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Association of Melanoma-Risk Variants with Primary Melanoma Tumor Prognostic Characteristics and Melanoma-Specific Survival in the GEM Study. Curr Oncol 2021; 28:4756-4771. [PMID: 34898573 PMCID: PMC8628692 DOI: 10.3390/curroncol28060401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/11/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWAS) and candidate pathway studies have identified low-penetrant genetic variants associated with cutaneous melanoma. We investigated the association of melanoma-risk variants with primary melanoma tumor prognostic characteristics and melanoma-specific survival. The Genes, Environment, and Melanoma Study enrolled 3285 European origin participants with incident invasive primary melanoma. For each of 47 melanoma-risk single nucleotide polymorphisms (SNPs), we used linear and logistic regression modeling to estimate, respectively, the per allele mean changes in log of Breslow thickness and odds ratios for presence of ulceration, mitoses, and tumor-infiltrating lymphocytes (TILs). We also used Cox proportional hazards regression modeling to estimate the per allele hazard ratios for melanoma-specific survival. Passing the false discovery threshold (p = 0.0026) were associations of IRF4 rs12203592 and CCND1 rs1485993 with log of Breslow thickness, and association of TERT rs2242652 with presence of mitoses. IRF4 rs12203592 also had nominal associations (p < 0.05) with presence of mitoses and melanoma-specific survival, as well as a borderline association (p = 0.07) with ulceration. CCND1 rs1485993 also had a borderline association with presence of mitoses (p = 0.06). MX2 rs45430 had nominal associations with log of Breslow thickness, presence of mitoses, and melanoma-specific survival. Our study indicates that further research investigating the associations of these genetic variants with underlying biologic pathways related to tumor progression is warranted.
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Landi MT, Bishop DT, MacGregor S, Machiela MJ, Stratigos AJ, Ghiorzo P, Brossard M, Calista D, Choi J, Fargnoli MC, Zhang T, Rodolfo M, Trower AJ, Menin C, Martinez J, Hadjisavvas A, Song L, Stefanaki I, Scolyer R, Yang R, Goldstein AM, Potrony M, Kypreou KP, Pastorino L, Queirolo P, Pellegrini C, Cattaneo L, Zawistowski M, Gimenez-Xavier P, Rodriguez A, Elefanti L, Manoukian S, Rivoltini L, Smith BH, Loizidou MA, Del Regno L, Massi D, Mandala M, Khosrotehrani K, Akslen LA, Amos CI, Andresen PA, Avril MF, Azizi E, Soyer HP, Bataille V, Dalmasso B, Bowdler LM, Burdon KP, Chen WV, Codd V, Craig JE, Dębniak T, Falchi M, Fang S, Friedman E, Simi S, Galan P, Garcia-Casado Z, Gillanders EM, Gordon S, Green A, Gruis NA, Hansson J, Harland M, Harris J, Helsing P, Henders A, Hočevar M, Höiom V, Hunter D, Ingvar C, Kumar R, Lang J, Lathrop GM, Lee JE, Li X, Lubiński J, Mackie RM, Malt M, Malvehy J, McAloney K, Mohamdi H, Molven A, Moses EK, Neale RE, Novaković S, Nyholt DR, Olsson H, Orr N, Fritsche LG, Puig-Butille JA, Qureshi AA, Radford-Smith GL, Randerson-Moor J, Requena C, Rowe C, Samani NJ, Sanna M, Schadendorf D, Schulze HJ, Simms LA, Smithers M, Song F, Swerdlow AJ, van der Stoep N, Kukutsch NA, Visconti A, Wallace L, Ward SV, Wheeler L, Sturm RA, Hutchinson A, Jones K, Malasky M, Vogt A, Zhou W, Pooley KA, Elder DE, Han J, Hicks B, Hayward NK, Kanetsky PA, Brummett C, Montgomery GW, Olsen CM, Hayward C, Dunning AM, Martin NG, Evangelou E, Mann GJ, Long G, Pharoah PDP, Easton DF, Barrett JH, Cust AE, Abecasis G, Duffy DL, Whiteman DC, Gogas H, De Nicolo A, Tucker MA, Newton-Bishop JA, Peris K, Chanock SJ, Demenais F, Brown KM, Puig S, Nagore E, Shi J, Iles MM, Law MH. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility. Nat Genet 2020; 52:494-504. [PMID: 32341527 PMCID: PMC7255059 DOI: 10.1038/s41588-020-0611-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
Most genetic susceptibility to cutaneous melanoma remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 cases of melanoma (67% newly genotyped) and 375,188 controls identified 54 significant (P < 5 × 10-8) loci with 68 independent single nucleotide polymorphisms. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with GWAS of nevus count and hair color, and transcriptome association approaches, uncovered 31 potential secondary loci for a total of 85 cutaneous melanoma susceptibility loci. These findings provide insights into cutaneous melanoma genetic architecture, reinforcing the importance of nevogenesis, pigmentation and telomere maintenance, together with identifying potential new pathways for cutaneous melanoma pathogenesis.
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Affiliation(s)
- Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexander J Stratigos
- Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Paola Ghiorzo
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Myriam Brossard
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Concetta Fargnoli
- Department of Dermatology & Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Adam J Trower
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Venito Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Andreas Hadjisavvas
- Department of EM/Molecular Pathology & The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Stefanaki
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Richard Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
- New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Rose Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miriam Potrony
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Katerina P Kypreou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Lorenza Pastorino
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Paola Queirolo
- Medical Oncology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Cristina Pellegrini
- Department of Dermatology & Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Laura Cattaneo
- Pathology Unit, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pol Gimenez-Xavier
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Arantxa Rodriguez
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Venito Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Maria A Loizidou
- Department of EM/Molecular Pathology & The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Laura Del Regno
- Institute of Dermatology, Catholic University, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Mario Mandala
- Department of Oncology, Giovanni XXIII Hospital, Bergamo, Italy
| | - Kiarash Khosrotehrani
- UQ Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Christopher I Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Per A Andresen
- Department of Pathology, Molecular Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marie-Françoise Avril
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service de Dermatologie, Université Paris Descartes, Paris, France
| | - Esther Azizi
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv, Israel
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H Peter Soyer
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Bruna Dalmasso
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Lisa M Bowdler
- Sample Processing, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Wei V Chen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Tadeusz Dębniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eitan Friedman
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarah Simi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Pilar Galan
- Université Paris 13, Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Institut National de la Santé et de la Recherche Médicale (INSERM U1153), Institut National de la Recherche Agronomique (INRA U1125), Conservatoire National des Arts et Métiers, Communauté d'Université Sorbonne Paris Cité, Bobigny, France
| | - Zaida Garcia-Casado
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Elizabeth M Gillanders
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Scott Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Adele Green
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- CRUK Manchester Institute, Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mark Harland
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jessica Harris
- Translational Research Institute, Institute of Health and Biomedical Innovation, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Per Helsing
- Department of Dermatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Anjali Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marko Hočevar
- Department of Surgical Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Lund, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Julie Lang
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
| | - G Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Jan Lubiński
- International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Rona M Mackie
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
- Department of Public Health, University of Glasgow, Glasgow, UK
| | - Maryrose Malt
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Josep Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Kerrie McAloney
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hamida Mohamdi
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Anders Molven
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Rachel E Neale
- Cancer Aetiology & Prevention, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Dale R Nyholt
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Håkan Olsson
- Department of Oncology/Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nicholas Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Lars G Fritsche
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Joan Anton Puig-Butille
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona,CIBERER, Barcelona, Spain
| | - Abrar A Qureshi
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Graham L Radford-Smith
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology and Hepatology, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
- University of Queensland School of Medicine, Herston Campus, Brisbane, Queensland, Australia
| | | | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Casey Rowe
- UQ Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Marianna Sanna
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
- German Consortium Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Hans-Joachim Schulze
- Department of Dermatology, Fachklinik Hornheide, Institute for Tumors of the Skin, University of Münster, Münster, Germany
| | - Lisa A Simms
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Smithers
- Queensland Melanoma Project, Princess Alexandra Hospital, The University of Queensland, St Lucia, Queensland, Australia
- Mater Research Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Fengju Song
- Departments of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, P. R. China
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nienke van der Stoep
- Department of Clinical Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nicole A Kukutsch
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Sarah V Ward
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lawrie Wheeler
- Translational Research Institute, Institute of Health and Biomedical Innovation, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Michael Malasky
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Karen A Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - David E Elder
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Nicholas K Hayward
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chad Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, Sydney, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georgina Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore Hospital, Sydney, Australia
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | | | - Anne E Cust
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Cancer Epidemiology and Prevention Research, Sydney School of Public Health, Sydney, Australia
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - David L Duffy
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Helen Gogas
- First Department of Internal Medicine, Laikon General Hospital Greece, National and Kapodistrian University of Athens, Athens, Greece
| | - Arcangela De Nicolo
- Cancer Genomics Program, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Ketty Peris
- Institute of Dermatology, Catholic University, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florence Demenais
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK.
