we present our results for acute myeloid leukemia (AML), breast cancer and prostate cancer. We compare these panels with other variant-driven gene panels obtained from Clinvar, Mastermind and others from literature, as well as with a panel identified with a classical differentially expressed genes (DEGs) approach. The results show that the panels obtained by the proposed framework yield better results than the other gene panels currently available in the literature.
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Affiliation(s)
- Nafiseh Saberian
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Adib Shafi
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Azam Peyvandipour
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
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18
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Tong Y, Tang Y, Li S, Zhao F, Ying J, Qu Y, Niu X, Mu D. Cumulative evidence of relationships between multiple variants in 8q24 region and cancer incidence. Medicine (Baltimore) 2020; 99:e20716. [PMID: 32590746 PMCID: PMC7328976 DOI: 10.1097/md.0000000000020716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple independent cancer susceptibility loci at chromosome 8q24. We aimed to evaluate the associations between variants in the 8q24 region and cancer susceptibility. A comprehensive research synopsis and meta-analysis was performed to evaluate associations between 28 variants in 8q24 and risk of 7 cancers using data from 103 eligible articles totaling 146,932 cancer cases and 219,724 controls. Results: 20 variants were significantly associated with risk of prostate cancer, colorectal cancer, thyroid cancer, breast cancer, bladder cancer, stomach cancer, and glioma, including 1 variant associated with prostate cancer, colorectal cancer, and thyroid cancer. Cumulative epidemiological evidence of an association was graded as strong for DG8S737 -8 allele, rs10090154, rs7000448 in prostate cancer, rs10808556 in colorectal cancer, rs55705857 in gliomas, rs9642880 in bladder cancer, moderate for rs16901979, rs1447295, rs6983267, rs7017300, rs7837688, rs1016343, rs620861, rs10086908 associated in prostate cancer, rs10505477, rs6983267 in colorectal cancer, rs6983267 in thyroid cancer, rs13281615 in breast cancer, and rs1447295 in stomach cancer, weak for rs6983561, rs13254738, rs7008482, rs4242384 in prostate cancer. Data from ENCODE suggested that these variants with strong evidence and other correlated variants might fall within putative functional regions. Our study provides summary evidence that common variants in the 8q24 are associated with risk of multiple cancers in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the mechanisms underlying variants in the 8q24 involved in various human cancers.
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Affiliation(s)
- Yu Tong
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Ying Tang
- Department of Pediatrics
- Department of Diagnostic Ultrasound
| | - Shiping Li
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Fengyan Zhao
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Junjie Ying
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Yi Qu
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Xiaoyu Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Dezhi Mu
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
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19
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Pathway Analysis of Genes Identified through Post-GWAS to Underpin Prostate Cancer Aetiology. Genes (Basel) 2020; 11:genes11050526. [PMID: 32397189 PMCID: PMC7291227 DOI: 10.3390/genes11050526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 01/22/2023] Open
Abstract
Understanding the functional role of risk regions identified by genome-wide association studies (GWAS) has made considerable recent progress and is referred to as the post-GWAS era. Annotation of functional variants to the genes, including cis or trans and understanding their biological pathway/gene network enrichments, is expected to give rich dividends by elucidating the mechanisms underlying prostate cancer. To this aim, we compiled and analysed currently available post-GWAS data that is validated through further studies in prostate cancer, to investigate molecular biological pathways enriched for assigned functional genes. In total, about 100 canonical pathways were significantly, at false discovery rate (FDR) < 0.05), enriched in assigned genes using different algorithms. The results have highlighted some well-known cancer signalling pathways, antigen presentation processes and enrichment in cell growth and development gene networks, suggesting risk loci may exert their functional effect on prostate cancer by acting through multiple gene sets and pathways. Additional upstream analysis of the involved genes identified critical transcription factors such as HDAC1 and STAT5A. We also investigated the common genes between post-GWAS and three well-annotated gene expression datasets to endeavour to uncover the main genes involved in prostate cancer development/progression. Post-GWAS generated knowledge of gene networks and pathways, although continuously evolving, if analysed further and targeted appropriately, will have an important impact on clinical management of the disease.
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20
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Skov L, Coll Macià M, Sveinbjörnsson G, Mafessoni F, Lucotte EA, Einarsdóttir MS, Jonsson H, Halldorsson B, Gudbjartsson DF, Helgason A, Schierup MH, Stefansson K. The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes. Nature 2020; 582:78-83. [DOI: 10.1038/s41586-020-2225-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/21/2020] [Indexed: 01/08/2023]
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21
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Beikzadeh B, Angaji SA, Abolhasani M. Association study between common variations in some candidate genes and prostate adenocarcinoma predisposition through multi-stage approach in Iranian population. BMC MEDICAL GENETICS 2020; 21:81. [PMID: 32295536 PMCID: PMC7161142 DOI: 10.1186/s12881-020-01014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/27/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Prostate cancer is one of the five common cancers and has the second incidence rate and the third mortality rate in Iranian population. The purpose of this study was to evaluate the association of rs16901979, rs4242382 and rs1447295 on 8q24 locus, rs2735839 (KLK3 gene) and rs721048 (EHBP1 gene) with prostate adenocarcinoma through multi-stage approach to identify the polymorphisms associated with prostate cancer and use them as screening factors. Screening tests can identify people who may have a chance of developing the disease before detection and any symptoms. METHODS The case-control study included 103 cases (prostate adenocarcinoma) and 100 controls (benign prostatic hyperplasia). Tetra-primer ARMS-PCR was used to genotyping of each participant. A Multi-stage approach was used for efficient genomic study. In this method, a smaller number of people can be used. Chi-squared, Fisher's exact test and logistic regression were used to investigate the SNPs associated with prostate cancer and Gleason score. RESULTS In the first stage (59 men), the frequency of polymorphisms rs16901979, rs4242382, rs1447295, rs2735839 and rs721048 in the prostate adenocarcinoma group was evaluated compared to the control group (P-value < 0.3) in order to select meaningful polymorphisms. There was not any significant difference between genotype frequency rs16901979 (P = 0.671) and rs721048 (P = 0.474) in the case group compared to BPH. Therefore, these polymorphisms were eliminated, and in the second step (144 men), rs4242382, rs2735839 and rs1447295 were evaluated (P-value < 0.05). According to the total population (203 men), there was significant difference between genotype frequency rs4242382 (P = 0.001), rs2735839 (P = 0.000) and rs1447295 (P = 0.005) even after using Bonferroni correction (p = 0.016). The effect of these three polymorphisms on prostate cancer was not modified by age and PSA. There was a significant difference between the allelic frequency of A vs G (rs4242382, rs2735839) at all classes of Gleason score and A vs C (rs1447295) at Gleason score ≥ 8. CONCLUSIONS The results of this study for rs2735839, rs4242382 and rs1447295 indicate the association of these polymorphisms with prostate adenocarcinoma predisposition in Iranian population. Exposure effect is homogeneous between different ages and PSA level categories. These three polymorphisms should be studied in a larger population to confirm these results.
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Affiliation(s)
- Behnaz Beikzadeh
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Seyed Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Maryam Abolhasani
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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22
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Selenium Supplementation and Prostate Health in a New Zealand Cohort. Nutrients 2019; 12:nu12010002. [PMID: 31861307 PMCID: PMC7019779 DOI: 10.3390/nu12010002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 01/23/2023] Open
Abstract
Background: There is variable reporting on the benefits of a 200 μg/d selenium supplementation towards reducing prostate cancer impacts. The current analysis is to understand whether stratified groups receive supplementation benefits on prostate health. Methods: 572 men were supplemented with 200 µg/d selenium as selinized yeast for six months, and 481 completed the protocol. Selenium and prostate-specific antigen (PSA) levels were measured in serum at pre- and post-supplementation. Changes in selenium and PSA levels subsequent to supplementation were assessed with and without demographic, lifestyle, genetic and dietary stratifications. Results: The post-supplementation selenium (p = 0.002) and the gain in selenium (p < 0.0001) by supplementation were significantly dependent on the baseline selenium level. Overall, there was no significant correlation between changes in PSA and changes in selenium levels by supplementation. However, stratified analyses showed a significant inverse correlation between changes in PSA and changes in selenium in men below the median age (p = 0.048), never-smokers (p = 0.031), men carrying the GPX1 rs1050450 T allele (CT, p = 0.022 and TT, p = 0.011), dietary intakes above the recommended daily intake (RDI) for zinc (p < 0.05), and below the RDI for vitamin B12 (p < 0.001). Conclusions: The current analysis shows the influence of life factors on prostate health benefits of supplemental selenium.
