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Rao SR, Protheroe A, Cerundolo L, Maldonado-Perez D, Browning L, Lamb AD, Bryant RJ, Mills IG, Woodcock DJ, Hamdy FC, Tomlinson IPM, Verrill C. Genomic Evolution and Transcriptional Changes in the Evolution of Prostate Cancer into Neuroendocrine and Ductal Carcinoma Types. Int J Mol Sci 2023; 24:12722. [PMID: 37628903 PMCID: PMC10454593 DOI: 10.3390/ijms241612722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Prostate cancer is typically of acinar adenocarcinoma type but can occasionally present as neuroendocrine and/or ductal type carcinoma. These are associated with clinically aggressive disease, and the former often arises on a background of androgen deprivation therapy, although it can also arise de novo. Two prostate cancer cases were sequenced by exome capture from archival tissue. Case 1 was de novo small cell neuroendocrine carcinoma and ductal adenocarcinoma with three longitudinal samples over 5 years. Case 2 was a single time point after the development of treatment-related neuroendocrine prostate carcinoma. Case 1 showed whole genome doubling in all samples and focal amplification of AR in all samples except the first time point. Phylogenetic analysis revealed a common ancestry for ductal and small cell carcinoma. Case 2 showed 13q loss (involving RB1) in both adenocarcinoma and small cell carcinoma regions, and 3p gain, 4p loss, and 17p loss (involving TP53) in the latter. By using highly curated samples, we demonstrate for the first time that small-cell neuroendocrine and ductal prostatic carcinoma can have a common ancestry. We highlight whole genome doubling in a patient with prostate cancer relapse, reinforcing its poor prognostic nature.
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Affiliation(s)
- Srinivasa R. Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Andrew Protheroe
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | | | - Lisa Browning
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Alastair D. Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Richard J. Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Ian G. Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Dan J. Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | | | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
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2
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Palles C, West HD, Chew E, Galavotti S, Flensburg C, Grolleman JE, Jansen EAM, Curley H, Chegwidden L, Arbe-Barnes EH, Lander N, Truscott R, Pagan J, Bajel A, Sherwood K, Martin L, Thomas H, Georgiou D, Fostira F, Goldberg Y, Adams DJ, van der Biezen SAM, Christie M, Clendenning M, Thomas LE, Deltas C, Dimovski AJ, Dymerska D, Lubinski J, Mahmood K, van der Post RS, Sanders M, Weitz J, Taylor JC, Turnbull C, Vreede L, van Wezel T, Whalley C, Arnedo-Pac C, Caravagna G, Cross W, Chubb D, Frangou A, Gruber AJ, Kinnersley B, Noyvert B, Church D, Graham T, Houlston R, Lopez-Bigas N, Sottoriva A, Wedge D, Jenkins MA, Kuiper RP, Roberts AW, Cheadle JP, Ligtenberg MJL, Hoogerbrugge N, Koelzer VH, Rivas AD, Winship IM, Ponte CR, Buchanan DD, Power DG, Green A, Tomlinson IPM, Sampson JR, Majewski IJ, de Voer RM. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome. Am J Hum Genet 2022; 109:953-960. [PMID: 35460607 PMCID: PMC9118112 DOI: 10.1016/j.ajhg.2022.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.
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Affiliation(s)
- Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Edward Chew
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Sara Galavotti
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Helen Curley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Laura Chegwidden
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Edward H Arbe-Barnes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Nicola Lander
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Rebekah Truscott
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Judith Pagan
- Molecular Genetics Laboratory, South East Scotland Genetic Service, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ashish Bajel
- Peter MacCallum Cancer Center and Royal Melbourne Hospital, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Lynn Martin
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Huw Thomas
- St Mark's Hospital, Imperial College London, London, UK
| | - Demetra Georgiou
- Genomic Medicine, Imperial College Healthcare Trust and North West Thames Regional Genetics Service, Northwick Park, Harrow, UK
| | | | - Yael Goldberg
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simone A M van der Biezen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Michael Christie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Laura E Thomas
- Institute of Life Sciences, Swansea University, Swansea SA28PP, UK
| | - Constantinos Deltas
- Center of Excellence in Biobanking and Biomedical Research and Molecular Medicine Research Center, University of Cyprus Medical School, Nicosia, Cyprus
| | - Aleksandar J Dimovski
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Dagmara Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Rachel S van der Post
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Mathijs Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jürgen Weitz
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jenny C Taylor
- Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Clare Turnbull
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Lilian Vreede
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 Leiden, the Netherlands
| | - Celina Whalley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Giulio Caravagna
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - William Cross
- Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Daniel Chubb
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Anna Frangou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Andreas J Gruber
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
| | - Ben Kinnersley
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Boris Noyvert
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David Church
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Trevor Graham
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard Houlston
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Sottoriva
- Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - David Wedge
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
| | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 Utrecht, the Netherlands
| | - Andrew W Roberts
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Molecular Genetics Laboratory, South East Scotland Genetic Service, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia; University of Melbourne, Department of Medical Biology, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Jeremy P Cheadle
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Andres Dacal Rivas
- Servicio de Digestivo, Hospital Lucus Augusti, Instituto de Investigación Sanitaria de Santiago, Lugo, Galicia, Spain
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia; Department of Medicine, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Clara Ruiz Ponte
- Fundación Pública Galega de Medicina Xenómica SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago, Centro de Investigación Biomédica en Red de Enfermedades Raras, Santiago de Compostela, Galicia, Spain
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Derek G Power
- Department of Medical Oncology, Cork University Hospital, Cork, Ireland
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland; School of Medicine University College, Dublin, Ireland
| | - Ian P M Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK.