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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Inherited Melanoma Risk Variants Associated with Histopathologically Amelanotic Melanoma. J Invest Dermatol 2019; 140:918-922.e7. [PMID: 31568773 DOI: 10.1016/j.jid.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 01/26/2023]
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Thomas NE, Edmiston SN, Orlow I, Kanetsky PA, Luo L, Gibbs DC, Parrish EA, Hao H, Busam KJ, Armstrong BK, Kricker A, Cust AE, Anton-Culver H, Gruber SB, Gallagher RP, Zanetti R, Rosso S, Sacchetto L, Dwyer T, Ollila DW, Begg CB, Berwick M, Conway K. Inherited Genetic Variants Associated with Melanoma BRAF/NRAS Subtypes. J Invest Dermatol 2018; 138:2398-2404. [PMID: 29753029 PMCID: PMC6200630 DOI: 10.1016/j.jid.2018.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 04/08/2018] [Indexed: 10/16/2022]
Abstract
BRAF and NRAS mutations arise early in melanoma development, but their associations with low-penetrance melanoma susceptibility loci remain unknown. In the Genes, Environment and Melanoma Study, 1,223 European-origin participants had their incident invasive primary melanomas screened for BRAF/NRAS mutations and germline DNA genotyped for 47 single-nucleotide polymorphisms identified as low-penetrant melanoma-risk variants. We used multinomial logistic regression to simultaneously examine each single-nucleotide polymorphism's relationship to BRAF V600E, BRAF V600K, BRAF other, and NRAS+ relative to BRAF-/NRAS- melanoma adjusted for study features. IRF4 rs12203592*T was associated with BRAF V600E (odds ratio [OR] = 0.59, 95% confidence interval [CI] = 0.43-0.79) and V600K (OR = 0.65, 95% CI = 0.41-1.03), but not BRAF other or NRAS+ melanoma. A global test of etiologic heterogeneity (Pglobal = 0.001) passed false discovery (Pglobal = 0.0026). PLA2G6 rs132985*T was associated with BRAF V600E (OR = 1.32, 95% CI = 1.05-1.67) and BRAF other (OR = 1.82, 95% CI = 1.11-2.98), but not BRAF V600K or NRAS+ melanoma. The test for etiologic heterogeneity (Pglobal) was 0.005. The IRF4 rs12203592 associations were slightly attenuated after adjustment for melanoma-risk phenotypes. The PLA2G6 rs132985 associations were independent of phenotypes. IRF4 and PLA2G6 inherited genotypes may influence melanoma BRAF/NRAS subtype development.
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Affiliation(s)
- Nancy E Thomas
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
| | - Sharon N Edmiston
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Li Luo
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | - David C Gibbs
- Department of Epidemiology, Emory University, Atlanta, Georgia, USA
| | - Eloise A Parrish
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Honglin Hao
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Bruce K Armstrong
- School of Public and Global Health, The University of Western Australia, Perth, Australia
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Anne E Cust
- Sydney School of Public Health, The University of Sydney, Sydney, Australia; Melanoma Institute Australia, The University of Sydney, North Sydney, Australia
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California, Irvine, California, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Richard P Gallagher
- British Columbia Cancer and Department of Dermatology and Skin Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roberto Zanetti
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - Stefano Rosso
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - Lidia Sacchetto
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy; Politecnico di Torino, Turin, Italy
| | - Terence Dwyer
- George Institute for Global Health, Nuffield Department of Obstetrics and Gynecology, University of Oxford, Oxford, UK
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Surgery, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | - Kathleen Conway
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
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5
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Yu Y, Hu H, Chen JS, Hu F, Fowler J, Scheet P, Zhao H, Huff CD. Integrated case-control and somatic-germline interaction analyses of melanoma susceptibility genes. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2247-2254. [PMID: 29317335 DOI: 10.1016/j.bbadis.2018.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/20/2017] [Accepted: 01/04/2018] [Indexed: 12/18/2022]
Abstract
While a number of genes have been implicated in melanoma susceptibility, the role of protein-coding variation in melanoma development and progression remains underexplored. To better characterize the role of germline coding variation in melanoma, we conducted a whole-exome case-control and somatic-germline interaction study involving 322 skin cutaneous melanoma cases from The Cancer Genome Atlas and 3607 controls of European ancestry. We controlled for cross-platform technological stratification using XPAT and conducted gene-based association tests using VAAST 2. Four established melanoma susceptibility genes achieved nominal statistical significance, MC1R (p = .0014), MITF (p = .0165) BRCA2 (p = .0206), and MTAP (p = .0393). We also observed a suggestive association for FANCA (p = .002), a gene previously implicated in melanoma survival. The association signal for BRCA2 was driven primarily by likely gene disrupting (LGD) variants, with an Odds Ratio (OR) of 5.62 (95% Confidence Interval (CI) 1.03-30.1). In contrast, the association signals for MC1R and MITF were driven primarily by predicted pathogenic missense variants, with estimated ORs of 1.4 to 3.0 for MC1R and 4.1 for MITF. MTAP exhibited an excess of both LGD and predicted damaging missense variants among cases, with ORs of 5.62 and 3.72, respectively, although neither category was significant. For individuals with known or predicted damaging variants, age of disease onset was significantly lower for two of the four genes, MC1R (p = .005) and MTAP (p = .035). In an analysis of germline carrier status and overlapping copy number alterations, we observed no evidence to support a two-hit model of carcinogenesis in any of the four genes. Although MC1R carriers were represented proportionally among the four molecular tumor subtypes, these individuals accounted for 69% of ultraviolet (UV) radiation mutational signatures among triple-wild type tumors (p = .040), highlighting the increased sensitivity to UV exposure among individuals with loss-of-function variants in MC1R.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Fulan Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Montgomery GW. Discovery of genetic risk factors for disease. J R Soc N Z 2017. [DOI: 10.1080/03036758.2017.1392324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Grant W. Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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7
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Liang WS, Hendricks W, Kiefer J, Schmidt J, Sekar S, Carpten J, Craig DW, Adkins J, Cuyugan L, Manojlovic Z, Halperin RF, Helland A, Nasser S, Legendre C, Hurley LH, Sivaprakasam K, Johnson DB, Crandall H, Busam KJ, Zismann V, Deluca V, Lee J, Sekulic A, Ariyan CE, Sosman J, Trent J. Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. Genome Res 2017; 27:524-532. [PMID: 28373299 PMCID: PMC5378171 DOI: 10.1101/gr.213348.116] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/24/2017] [Indexed: 12/25/2022]
Abstract
Genomic analyses of cutaneous melanoma (CM) have yielded biological and therapeutic insights, but understanding of non-ultraviolet (UV)-derived CMs remains limited. Deeper analysis of acral lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic and transcriptomic analysis of 34 ALM patients. Unlike CM, somatic alterations were dominated by structural variation and absence of UV-derived mutation signatures. Only 38% of patients demonstrated driver BRAF/NRAS/NF1 mutations. In contrast with CM, we observed PAK1 copy gains in 15% of patients, and somatic TERT translocations, copy gains, and missense and promoter mutations, or germline events, in 41% of patients. We further show that in vitro TERT inhibition has cytotoxic effects on primary ALM cells. These findings provide insight into the role of TERT in ALM tumorigenesis and reveal preliminary evidence that TERT inhibition represents a potential therapeutic strategy in ALM.
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Affiliation(s)
- Winnie S. Liang
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - William Hendricks
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jeffrey Kiefer
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | | | - Shobana Sekar
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - John Carpten
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - David W. Craig
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jonathan Adkins
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Zarko Manojlovic
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | | | - Adrienne Helland
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | | | | | | | | | - Holly Crandall
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Klaus J. Busam
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Victoria Zismann
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Valerie Deluca
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jeeyun Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea
| | - Aleksandar Sekulic
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA;,Mayo Clinic, Scottsdale, Arizona 85259, USA
| | | | - Jeffrey Sosman
- Northwestern University, Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois 60611, USA
| | - Jeffrey Trent
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
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8
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Zhang T, Dutton-Regester K, Brown KM, Hayward NK. The genomic landscape of cutaneous melanoma. Pigment Cell Melanoma Res 2016; 29:266-83. [PMID: 26833684 DOI: 10.1111/pcmr.12459] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/25/2016] [Indexed: 12/31/2022]
Abstract
Somatic mutation analysis of melanoma has been performed at the single gene level extensively over the past several decades. This has provided considerable insight into the critical pathways controlling melanoma initiation and progression. During the last 5 yr, next-generation sequencing (NGS) has enabled even more comprehensive mutational screening at the level of multigene panels, exomes and genomes. These studies have uncovered many new and unexpected players in melanoma development. The recent landmark study from The Cancer Genome Atlas (TCGA) consortium describing the genomic architecture of 333 cutaneous melanomas provides the largest and broadest analysis to date on the somatic aberrations underlying melanoma genesis. It thus seems timely to review the mutational landscape of melanoma and highlight the key genes and cellular pathways that appear to drive this cancer.