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Yazdani M, Angaji A, Abolhasani M, Fathi Z, Madjd Z, Roviello G, Roudi R, Asgari M. The relationship between KLK3 rs17632542 and PRNCR1 rs16901979 polymorphisms with susceptibility to prostate cancer. Meta Gene 2019; 21:100595. [DOI: 10.1016/j.mgene.2019.100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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24
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Motamedi RK, Sarhangi N, Afshari M, Sattari M, Jamaldini SH, Samzadeh M, Mohsen Ziaei SA, Pourmand GR, Hasanzad M. Kallikarein-related peptidase 3 common genetic variant and the risk of prostate cancer. J Cell Biochem 2019; 120:14822-14830. [PMID: 31017705 DOI: 10.1002/jcb.28743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/17/2019] [Accepted: 03/22/2019] [Indexed: 11/10/2022]
Abstract
Kallikarein-related peptidase 3 (KLK3) gene polymorphisms seem to play a role in susceptibility to prostate cancer (PC). The purpose of this study was to investigate the association between rs2735839 polymorphism of KLK3 gene and risk of PC in an Iranian population. In this case-control study, rs2735839 was genotyped in 532 patients with PC and 602 controls with benign prostate hyperplasia (BPH) using polymerase chain reaction-restriction fragment length polymorphism assay. The frequency of GG, AG, and AA genotypes of KLK3 polymorphism was 24.6% and 76.2%, 46.6% and 21.7%, and 28.8% and 2.1%, in patients with BPH and PC, respectively (P < 0.001). The frequency of G allele in patients with BPH and PC was 47.9% and 87%, respectively (odds ratio: 7.31; confidence interval: 5.88-9.10; P < 0.001). Patients with AG and GG genotypes had a higher total serum level of prostate-specific antigen (PSA) compared to those with AA genotype (P < 0.001). Patients with this polymorphism had higher risk of tumor with higher grade (P = 0.23), advanced stage (P = 0.11), perineural invasion (P = 0.07), and vascular invasion (P = 0.07) compared to those without it but this difference was not statistically significant. Based on our results, KLK3 gene polymorphism was associated with the risk of PC. Higher levels of PSA in the presence of KLK3 polymorphism in patients with PC indicated that rs2735839 polymorphism could be a risk factor for increased levels of PSA.
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Affiliation(s)
- Rouhollah K Motamedi
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Negar Sarhangi
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Afshari
- Department of Community Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Mahshid Sattari
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Seyed H Jamaldini
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad Samzadeh
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Seyed A Mohsen Ziaei
- Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gholam R Pourmand
- Urology Research center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mandana Hasanzad
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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25
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DeRycke MS, Larson MC, Nair AA, McDonnell SK, French AJ, Tillmans LS, Riska SM, Baheti S, Fogarty ZC, Larson NB, O’Brien DR, Cheville JC, Wang L, Schaid DJ, Thibodeau SN. An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set. PLoS One 2019; 14:e0214588. [PMID: 30958860 PMCID: PMC6453468 DOI: 10.1371/journal.pone.0214588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/17/2019] [Indexed: 01/01/2023] Open
Abstract
Prostate cancer (PrCa) is highly heritable; 284 variants have been identified to date that are associated with increased prostate cancer risk, yet few genes contributing to its development are known. Expression quantitative trait loci (eQTL) studies link variants with affected genes, helping to determine how these variants might regulate gene expression and may influence prostate cancer risk. In the current study, we performed eQTL analysis on 471 normal prostate epithelium samples and 249 PrCa-risk variants in 196 risk loci, utilizing RNA sequencing transcriptome data based on ENSEMBL gene definition and genome-wide variant data. We identified a total of 213 genes associated with known PrCa-risk variants, including 141 protein-coding genes, 16 lncRNAs, and 56 other non-coding RNA species with differential expression. Compared to our previous analysis, where RefSeq was used for gene annotation, we identified an additional 130 expressed genes associated with known PrCa-risk variants. We detected an eQTL signal for more than half (n = 102, 52%) of the 196 loci tested; 52 (51%) of which were a Group 1 signal, indicating high linkage disequilibrium (LD) between the peak eQTL variant and the PrCa-risk variant (r2>0.5) and may help explain how risk variants influence the development of prostate cancer.
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Affiliation(s)
- Melissa S. DeRycke
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Melissa C. Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Asha A. Nair
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Shannon K. McDonnell
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Amy J. French
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Lori S. Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Shaun M. Riska
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Saurabh Baheti
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Zachary C. Fogarty
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Nicholas B. Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Daniel R. O’Brien
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - John C. Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Daniel J. Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
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26
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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27
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Srinivasan S, Stephens C, Wilson E, Panchadsaram J, DeVoss K, Koistinen H, Stenman UH, Brook MN, Buckle AM, Klein RJ, Lilja H, Clements J, Batra J. Prostate Cancer Risk-Associated Single-Nucleotide Polymorphism Affects Prostate-Specific Antigen Glycosylation and Its Function. Clin Chem 2018; 65:e1-e9. [PMID: 30538125 DOI: 10.1373/clinchem.2018.295790] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/15/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND Genetic association studies have reported single-nucleotide polymorphisms (SNPs) at chromosome 19q13.3 to be associated with prostate cancer (PCa) risk. Recently, the rs61752561 SNP (Asp84Asn substitution) in exon 3 of the kallikrein-related peptidase 3 (KLK3) gene encoding prostate-specific antigen (PSA) was reported to be strongly associated with PCa risk (P = 2.3 × 10-8). However, the biological contribution of the rs61752561 SNP to PCa risk has not been elucidated. METHODS Recombinant PSA protein variants were generated to assess the SNP-mediated biochemical changes by stability and substrate activity assays. PC3 cell-PSA overexpression models were established to evaluate the effect of the SNP on PCa pathogenesis. Genotype-specific correlation of the SNP with total PSA (tPSA) concentrations and free/total (F/T) PSA ratio were determined from serum samples. RESULTS Functional analysis showed that the rs61752561 SNP affects PSA stability and structural conformation and creates an extra glycosylation site. This PSA variant had reduced enzymatic activity and the ability to stimulate proliferation and migration of PCa cells. Interestingly, the minor allele is associated with lower tPSA concentrations and high F/T PSA ratio in serum samples, indicating that the amino acid substitution may affect PSA immunoreactivity to the antibodies used in the clinical immunoassays. CONCLUSIONS The rs61752561 SNP appears to have a potential role in PCa pathogenesis by changing the glycosylation, protein stability, and PSA activity and may also affect the clinically measured F/T PSA ratio. Accounting for these effects on tPSA concentration and F/T PSA ratio may help to improve the accuracy of the current PSA test.