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK.
| | - Ian J Majewski
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
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3
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Zhang X, Li X, He Y, Law PJ, Farrington SM, Campbell H, Tomlinson IPM, Houlston RS, Dunlop MG, Timofeeva M, Theodoratou E. Phenome-wide association study (PheWAS) of colorectal cancer risk SNP effects on health outcomes in UK Biobank. Br J Cancer 2022; 126:822-830. [PMID: 34912076 PMCID: PMC8888597 DOI: 10.1038/s41416-021-01655-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Associations between colorectal cancer (CRC) and other health outcomes have been reported, but these may be subject to biases, or due to limitations of observational studies. METHODS We set out to determine whether genetic predisposition to CRC is also associated with the risk of other phenotypes. Under the phenome-wide association study (PheWAS) and tree-structured phenotypic model (TreeWAS), we studied 334,385 unrelated White British individuals (excluding CRC patients) from the UK Biobank cohort. We generated a polygenic risk score (PRS) from CRC genome-wide association studies as a measure of CRC risk. We performed sensitivity analyses to test the robustness of the results and searched the Danish Disease Trajectory Browser (DTB) to replicate the observed associations. RESULTS Eight PheWAS phenotypes and 21 TreeWAS nodes were associated with CRC genetic predisposition by PheWAS and TreeWAS, respectively. The PheWAS detected associations were from neoplasms and digestive system disease group (e.g. benign neoplasm of colon, anal and rectal polyp and diverticular disease). The results from the TreeWAS corroborated the results from the PheWAS. These results were replicated in the observational data within the DTB. CONCLUSIONS We show that benign colorectal neoplasms share genetic aetiology with CRC using PheWAS and TreeWAS methods. Additionally, CRC genetic predisposition is associated with diverticular disease.
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Affiliation(s)
- Xiaomeng Zhang
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Xue Li
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- School of Public Health and the Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yazhou He
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Oncology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Ian P M Tomlinson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- Danish Institute for Advanced Study (DIAS), Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK.
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Zhang X, Theodoratou E, Li X, Farrington SM, Law PJ, Broderick P, Walker M, Klimentidis YC, Rees JMB, Houlston RS, Tomlinson IPM, Burgess S, Campbell H, Dunlop MG, Timofeeva M. Genetically predicted physical activity levels are associated with lower colorectal cancer risk: a Mendelian randomisation study. Br J Cancer 2021; 124:1330-1338. [PMID: 33510439 PMCID: PMC8007642 DOI: 10.1038/s41416-020-01236-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND We conducted a Mendelian randomisation (MR) study to investigate whether physical activity (PA) causes a reduction of colorectal cancer risk and to understand the contributions of effects mediated through changes in body fat. METHODS Common genetic variants associated with self-reported moderate-to-vigorous PA (MVPA), acceleration vector magnitude PA (AMPA) and sedentary time were used as instrumental variables. To control for confounding effects of obesity, we included instrumental variables for body mass index (BMI), body fat percentage, waist circumference and arm, trunk and leg fat ratios. We analysed the effect of these instrumental variables in a colorectal cancer genome-wide association study comprising 31,197 cases and 61,770 controls of European ancestry by applying two-sample and multivariable MR study designs. RESULTS We found decreased colorectal cancer risk for genetically represented measures of MVPA and AMPA that were additional to effects mediated through genetic measures of obesity. Odds ratio and 95% confidence interval (CI) per standard deviation increase in MVPA and AMPA was 0.56 (0.31, 1.01) and 0.60 (0.41, 0.88), respectively. No association has been found between sedentary time and colorectal cancer risk. The proportion of effect mediated through BMI was 2% (95% CI: 0, 14) and 32% (95% CI: 12, 46) for MVPA and AMPA, respectively. CONCLUSION These findings provide strong evidence to reinforce public health measures on preventing colorectal cancer that promote PA at a population level regardless of body fatness.
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Affiliation(s)
- Xiaomeng Zhang
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Xue Li
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- School of Public Health and the Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Yann C Klimentidis
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Jessica M B Rees
- Edinburgh Clinical Trials Unit, Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Ian P M Tomlinson
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Department of Public Health, Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Odense, Denmark.