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Affiliation(s)
- Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ken Dutton-Regester
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
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9
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Gibbs DC, Orlow I, Bramson JI, Kanetsky PA, Luo L, Kricker A, Armstrong BK, Anton-Culver H, Gruber SB, Marrett LD, Gallagher RP, Zanetti R, Rosso S, Dwyer T, Sharma A, La Pilla E, From L, Busam KJ, Cust AE, Ollila DW, Begg CB, Berwick M, Thomas NE. Association of Interferon Regulatory Factor-4 Polymorphism rs12203592 With Divergent Melanoma Pathways. J Natl Cancer Inst 2016; 108:djw004. [PMID: 26857527 DOI: 10.1093/jnci/djw004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/05/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Solar elastosis and neval remnants are histologic markers characteristic of divergent melanoma pathways linked to differences in age at onset, host phenotype, and sun exposure. However, the association between these pathway markers and newly identified low-penetrance melanoma susceptibility loci remains unknown. METHODS In the Genes, Environment and Melanoma (GEM) Study, 2103 Caucasian participants had first primary melanomas that underwent centralized pathology review. For 47 single-nucleotide polymorphisms (SNPs) previously identified as low-penetrant melanoma risk variants, we used multinomial logistic regression to compare melanoma with solar elastosis and melanoma with neval remnants simultaneously to melanoma with neither of these markers, excluding melanomas with both markers. All statistical tests were two-sided. RESULTS IRF4 rs12203592 was the only SNP to pass the false discovery threshold in baseline models adjusted for age, sex, and study center. rs12203592*T was associated positively with melanoma with solar elastosis (odds ratio [OR] = 1.47, 95% confidence interval [CI] = 1.18 to 1.82) and inversely with melanoma with neval remnants (OR = 0.65, 95% CI = 0.48 to 0.87) compared with melanoma with neither marker (P global = 3.78 x 10(-08)). Adjusting for phenotypic characteristics and total sun exposure hours did not materially affect rs12203592's associations. Distinct early- and late-onset age distributions were observed in patients with IRF4 rs12203592 [CC] and [TT] genotypes, respectively. CONCLUSIONS Our findings suggest a role of IRF4 rs12203592 in pathway-specific risk for melanoma development. We hypothesize that IRF4 rs12203592 could underlie in part the bimodal age distribution reported for melanoma and linked to the divergent pathways.
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Affiliation(s)
- David C Gibbs
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Irene Orlow
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Jennifer I Bramson
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Peter A Kanetsky
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Li Luo
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Anne Kricker
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Bruce K Armstrong
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Hoda Anton-Culver
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Stephen B Gruber
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Loraine D Marrett
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Richard P Gallagher
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Roberto Zanetti
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Stefano Rosso
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Terence Dwyer
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Ajay Sharma
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Emily La Pilla
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Lynn From
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Klaus J Busam
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Anne E Cust
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - David W Ollila
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Colin B Begg
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Marianne Berwick
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Nancy E Thomas
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF).
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Zhang M, Wu X, Lu W, Ge Y, Wang X, Cai Z, Wu S. Rs401681 polymorphism in TERT-CLPTM1L was associated with bladder cancer risk: A meta-analysis. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2015; 18:1130-6. [PMID: 26949502 PMCID: PMC4764116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Genome-wide association studies have identified a number of genetic variants of telomerase reverse transcriptase (TERT), cleft lip and palate transmembrane1-like (CLPTM1L) associated with the risk of bladder cancer. Rs401681 polymorphism in TERT-CLPTM1L was of special interest for bladder cancer risk, whereas the results were inconclusive. MATERIALS AND METHODS Publications illustrating the association between rs401681 polymorphism and bladder cancer risk were collected from the Embase, PubMed and Google scholar. Three independent reviewers worked on the data extraction. The meta-analysis was performed by STATA 12.0. The odds ratio (OR) with 95% confidence interval (CI) was calculated for these data. RESULTS Six case-control studies were retrieved reporting a total of 9196 bladder cancer patients and 42570 controls. The strength of the relevance between rs401681 polymorphism and bladder cancer risk was evaluated by Stata 12.0 software. Rs401681[C] allele was identified marginally associated with increased bladder cancer risk, with per allele OR of 1.132 (95% CI=1.080-1.187, P heterogeneity=0.701); in the stratified analysis by ethnicity, the increased cancer risk was revealed in Asian and Caucasian groups. Moreover, we also revealed that rs401681 polymorphism was associated with an increased risk of bladder cancer in Asian population with three publications under allele model (OR=3.722, 95% CI=1.311-10.568, P=0.014), whereas a decreased risk was identified in homozygote model (OR=0.692, 95 % CI=0.513-0.934, P= 0.016) and recessive model (OR=0.728, 95% CI=0.541-0.980, P=0.036). CONCLUSION In summary, our study provided evidence that rs401681 polymorphism is associated with the risk of bladder cancer.
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Affiliation(s)
- Meng Zhang
- Anhui Medical University, Hefei, Anhui, China (230032),BGI-Shenzhen, Shenzhen, China (518000)
| | - Xun Wu
- BGI-Shenzhen, Shenzhen, China (518000),Department of Anatomy, School of Basic Medicine Science, Southern Medical University, Guangzhou, China (510000)
| | - Wei Lu
- Anhui Medical University, Hefei, Anhui, China (230032),BGI-Shenzhen, Shenzhen, China (518000)
| | - Yukun Ge
- BGI-Shenzhen, Shenzhen, China (518000),Department of Urology, Zhujiang Hospital, Southern Medical University, China
| | - Xiang Wang
- Anhui Medical University, Hefei, Anhui, China (230032),BGI-Shenzhen, Shenzhen, China (518000)
| | - Zhiming Cai
- Anhui Medical University, Hefei, Anhui, China (230032)
| | - Song Wu
- Anhui Medical University, Hefei, Anhui, China (230032),Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China (510000),Corresponding author: Song Wu. Department of Urology Surgery, Futian District, North Road, Shenzhen, Guangdong, CHINA. Tel: +0086010075583669030; Fax: +0086010075583669030;
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11
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Ribero S, Davies JR, Requena C, Carrera C, Glass D, Rull R, Vidal‐Sicart S, Vilalta A, Alos L, Soriano V, Quaglino P, Traves V, Newton‐Bishop JA, Nagore E, Malvehy J, Puig S, Bataille V. High nevus counts confer a favorable prognosis in melanoma patients. Int J Cancer 2015; 137:1691-8. [PMID: 25809795 PMCID: PMC4503475 DOI: 10.1002/ijc.29525] [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: 01/14/2015] [Accepted: 03/06/2015] [Indexed: 01/31/2023]
Abstract
A high number of nevi is the most significant phenotypic risk factor for melanoma and is in part genetically determined. The number of nevi decreases from middle age onward but this senescence can be delayed in patients with melanoma. We investigated the effects of nevus number count on sentinel node status and melanoma survival in a large cohort of melanoma cases. Out of 2,184 melanoma cases, 684 (31.3%) had a high nevus count (>50). High nevus counts were associated with favorable prognostic factors such as lower Breslow thickness, less ulceration and lower mitotic rate, despite adjustment for age. Nevus count was not predictive of sentinel node status. The crude 5- and 10-year melanoma-specific survival rate was higher in melanomas cases with a high nevus count compared to those with a low nevus count (91.2 vs. 86.4% and 87.2 vs. 79%, respectively). The difference in survival remained significant after adjusting for all known melanoma prognostic factors (hazard ratio [HR] = 0.43, confidence interval [CI] = 0.21-0.89). The favorable prognostic value of a high nevus count was also seen within the positive sentinel node subgroup of patients (HR = 0.22, CI = 0.08-0.60). High nevus count is associated with a better melanoma survival, even in the subgroup of patients with positive sentinel lymph node. This suggests a different biological behavior of melanoma tumors in patients with an excess of nevi.