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Affiliation(s)
- Srilakshmi Srinivasan
- Australian Prostate Cancer Research Centre-Queensland and Cancer Program, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Carson Stephens
- Australian Prostate Cancer Research Centre-Queensland and Cancer Program, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Emily Wilson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Janaththani Panchadsaram
- Australian Prostate Cancer Research Centre-Queensland and Cancer Program, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Kerry DeVoss
- Endocrinology, QML Pathology, Mansfield, Queensland, Australia
| | - Hannu Koistinen
- Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Robert J Klein
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Hans Lilja
- Departments of Laboratory Medicine, Surgery (Urology Service) and Medicine (Genitourinary Oncology), Memorial Sloan Kettering Cancer Center, New York, NY.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Judith Clements
- Australian Prostate Cancer Research Centre-Queensland and Cancer Program, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Queensland and Cancer Program, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia; .,Translational Research Institute, Woolloongabba, Queensland, Australia
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28
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Dias A, Kote-Jarai Z, Mikropoulos C, Eeles R. Prostate Cancer Germline Variations and Implications for Screening and Treatment. Cold Spring Harb Perspect Med 2018; 8:a030379. [PMID: 29101112 PMCID: PMC6120689 DOI: 10.1101/cshperspect.a030379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is a highly heritable disease, and rapid evolution of sequencing technologies has enabled marked progression of our understanding of its genetic inheritance. A complex polygenic model that involves common low-penetrance susceptibility alleles causing individually small but cumulatively significant risk and rarer genetic variants causing greater risk represent the current most accepted model. Through genome-wide association studies, more than 100 single-nucleotide polymorphisms (SNPs) associated with PCa risk have been identified. Consistent reports have identified germline mutations in the genes BRCA1, BRCA2, MMR, HOXB13, CHEK2, and NBS1 as conferring moderate risks, with some leading to a more aggressive disease behavior. Considering this knowledge, several research strategies have been developed to determine whether targeted prostate screening using genetic information can overcome the limitations of population-based prostate-specific antigen (PSA) screening. Germline DNA-repair mutations are more frequent in men with metastatic disease than previously thought, and these patients have a more favorable response to therapy with poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitors. Genomic information is a practical tool that has the potential to enable the concept of precision medicine to become a reality in all steps of PCa patient care.
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Affiliation(s)
- Alexander Dias
- The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
- The Institute of Cancer Research and Royal Marsden National Health Service (NHS) Foundation Trust, Academic Urology Unit and The Oncogenetics Team, London SW3 6JJ, United Kingdom
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | | | - Ros Eeles
- The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
- The Institute of Cancer Research and Royal Marsden National Health Service (NHS) Foundation Trust, Academic Urology Unit and The Oncogenetics Team, London SW3 6JJ, United Kingdom
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29
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Dadaev T, Saunders EJ, Newcombe PJ, Anokian E, Leongamornlert DA, Brook MN, Cieza-Borrella C, Mijuskovic M, Wakerell S, Olama AAA, Schumacher FR, Berndt SI, Benlloch S, Ahmed M, Goh C, Sheng X, Zhang Z, Muir K, Govindasami K, Lophatananon A, Stevens VL, Gapstur SM, Carter BD, Tangen CM, Goodman P, Thompson IM, Batra J, Chambers S, Moya L, Clements J, Horvath L, Tilley W, Risbridger G, Gronberg H, Aly M, Nordström T, Pharoah P, Pashayan N, Schleutker J, Tammela TLJ, Sipeky C, Auvinen A, Albanes D, Weinstein S, Wolk A, Hakansson N, West C, Dunning AM, Burnet N, Mucci L, Giovannucci E, Andriole G, Cussenot O, Cancel-Tassin G, Koutros S, Freeman LEB, Sorensen KD, Orntoft TF, Borre M, Maehle L, Grindedal EM, Neal DE, Donovan JL, Hamdy FC, Martin RM, Travis RC, Key TJ, Hamilton RJ, Fleshner NE, Finelli A, Ingles SA, Stern MC, Rosenstein B, Kerns S, Ostrer H, Lu YJ, Zhang HW, Feng N, Mao X, Guo X, Wang G, Sun Z, Giles GG, Southey MC, MacInnis RJ, FitzGerald LM, Kibel AS, Drake BF, Vega A, Gómez-Caamaño A, Fachal L, Szulkin R, Eklund M, Kogevinas M, Llorca J, Castaño-Vinyals G, Penney KL, Stampfer M, Park JY, Sellers TA, et alDadaev T, Saunders EJ, Newcombe PJ, Anokian E, Leongamornlert DA, Brook MN, Cieza-Borrella C, Mijuskovic M, Wakerell S, Olama AAA, Schumacher FR, Berndt SI, Benlloch S, Ahmed M, Goh C, Sheng X, Zhang Z, Muir K, Govindasami K, Lophatananon A, Stevens VL, Gapstur SM, Carter BD, Tangen CM, Goodman P, Thompson IM, Batra J, Chambers S, Moya L, Clements J, Horvath L, Tilley W, Risbridger G, Gronberg H, Aly M, Nordström T, Pharoah P, Pashayan N, Schleutker J, Tammela TLJ, Sipeky C, Auvinen A, Albanes D, Weinstein S, Wolk A, Hakansson N, West C, Dunning AM, Burnet N, Mucci L, Giovannucci E, Andriole G, Cussenot O, Cancel-Tassin G, Koutros S, Freeman LEB, Sorensen KD, Orntoft TF, Borre M, Maehle L, Grindedal EM, Neal DE, Donovan JL, Hamdy FC, Martin RM, Travis RC, Key TJ, Hamilton RJ, Fleshner NE, Finelli A, Ingles SA, Stern MC, Rosenstein B, Kerns S, Ostrer H, Lu YJ, Zhang HW, Feng N, Mao X, Guo X, Wang G, Sun Z, Giles GG, Southey MC, MacInnis RJ, FitzGerald LM, Kibel AS, Drake BF, Vega A, Gómez-Caamaño A, Fachal L, Szulkin R, Eklund M, Kogevinas M, Llorca J, Castaño-Vinyals G, Penney KL, Stampfer M, Park JY, Sellers TA, Lin HY, Stanford JL, Cybulski C, Wokolorczyk D, Lubinski J, Ostrander EA, Geybels MS, Nordestgaard BG, Nielsen SF, Weisher M, Bisbjerg R, Røder MA, Iversen P, Brenner H, Cuk K, Holleczek B, Maier C, Luedeke M, Schnoeller T, Kim J, Logothetis CJ, John EM, Teixeira MR, Paulo P, Cardoso M, Neuhausen SL, Steele L, Ding YC, De Ruyck K, De Meerleer G, Ost P, Razack A, Lim J, Teo SH, Lin DW, Newcomb LF, Lessel D, Gamulin M, Kulis T, Kaneva R, Usmani N, Slavov C, Mitev V, Parliament M, Singhal S, Claessens F, Joniau S, Van den Broeck T, Larkin S, Townsend PA, Aukim-Hastie C, Gago-Dominguez M, Castelao JE, Martinez ME, Roobol MJ, Jenster G, van Schaik RHN, Menegaux F, Truong T, Koudou YA, Xu J, Khaw KT, Cannon-Albright L, Pandha H, Michael A, Kierzek A, Thibodeau SN, McDonnell SK, Schaid DJ, Lindstrom S, Turman C, Ma J, Hunter DJ, Riboli E, Siddiq A, Canzian F, Kolonel LN, Le Marchand L, Hoover RN, Machiela MJ, Kraft P, Freedman M, Wiklund F, Chanock S, Henderson BE, Easton DF, Haiman CA, Eeles RA, Conti DV, Kote-Jarai Z. Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants. Nat Commun 2018; 9:2256. [PMID: 29892050 PMCID: PMC5995836 DOI: 10.1038/s41467-018-04109-8] [Show More Authors] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.