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5
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Li X, Timofeeva M, Spiliopoulou A, McKeigue P, He Y, Zhang X, Svinti V, Campbell H, Houlston RS, Tomlinson IPM, Farrington SM, Dunlop MG, Theodoratou E. Prediction of colorectal cancer risk based on profiling with common genetic variants. Int J Cancer 2020; 147:3431-3437. [PMID: 32638365 DOI: 10.1002/ijc.33191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/06/2020] [Accepted: 06/15/2020] [Indexed: 12/26/2022]
Abstract
Increasing numbers of common genetic variants associated with colorectal cancer (CRC) have been identified. Our study aimed to determine whether risk prediction based on common genetic variants might enable stratification for CRC risk. Meta-analysis of 11 genome-wide association studies comprising 16 871 cases and 26 328 controls was performed to capture CRC susceptibility variants. Genetic prediction models with several candidate polygenic risk scores (PRSs) were generated from Scottish CRC case-control studies (6478 cases and 11 043 controls) and the score with the best performance was then tested in UK Biobank (UKBB) (4800 cases and 20 287 controls). A weighted PRS of 116 CRC single nucleotide polymorphisms (wPRS116 ) was found with the best predictive performance, reporting a c-statistics of 0.60 and an odds ratio (OR) of 1.46 (95% confidence interval [CI] = 1.41-1.50, per SD increase) in Scottish data set. The predictive performance of this wPRS116 was consistently validated in UKBB data set with c-statistics of 0.61 and an OR of 1.49 (95% CI = 1.44-1.54, per SD increase). Modeling the levels of PRS with age and sex in the general UK population shows that employing genetic risk profiling can achieve a moderate degree of risk discrimination that could be helpful to identify a subpopulation with higher CRC risk due to genetic susceptibility.
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Affiliation(s)
- Xue Li
- School of Public Health, Zhejiang University, Hangzhou, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study (DIAS), Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Athina Spiliopoulou
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Paul McKeigue
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Yazhou He
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Xiaomeng Zhang
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Ian P M Tomlinson
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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Reijns MAM, Thompson L, Acosta JC, Black HA, Sanchez-Luque FJ, Diamond A, Parry DA, Daniels A, O'Shea M, Uggenti C, Sanchez MC, O'Callaghan A, McNab MLL, Adamowicz M, Friman ET, Hurd T, Jarman EJ, Chee FLM, Rainger JK, Walker M, Drake C, Longman D, Mordstein C, Warlow SJ, McKay S, Slater L, Ansari M, Tomlinson IPM, Moore D, Wilkinson N, Shepherd J, Templeton K, Johannessen I, Tait-Burkard C, Haas JG, Gilbert N, Adams IR, Jackson AP. A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection. PLoS Biol 2020; 18:e3001030. [PMID: 33320856 PMCID: PMC7771873 DOI: 10.1371/journal.pbio.3001030] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 11/05/2020] [Revised: 12/29/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
With the ongoing COVID-19 (Coronavirus Disease 2019) pandemic, caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), there is a need for sensitive, specific, and affordable diagnostic tests to identify infected individuals, not all of whom are symptomatic. The most sensitive test involves the detection of viral RNA using RT-qPCR (quantitative reverse transcription PCR), with many commercial kits now available for this purpose. However, these are expensive, and supply of such kits in sufficient numbers cannot always be guaranteed. We therefore developed a multiplex assay using well-established SARS-CoV-2 targets alongside a human cellular control (RPP30) and a viral spike-in control (Phocine Herpes Virus 1 [PhHV-1]), which monitor sample quality and nucleic acid extraction efficiency, respectively. Here, we establish that this test performs as well as widely used commercial assays, but at substantially reduced cost. Furthermore, we demonstrate >1,000-fold variability in material routinely collected by combined nose and throat swabbing and establish a statistically significant correlation between the detected level of human and SARS-CoV-2 nucleic acids. The inclusion of the human control probe in our assay therefore provides a quantitative measure of sample quality that could help reduce false-negative rates. We demonstrate the feasibility of establishing a robust RT-qPCR assay at approximately 10% of the cost of equivalent commercial assays, which could benefit low-resource environments and make high-volume testing affordable.
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Affiliation(s)
- Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Louise Thompson
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Juan Carlos Acosta
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Holly A. Black
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Francisco J. Sanchez-Luque
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
- Centre Pfizer-University of Granada-Andalusian Government for Genomics and Oncological Research (Genyo), Granada, Spain
| | - Austin Diamond
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Daniels
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Marie O'Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Carolina Uggenti
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Maria C. Sanchez
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alan O'Callaghan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michelle L. L. McNab
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Martyna Adamowicz
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Elias T. Friman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Hurd
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Edward J. Jarman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Frederic Li Mow Chee
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jacqueline K. Rainger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Marion Walker
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Camilla Drake
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Dasa Longman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Christine Mordstein
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sophie J. Warlow
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stewart McKay
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Louise Slater
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Morad Ansari
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Ian P. M. Tomlinson
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - David Moore
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Nadine Wilkinson
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Jill Shepherd
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Kate Templeton
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Ingolfur Johannessen
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jürgen G. Haas
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Nick Gilbert
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ian R. Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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7
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Watkins TBK, Lim EL, Petkovic M, Elizalde S, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM, Demeulemeester J, Dentro SC, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir MA, Xu H, Litchfield K, Lu WT, Mourikis TP, Dietzen M, Spain L, Cresswell GD, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates LR, Caramia F, Jaulin F, Vicier C, Tomlinson IPM, Brastianos PK, Cho RJ, Bastian BC, Dyrskjøt L, Jönsson GB, Savas P, Loi S, Campbell PJ, Andre F, Luscombe NM, Steeghs N, Tjan-Heijnen VCG, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum SF, Schwarz RF, McGranahan N, Swanton C. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 2020; 587:126-132. [PMID: 32879494 PMCID: PMC7611706 DOI: 10.1038/s41586-020-2698-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.