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Affiliation(s)
- Simone Ribero
- Department of Twin Research & Genetic EpidemiologyKing's College LondonLondonUnited Kingdom
- Department of Medical Sciences, Section of DermatologyUniversity of TurinTurinItaly
- Department of DermatologyLondon North West Healthcare NHS Trust Northwick Park HospitalLondonUnited Kingdom
- Imperial College LondonLondonUnited Kingdom
| | - John R. Davies
- Section of Epidemiology and BiostatisticsLICAP, University of LeedsLeedsUnited Kingdom
| | - Celia Requena
- Department of DermatologyInstituto Valenciano De OncologıaValenciaSpain
| | - Cristina Carrera
- Department of DermatologyMelanoma Unit, Hospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Daniel Glass
- Department of Twin Research & Genetic EpidemiologyKing's College LondonLondonUnited Kingdom
- Department of DermatologyLondon North West Healthcare NHS Trust Northwick Park HospitalLondonUnited Kingdom
- Imperial College LondonLondonUnited Kingdom
| | - Ramon Rull
- Department of SurgeryMelanoma UnitHospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Sergi Vidal‐Sicart
- Department of Nuclear Medicine ServiceMelanoma Unit, Hospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Antonio Vilalta
- Department of DermatologyMelanoma Unit, Hospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Lucia Alos
- Department of Pathology ServiceMelanoma Unit, Hospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Virtudes Soriano
- Department of OncologyInstituto Valenciano De OncologıaValenciaSpain
| | - Pietro Quaglino
- Department of Medical Sciences, Section of DermatologyUniversity of TurinTurinItaly
| | - Victor Traves
- Department of PathologyInstituto Valenciano De OncologıaValenciaSpain
| | | | - Eduardo Nagore
- Department of DermatologyInstituto Valenciano De OncologıaValenciaSpain
| | - Josep Malvehy
- Department of DermatologyMelanoma Unit, Hospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
- Instituto de Salud Carlos IIICIBER on Rare DiseasesBarcelonaSpain
| | - Susana Puig
- Department of DermatologyMelanoma Unit, Hospital Clinic & IDIBAPS, University of BarcelonaBarcelonaSpain
- Instituto de Salud Carlos IIICIBER on Rare DiseasesBarcelonaSpain
| | - Veronique Bataille
- Department of Twin Research & Genetic EpidemiologyKing's College LondonLondonUnited Kingdom
- Department of DermatologyWest Herts NHS TrustHertfordshireUnited Kingdom
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12
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Abstract
Approximately 10% of melanoma cases report a relative affected with melanoma, and a positive family history is associated with an increased risk of developing melanoma. Although the majority of genetic alterations associated with melanoma development are somatic, the underlying presence of heritable melanoma risk genes is an important component of disease occurrence. Susceptibility for some families is due to mutation in one of the known high penetrance melanoma predisposition genes: CDKN2A, CDK4, BAP1, POT1, ACD, TERF2IP and TERT. However, despite such mutations being implicated in a combined total of approximately 50% of familial melanoma cases, the underlying genetic basis is unexplained for the remainder of high-density melanoma families. Aside from the possibility of extremely rare mutations in a few additional high penetrance genes yet to be discovered, this suggests a likely polygenic component to susceptibility, and a unique level of personal melanoma risk influenced by multiple low-risk alleles and genetic modifiers. In addition to conferring a risk of cutaneous melanoma, some 'melanoma' predisposition genes have been linked to other cancers, with cancer clustering observed in melanoma families at rates greater than expected by chance. The most extensively documented association is between CDKN2A germ line mutations and pancreatic cancer, and a cancer syndrome including cutaneous melanoma, uveal melanoma and mesothelioma has been proposed for BAP1 germ line mutations. Other medium to high penetrance melanoma predisposition genes have been associated with renal cell carcinoma (MITF, BAP1) and glioma (POT1). These associations between melanoma and other cancers hint at the possibility of common pathways for oncogenesis, and better knowledge of these pathways may improve understanding of the genetic basis underpinning familial melanoma. It is likely that 'melanoma' risk genes will impact on mutation screening and genetic counselling not only for melanoma but also a range of other cancers.
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Affiliation(s)
- Jazlyn Read
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia The University of Queensland, Brisbane, Queensland, Australia
| | - Karin A W Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Law MH, Bishop DT, Lee JE, Brossard M, Martin NG, Moses EK, Song F, Barrett JH, Kumar R, Easton DF, Pharoah PDP, Swerdlow AJ, Kypreou KP, Taylor JC, Harland M, Randerson-Moor J, Akslen LA, Andresen PA, Avril MF, Azizi E, Scarrà GB, Brown KM, Dȩbniak T, Duffy DL, Elder DE, Fang S, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Kanetsky PA, Chen WV, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Mann GJ, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, Qureshi AA, Radford-Smith GL, van der Stoep N, van Doorn R, Whiteman DC, Craig JE, Schadendorf D, Simms LA, Burdon KP, Nyholt DR, Pooley KA, Orr N, Stratigos AJ, Cust AE, Ward SV, Hayward NK, Han J, Schulze HJ, Dunning AM, Bishop JAN, Demenais F, Amos CI, MacGregor S, Iles MM. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma. Nat Genet 2015; 47:987-995. [PMID: 26237428 PMCID: PMC4557485 DOI: 10.1038/ng.3373] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 07/09/2015] [Indexed: 12/17/2022]
Abstract
Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.
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Barón AE, Asdigian NL, Gonzalez V, Aalborg J, Terzian T, Stiegmann RA, Torchia EC, Berwick M, Dellavalle RP, Morelli JG, Mokrohisky ST, Crane LA, Box NF. Interactions between ultraviolet light and MC1R and OCA2 variants are determinants of childhood nevus and freckle phenotypes. Cancer Epidemiol Biomarkers Prev 2015; 23:2829-39. [PMID: 25410285 DOI: 10.1158/1055-9965.epi-14-0633] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Melanocytic nevi (moles) and freckles are well known biomarkers of melanoma risk, and they are influenced by similar UV light exposures and genetic susceptibilities to those that increase melanoma risk. Nevertheless, the selective interactions between UV exposures and nevus and freckling genes remain largely undescribed. METHODS We conducted a longitudinal study from ages 6 through 10 years in 477 Colorado children who had annual information collected for sun exposure, sun protection behaviors, and full body skin exams. MC1R and HERC2/OCA2 rs12913832 were genotyped and linear mixed models were used to identify main and interaction effects. RESULTS All measures of sun exposure (chronic, sunburns, and waterside vacations) contributed to total nevus counts, and cumulative chronic exposure acted as the major driver of nevus development. Waterside vacations strongly increased total nevus counts in children with rs12913832 blue eye color alleles and facial freckling scores in those with MC1R red hair color variants. Sunburns increased the numbers of larger nevi (≥2 mm) in subjects with certain MC1R and rs12913832 genotypes. CONCLUSIONS Complex interactions between different UV exposure profiles and genotype combinations determine nevus numbers and size, and the degree of facial freckling. IMPACT Our findings emphasize the importance of implementing sun-protective behavior in childhood regardless of genetic make-up, although children with particular genetic variants may benefit from specifically targeted preventive measures to counteract their inherent risk of melanoma. Moreover, we demonstrate, for the first time, that longitudinal studies are a highly powered tool to uncover new gene-environment interactions that increase cancer risk.
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Affiliation(s)
- Anna E Barón
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Nancy L Asdigian
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Victoria Gonzalez
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jenny Aalborg
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Tamara Terzian
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Regan A Stiegmann
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Enrique C Torchia
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Marianne Berwick
- Division of Epidemiology, University of New Mexico, Albuquerque, New Mexico
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Dermatology Service, Department of Veterans Affairs, Eastern Colorado Health Care System, Denver, Colorado. Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Joseph G Morelli
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Lori A Crane
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Neil F Box
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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15
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Kocarnik JM, Park SL, Han J, Dumitrescu L, Cheng I, Wilkens LR, Schumacher FR, Kolonel L, Carlson CS, Crawford DC, Goodloe RJ, Dilks HH, Baker P, Richardson D, Matise TC, Ambite JL, Song F, Qureshi AA, Zhang M, Duggan D, Hutter C, Hindorff L, Bush WS, Kooperberg C, Le Marchand L, Peters U. Pleiotropic and sex-specific effects of cancer GWAS SNPs on melanoma risk in the population architecture using genomics and epidemiology (PAGE) study. PLoS One 2015; 10:e0120491. [PMID: 25789475 PMCID: PMC4366224 DOI: 10.1371/journal.pone.0120491] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/22/2015] [Indexed: 11/19/2022] Open
Abstract
Background Several regions of the genome show pleiotropic associations with multiple cancers. We sought to evaluate whether 181 single-nucleotide polymorphisms previously associated with various cancers in genome-wide association studies were also associated with melanoma risk. Methods We evaluated 2,131 melanoma cases and 20,353 controls from three studies in the Population Architecture using Genomics and Epidemiology (PAGE) study (EAGLE-BioVU, MEC, WHI) and two collaborating studies (HPFS, NHS). Overall and sex-stratified analyses were performed across studies. Results We observed statistically significant associations with melanoma for two lung cancer SNPs in the TERT-CLPTM1L locus (Bonferroni-corrected p<2.8x10-4), replicating known pleiotropic effects at this locus. In sex-stratified analyses, we also observed a potential male-specific association between prostate cancer risk variant rs12418451 and melanoma risk (OR=1.22, p=8.0x10-4). No other variants in our study were associated with melanoma after multiple comparisons adjustment (p>2.8e-4). Conclusions We provide confirmatory evidence of pleiotropic associations with melanoma for two SNPs previously associated with lung cancer, and provide suggestive evidence for a male-specific association with melanoma for prostate cancer variant rs12418451. This SNP is located near TPCN2, an ion transport gene containing SNPs which have been previously associated with hair pigmentation but not melanoma risk. Previous evidence provides biological plausibility for this association, and suggests a complex interplay between ion transport, pigmentation, and melanoma risk that may vary by sex. If confirmed, these pleiotropic relationships may help elucidate shared molecular pathways between cancers and related phenotypes.