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Affiliation(s)
- Tokhir Dadaev
- The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Paul J Newcombe
- MRC Biostatistics Unit, University of Cambridge, Robinson Way, Cambridge, CB2 0SR, UK
| | | | - Daniel A Leongamornlert
- The Institute of Cancer Research, London, SW7 3RP, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark N Brook
- The Institute of Cancer Research, London, SW7 3RP, UK
| | | | | | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106-7219, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, 44106, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sara Benlloch
- The Institute of Cancer Research, London, SW7 3RP, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Mahbubl Ahmed
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - Chee Goh
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Zhuo Zhang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Artitaya Lophatananon
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, 250 Williams Street, Atlanta, GA, 30303, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, 250 Williams Street, Atlanta, GA, 30303, USA
| | - Brian D Carter
- Epidemiology Research Program, American Cancer Society, 250 Williams Street, Atlanta, GA, 30303, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Phyllis Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ian M Thompson
- CHRISTUS Santa Rosa Hospital - Medical Center, San Antonio, TX, 78229, USA
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, 4059, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Suzanne Chambers
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
- Cancer Council Queensland, Fortitude Valley, QLD, 4006, Australia
| | - Leire Moya
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, 4059, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Judith Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, 4059, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Lisa Horvath
- Chris O'Brien Lifehouse (COBLH), Camperdown, Sydney, NSW, 2010, Australia
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Centre, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Gail Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Urology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Tobias Nordström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
- Department of Clinical Sciences at Danderyd Hospital, Karolinska Institutet, 182 88, Stockholm, Sweden
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, FI-20014, Turku, Finland
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, 20521, Turku, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital, University of Tampere, Kalevantie 4, FI-33014, Tampere, Finland
| | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, FI-20014, Turku, Finland
| | - Anssi Auvinen
- Department of Epidemiology, School of Health Sciences, University of Tampere, FI-33014, Tampere, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Niclas Hakansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catharine West
- Division of Cancer Sciences, Manchester Academic Health Science Centre, Radiotherapy Related Research, Manchester NIHR Biomedical Research Centre, The Christie Hospital NHS Foundation Trust, University of Manchester, Manchester, M13 9PL, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Neil Burnet
- University of Cambridge Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB1 8RN, UK
| | - Lorelei Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Gerald Andriole
- Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Olivier Cussenot
- GRC N°5 ONCOTYPE-URO, UPMC Univ Paris 06, Tenon Hospital, F-75020, Paris, France
- CeRePP, Tenon Hospital, F-75020, Paris, France
| | - Géraldine Cancel-Tassin
- GRC N°5 ONCOTYPE-URO, UPMC Univ Paris 06, Tenon Hospital, F-75020, Paris, France
- CeRePP, Tenon Hospital, F-75020, Paris, France
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
| | - Torben Falck Orntoft
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
- Department of Urology, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Eli Marie Grindedal
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - David E Neal
- Department of Oncology, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
| | - Jenny L Donovan
- School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol, BS8 2PS, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
- Faculty of Medical Science, John Radcliffe Hospital, University of Oxford, Oxford, OX1 2JD, UK
| | - Richard M Martin
- School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol, BS8 2PS, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre, University of Bristol, Bristol, BS8 1TH, UK
| | - Ruth C Travis
- Cancer Epidemiology, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Tim J Key
- Cancer Epidemiology, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Robert J Hamilton
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2M9, Canada
| | - Neil E Fleshner
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2M9, Canada
| | - Antonio Finelli
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2M9, Canada
| | - Sue Ann Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Mariana C Stern
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Barry Rosenstein
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Sarah Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, NY, 14620, USA
| | - Harry Ostrer
- Professor of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Hong-Wei Zhang
- Second Military Medical University, Shanghai, 200433, P. R. China
| | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, Jiangzhu, 214003, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Xin Guo
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 200032, China
- The People's Hospital of Liaoning Province and The People's Hospital of China Medical University, Shenyang, 110001, China
| | - Guomin Wang
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Zan Sun
- The People's Hospital of Liaoning Province and The People's Hospital of China Medical University, Shenyang, 110001, China
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Melissa C Southey
- Precision Medicine, School and Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Robert J MacInnis
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Liesel M FitzGerald
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, 02115, USA
| | - Bettina F Drake
- Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, 15706, Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, 15706, Santiago de Compostela, Spain
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, 15706, Spain
| | - Robert Szulkin
- Division of Family Medicine, Department of Neurobiology, Care Science and Society, Karolinska Institutet, Huddinge, SE-171 77, Stockholm, Sweden
- Scandinavian Development Services, 182 33, Danderyd, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Manolis Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona Institute for Global Health (ISGlobal), 08003, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- IMIM (Hospital del Mar Research Institute), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Javier Llorca
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- University of Cantabria-IDIVAL, 39005, Santander, Spain
| | - Gemma Castaño-Vinyals
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona Institute for Global Health (ISGlobal), 08003, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- IMIM (Hospital del Mar Research Institute), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02184, USA
| | - Meir Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02184, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Hui-Yi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-115, Szczecin, Poland
| | - Dominika Wokolorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-115, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-115, Szczecin, Poland
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Sune F Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Maren Weisher
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Rasmus Bisbjerg
- Department of Urology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Martin Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, DK-2730, Herlev, Denmark
| | - Peter Iversen
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, DK-2730, Herlev, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | | | - Christiane Maier
- Institute for Human Genetics, University Hospital Ulm, 89075, Ulm, Germany
| | - Manuel Luedeke
- Institute for Human Genetics, University Hospital Ulm, 89075, Ulm, Germany
| | | | - Jeri Kim
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, 94538, USA
- Department of Health Research & Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305-5101, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto, 4200-072, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute of Porto, 4200-072, Porto, Portugal
| | - Marta Cardoso
- Department of Genetics, Portuguese Oncology Institute of Porto, 4200-072, Porto, Portugal
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, B-9000, Gent, Belgium
| | - Gert De Meerleer
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, B-9000, Gent, Belgium
| | - Piet Ost
- Department of Radiotherapy, Ghent University Hospital, B-9000, Gent, Belgium
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, 47500, Subang Jaya, Selangor, Malaysia
| | - Daniel W Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Urology, University of Washington, Seattle, WA, 98195, USA
| | - Lisa F Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Urology, University of Washington, Seattle, WA, 98195, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, D-20246, Hamburg, Germany
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology at the University Hospital Centre Zagreb, Šalata 2, 10000, Zagreb, Croatia
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Šalata 2, 10000, Zagreb, Croatia
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, BE-3000, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, BE-3000, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, BE-3000, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, BE-3000, Leuven, Belgium
| | - Samantha Larkin
- Southampton General Hospital, The University of Southampton, Southampton, SO16 6YD, UK
| | - Paul A Townsend
- Manchester Cancer Research Centre, Faculty of Biology Medicine & Health, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Health Innovation Manchester, University of Manchester, Manchester, M13 9WL, UK
| | | | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, 15706, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), 36204, Vigo (Pontevedra), Spain
| | - Maria Elena Martinez
- Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, 92093-0012, USA
| | - Monique J Roobol
- Department of Urology, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Florence Menegaux
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, 94807, Villejuif Cédex, France
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, 94807, Villejuif Cédex, France
| | - Yves Akoli Koudou
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, 94807, Villejuif Cédex, France
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, 60201, USA
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
| | - Hardev Pandha
- The University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | | | | | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shannon K McDonnell
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Daniel J Schaid
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jing Ma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02184, USA
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, SW7 2AZ, UK
| | - Afshan Siddiq
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | | | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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Netto GJ, Eich ML, Varambally S. Prostate Cancer: An Update on Molecular Pathology with Clinical Implications. EUR UROL SUPPL 2017. [DOI: 10.1016/j.eursup.2017.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Koistinen H, Wallén E, Ylikangas H, Meinander K, Lahtela-Kakkonen M, Närvänen A, Stenman UH. Development of molecules stimulating the activity of KLK3 - an update. Biol Chem 2017; 397:1229-1235. [PMID: 27383882 DOI: 10.1515/hsz-2016-0189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023]
Abstract
Kallikrein-related peptidase-3 (KLK3, known also as prostate-specific antigen, PSA) is highly expressed in the prostate. KLK3 possess antiangiogenic activity, which we have found to be related to its proteolytic activity. Thus, it may be possible to slow down the growth of prostatic tumors by enhancing this activity. We have developed peptides that enhance the proteolytic activity of KLK3. As these peptides are degraded in circulation and rapidly excreted, we have started to modify them and have succeeded in creating bioactive and more stable pseudopeptides. We have also identified small molecules stimulating the activity of KLK3, especially in synergy with peptides.
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Vaidyanathan V, Naidu V, Kao CHJ, Karunasinghe N, Bishop KS, Wang A, Pallati R, Shepherd P, Masters J, Zhu S, Goudie M, Krishnan M, Jabed A, Marlow G, Narayanan A, Ferguson LR. Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men - a genotypic approach. MOLECULAR BIOSYSTEMS 2017; 13:681-698. [PMID: 28252132 DOI: 10.1039/c6mb00873a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Prostate cancer is one of the most significant health concerns for men worldwide. Numerous researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms (SNPs) are increasingly becoming strong biomarker candidates to identify susceptibility to prostate cancer. We carried out a gene × environment interaction analysis linked to aggressive and non-aggressive prostate cancer (PCa) with a number of SNPs. By using this method, we identified the susceptible alleles in a New Zealand population, and examined the interaction with environmental factors. We have identified a number of SNPs that have risk associations both with and without environmental interaction. The results indicate that certain SNPs are associated with disease vulnerability based on behavioral factors. The list of genes with SNPs identified as being associated with the risk of PCa in a New Zealand population is provided in the graphical abstract.