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Affiliation(s)
- Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marina Petkovic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sergi Elizalde
- Department of Mathematics, Dartmouth College, Hanover, NH, USA
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sally M Dewhurst
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Lewis Au
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Mickael Escudero
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hang Xu
- Stanford Cancer Institute, Stanford, CA, USA
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Wei Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thanos P Mourikis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Lavinia Spain
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - George D Cresswell
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Philippe Lamy
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Katja Harbst
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lucy R Yates
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Clinical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Ian P M Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Priscilla K Brastianos
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Göran B Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Peter Savas
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Fabrice Andre
- INSERM U981, PRISM Institute, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
- Medical School, Université Paris Saclay, Kremlin Bicetre, France
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute of Science & Technology, Okinawa, Japan
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, School of GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- 2nd Department of Pathology, SE-NAP Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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8
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Jiang X, Tomlinson IPM. Why is cancer not more common? A changing microenvironment may help to explain why, and suggests strategies for anti-cancer therapy. Open Biol 2020; 10:190297. [PMID: 32289242 PMCID: PMC7241076 DOI: 10.1098/rsob.190297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
One of the great unsolved puzzles in cancer biology is not why cancers occur, but rather explaining why so few cancers occur compared with the theoretical number that could occur, given the number of progenitor cells in the body and the normal mutation rate. We hypothesized that a contributory explanation is that the tumour microenvironment (TME) is not fixed due to factors such as immune cell infiltration, and that this could impair the ability of neoplastic cells to retain a high enough fitness to become a cancer. The TME has implicitly been assumed to be static in most cancer evolution models, and we therefore developed a mathematical model of spatial cancer evolution assuming that the TME, and thus the optimum cancer phenotype, changes over time. Based on simulations, we show how cancer cell populations adapt to diverse changing TME conditions and fitness landscapes. Compared with static TMEs, which generate neutral dynamics, changing TMEs lead to complex adaptations with characteristic spatio-temporal heterogeneity involving variable fitness effects of driver mutations, subclonal mixing, subclonal competition and phylogeny patterns. In many cases, cancer cell populations fail to grow or undergo spontaneous regression, and even extinction. Our analyses predict that cancer evolution in a changing TME is challenging, and can help to explain why cancer is neither inevitable nor as common as expected. Should cancer driver mutations with effects dependent of the TME exist, they are likely to be selected. Anti-cancer prevention and treatment strategies based on changing the TME are feasible and potentially effective.
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Affiliation(s)
| | - Ian P. M. Tomlinson
- Edinburgh Cancer Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
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9
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Werner B, Case J, Williams MJ, Chkhaidze K, Temko D, Fernández-Mateos J, Cresswell GD, Nichol D, Cross W, Spiteri I, Huang W, Tomlinson IPM, Barnes CP, Graham TA, Sottoriva A. Measuring single cell divisions in human tissues from multi-region sequencing data. Nat Commun 2020; 11:1035. [PMID: 32098957 PMCID: PMC7042311 DOI: 10.1038/s41467-020-14844-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/29/2020] [Indexed: 01/06/2023] Open
Abstract
Both normal tissue development and cancer growth are driven by a branching process of cell division and mutation accumulation that leads to intra-tissue genetic heterogeneity. However, quantifying somatic evolution in humans remains challenging. Here, we show that multi-sample genomic data from a single time point of normal and cancer tissues contains information on single-cell divisions. We present a new theoretical framework that, applied to whole-genome sequencing data of healthy tissue and cancer, allows inferring the mutation rate and the cell survival/death rate per division. On average, we found that cells accumulate 1.14 mutations per cell division in healthy haematopoiesis and 1.37 mutations per division in brain development. In both tissues, cell survival was maximal during early development. Analysis of 131 biopsies from 16 tumours showed 4 to 100 times increased mutation rates compared to healthy development and substantial inter-patient variation of cell survival/death rates.