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Affiliation(s)
- Jonathan M. Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - S. Lani Park
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, United States of America
| | - Logan Dumitrescu
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Fredrick R. Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Laurence Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Chris S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Dana C. Crawford
- Department of Epidemiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Biostatistics Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Robert J. Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Holli H. Dilks
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Paxton Baker
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Danielle Richardson
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, California, United States of America
| | - Fengju Song
- Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Abrar A. Qureshi
- Department of Dermatology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Mingfeng Zhang
- Department of Dermatology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Carolyn Hutter
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, NCI, NIH, Bethesda, Maryland, United States of America
| | - Lucia Hindorff
- Division of Genomic Medicine, NHGRI, NIH, Bethesda, Maryland, Untied States of America
| | - William S. Bush
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Liu T, Jiang L, Lv X, Li J, Li Y, Li W, Li X, Li J. Association of CRR9 locus with elevated risk of squamous cell carcinoma and basal cell carcinoma. Int J Clin Exp Med 2015; 8:3761-3768. [PMID: 26064272 PMCID: PMC4443106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Published studies have generated inconsistent results related to the contribution of CRR9 rs401681 C allele to the risk of developing non-melanoma skin cancer (NMSC), and it is the inconsistency that promoted us to undertake a meta-analysis to identify the degree of impact the C allele has on NMSC. METHOD The PubMed, Science Direct, Embase and Cochrane Library were thoroughly searched from the start of November 2013 to the end of April 2014 by using CRR9, polymorphism, skin cancer and their synonyms. Based on a total of 44,036 subjects, we calculated ORs and 95% CIs to measure the influence of the C allele on NMSC predisposition. RESULTS Overall, individuals carrying the risk C allele at rs401681 had 1.16 times (OR = 1.16, 95% CI: 1.10-1.21, heterogeneity: P = 0.298 and I2 = 0.166, Figure 2) greater risk of NMSC compared to the common T allele. In the further stratified analyses, we found a significant association between the C allele and BCC, Icelanders, and non-Icelanders. CONCLUSION The results of this meta-analysis suggest that the C allele at rs401681 is likely to modify the genetic predisposition to NMSC.
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Affiliation(s)
- Tao Liu
- Department of Dermatology, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Li Jiang
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Xiaoxing Lv
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Jinqing Li
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Yuejun Li
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Wangzhou Li
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Xueyong Li
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
| | - Jing Li
- Department of Burns and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University569 Xinsi Road, Xi’an 710038, China
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Aoude LG, Wadt KAW, Pritchard AL, Hayward NK. Genetics of familial melanoma: 20 years after CDKN2A. Pigment Cell Melanoma Res 2015; 28:148-60. [PMID: 25431349 DOI: 10.1111/pcmr.12333] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/24/2014] [Indexed: 01/29/2023]
Abstract
Twenty years ago, the first familial melanoma susceptibility gene, CDKN2A, was identified. Two years later, another high-penetrance gene, CDK4, was found to be responsible for melanoma development in some families. Progress in identifying new familial melanoma genes was subsequently slow; however, with the advent of next-generation sequencing, a small number of new high-penetrance genes have recently been uncovered. This approach has identified the lineage-specific oncogene MITF as a susceptibility gene both in melanoma families and in the general population, as well as the discovery of telomere maintenance as a key pathway underlying melanoma predisposition. Given these rapid recent advances, this approach seems likely to continue to pay dividends. Here, we review the currently known familial melanoma genes, providing evidence that most additionally confer risk to other cancers, indicating that they are likely general tumour suppressor genes or oncogenes, which has significant implications for surveillance and screening.
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Affiliation(s)
- Lauren G Aoude
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia; University of Queensland, Brisbane, Qld, Australia
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18
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Llorca-Cardeñosa MJ, Peña-Chilet M, Mayor M, Gomez-Fernandez C, Casado B, Martin-Gonzalez M, Carretero G, Lluch A, Martinez-Cadenas C, Ibarrola-Villava M, Ribas G. Long telomere length and a TERT-CLPTM1 locus polymorphism association with melanoma risk. Eur J Cancer 2014; 50:3168-77. [PMID: 25457634 DOI: 10.1016/j.ejca.2014.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/02/2014] [Accepted: 09/28/2014] [Indexed: 11/22/2022]
Abstract
Telomere length has been associated with the development of cancer. Studies have shown that shorter telomere length may be related to a decreased risk of cutaneous melanoma. Furthermore, deregulation of the telomere-maintaining gene complexes, has been related to this oncogenic process. Some variants in these genes seem to be correlated with a change in telomerase expression. We examined the effect of 10 single nucleotide polymorphisms (SNPs) in the TERT gene (encoding telomerase), one SNP in the related TERT-CLPTM1L locus and one SNP in the TRF1 gene with telomere length, and its influence on melanoma risk in 970 Spanish cases and 733 Spanish controls. Genotypes were determined using KASP technology, and telomere length was measured by quantitative polymerase chain reaction (PCR) on DNA extracted from peripheral blood leucocytes. Our results demonstrate that shorter telomere length is associated with a decreased risk of melanoma in our population (global p-value, 2.69×10(-11)), which may be caused by a diminution of proliferative potential of nevi (melanoma precursor cells). We also obtained significant results when we tested the association between rs401681 variant (TERT-CLPTM1L locus) with melanoma risk (Odds ratio, OR; 95% confidence interval, CI=1.24 (1.08-1.43); p-value, 3×10(-3)). This is the largest telomere-related study undertaken in a Spanish population to date. Furthermore, this study represents a comprehensive analysis of some of the most relevant telomere pathway genes in relation to cutaneous melanoma susceptibility.
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Affiliation(s)
- Marta J Llorca-Cardeñosa
- Department of Hematology and Medical Oncology, Health Research Institute-INCLIVA, Valencia, Spain
| | - Maria Peña-Chilet
- Department of Hematology and Medical Oncology, Health Research Institute-INCLIVA, Valencia, Spain
| | - Matias Mayor
- Dermatology Unit, La Paz Hospital, Madrid, Spain
| | | | | | | | | | - Ana Lluch
- Department of Hematology and Medical Oncology, Health Research Institute-INCLIVA, Valencia, Spain
| | | | - Maider Ibarrola-Villava
- Department of Hematology and Medical Oncology, Health Research Institute-INCLIVA, Valencia, Spain
| | - Gloria Ribas
- Department of Hematology and Medical Oncology, Health Research Institute-INCLIVA, Valencia, Spain.
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19
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Pergoli L, Favero C, Ruth M. P, Tarantini L, Calista D, Cavalleri T, Angelici L, Consonni D, Pier A. B, Angela C. P, Maria T. L, Bollati V. Blood DNA methylation, nevi number, and the risk of melanoma. Melanoma Res 2014; 24:480-7. [PMID: 25026000 PMCID: PMC6857929 DOI: 10.1097/cmr.0000000000000112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Germline mutations determining increased cutaneous malignant melanoma (CMM) risk have been identified in familial and sporadic CMM cases, but they account only for a small proportion of CMM cases. Recent evidence suggests that germline epimutations (e.g. DNA methylation alterations), which can be inherited similarly to genomic mutations and can be detected in normal body cells (including blood), might increase susceptibility to cancer. The aim of the study was to identify germline epimutations of genes that were found to be mutated in familial CMM (p16, p14, CDK4, MC1R, hTERT), immune and inflammatory genes (ICAM-1, TNFα), DNA mismatch repair gene (MLH1), and repetitive elements (ALU, LINE-1, HERV-w). We measured DNA methylation using bisulfite pyrosequencing in peripheral blood mononuclear cells from 167 CMM cases and 164 sex-matched and age-matched controls. We used multivariable logistic regression models to evaluate the association between methylation levels and CMM status or presence of dysplastic nevi. We found an association between the risk of CMM and peripheral blood mononuclear cell methylation levels of TNFα [odds ratio (OR)=1.11, 95% confidence interval (CI)=1.03-1.18], CDK4 (OR=0.76, 95% CI=0.64-0.91), and MLH1 (OR=1.12, 95% CI=1.02-1.22). In control participants, the risk of developing dysplastic nevi was associated with methylation levels of TNFα (OR=0.81, 95% CI=0.69-0.95), hTERT (OR=0.90, 95% CI=0.82-0.99), and ALU (OR=1.56, 95% CI=1.02-2.39). Epimutations in CMM susceptibility genes and in genes involved in response to oxidative damage are associated with the risk of developing CMM or dysplastic nevi. Further studies measuring methylation levels of these genes in prospectively collected samples are warranted to further elucidate their role in the development and progression of CMM.
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Affiliation(s)
- Laura Pergoli
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Chiara Favero
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Pfeiffer Ruth M.
