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Painter JN, O'Mara TA, Batra J, Cheng T, Lose FA, Dennis J, Michailidou K, Tyrer JP, Ahmed S, Ferguson K, Healey CS, Kaufmann S, Hillman KM, Walpole C, Moya L, Pollock P, Jones A, Howarth K, Martin L, Gorman M, Hodgson S, De Polanco MME, Sans M, Carracedo A, Castellvi-Bel S, Rojas-Martinez A, Santos E, Teixeira MR, Carvajal-Carmona L, Shu XO, Long J, Zheng W, Xiang YB, Montgomery GW, Webb PM, Scott RJ, McEvoy M, Attia J, Holliday E, Martin NG, Nyholt DR, Henders AK, Fasching PA, Hein A, Beckmann MW, Renner SP, Dörk T, Hillemanns P, Dürst M, Runnebaum I, Lambrechts D, Coenegrachts L, Schrauwen S, Amant F, Winterhoff B, Dowdy SC, Goode EL, Teoman A, Salvesen HB, Trovik J, Njolstad TS, Werner HMJ, Ashton K, Proietto T, Otton G, Tzortzatos G, Mints M, Tham E, Hall P, Czene K, Liu J, Li J, Hopper JL, Southey MC, Ekici AB, Ruebner M, Johnson N, Peto J, Burwinkel B, Marme F, Brenner H, Dieffenbach AK, Meindl A, Brauch H, Lindblom A, Depreeuw J, Moisse M, Chang-Claude J, Rudolph A, Couch FJ, Olson JE, Giles GG, Bruinsma F, Cunningham JM, Fridley BL, Børresen-Dale AL, Kristensen VN, Cox A, Swerdlow AJ, Orr N, Bolla MK, Wang Q, Weber RP, Chen Z, Shah M, French JD, Pharoah PDP, Dunning AM, Tomlinson I, Easton DF, Edwards SL, Thompson DJ, Spurdle AB. Fine-mapping of the HNF1B multicancer locus identifies candidate variants that mediate endometrial cancer risk. Hum Mol Genet 2015; 24:1478-92. [PMID: 25378557 PMCID: PMC4321445 DOI: 10.1093/hmg/ddu552] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 10/13/2014] [Accepted: 10/24/2014] [Indexed: 12/14/2022] Open
Abstract
Common variants in the hepatocyte nuclear factor 1 homeobox B (HNF1B) gene are associated with the risk of Type II diabetes and multiple cancers. Evidence to date indicates that cancer risk may be mediated via genetic or epigenetic effects on HNF1B gene expression. We previously found single-nucleotide polymorphisms (SNPs) at the HNF1B locus to be associated with endometrial cancer, and now report extensive fine-mapping and in silico and laboratory analyses of this locus. Analysis of 1184 genotyped and imputed SNPs in 6608 Caucasian cases and 37 925 controls, and 895 Asian cases and 1968 controls, revealed the best signal of association for SNP rs11263763 (P = 8.4 × 10(-14), odds ratio = 0.86, 95% confidence interval = 0.82-0.89), located within HNF1B intron 1. Haplotype analysis and conditional analyses provide no evidence of further independent endometrial cancer risk variants at this locus. SNP rs11263763 genotype was associated with HNF1B mRNA expression but not with HNF1B methylation in endometrial tumor samples from The Cancer Genome Atlas. Genetic analyses prioritized rs11263763 and four other SNPs in high-to-moderate linkage disequilibrium as the most likely causal SNPs. Three of these SNPs map to the extended HNF1B promoter based on chromatin marks extending from the minimal promoter region. Reporter assays demonstrated that this extended region reduces activity in combination with the minimal HNF1B promoter, and that the minor alleles of rs11263763 or rs8064454 are associated with decreased HNF1B promoter activity. Our findings provide evidence for a single signal associated with endometrial cancer risk at the HNF1B locus, and that risk is likely mediated via altered HNF1B gene expression.