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Affiliation(s)
- Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolutionary Dynamics Group, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Jack Case
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- University of Cambridge, Cambridge, UK
| | - Marc J Williams
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Ketevan Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Temko
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Javier Fernández-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - William Cross
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, 510060, Guangzhou, China
- School of Mathematical Sciences, Queen Mary University London, London, UK
| | - Ian P M Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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10
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Cornish AJ, Tomlinson IPM, Houlston RS. Mendelian randomisation: A powerful and inexpensive method for identifying and excluding non-genetic risk factors for colorectal cancer. Mol Aspects Med 2019; 69:41-47. [PMID: 30710596 PMCID: PMC6856712 DOI: 10.1016/j.mam.2019.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/28/2019] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer in economically developed countries and a major cause of cancer-related mortality. The importance of lifestyle and diet as major determinants of CRC risk is suggested by differences in CRC incidence between countries and in migration studies. Previous observational epidemiological studies have identified associations between modifiable environmental risk factors and CRC, but these studies can be susceptible to reverse causation and confounding, and their results can therefore conflict. Mendelian randomisation (MR) analysis represents an approach complementary to conventional observational studies examining associations between exposures and disease. The MR strategy employs allelic variants as instrumental variables (IVs), which act as proxies for non-genetic exposures. These allelic variants are randomly assigned during meiosis and can therefore inform on life-long exposure, whilst not being subject to reverse causation. In previous studies MR frameworks have associated several modifiable factors with CRC risk, including adiposity, hyperlipidaemia, fatty acid profile and alcohol consumption. In this review we detail the use of MR to investigate and discover CRC risk factors, and its future applications.
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Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
| | - Ian P M Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Department of Histopathology, University Hospitals Birmingham, Birmingham, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
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11
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Baker AM, Cross W, Curtius K, Al Bakir I, Choi CHR, Davis HL, Temko D, Biswas S, Martinez P, Williams MJ, Lindsay JO, Feakins R, Vega R, Hayes SJ, Tomlinson IPM, McDonald SAC, Moorghen M, Silver A, East JE, Wright NA, Wang LM, Rodriguez-Justo M, Jansen M, Hart AL, Leedham SJ, Graham TA. Evolutionary history of human colitis-associated colorectal cancer. Gut 2019; 68:985-995. [PMID: 29991641 PMCID: PMC6580738 DOI: 10.1136/gutjnl-2018-316191] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE IBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing. DESIGN Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using single nucleotide polymorphism arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC. RESULTS 10/12 tumours were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNA) per Mb, ~20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated ageing-associated mutational processes. Non-dysplastic mucosa had considerable mutation burden (median 47 SNAs), including mutations shared with the neighbouring CA-CRC, indicating a precancer mutational field. CA-CRCs were often near triploid (40%) or near tetraploid (20%) and phylogenetic analysis revealed that copy number alterations (CNAs) began to accrue in non-dysplastic bowel, but the LGD/HGD transition often involved a punctuated 'catastrophic' CNA increase. CONCLUSIONS Evolutionary genomic analysis revealed precancer clones bearing extensive SNAs and CNAs, with progression to cancer involving a dramatic accrual of CNAs at HGD. Detection of the cancerised field is an encouraging prospect for surveillance, but punctuated evolution may limit the window for early detection.
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Affiliation(s)
- Ann-Marie Baker
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - William Cross
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kit Curtius
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ibrahim Al Bakir
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | - Chang-Ho Ryan Choi
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | | | - Daniel Temko
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Computer Science, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Sujata Biswas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pierre Martinez
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Marc J Williams
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
| | - James O Lindsay
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Roger Feakins
- Department of Histopathology, The Royal London Hospital, London, UK
| | - Roser Vega
- Department of Gastroenterology, University College London Hospital, London, UK
| | - Stephen J Hayes
- Department of Histopathology, Salford Royal NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Ian P M Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Stuart A C McDonald
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Morgan Moorghen
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | - Andrew Silver
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - James E East
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nicholas A Wright
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Lai Mun Wang
- Cellular Pathology, John Radcliffe Hospital, Oxford, UK
| | | | - Marnix Jansen
- Department of Histopathology, University College London Hospital, London, UK
| | - Ailsa L Hart
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | - Simon J Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Trevor A Graham
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C, Anderson AR, Koelzer VH, Martinez P, Jiang X, Domingo E, Woodcock DJ, Feng Y, Kovacova M, Maughan T, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA, Tomlinson IPM. The evolutionary landscape of colorectal tumorigenesis. Nat Ecol Evol 2018; 2:1661-1672. [PMID: 30177804 PMCID: PMC6152905 DOI: 10.1038/s41559-018-0642-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [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: 04/17/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023]
Abstract
The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colorectal tumours, we investigate the evolutionary fitness landscape occupied by these neoplasms. Unlike carcinomas, advanced adenomas frequently harbour sub-clonal driver mutations-considered to be functionally important in the carcinogenic process-that have not swept to fixation, and have relatively high genetic heterogeneity. Carcinomas are distinguished from adenomas by widespread aneusomies that are usually clonal and often accrue in a 'punctuated' fashion. We conclude that adenomas evolve across an undulating fitness landscape, whereas carcinomas occupy a sharper fitness peak, probably owing to stabilizing selection.