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Letizia Tarantini
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | | | - Tommaso Cavalleri
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Laura Angelici
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Bertazzi Pier A.
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Pesatori Angela C.
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Landi Maria T.
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Valentina Bollati
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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20
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Correlation of CLPTM1L polymorphisms with lung cancer susceptibility and response to cisplatin-based chemotherapy in a Chinese Han population. Tumour Biol 2014; 35:12075-82. [PMID: 25155038 DOI: 10.1007/s13277-014-2508-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022] Open
Abstract
The implication of genetic factors in predisposition to cancer is a recognized fact. The Cleft lip and palate transmembrane 1-like (CLPTM1L) gene resides in a locus in the chromosome 5p15.33 region that is associated with lung cancer susceptibility and has a role in carcinogenesis. We conducted a case-control study in a Chinese population of 309 pathologically confirmed lung cancer patients and 310 controls to investigate the effect of variant genotypes within the CLPTM1L locus on susceptibility to lung cancer and sensitivity to cisplatin-based chemotherapy. We genotyped nine single nucleotide polymorphisms (SNPs) within the CLPTM1L locus and examined their correlation with lung cancer risk and treatment response using χ (2) and unconditional logistic regression analysis. We identified rs451360 as a novel SNP associated with lung cancer risk in the Chinese Han population. The "T" allele of rs451360 was associated with decreased risk of lung cancer (p = 0.007, odd ratio (OR) = 0.59, 95 % confidence interval (CI): 0.40-0.87). Significant multiplicative interactions were observed between gender and polymorphisms of rs402710, the "T/T" genotype of which was associated with decreased lung cancer risk in male patients (p = 0.016, OR = 0.35, 95 % CI: 0.17-0.73). CLPTM1L polymorphisms did not affect the tumor sensitivity to cisplatin combination chemotherapy in our study patients. The results of the present study suggest a potential association between CLPTM1L variants and lung cancer risk in the Chinese Han populations.
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21
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Yin J, Wang L, Zheng L, Wang X, Shi Y, Shao A, Ding G, Liu C, Chen S, Tang W, Gu H. TERT-CLPTM1L Rs401681 C>T polymorphism was associated with a decreased risk of esophageal cancer in a Chinese population. PLoS One 2014; 9:e100667. [PMID: 25007268 PMCID: PMC4089909 DOI: 10.1371/journal.pone.0100667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
Background Esophageal cancer was the fifth most commonly diagnosed cancer and the fourth leading cause of cancer-related death in China in 2009. Esophageal squamous cell carcinoma (ESCC) accounts for more than 90 percent of esophageal cancers. Genetic factors probably play an important role in the ESCC carcinogenesis. Methods We conducted a hospital based case-control study to evaluate functional hTERT rs2736098 G>A and TERT-CLPTM1L rs401681 C>T single nucleotide polymorphisms (SNPs) on the risk of ESCC. Six hundred and twenty-nine ESCC cases and 686 controls were recruited. Their genotypes were determined using the ligation detection reaction (LDR) method. Results When the TERT-CLPTM1L rs401681 CC homozygote genotype was used as the reference group, the CT genotype was associated with a significantly decreased risk of ESCC (adjusted OR = 0.74, 95% CI = 0.58–0.94, p = 0.012); the CT/TT variants were associated with a 26% decreased risk of ESCC (adjusted OR = 0.74, 95% CI = 0.59–0.93, P = 0.009). The significantly decreased risk of ESCC associated with the TERT-CLPTM1L rs401681 C>T polymorphism was associated with male sex, young age (<63 years in our study) and alcohol consumption. No association between the hTERT rs2736098 G>A polymorphism and ESCC risk was observed. Conclusion TERT-CLPTM1L rs401681 CT and CT/TT genotypes were associated with decreased risk of ESCC, particularly among men, young patients and those reported to be drinkers. However, our results are preliminary conclusions. Larger studies with more rigorous study designs are required to confirm the current findings.
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Affiliation(s)
- Jun Yin
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Liming Wang
- Cancer institute, Department of chemotherapy, People's Hospital Affiliated to Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Liang Zheng
- Department of Cardiothoracic Surgery, The First People's Hospital of Changzhou and The Third Affiliated Hospital of Suzhou University, Changzhou, Jiangsu Province, China
| | - Xu Wang
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yijun Shi
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Aizhong Shao
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Guowen Ding
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chao Liu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Suocheng Chen
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Weifeng Tang
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
- * (WT); (HG)
| | - Haiyong Gu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
- * (WT); (HG)
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22
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A large French case-control study emphasizes the role of rare Mc1R variants in melanoma risk. BIOMED RESEARCH INTERNATIONAL 2014; 2014:925716. [PMID: 24982914 PMCID: PMC4003837 DOI: 10.1155/2014/925716] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/12/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND The MC1R gene implicated in melanogenesis and skin pigmentation is highly polymorphic. Several alleles are associated with red hair and fair skin phenotypes and contribute to melanoma risk. OBJECTIVE This work aims to assess the effect of different classes of MC1R variants, notably rare variants, on melanoma risk. Methods. MC1R coding region was sequenced in 1131 melanoma patients and 869 healthy controls. MC1R variants were classified as RHC (R) and non-RHC (r). Rare variants (frequency < 1%) were subdivided into two subgroups, predicted to be damaging (D) or not (nD). RESULTS Both R and r alleles were associated with melanoma (OR = 2.66 [2.20-3.23] and 1.51 [1.32-1.73]) and had similar population attributable risks (15.8% and 16.6%). We also identified 69 rare variants, of which 25 were novel. D variants were strongly associated with melanoma (OR = 2.38 [1.38-4.15]) and clustered in the same MC1R domains as R alleles (intracellular 2, transmembrane 2 and 7). CONCLUSION This work confirms the role of R and r alleles in melanoma risk in the French population and proposes a novel class of rare D variants as important melanoma risk factors. These findings may improve the definition of high-risk subjects that could be targeted for melanoma prevention and screening.
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23
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Burke LS, Hyland PL, Pfeiffer RM, Prescott J, Wheeler W, Mirabello L, Savage SA, Burdette L, Yeager M, Chanock S, De Vivo I, Tucker MA, Goldstein AM, Yang XR. Telomere length and the risk of cutaneous malignant melanoma in melanoma-prone families with and without CDKN2A mutations. PLoS One 2013; 8:e71121. [PMID: 23990928 PMCID: PMC3747185 DOI: 10.1371/journal.pone.0071121] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/25/2013] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Recent evidence suggests a link between constitutional telomere length (TL) and cancer risk. Previous studies have suggested that longer telomeres were associated with an increased risk of melanoma and larger size and number of nevi. The goal of this study was to examine whether TL modified the risk of melanoma in melanoma-prone families with and without CDKN2A germline mutations. MATERIALS AND METHODS We measured TL in blood DNA in 119 cutaneous malignant melanoma (CMM) cases and 208 unaffected individuals. We also genotyped 13 tagging SNPs in TERT. RESULTS We found that longer telomeres were associated with an increased risk of CMM (adjusted OR = 2.81, 95% CI = 1.02-7.72, P = 0.04). The association of longer TL with CMM risk was seen in CDKN2A- cases but not in CDKN2A+ cases. Among CMM cases, the presence of solar injury was associated with shorter telomeres (P = 0.002). One SNP in TERT, rs2735940, was significantly associated with TL (P = 0.002) after Bonferroni correction. DISCUSSION Our findings suggest that TL regulation could be variable by CDKN2A mutation status, sun exposure, and pigmentation phenotype. Therefore, TL measurement alone may not be a good marker for predicting CMM risk.
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Affiliation(s)
- Laura S. Burke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Paula L. Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
- Cancer Prevention Fellowship Program, Office of Directors, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Jennifer Prescott
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - William Wheeler
- Information Management Services, Inc., Rockville, Maryland, United States of America
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Laurie Burdette
- Core Genotyping Facility, SAIC-Frederick, Inc., National Cancer Institute -Frederick, Frederick, Maryland, United States of America
| | - Meredith Yeager
- Core Genotyping Facility, SAIC-Frederick, Inc., National Cancer Institute -Frederick, Frederick, Maryland, United States of America
| | - Stephen Chanock
- Core Genotyping Facility, SAIC-Frederick, Inc., National Cancer Institute -Frederick, Frederick, Maryland, United States of America
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Margaret A. Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, United States of America
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24
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Glass D, Viñuela A, Davies MN, Ramasamy A, Parts L, Knowles D, Brown AA, Hedman ÅK, Small KS, Buil A, Grundberg E, Nica AC, Di Meglio P, Nestle FO, Ryten M, Durbin R, McCarthy MI, Deloukas P, Dermitzakis ET, Weale ME, Bataille V, Spector TD. Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol 2013; 14:R75. [PMID: 23889843 PMCID: PMC4054017 DOI: 10.1186/gb-2013-14-7-r75] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/13/2013] [Accepted: 07/26/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age. RESULTS Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential expression with age in both skin and brain tissue and three common to adipose and brain tissues. CONCLUSIONS Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.