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Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Vijay Naidu
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Chi Hsiu-Juei Kao
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | | | - Karen S Bishop
- Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Alice Wang
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Radha Pallati
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Phillip Shepherd
- Sequenom Facility, Liggins Institute, University of Auckland, Auckland 1023, New Zealand.
| | - Jonathan Masters
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Shuotun Zhu
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Megan Goudie
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Mohanraj Krishnan
- Department of Obstetrics and Gynaecology, FMHS, University of Auckland, Auckland 1023, New Zealand.
| | - Anower Jabed
- Department of Molecular Medicine and Pathology, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Gareth Marlow
- Experimental Cancer Medicine Centre, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ajit Narayanan
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
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Zhu Q, Shepherd L, Lunetta KL, Yao S, Liu Q, Hu Q, Haddad SA, Sucheston-Campbell L, Bensen JT, Bandera EV, Rosenberg L, Liu S, Haiman CA, Olshan AF, Palmer JR, Ambrosone CB. Trans-ethnic follow-up of breast cancer GWAS hits using the preferential linkage disequilibrium approach. Oncotarget 2016; 7:83160-83176. [PMID: 27825120 PMCID: PMC5341253 DOI: 10.18632/oncotarget.13075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Leveraging population-distinct linkage equilibrium (LD) patterns, trans-ethnic follow-up of variants discovered from genome-wide association studies (GWAS) has proved to be useful in facilitating the identification of bona fide causal variants. We previously developed the preferential LD approach, a novel method that successfully identified causal variants driving the GWAS signals within European-descent populations even when the causal variants were only weakly linked with the GWAS-discovered variants. To evaluate the performance of our approach in a trans-ethnic setting, we applied it to follow up breast cancer GWAS hits identified mostly from populations of European ancestry in African Americans (AA). We evaluated 74 breast cancer GWAS variants in 8,315 AA women from the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Only 27% of them were associated with breast cancer risk at significance level α=0.05, suggesting race-specificity of the identified breast cancer risk loci. We followed up on those replicated GWAS hits in the AMBER consortium utilizing the preferential LD approach, to search for causal variants or better breast cancer markers from the 1000 Genomes variant catalog. Our approach identified stronger breast cancer markers for 80% of the GWAS hits with at least nominal breast cancer association, and in 81% of these cases, the marker identified was among the top 10 of all 1000 Genomes variants in the corresponding locus. The results support trans-ethnic application of the preferential LD approach in search for candidate causal variants, and may have implications for future genetic research of breast cancer in AA women.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Lori Shepherd
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qian Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Lara Sucheston-Campbell
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
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Heger Z, Merlos Rodrigo MA, Michalek P, Polanska H, Masarik M, Vit V, Plevova M, Pacik D, Eckschlager T, Stiborova M, Adam V. Sarcosine Up-Regulates Expression of Genes Involved in Cell Cycle Progression of Metastatic Models of Prostate Cancer. PLoS One 2016; 11:e0165830. [PMID: 27824899 PMCID: PMC5100880 DOI: 10.1371/journal.pone.0165830] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
The effects of sarcosine on the processes driving prostate cancer (PCa) development remain still unclear. Herein, we show that a supplementation of metastatic PCa cells (androgen independent PC-3 and androgen dependent LNCaP) with sarcosine stimulates cells proliferation in vitro. Similar stimulatory effects were observed also in PCa murine xenografts, in which sarcosine treatment induced a tumor growth and significantly reduced weight of treated mice (p < 0.05). Determination of sarcosine metabolism-related amino acids and enzymes within tumor mass revealed significantly increased glycine, serine and sarcosine concentrations after treatment accompanied with the increased amount of sarcosine dehydrogenase. In both tumor types, dimethylglycine and glycine-N-methyltransferase were affected slightly, only. To identify the effects of sarcosine treatment on the expression of genes involved in any aspect of cancer development, we further investigated expression profiles of excised tumors using cDNA electrochemical microarray followed by validation using the semi-quantitative PCR. We found 25 differentially expressed genes in PC-3, 32 in LNCaP tumors and 18 overlapping genes. Bioinformatical processing revealed strong sarcosine-related induction of genes involved particularly in a cell cycle progression. Our exploratory study demonstrates that sarcosine stimulates PCa metastatic cells irrespectively of androgen dependence. Overall, the obtained data provides valuable information towards understanding the role of sarcosine in PCa progression and adds another piece of puzzle into a picture of sarcosine oncometabolic potential.
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Affiliation(s)
- Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
| | - Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
| | - Petr Michalek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
| | - Hana Polanska
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Michal Masarik
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Vitezslav Vit
- Department of Urology, University Hospital Brno, Jihlavska 20, Brno, CZ-625 00, Czech Republic
| | - Mariana Plevova
- Department of Urology, University Hospital Brno, Jihlavska 20, Brno, CZ-625 00, Czech Republic
| | - Dalibor Pacik
- Department of Urology, University Hospital Brno, Jihlavska 20, Brno, CZ-625 00, Czech Republic
| | - Tomas Eckschlager
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, V Uvalu 84, CZ-150 06, Prague 5, Czech Republic
| | - Marie Stiborova
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ-128 40, Prague 2, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
- * E-mail:
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36
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Rodriguez S, Al-Ghamdi OA, Guthrie PA, Shihab HA, McArdle W, Gaunt T, Alharbi KK, Day IN. Frequency of KLK3 gene deletions in the general population. Ann Clin Biochem 2016; 54:472-480. [PMID: 27555663 DOI: 10.1177/0004563216666999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background One of the kallikrein genes ( KLK3) encodes prostate-specific antigen, a key biomarker for prostate cancer. A number of factors, both genetic and non-genetic, determine variation of serum prostate-specific antigen concentrations in the population. We have recently found three KLK3 deletions in individuals with very low prostate-specific antigen concentrations, suggesting a link between abnormally reduced KLK3 expression and deletions of KLK3. Here, we aim to determine the frequency of kallikrein gene 3 deletions in the general population. Methods The frequency of KLK3 deletions in the general population was estimated from the 1958 Birth Cohort sample ( n = 3815) using amplification ratiometry control system. In silico analyses using PennCNV were carried out in the same cohort and in NBS-WTCCC2 in order to provide an independent estimation of the frequency of KLK3 deletions in the general population. Results Amplification ratiometry control system results from the 1958 cohort indicated a frequency of KLK3 deletions of 0.81% (3.98% following a less stringent calling criterion). From in silico analyses, we found that potential deletions harbouring the KLK3 gene occurred at rates of 2.13% (1958 Cohort, n = 2867) and 0.99% (NBS-WTCCC2, n = 2737), respectively. These results are in good agreement with our in vitro experiments. All deletions found were in heterozygosis. Conclusions We conclude that a number of individuals from the general population present KLK3 deletions in heterozygosis. Further studies are required in order to know if interpretation of low serum prostate-specific antigen concentrations in individuals with KLK3 deletions may offer false-negative assurances with consequences for prostate cancer screening, diagnosis and monitoring.