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Affiliation(s)
- Jodie N Painter
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tracy A O'Mara
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation, and School of Biomedical Science and
| | - Timothy Cheng
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Felicity A Lose
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Shahana Ahmed
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kaltin Ferguson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Catherine S Healey
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Susanne Kaufmann
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Carina Walpole
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation, and School of Biomedical Science and
| | - Leire Moya
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation, and School of Biomedical Science and
| | - Pamela Pollock
- Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Angela Jones
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberley Howarth
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Shirley Hodgson
- Department of Clinical Genetics, St George's Hospital Medical School, London, UK
| | | | - Monica Sans
- Department of Biological Anthropology, College of Humanities and Educational Sciences, University of the Republic, Magallanes, Montevideo, Uruguay
| | - Angel Carracedo
- Grupo de Medicina Xenómica, Fundación Galega de Medicina Xenómica (SERGAS) and CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, KSA
| | - Sergi Castellvi-Bel
- Genetic Predisposition to Colorectal Cancer Group, Gastrointestinal & Pancreatic Oncology Team, IDIBAPS/CIBERehd/Hospital Clínic, Centre Esther Koplowitz (CEK), Barcelona, Spain
| | - Augusto Rojas-Martinez
- Universidad Autónoma de Nuevo León, Pedro de Alba s/n, San Nicolás de Los Garza, Nuevo León, Mexico
| | | | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal, Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Luis Carvajal-Carmona
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK, Grupo de Investigación Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Tolima, Colombia, Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | | | - Penelope M Webb
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Rodney J Scott
- Hunter Medical Research Institute and, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia, Centre for Information Based Medicine and School of Biomedical Science and Pharmacy
| | - Mark McEvoy
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health
| | - John Attia
- Hunter Medical Research Institute and, Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health
| | - Elizabeth Holliday
- Hunter Medical Research Institute and, Centre for Information Based Medicine and School of Medicine and Public Health
| | | | - Dale R Nyholt
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anjali K Henders
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Peter A Fasching
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alexander Hein
- University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Stefan P Renner
- University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Peter Hillemanns
- Clinics of Gynaecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Matthias Dürst
- Dept. of Gynaecology, Friedrich Schiller University Jena, Jena, Germany
| | - Ingo Runnebaum
- Dept. of Gynaecology, Friedrich Schiller University Jena, Jena, Germany
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium, Department of Oncology, Laboratory for Translational Genetics
| | - Lieve Coenegrachts
- Division of Gynaecological Oncology, Department of Oncology, University Hospital Leuven, KU Leuven, Belgium
| | - Stefanie Schrauwen
- Division of Gynaecological Oncology, Department of Oncology, University Hospital Leuven, KU Leuven, Belgium
| | - Frederic Amant
- Division of Gynaecological Oncology, Department of Oncology, University Hospital Leuven, KU Leuven, Belgium
| | - Boris Winterhoff
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology
| | - Sean C Dowdy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology
| | - Ellen L Goode
- Division of Epidemiology, Department of Health Science Research and
| | - Attila Teoman
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology
| | - Helga B Salvesen
- Department of Clinical Science, Centre for Cancerbiomarkers, The University of Bergen, Norway, Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Jone Trovik
- Department of Clinical Science, Centre for Cancerbiomarkers, The University of Bergen, Norway, Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Tormund S Njolstad
- Department of Clinical Science, Centre for Cancerbiomarkers, The University of Bergen, Norway, Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Henrica M J Werner
- Department of Clinical Science, Centre for Cancerbiomarkers, The University of Bergen, Norway, Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Katie Ashton
- Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia, Faculty of Health, Centre for Information Based Medicine and the Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy and
| | - Tony Proietto
- Faculty of Health, School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Geoffrey Otton
- Faculty of Health, School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | | | | | - Emma Tham
- Department of Molecular Medicine and Surgery and
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health and
| | - Melissa C Southey
- Department of Pathology, Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, VIC, Australia
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital, Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias Ruebner
- University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Julian Peto
- London School of Hygiene and Tropical Medicine, London, UK
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Molecular Epidemiology, C080
| | - Frederik Marme
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aida K Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alfons Meindl
- Division of Tumor Genetics, Department of Obstetrics and Gynecology, Technical University of Munich, Munich, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart, University of Tuebingen, Germany
| | | | | | | | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Rudolph
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J Couch
- Departments of Laboratory Medicine and Pathology, and Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Janet E Olson
- Division of Epidemiology, Department of Health Science Research and
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health and Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia, Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia
| | - Julie M Cunningham
- Departments of Laboratory Medicine and Pathology, and Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway, Faculty of Medicine, The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway, Faculty of Medicine, The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway, Division of Medicine, Department of Clinical Molecular Oncology, Akershus University Hospital, Ahus, Norway
| | - Angela Cox
- Department of Oncology, Sheffield Cancer Research Centre, University of Sheffield, Sheffield, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology and, Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Nicholas Orr
- Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Zhihua Chen
- Division of Population Sciences, Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Juliet D French
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stacey L Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,
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