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Affiliation(s)
- Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
- North West London Hospitals NHS Trust, Northwick Park Hospital, Watford Road, Harrow HA1 3UJ, UK
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | - Matthew N Davies
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | - Adaikalavan Ramasamy
- Department of Medical ƒ Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | | | - David Knowles
- Stanford University, 450 Serra MallStanford, CA 94305, USA
| | | | - Åsa K Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
- Wellcome Trust Sanger Institute, HinxtonCB10 1SA,UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet (CMU office 9088), Geneva 1211, Switzerland
| | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
- Wellcome Trust Sanger Institute, HinxtonCB10 1SA,UK
| | - Alexandra C Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet (CMU office 9088), Geneva 1211, Switzerland
| | - Paola Di Meglio
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Frank O Nestle
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Mina Ryten
- Department of Medical ƒ Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - the UK Brain Expression consortium
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | | | | | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology ƒ Metabolism, University of Oxford, Churchill Hospital, Oxford, Headington OX3 7LJ,UK
| | | | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet (CMU office 9088), Geneva 1211, Switzerland
| | - Michael E Weale
- Department of Medical ƒ Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
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25
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Hill VK, Gartner JJ, Samuels Y, Goldstein AM. The genetics of melanoma: recent advances. Annu Rev Genomics Hum Genet 2013; 14:257-79. [PMID: 23875803 DOI: 10.1146/annurev-genom-091212-153429] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cutaneous malignant melanoma results from the interplay of genetic, host, and environmental factors. Genetic factors implicated in melanoma etiology include inherited high-, intermediate-, and low-risk susceptibility genes as well as numerous somatic mutations in melanoma tumors. CDKN2A is the major high-risk melanoma susceptibility gene identified to date. Recent identification of low-risk loci has been accomplished predominantly through genome-wide association studies. Whole-exome and whole-genome studies have identified numerous genes somatically altered in melanoma tumors and highlighted a higher mutation load in melanoma tumors compared with those in other cancers. This higher load is believed to be attributable to the preponderance of cytosine-to-thymine nucleotide substitutions as a result of UV radiation exposure. Technological advances, particularly next-generation sequencing, have increased the opportunities for germline and somatic gene discovery in melanoma and are opening up new avenues for understanding melanoma pathogenesis as well as leading to new opportunities for treatment.
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Affiliation(s)
- Victoria K Hill
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
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26
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Bataille V. Melanoma. Shall we move away from the sun and focus more on embryogenesis, body weight and longevity? Med Hypotheses 2013; 81:846-50. [PMID: 23796690 PMCID: PMC3828598 DOI: 10.1016/j.mehy.2013.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/16/2013] [Accepted: 05/23/2013] [Indexed: 12/20/2022]
Abstract
There are many observations regarding the behaviour of melanoma which points away from sunshine as the main cause of this tumour. Incidence data shows that the increase is mostly seen for thin melanomas which cannot be attributed to sun exposure but increasing screening over the last 20 years. Melanoma behaves in a similar fashion all over the world regarding age of onset, gender differences and histological subtypes. An excess of naevi is the strongest risk factor for melanoma and their appearance and involution throughout life, and the differences in naevus distribution according to gender is giving us a lot of clues about melanoma biology. Melanoma like all cancers is a complex disease with the involvement of many common and low penetrance genes many of them involved in pigmentation and naevogenesis but these only explain a very small portion of melanoma susceptibility. Genes involved in melanocyte differentiation early on in embryogenesis are also becoming relevant for melanoma initiation and progression. Reduced senescence and longevity as well as body weight and energy expenditure are also relevant for melanoma susceptibility. These observations with links between melanoma and non-sun related phenotypes as well as gene discoveries should help to assess the relative contribution of genetic and environmental factors in its causation.
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Affiliation(s)
- Veronique Bataille
- Twin Research and Genetic Epidemiology Unit, St. Thomas Hospital, Kings College, London, UK; Dermatology Department, Hemel Hempstead General Hospital, West Herts NHS Trust, Herts, UK.
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27
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Ruark E, Seal S, McDonald H, Zhang F, Elliot A, Lau K, Perdeaux E, Rapley E, Eeles R, Peto J, Kote-Jarai Z, Muir K, Nsengimana J, Shipley J, Bishop DT, Stratton MR, Easton DF, Huddart RA, Rahman N, Turnbull C. Identification of nine new susceptibility loci for testicular cancer, including variants near DAZL and PRDM14. Nat Genet 2013; 45:686-9. [PMID: 23666240 PMCID: PMC3680037 DOI: 10.1038/ng.2635] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/10/2013] [Indexed: 01/16/2023]
Abstract
Testicular germ cell tumor (TGCT) is the most common cancer in young men and is notable for its high familial risks. So far, six loci associated with TGCT have been reported. From genome-wide association study (GWAS) analysis of 307,291 SNPs in 986 TGCT cases and 4,946 controls, we selected for follow-up 694 SNPs, which we genotyped in a further 1,064 TGCT cases and 10,082 controls from the UK. We identified SNPs at nine new loci (1q22, 1q24.1, 3p24.3, 4q24, 5q31.1, 8q13.3, 16q12.1, 17q22 and 21q22.3) showing association with TGCT (P < 5 × 10(-8)), which together account for an additional 4-6% of the familial risk of TGCT. The loci include genes plausibly related to TGCT development. PRDM14, at 8q13.3, is essential for early germ cell specification, and DAZL, at 3p24.3, is required for the regulation of germ cell development. Furthermore, PITX1, at 5q31.1, regulates TERT expression and is the third TGCT-associated locus implicated in telomerase regulation.
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Affiliation(s)
- Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
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28
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Abstract
Cutaneous malignant melanoma (CMM) has been increasing steadily in incidence over the past 30 years. Recent studies have explored associations between CMM and varying physiologic risk factors, such as nevi or hair and eye color, in addition to historical features such as a personal history of nonmelanoma skin cancer (NMSC), childhood cancers, Parkinson's Disease, hormone exposure and family history of CMM. Genome-wide association studies have also uncovered many genetic determinants of CMM risk. Ultimately, ultraviolet (UV) radiation exposure remains the most important modifiable risk factor for CMM. Organ transplant recipients, and nonsteroidal anti-inflammatory usage may also play a role. While risk factors are important to identify, effective campaigns to reduce the burden of disease through early detection and prevention are essential. We present detailed data regarding these facets of care for the CMM patient, and provide an update on the epidemiology of CMM.
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Affiliation(s)
- Steven T Chen
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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29
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Wang H, Zhao Y, Ma J, Zhang G, Mu Y, Qi G, Fang Z, Wang L, Fan Q, Ma Z. Short Communication The genetic variant rs401681C/T is associated with the risk of non-small cell lung cancer in a Chinese mainland population. GENETICS AND MOLECULAR RESEARCH 2013; 12:67-73. [DOI: 10.4238/2013.january.22.5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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Ni Z, Tao K, Chen G, Chen Q, Tang J, Luo X, Yin P, Tang J, Wang X. CLPTM1L is overexpressed in lung cancer and associated with apoptosis. PLoS One 2012; 7:e52598. [PMID: 23300716 PMCID: PMC3530437 DOI: 10.1371/journal.pone.0052598] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/16/2012] [Indexed: 11/18/2022] Open
Abstract
CLPTM1L is believed to be associated with lung cancer. However, there is little information regarding its expression and function. Here using immunohistochemistry, we found that CLPTM1L expression was markedly increased in lung cancer tissues relative to normal tissues, especially in lung adenocarcinoma. CLPTM1L expression was not found to be associated with stages, smoking status, lymph node metastasis, or T lymphocyte infiltration but with differentiation stage. We found CLPTM1L to be enriched in the mitochondrial compared with plasma membrane protein extracts. CLPTM1L-EGFP transfection showed that the molecule product was expressed in cytoplasm and indicated the mitochondrial localization stained with mitochondrial marker MitoTracker. CLPTM1L transferred lung cancer cell line 95-D showed no growth inhibition or cell apoptosis, but it did show inhibited sensitivity to cis-diamminedichloroplatinum(II) (cisplatin, CDDP). Knockdown of CLPTM1L by RNAi did not interfere with cell proliferation but it did increase cell sensitivity to CDDP and activation of caspase-9 and caspase-3/7. These data indicate CLPTM1L is a mitochondria protein and that it may be associated with anti-apoptotic mechanism which affects drug-resistance in turn.