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Affiliation(s)
- Santiago Rodriguez
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Osama A Al-Ghamdi
- 2 Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.,3 School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Philip Ai Guthrie
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Hashem A Shihab
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Wendy McArdle
- 3 School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tom Gaunt
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Khalid K Alharbi
- 2 Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ian Nm Day
- 3 School of Social and Community Medicine, University of Bristol, Bristol, UK
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37
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Abstract
Although prostate cancer is the most common malignancy to affect men in the Western world, the molecular mechanisms underlying its development and progression remain poorly understood. Like all cancers, prostate cancer is a genetic disease that is characterized by multiple genomic alterations, including point mutations, microsatellite variations, and chromosomal alterations such as translocations, insertions, duplications, and deletions. In prostate cancer, but not other carcinomas, these chromosome alterations result in a high frequency of gene fusion events. The development and application of novel high-resolution technologies has significantly accelerated the detection of genomic alterations, revealing the complex nature and heterogeneity of the disease. The clinical heterogeneity of prostate cancer can be partly explained by this underlying genetic heterogeneity, which has been observed between patients from different geographical and ethnic populations, different individuals within these populations, different tumour foci within the same patient, and different cells within the same tumour focus. The highly heterogeneous nature of prostate cancer provides a real challenge for clinical disease management and a detailed understanding of the genetic alterations in all cells, including small subpopulations, would be highly advantageous.
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38
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Ahmed M, Eeles R. Germline genetic profiling in prostate cancer: latest developments and potential clinical applications. Future Sci OA 2016; 2:FSO87. [PMID: 28031937 PMCID: PMC5137984 DOI: 10.4155/fso.15.87] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 11/10/2015] [Indexed: 12/16/2022] Open
Abstract
Familial and twin studies have demonstrated a significant inherited component to prostate cancer predisposition. Genome wide association studies have shown that there are 100 single nucleotide polymorphisms which have been associated with the development of prostate cancer. This review aims to discuss the scientific methods used to identify these susceptibility loci. It will also examine the current clinical utility of these loci, which include the development of risk models as well as predicting treatment efficacy and toxicity. In order to refine the clinical utility of the susceptibility loci, international consortia have been developed to combine statistical power as well as skills and knowledge to further develop models that could be used to predict risk and treatment outcomes.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, London SM2 5NG, UK
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39
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Bu H, Narisu N, Schlick B, Rainer J, Manke T, Schäfer G, Pasqualini L, Chines P, Schweiger MR, Fuchsberger C, Klocker H. Putative Prostate Cancer Risk SNP in an Androgen Receptor-Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites. Hum Mutat 2016; 37:52-64. [PMID: 26411452 PMCID: PMC4715509 DOI: 10.1002/humu.22909] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 09/16/2015] [Indexed: 01/17/2023]
Abstract
Genome-wide association studies have identified genomic loci, whose single-nucleotide polymorphisms (SNPs) predispose to prostate cancer (PCa). However, the mechanisms of most of these variants are largely unknown. We integrated chromatin-immunoprecipitation-coupled sequencing and microarray expression profiling in TMPRSS2-ERG gene rearrangement positive DUCaP cells with the GWAS PCa risk SNPs catalog to identify disease susceptibility SNPs localized within functional androgen receptor-binding sites (ARBSs). Among the 48 GWAS index risk SNPs and 3,917 linked SNPs, 80 were found located in ARBSs. Of these, rs11891426:T>G in an intron of the melanophilin gene (MLPH) was within a novel putative auxiliary AR-binding motif, which is enriched in the neighborhood of canonical androgen-responsive elements. T→G exchange attenuated the transcriptional activity of the ARBS in an AR reporter gene assay. The expression of MLPH in primary prostate tumors was significantly lower in those with the G compared with the T allele and correlated significantly with AR protein. Higher melanophilin level in prostate tissue of patients with a favorable PCa risk profile points out a tumor-suppressive effect. These results unravel a hidden link between AR and a functional putative PCa risk SNP, whose allele alteration affects androgen regulation of its host gene MLPH.
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Affiliation(s)
- Huajie Bu
- Department of UrologyDivision of Experimental UrologyMedical University of InnsbruckInnsbruckAustria
- Research Institute for Biomedical Aging ResearchUniversity of InnsbruckInnsbruckAustria
| | - Narisu Narisu
- Medical Genomics and Metabolic Genetics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland
| | - Bettina Schlick
- Department of UrologyDivision of Experimental UrologyMedical University of InnsbruckInnsbruckAustria
- OncotyrolCenter for Personalized Cancer MedicineInnsbruckAustria
| | - Johannes Rainer
- Biocenter InnsbruckSection for Molecular PathophysiologyMedical University of InnsbruckInnsbruckAustria
- Center for BiomedicineEURAC ResearchBolzanoItaly
| | - Thomas Manke
- Max Planck Institute for Molecular GeneticsBerlinGermany
- Max Planck Institute for Immunobiology and EpigeneticsFreiburgGermany
| | - Georg Schäfer
- Department of UrologyDivision of Experimental UrologyMedical University of InnsbruckInnsbruckAustria
- Department of PathologyMedical University of InnsbruckInnsbruckAustria
| | - Lorenza Pasqualini
- Department of UrologyDivision of Experimental UrologyMedical University of InnsbruckInnsbruckAustria
| | - Peter Chines
- Medical Genomics and Metabolic Genetics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland
| | - Michal R. Schweiger
- Max Planck Institute for Molecular GeneticsBerlinGermany
- Cologne Center for GenomicsUniversity of CologneGermany
| | - Christian Fuchsberger
- Center for BiomedicineEURAC ResearchBolzanoItaly
- Department of BiostatisticsUniversity of MichiganAnn ArborMichigan
| | - Helmut Klocker
- Department of UrologyDivision of Experimental UrologyMedical University of InnsbruckInnsbruckAustria
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40
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Abstract
A wide array of molecular markers and genomic signatures, reviewed in this article, may soon be used as adjuncts to currently established screening strategies, prognostic parameters, and early detection markers. Markers of genetic susceptibility to PCA, recurrent epigenetic and genetic alterations, including ETS gene fusions, PTEN alterations, and urine-based early detection marker PCA3, are discussed. Impact of recent genome-wide assessment on our understanding of key pathways of PCA development and progression and their potential clinical implications are highlighted.
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41
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Han Y, Hazelett DJ, Wiklund F, Schumacher FR, Stram DO, Berndt SI, Wang Z, Rand KA, Hoover RN, Machiela MJ, Yeager M, Burdette L, Chung CC, Hutchinson A, Yu K, Xu J, Travis RC, Key TJ, Siddiq A, Canzian F, Takahashi A, Kubo M, Stanford JL, Kolb S, Gapstur SM, Diver WR, Stevens VL, Strom SS, Pettaway CA, Al Olama AA, Kote-Jarai Z, Eeles RA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, Isaacs WB, Chen C, Lindstrom S, Le Marchand L, Giovannucci EL, Pomerantz M, Long H, Li F, Ma J, Stampfer M, John EM, Ingles SA, Kittles RA, Murphy AB, Blot WJ, Signorello LB, Zheng W, Albanes D, Virtamo J, Weinstein S, Nemesure B, Carpten J, Leske MC, Wu SY, Hennis AJM, Rybicki BA, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Zheng SL, Witte JS, Casey G, Riboli E, Li Q, Freedman ML, Hunter DJ, Gronberg H, Cook MB, Nakagawa H, Kraft P, Chanock SJ, Easton DF, Henderson BE, Coetzee GA, Conti DV, Haiman CA. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. Hum Mol Genet 2015; 24:5603-18. [PMID: 26162851 PMCID: PMC4572069 DOI: 10.1093/hmg/ddv269] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/07/2015] [Indexed: 01/27/2023] Open
Abstract
Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.
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Affiliation(s)
- Ying Han
- Department of Preventive Medicine, Keck School of Medicine
| | | | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Merideth Yeager
- Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | | | - Curtis A Pettaway
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK, Royal Marsden National Health Services (NHS) Foundation Trust, London and Sutton, UK
| | - Edward D Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Richard B Biritwum
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Andrew A Adjei
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | | | | | | | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Henry Long
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fugen Li
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Ma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Rick A Kittles
- University of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, AZ, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - William J Blot
- International Epidemiology Institute, Rockville, MD, USA, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J M Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA, Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | | | - Ann W Hsing
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric A Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, CA, USA and
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China
| | | | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center,
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42
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Amin Al Olama A, Dadaev T, Hazelett DJ, Li Q, Leongamornlert D, Saunders EJ, Stephens S, Cieza-Borrella C, Whitmore I, Benlloch Garcia S, Giles GG, Southey MC, Fitzgerald L, Gronberg H, Wiklund F, Aly M, Henderson BE, Schumacher F, Haiman CA, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, Mcdonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokołorczyk D, Kluzniak W, Cannon-Albright L, Brenner H, Butterbach K, Arndt V, Park JY, Sellers T, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Clements JA, Spurdle A, Teixeira MR, Paulo P, Maia S, Pandha H, Michael A, Kierzek A, Govindasami K, Guy M, Lophatonanon A, Muir K, Viñuela A, Brown AA, Freedman M, Conti DV, Easton D, Coetzee GA, Eeles RA, Kote-Jarai Z. Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum Mol Genet 2015; 24:5589-602. [PMID: 26025378 PMCID: PMC4572072 DOI: 10.1093/hmg/ddv203] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same region.