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Affiliation(s)
- William Cross
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michal Kovac
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - Daniel Temko
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- CoMPLEX, Department of Computer Science, University College London, London, UK
| | - Hayley Davis
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sujata Biswas
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Roland Arnold
- Cancer Bioinfomatics Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Chandler Gatenbee
- Integrated Mathematical Oncology Department, Moffitt Comprehensive Cancer Centre, Tampa, FL, USA
| | - Alexander R Anderson
- Integrated Mathematical Oncology Department, Moffitt Comprehensive Cancer Centre, Tampa, FL, USA
| | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Xiaowei Jiang
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Enric Domingo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Yun Feng
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Monika Kovacova
- Institute of Mathematics and Physics, Faculty of Mechanical Engineering, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - Tim Maughan
- Department of Oncology, University of Oxford, Oxford, UK
| | - Marnix Jansen
- Department of Research Pathology, Cancer Institute, University College London, London, UK
| | - Manuel Rodriguez-Justo
- Department of Research Pathology, Cancer Institute, University College London, London, UK
| | - Shazad Ashraf
- Department of Surgery, University Hospitals Birmingham, Birmingham, UK
| | - Richard Guy
- Department of Colorectal Surgery, Cancer Centre, Churchill Hospital, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Christopher Cunningham
- Department of Colorectal Surgery, Cancer Centre, Churchill Hospital, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - James E East
- Translational Gastroenterology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford, UK
| | - Lai Mun Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Karl Heinimann
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Simon J Leedham
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Ian P M Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Department of Histopathology, University Hospitals Birmingham, Birmingham, UK.
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13
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Van Gool IC, Rayner E, Osse EM, Nout RA, Creutzberg CL, Tomlinson IPM, Church DN, Smit VTHBM, de Wind N, Bosse T, Drost M. Adjuvant Treatment for POLE Proofreading Domain-Mutant Cancers: Sensitivity to Radiotherapy, Chemotherapy, and Nucleoside Analogues. Clin Cancer Res 2018; 24:3197-3203. [PMID: 29559562 DOI: 10.1158/1078-0432.ccr-18-0266] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/08/2018] [Accepted: 03/14/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Pathogenic POLE proofreading domain mutations are found in many malignancies where they are associated with ultramutation and favorable prognosis. The extent to which this prognosis depends on their sensitivity to adjuvant treatment is unknown, as is the optimal therapy for advanced-staged or recurrent POLE-mutant cancers.Experimental Design: We examined the recurrence-free survival of women with POLE-mutant and POLE-wild-type endometrial cancers (EC) in the observation arm of the randomized PORTEC-1 endometrial cancer trial (N = 245 patients with stage I endometrial cancer for analysis). Sensitivity to radiotherapy and selected chemotherapeutics was compared between Pole-mutant mouse-derived embryonic stem (mES) cells, generated using CRISPR-Cas9 (Pole mutations D275A/E275A, and cancer-associated P286R, S297F, V411L) and isogenic wild-type cell lines.Results: In the observation arm of the PORTEC-1 trial (N = 245), women with POLE-mutant endometrial cancers (N = 16) had an improved recurrence-free survival (10-year recurrence-free survival 100% vs. 80.1% for POLE-wild-type; HR, 0.143; 95% confidence interval, 0.001-0.996; P = 0.049). Pole mutations did not increase sensitivity to radiotherapy nor to chemotherapeutics in mES cells. In contrast, Pole-mutant cells displayed significantly increased sensitivity to cytarabine and fludarabine (IC50Pole P286R-mutant vs. wild-type: 0.05 vs. 0.17 μmol/L for cytarabine, 4.62 vs. 11.1 μmol/L for fludarabine; P < 0.001 for both comparisons).Conclusions: The favorable prognosis of POLE-mutant cancers cannot be explained by increased sensitivity to currently used adjuvant treatments. These results support studies exploring minimization of adjuvant therapy for early-stage POLE-mutant cancers, including endometrial and colorectal cancers. Conversely, POLE mutations result in hypersensitivity to nucleoside analogues, suggesting the use of these compounds as a potentially effective targeted treatment for advanced-stage POLE-mutant cancers. Clin Cancer Res; 24(13); 3197-203. ©2018 AACR.
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Affiliation(s)
- Inge C Van Gool
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Emily Rayner
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elisabeth M Osse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Remi A Nout
- Department of Clinical and Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carien L Creutzberg
- Department of Clinical and Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ian P M Tomlinson
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - David N Church
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Cancer Centre, Churchill Hospital, Oxford, United Kingdom
| | - Vincent T H B M Smit
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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14
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Temko D, Tomlinson IPM, Severini S, Schuster-Böckler B, Graham TA. The effects of mutational processes and selection on driver mutations across cancer types. Nat Commun 2018; 9:1857. [PMID: 29748584 PMCID: PMC5945620 DOI: 10.1038/s41467-018-04208-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 04/11/2018] [Indexed: 11/17/2022] Open
Abstract
Epidemiological evidence has long associated environmental mutagens with increased cancer risk. However, links between specific mutation-causing processes and the acquisition of individual driver mutations have remained obscure. Here we have used public cancer sequencing data from 11,336 cancers of various types to infer the independent effects of mutation and selection on the set of driver mutations in a cancer type. First, we detect associations between a range of mutational processes, including those linked to smoking, ageing, APOBEC and DNA mismatch repair (MMR) and the presence of key driver mutations across cancer types. Second, we quantify differential selection between well-known alternative driver mutations, including differences in selection between distinct mutant residues in the same gene. These results show that while mutational processes have a large role in determining which driver mutations are present in a cancer, the role of selection frequently dominates.