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Affiliation(s)
- Zhenhua Ni
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kun Tao
- Department of Pathology, Shanghai Changning Central Hospital, Shanghai, China
| | - Guo Chen
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qingge Chen
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jianmin Tang
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xuming Luo
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Peihao Yin
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jihong Tang
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiongbiao Wang
- Central Lab, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- * E-mail:
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31
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Bourillon A, Hu HH, Hetet G, Lacapere JJ, André J, Descamps V, Basset-Seguin N, Ogbah Z, Puig S, Saiag P, Bagot M, Bensussan A, Grandchamp B, Dumaz N, Soufir N. Genetic variation at KIT locus may predispose to melanoma. Pigment Cell Melanoma Res 2012; 26:88-96. [PMID: 23020152 DOI: 10.1111/pcmr.12032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 09/28/2012] [Indexed: 01/06/2023]
Abstract
As loss of KIT frequently occurs in melanoma progression, we hypothesized that KIT is implicated in predisposition to melanoma (MM). Thus, we sequenced the KIT coding region in 112 familial MM cases and 143 matched controls and genotyped tag single-nucleotide polymorphisms (SNPs) in two cohorts of melanoma patients and matched controls. Five rare KIT substitutions, all predicted possibly or probably deleterious, were identified in five patients, but none in controls [RR = 2.26 (1.26-2.26)]. Expressed in melanocyte lines, three substitutions inhibited KIT signaling. Comparison with exomes database (7020 alleles) confirmed a significant excess of rare deleterious KIT substitutions in patients. Additionally, a common SNP, rs2237028, was associated with MM risk, and 6 KIT variants were associated with nevus count. Our data strongly suggest that rare KIT substitutions predispose to melanoma and that common variants at KIT locus may also impact nevus count and melanoma risk.
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Affiliation(s)
- Agnes Bourillon
- Département de Génétique, Hôpital Bichat-Claude Bernard, APHP, Paris, France
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32
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Fredebohm J, Boettcher M, Eisen C, Gaida MM, Heller A, Keleg S, Tost J, Greulich-Bode KM, Hotz-Wagenblatt A, Lathrop M, Giese NA, Hoheisel JD. Establishment and characterization of a highly tumourigenic and cancer stem cell enriched pancreatic cancer cell line as a well defined model system. PLoS One 2012; 7:e48503. [PMID: 23152778 PMCID: PMC3495919 DOI: 10.1371/journal.pone.0048503] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/26/2012] [Indexed: 12/12/2022] Open
Abstract
Standard cancer cell lines do not model the intratumoural heterogeneity situation sufficiently. Clonal selection leads to a homogeneous population of cells by genetic drift. Heterogeneity of tumour cells, however, is particularly critical for therapeutically relevant studies, since it is a prerequisite for acquiring drug resistance and reoccurrence of tumours. Here, we report the isolation of a highly tumourigenic primary pancreatic cancer cell line, called JoPaca-1 and its detailed characterization at multiple levels. Implantation of as few as 100 JoPaca-1 cells into immunodeficient mice gave rise to tumours that were histologically very similar to the primary tumour. The high heterogeneity of JoPaca-1 was reflected by diverse cell morphology and a substantial number of chromosomal aberrations. Comparative whole-genome sequencing of JoPaca-1 and BxPC-3 revealed mutations in genes frequently altered in pancreatic cancer. Exceptionally high expression of cancer stem cell markers and a high clonogenic potential in vitro and in vivo was observed. All of these attributes make this cell line an extremely valuable model to study the biology of and pharmaceutical effects on pancreatic cancer.
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MESH Headings
- AC133 Antigen
- Aldehyde Dehydrogenase 1 Family
- Alleles
- Animals
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antimetabolites, Antineoplastic/pharmacology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Deoxycytidine/analogs & derivatives
- Deoxycytidine/pharmacology
- Disease Models, Animal
- Drug Resistance, Neoplasm/genetics
- GPI-Linked Proteins/genetics
- GPI-Linked Proteins/metabolism
- Genomic Instability
- Glycoproteins/genetics
- Glycoproteins/metabolism
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Keratins/genetics
- Keratins/metabolism
- Male
- Mesothelin
- Mice
- Middle Aged
- Mutation
- Neoplasm Metastasis
- Neoplastic Stem Cells/metabolism
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- Peptides/genetics
- Peptides/metabolism
- Polyploidy
- Retinal Dehydrogenase/genetics
- Retinal Dehydrogenase/metabolism
- Transplantation, Heterologous
- Tumor Microenvironment
- Gemcitabine
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Affiliation(s)
- Johannes Fredebohm
- Functional Genome Analysis, German Cancer Research Center, Heidelberg, Germany.
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33
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Mangino M, Hwang SJ, Spector TD, Hunt SC, Kimura M, Fitzpatrick AL, Christiansen L, Petersen I, Elbers CC, Harris T, Chen W, Srinivasan SR, Kark JD, Benetos A, El Shamieh S, Visvikis-Siest S, Christensen K, Berenson GS, Valdes AM, Viñuela A, Garcia M, Arnett DK, Broeckel U, Province MA, Pankow JS, Kammerer C, Liu Y, Nalls M, Tishkoff S, Thomas F, Ziv E, Psaty BM, Bis JC, Rotter JI, Taylor KD, Smith E, Schork NJ, Levy D, Aviv A. Genome-wide meta-analysis points to CTC1 and ZNF676 as genes regulating telomere homeostasis in humans. Hum Mol Genet 2012; 21:5385-94. [PMID: 23001564 PMCID: PMC3510758 DOI: 10.1093/hmg/dds382] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Leukocyte telomere length (LTL) is associated with a number of common age-related diseases and is a heritable trait. Previous genome-wide association studies (GWASs) identified two loci on chromosomes 3q26.2 (TERC) and 10q24.33 (OBFC1) that are associated with the inter-individual LTL variation. We performed a meta-analysis of 9190 individuals from six independent GWAS and validated our findings in 2226 individuals from four additional studies. We confirmed previously reported associations with OBFC1 (rs9419958 P = 9.1 × 10−11) and with the telomerase RNA component TERC (rs1317082, P = 1.1 × 10−8). We also identified two novel genomic regions associated with LTL variation that map near a conserved telomere maintenance complex component 1 (CTC1; rs3027234, P = 3.6 × 10−8) on chromosome17p13.1 and zinc finger protein 676 (ZNF676; rs412658, P = 3.3 × 10−8) on 19p12. The minor allele of rs3027234 was associated with both shorter LTL and lower expression of CTC1. Our findings are consistent with the recent observations that point mutations in CTC1 cause short telomeres in both Arabidopsis and humans affected by a rare Mendelian syndrome. Overall, our results provide novel insights into the genetic architecture of inter-individual LTL variation in the general population.
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Affiliation(s)
- Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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Association between TERT-CLPTM1L rs401681[C] allele and NMSC cancer risk: a meta-analysis including 45,184 subjects. Arch Dermatol Res 2012; 305:49-52. [PMID: 22893025 DOI: 10.1007/s00403-012-1275-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 07/01/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Single-nucleotide polymorphism of CLPTM1L-rs401681(C > T) at the 5p15.33 locus is significantly associated with cancer risk as reported in genome-wide association studies, but the reported studies for non-melanoma skin cancer (NMSC) are inconclusive. To assess the association between rs401681[C] allele and NMSC risk, we performed this meta-analysis with four case-control studies involving 5,469 cases and 39,715 controls. Our meta-analysis showed that rs401681[C] allele was associated with NMSC susceptibility in the overall subjects (C vs. T, OR 1.13, 95 % CI 1.07-1.20). In the stratified analysis, the rs401681[C] allele confers susceptibility in Icelanders (C vs. T, OR 1.15, 95 % CI 1.06-1.26) and non-Icelanders (C vs. T, OR 1.13, 95 % CI 1.03-1.24). In the subtype analysis, we found that rs401681[C] allele was a risk factor for BCC, but not SCC in the overall subjects.
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Abstract
Background: Polymorphic variation at the 5p15.33 (TERT–CLPTM1L) locus is associated
with the risk of many cancers but a relationship with colorectal cancer (CRC) risk has
yet to be defined. Methods: We used data from six genome-wide association studies (GWAS) of CRC, linkage
disequilibrium mapping and imputation, to examine the relationship between 73
single-nucleotide polymorphisms at 5p15.33 and CRC risk in detail. Results: rs2736100, which localises to intron 2 of TERT, provided the strongest
evidence of an association with CRC (P=2.28 ×
10−4). The association was also shown in an independent series of
10 047 CRC cases and 6918 controls (P=0.02). A meta-analysis of
all seven studies (totalling 16 039 cases, 16 430 controls) provided
increased evidence of association (P=2.49 × 10−5;
per allele odds ratio=1.07). The association of rs2736100 on CRC risk was shown
to be independent of 15 low-penetrance variants previously identified. Conclusion: The rs2736100 association demonstrates an influence of variation at 5p15.33 on CRC risk
and further evidence that the 5p15.33 (TERT–CLPTM1L) locus has
pleiotropic effects (reflecting generic or lineage-specific effects) on cancer risk.
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Melanoma Genetics: Recent Findings Take Us Beyond Well-Traveled Pathways. J Invest Dermatol 2012; 132:1763-74. [DOI: 10.1038/jid.2012.75] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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