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Affiliation(s)
- Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Dennis J Hazelett
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Qiuyan Li
- Medical College, Xiamen University, Xiamen, China
| | - Daniel Leongamornlert
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Edward J Saunders
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Sarah Stephens
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Clara Cieza-Borrella
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Ian Whitmore
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Sara Benlloch Garcia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden, Department of Clinical Sciences, Danderyds Hospital, Stockholm, Sweden
| | - Brian E Henderson
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics Institute of Biomedicine, University of Turku, Turku, Finland, BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Teuvo L Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim J Key
- Cancer Epidemiology, Nuffield Department of Population Health
| | - Ruth C Travis
- Cancer Epidemiology, Nuffield Department of Population Health
| | - David E Neal
- Department of Oncology, Addenbrooke's Hospital, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK, Faculty of Medical Science, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, Department of Applied Health Research, University College London, London, UK
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Walther Vogel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Kluzniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- Biostatistics Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University, Sofia, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - Judith A Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal, Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | | | | | | | - Koveela Govindasami
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Michelle Guy
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Artitaya Lophatonanon
- Institute of Population Health, University of Manchester, Manchester, UK, Warwick Medical School, University of Warwick, Coventry, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, UK, Warwick Medical School, University of Warwick, Coventry, UK
| | - Ana Viñuela
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andrew A Brown
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway, Department of Genetic Medicine and Development, University of Geneva, Switzerland and
| | | | - David V Conti
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Gerhard A Coetzee
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK,
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Srinivasan S, Clements JA, Batra J. Single nucleotide polymorphisms in clinics: Fantasy or reality for cancer? Crit Rev Clin Lab Sci 2015; 53:29-39. [DOI: 10.3109/10408363.2015.1075469] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Sullivan J, Kopp R, Stratton K, Manschreck C, Corines M, Rau-Murthy R, Hayes J, Lincon A, Ashraf A, Thomas T, Schrader K, Gallagher D, Hamilton R, Scher H, Lilja H, Scardino P, Eastham J, Offit K, Vijai J, Klein RJ. An analysis of the association between prostate cancer risk loci, PSA levels, disease aggressiveness and disease-specific mortality. Br J Cancer 2015; 113:166-72. [PMID: 26068399 PMCID: PMC4647539 DOI: 10.1038/bjc.2015.199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/24/2015] [Accepted: 05/05/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Genome-wide association studies have identified multiple single-nucleotide polymorphsims (SNPs) associated with prostate cancer (PCa). Although these SNPs have been clearly associated with disease risk, their relationship with clinical outcomes is less clear. Our aim was to assess the frequency of known PCa susceptibility alleles within a single institution ascertainment and to correlate risk alleles with disease-specific outcomes. METHODS We genotyped 1354 individuals treated for localised PCa between June 1988 and December 2007. Blood samples were prospectively collected and de-identified before being genotyped and matched to phenotypic data. We investigated associations between 61 SNPs and disease-specific end points using multivariable analysis and also determined if SNPs were associated with PSA at diagnosis. RESULTS Seven SNPs showed associations on multivariable analysis (P<0.05), rs13385191 with both biochemical recurrence (BR) and castrate metastasis (CM), rs339331 (BR), rs1894292, rs17178655 and rs11067228 (CM), and rs11902236 and rs4857841 PCa-specific mortality. After applying a Bonferroni correction for number of SNPs (P<0.0008), the only persistent significant association was between rs17632542 (KLK3) and PSA levels at diagnosis (P=1.4 × 10(-5)). CONCLUSIONS We confirmed that rs17632542 in KLK3 is associated with PSA at diagnosis. No significant association was seen between loci and disease-specific end points when accounting for multiple testing. This provides further evidence that known PCa risk SNPs do not predict likelihood of disease progression.
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Affiliation(s)
- J Sullivan
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - R Kopp
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - K Stratton
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - C Manschreck
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - M Corines
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - R Rau-Murthy
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - J Hayes
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - A Lincon
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - A Ashraf
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - T Thomas
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - K Schrader
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - D Gallagher
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - R Hamilton
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - H Scher
- Department of Medicine, Genitourinary Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - H Lilja
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - P Scardino
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - J Eastham
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - K Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - J Vijai
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - R J Klein
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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45
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Berndt SI, Wang Z, Yeager M, Alavanja MC, Albanes D, Amundadottir L, Andriole G, Beane Freeman L, Campa D, Cancel-Tassin G, Canzian F, Cornu JN, Cussenot O, Diver WR, Gapstur SM, Grönberg H, Haiman CA, Henderson B, Hutchinson A, Hunter DJ, Key TJ, Kolb S, Koutros S, Kraft P, Le Marchand L, Lindström S, Machiela MJ, Ostrander EA, Riboli E, Schumacher F, Siddiq A, Stanford JL, Stevens VL, Travis RC, Tsilidis KK, Virtamo J, Weinstein S, Wilkund F, Xu J, Lilly Zheng S, Yu K, Wheeler W, Zhang H, Sampson J, Black A, Jacobs K, Hoover RN, Tucker M, Chanock SJ. Two susceptibility loci identified for prostate cancer aggressiveness. Nat Commun 2015; 6:6889. [PMID: 25939597 PMCID: PMC4422072 DOI: 10.1038/ncomms7889] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 03/10/2015] [Indexed: 01/06/2023] Open
Abstract
Most men diagnosed with prostate cancer will experience indolent disease; hence, discovering genetic variants that distinguish aggressive from nonaggressive prostate cancer is of critical clinical importance for disease prevention and treatment. In a multistage, case-only genome-wide association study of 12,518 prostate cancer cases, we identify two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49 × 10(-9)) and rs78943174 at 3q26.31 (NAALADL2, P=4.18 × 10(-8)). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85 × 10(-5)) with no association for nonaggressive prostate cancer compared with controls (P=0.57). The proximity of these loci to genes involved in vascular disease suggests potential biological mechanisms worthy of further investigation.
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Affiliation(s)
- Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Zhaoming Wang
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA [2] Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Meredith Yeager
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA [2] Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Michael C Alavanja
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Gerald Andriole
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Laura Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jean-Nicolas Cornu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Olivier Cussenot
- CeRePP, Assistance Publique-Hôpitaux de Paris, UPMC University Paris 6, Paris, France
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 17177, Sweden
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Brian Henderson
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Sara Lindström
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London SW7 2AZ, UK
| | - Fred Schumacher
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Janet L Stanford
- 1] Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA [2] Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington 98195, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Konstantinos K Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Fredrik Wilkund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 17177, Sweden
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - William Wheeler
- Information Management Services Inc., Rockville, Maryland 20852, USA
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Kevin Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
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Stegeman S, Amankwah E, Klein K, O'Mara TA, Kim D, Lin HY, Permuth-Wey J, Sellers TA, Srinivasan S, Eeles R, Easton D, Kote-Jarai Z, Amin Al Olama A, Benlloch S, Muir K, Giles GG, Wiklund F, Gronberg H, Haiman CA, Schleutker J, Nordestgaard BG, Travis RC, Neal D, Pharoah P, Khaw KT, Stanford JL, Blot WJ, Thibodeau S, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Brenner H, Kaneva R, Teixeira MR, Spurdle AB, Clements JA, Park JY, Batra J. A Large-Scale Analysis of Genetic Variants within Putative miRNA Binding Sites in Prostate Cancer. Cancer Discov 2015; 5:368-79. [PMID: 25691096 PMCID: PMC4390388 DOI: 10.1158/2159-8290.cd-14-1057] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 02/02/2015] [Indexed: 02/02/2023]
Abstract
UNLABELLED Prostate cancer is the second most common malignancy among men worldwide. Genome-wide association studies have identified 100 risk variants for prostate cancer, which can explain approximately 33% of the familial risk of the disease. We hypothesized that a comprehensive analysis of genetic variations found within the 3' untranslated region of genes predicted to affect miRNA binding (miRSNP) can identify additional prostate cancer risk variants. We investigated the association between 2,169 miRSNPs and prostate cancer risk in a large-scale analysis of 22,301 cases and 22,320 controls of European ancestry from 23 participating studies. Twenty-two miRSNPs were associated (P<2.3×10(-5)) with risk of prostate cancer, 10 of which were within 7 genes previously not mapped by GWAS studies. Further, using miRNA mimics and reporter gene assays, we showed that miR-3162-5p has specific affinity for the KLK3 rs1058205 miRSNP T-allele, whereas miR-370 has greater affinity for the VAMP8 rs1010 miRSNP A-allele, validating their functional role. SIGNIFICANCE Findings from this large association study suggest that a focus on miRSNPs, including functional evaluation, can identify candidate risk loci below currently accepted statistical levels of genome-wide significance. Studies of miRNAs and their interactions with SNPs could provide further insights into the mechanisms of prostate cancer risk.