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Affiliation(s)
- Daniel Temko
- Evolution and Cancer laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Sq, London, EC1M 6BQ, UK.
- Department of Computer Science, University College London, London, WC1E 6BT, UK.
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, Gower Street, London, WC1E 6BT, UK.
| | - Ian P M Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Simone Severini
- Department of Computer Science, University College London, London, WC1E 6BT, UK
- Institute of Natural Sciences, Shanghai Jiao Tong University, Dong Chuan Road, Minhang District, Shanghai, 200240, UK
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Dr, Oxford, OX3 7DQ, USA.
| | - Trevor A Graham
- Evolution and Cancer laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Sq, London, EC1M 6BQ, UK.
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15
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16
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Timofeeva MN, Kinnersley B, Farrington SM, Whiffin N, Palles C, Svinti V, Lloyd A, Gorman M, Ooi LY, Hosking F, Barclay E, Zgaga L, Dobbins S, Martin L, Theodoratou E, Broderick P, Tenesa A, Smillie C, Grimes G, Hayward C, Campbell A, Porteous D, Deary IJ, Harris SE, Northwood EL, Barrett JH, Smith G, Wolf R, Forman D, Morreau H, Ruano D, Tops C, Wijnen J, Schrumpf M, Boot A, Vasen HFA, Hes FJ, van Wezel T, Franke A, Lieb W, Schafmayer C, Hampe J, Buch S, Propping P, Hemminki K, Försti A, Westers H, Hofstra R, Pinheiro M, Pinto C, Teixeira M, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo A, Castells A, Castellví-Bel S, Campbell H, Bishop DT, Tomlinson IPM, Dunlop MG, Houlston RS. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer. Sci Rep 2015; 5:16286. [PMID: 26553438 PMCID: PMC4639776 DOI: 10.1038/srep16286] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10(-7)), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10(-7)); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10(-7) and OR = 1.09, P = 7.4 × 10(-8)); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 × 10(-9)), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P < 2.90 × 10(-6)). We found an excess of rare, damaging variants in base-excision (P = 2.4 × 10(-4)) and DNA mismatch repair genes (P = 6.1 × 10(-4)) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC.
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Affiliation(s)
- Maria N. Timofeeva
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Victoria Svinti
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Amy Lloyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Li-Yin Ooi
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Fay Hosking
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Lina Zgaga
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Sara Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Evropi Theodoratou
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, United Kingdom
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Roslin EH25 9RG, United Kingdom
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Claire Smillie
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Graeme Grimes
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Archie Campbell
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - David Porteous
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Ian J. Deary
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Sarah E. Harris
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Emma L. Northwood
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Jennifer H. Barrett
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Gillian Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Roland Wolf
- Medical Research Institute, University of Dundee, Dundee, UK
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Juul Wijnen
- Department of Human Genetics, Leiden University Medical Center, The Netherlands
| | - Melanie Schrumpf
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Hans F A Vasen
- Department of Gastroenterology, Leiden University Medical Center, The Netherlands
| | - Frederik J. Hes
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wolgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University Kiel, Kiel
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Peter Propping
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 205 02 Malmö, Sweden
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 205 02 Malmö, Sweden
| | - Helga Westers
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Robert Hofstra
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, the Netherlands
| | - Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Manuel Teixeira
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Ceres Fernández-Rozadilla
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Angel Carracedo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Antoni Castells
- Servei de Gastroenterologia, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Servei de Gastroenterologia, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Harry Campbell
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, United Kingdom
| | - D. Timothy Bishop
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Ian P M Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
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17
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Guo X, Long J, Zeng C, Michailidou K, Ghoussaini M, Bolla MK, Wang Q, Milne RL, Shu XO, Cai Q, Beesley J, Kar SP, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Beeghly-Fadiel A, Benitez J, Blot W, Bogdanova N, Bojesen SE, Brauch H, Brenner H, Brinton L, Broeks A, Brüning T, Burwinkel B, Cai H, Canisius S, Chang-Claude J, Choi JY, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Devilee P, Droit A, Dörk T, Fasching PA, Fletcher O, Flyger H, Fostira F, Gaborieau V, García-Closas M, Giles GG, Grip M, Guénel P, Haiman CA, Hamann U, Hartman M, Hollestelle A, Hopper JL, Hsiung CN, Ito H, Jakubowska A, Johnson N, Kabisch M, Kang D, Khan S, Knight JA, Kosma VM, Lambrechts D, Le Marchand L, Li J, Lindblom A, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Margolin S, Marme F, Matsuo K, McLean CA, Meindl A, Muir K, Neuhausen SL, Nevanlinna H, Nord S, Olson JE, Orr N, Peterlongo P, Putti TC, Rudolph A, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Shen CY, Shi J, Shrubsole MJ, Southey MC, Swerdlow A, Teo SH, Thienpont B, Toland AE, Tollenaar RAEM, Tomlinson IPM, Truong T, Tseng CC, van den Ouweland A, Wen W, Winqvist R, Wu A, Yip CH, Zamora MP, Zheng Y, Hall P, Pharoah PDP, Simard J, Chenevix-Trench G, Dunning AM, Easton DF, Zheng W. Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk. Cancer Epidemiol Biomarkers Prev 2015; 24:1680-91. [PMID: 26354892 PMCID: PMC4633342 DOI: 10.1158/1055-9965.epi-15-0363] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/20/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. METHODS We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. RESULTS Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10(-4); OR, 1.04; 95% confidence interval (CI), 1.02-1.07] and rs77928427 (P = 1.86 × 10(-4); OR, 1.04; 95% CI, 1.02-1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r(2) ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. CONCLUSION Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. IMPACT Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Chenjie Zeng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. Centre for Epidemiology and Biostatistics, School of Population and Global health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jonathan Beesley