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Affiliation(s)
- Shane Stegeman
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Ernest Amankwah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Kerenaftali Klein
- Statistics Unit, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Tracy A O'Mara
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Donghwa Kim
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Hui-Yi Lin
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | | | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Srilakshmi Srinivasan
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Rosalind Eeles
- The Institute of Cancer Research, London, United Kingdom. Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, United Kingdom
| | - Doug Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | | | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland. Institute of Biomedical Technology/BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - David Neal
- Surgical Oncology (Uro-Oncology: S4), University of Cambridge, Addenbrooke's Hospital, Cambridge; Cancer Research UK, Cambridge Research Institute, Cambridge, United Kingdom
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | - Kay-Tee Khaw
- Cambridge Institute of Public Health, University of Cambridge, Cambridge, United Kingdom
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - William J Blot
- International Epidemiology Institute, Rockville, Maryland
| | | | - Christiane Maier
- Department of Urology, University Hospital Ulm, Ulm, Germany. Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Adam S Kibel
- Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts. Washington University, St. Louis, Missouri
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany. German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Radka Kaneva
- Molecular Medicine Center and Department of Medical Chemistry and Biochemistry, Medical University-Sofia, Sofia, Bulgaria
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto; Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Judith A Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, Australia.
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Gao P, Jin Z, Cheng Y, Cao X. RNA-Seq analysis identifies aberrant RNA splicing of TRIP12 in acute myeloid leukemia patients at remission. Tumour Biol 2014; 35:9585-90. [PMID: 24961348 DOI: 10.1007/s13277-014-2228-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/11/2014] [Indexed: 11/27/2022] Open
Abstract
Aberrant splicing events play important roles in the pathogenesis of acute myeloid leukemia (AML). To investigate the aberrant splicing events in AML during treatment, we carried out RNA sequencing in peripheral mononuclear cell samples from a patient with complete remission. In addition to the sequencing samples, selected splicing events were confirmed and validated with real-time quantitative RT-PCR in another seven pairs of samples. A total of 4.05 and 3.39 GB clean data of the AML and remission sample were generated, respectively, and 2,223 differentially expressed genes (DEGs) were identified. Integrated with gene expression profiling on T cells from AML patients compared with healthy donors, 82 DEGs were also differentially expressed in AML CD4 T cells and CD8 T cells. Twenty-three alternative splicing events were considered to be confidential, and they were involved in many biological processes, such as RNA processing, cellular macromolecule catabolic process, and DNA binding process. An exon3-skipping event in TRIP12 was detected in patients at remission and further validated in another three independent samples. TRIP12 is an ubiquitin ligase of ARF, which suppresses aberrant cell growth by activating p53 responses. The exon3-skipping isoform of TRIP12 increased significantly after treatment. Our results may provide new understanding of AML, and the confirmed alternative splicing event of TRIP12 may be used as potential target for future investigations.
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Affiliation(s)
- Panke Gao
- Department of Hematology, The Third Hospital Affiliated to Suzhou University, First People's Hospital of Changzhou, Changzhou, 213003, Jiangsu, China
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Reinhardt D, Helfand BT, Cooper PR, Roehl KA, Catalona WJ, Loeb S. Prostate cancer risk alleles are associated with prostate cancer volume and prostate size. J Urol 2014; 191:1733-6. [PMID: 24345439 PMCID: PMC4107200 DOI: 10.1016/j.juro.2013.12.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2013] [Indexed: 11/17/2022]
Abstract
PURPOSE Genome-wide association studies have identified an increasing number of single nucleotide polymorphisms associated with prostate cancer risk. Some of these genetic variants are also associated with serum prostate specific antigen levels and lower urinary tract symptoms, raising the question of whether they are truly prostate cancer biomarkers or simply lead to detection bias. Therefore, we determined whether single nucleotide polymorphisms associated with prostate cancer risk are more strongly associated with tumor or prostate volume. MATERIALS AND METHODS The genotypes of 38 validated prostate cancer risk single nucleotide polymorphisms were determined in 1,321 white men who underwent radical prostatectomy. Univariate and multivariate analyses were performed to compare the relationship of single nucleotide polymorphism frequency with total prostate and tumor volumes. RESULTS On multivariate analysis 2 single nucleotide polymorphisms on chromosome 8q24, rs16901979 (A) and rs6983267 (G), were significantly associated with increased tumor volume (p=0.01 and 0.02, respectively). In contrast, rs17632542 (T) near the PSA gene on 19q13 was associated with significantly lower tumor volume and rs10788160 (A) on 10q26 was associated with significantly larger prostate volume (p=0.02 and 0.01, respectively). CONCLUSIONS Analysis of 38 single nucleotide polymorphisms associated with prostate cancer risk revealed a significant association between several on chromosome 8q24 and increased tumor volume but not prostate volume. This suggests that they are bona fide markers of prostate cancer susceptibility and possibly more aggressive disease. Other prostate cancer risk alleles are associated with prostate specific antigen and increased prostate or decreased tumor volume, suggesting detection bias due to their phenotypic influence.
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Affiliation(s)
- Daniel Reinhardt
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Brian T Helfand
- Division of Urology, NorthShore University Healthcare System, Evanston, Illinois
| | - Phillip R Cooper
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kimberly A Roehl
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - William J Catalona
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stacy Loeb
- Department of Urology and Population Health, New York University and Manhattan Veterans Affairs, New York, New York.
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Helfand BT, Catalona WJ. The Epidemiology and Clinical Implications of Genetic Variation in Prostate Cancer. Urol Clin North Am 2014; 41:277-97. [DOI: 10.1016/j.ucl.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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50
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NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood 2014; 123:2816-25. [PMID: 24574459 DOI: 10.1182/blood-2013-02-481507] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our previous studies revealed an increase in alternative splicing of multiple RNAs in cells from patients with acute myeloid leukemia (AML) compared with CD34(+) bone marrow cells from normal donors. Aberrantly spliced genes included a number of oncogenes, tumor suppressor genes, and genes involved in regulation of apoptosis, cell cycle, and cell differentiation. Among the most commonly mis-spliced genes (>70% of AML patients) were 2, NOTCH2 and FLT3, that encode myeloid cell surface proteins. The splice variants of NOTCH2 and FLT3 resulted from complete or partial exon skipping and utilization of cryptic splice sites. Longitudinal analyses suggested that NOTCH2 and FLT3 aberrant splicing correlated with disease status. Correlation analyses between splice variants of these genes and clinical features of patients showed an association between NOTCH2-Va splice variant and overall survival of patients. Our results suggest that NOTCH2 and FLT3 mis-splicing is a common characteristic of AML and has the potential to generate transcripts encoding proteins with altered function. Thus, splice variants of these genes might provide disease markers and targets for novel therapeutics.
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