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Siddhartha P Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Matthias W Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain. Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee. International Epidemiology Institute, Rockville, Maryland
| | - Natalia Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Herlev, Denmark. Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark. Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany. University of Tübingen, Tübingen, Germany. German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany. German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany. Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum, Germany
| | - Barbara Burwinkel
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany. Molecular Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Sander Canisius
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands. Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnaud Droit
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec, Canada
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany. David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, California
| | - Olivia Fletcher
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", Athens, Greece
| | | | - Montserrat García-Closas
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom. Division of Genetics and Epidemiology, Institute of Cancer Research, London, United Kingdom
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. Centre for Epidemiology and Biostatistics, School of Population and Global health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Pascal Guénel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France. University Paris-Sud, Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore. Department of Surgery, National University Health System, Singapore
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Nichola Johnson
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sofia Khan
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Julia A Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada. Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland; Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Diether Lambrechts
- Vesalius Research Center, Leuven, Belgium. Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | | | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland; Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Frederik Marme
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany. Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Catriona A McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Kenneth Muir
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy. Institute of Population Health, University of Manchester, Manchester, United Kingdom
| | | | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Ullernchausseen, Oslo, Norway. K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Kirkeveien, Oslo, Norway
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Nick Orr
- Division of Breast Cancer Research, Institute of Cancer Research, London, United Kingdom; Cancer Research, Institute of Cancer Research, London, United Kingdom
| | | | | | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, United Kingdom
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Rita K Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany. Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany. Center for Molecular Medicine, University Hospital of Cologne, Cologne, Germany. Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Chen-Yang Shen
- School of Public Health, China Medical University, Taichung, Taiwan. Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology and Division of Breast Cancer Research, Institute of Cancer Research, London, United Kingdom
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia. Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Bernard Thienpont
- Vesalius Research Center, Leuven, Belgium. Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Amanda Ewart Toland
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Robert A E M Tollenaar
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ian P M Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Thérèse Truong
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France. University Paris-Sud, Villejuif, France
| | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ans van den Ouweland
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry, University of Oulu, Oulu, Finland. Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - Anna Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Cheng Har Yip
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, PR China
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec, Canada
| | | | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
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18
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Beggs AD, Dilworth MP, Domingo E, Midgley R, Kerr D, Tomlinson IPM, Middleton GW. Methylation changes in the TFAP2E promoter region are associated with BRAF mutation and poorer overall & disease free survival in colorectal cancer. Oncoscience 2015; 2:508-16. [PMID: 26097884 PMCID: PMC4468337 DOI: 10.18632/oncoscience.149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/16/2015] [Indexed: 01/10/2023] Open
Abstract
INTRODUCTION BRAF mutant colorectal cancer carries a poor prognosis which is thought to be related to poor response to conventional chemotherapy. BRAF mutation is associated with the serrated tumour phenotype. We hypothesised that one of the mechanisms by which BRAF mutant colorectal cancer demonstrate poor outcomes with chemotherapy is abnormal gene methylation. METHODS The Cancer Genome Atlas (TCGA) methylation data was analysed using a linear regression model with BRAF mutation as an independent variable. Expression datasets were also obtained to correlate functional changes. Top differentially methylated probes were taken forward for validation by methylation pyrosequencing. These probes were analysed on a cohort of patients enriched for BRAF mutations taken from the VICTOR and QUASAR2 studies. RESULTS In an analysis of 91 tumours (9 BRAF mutant, 82 wild type), the Illumina probe cg11835197 was the probe identified as top differentially methylated (p = 2.56×10-7, Bayes Factor (BF) =6.54). This probe covered a region -413bp from the promoter region of TFAP2E. We found a complex pattern of CpG specific methylation of this region which was associated with both overall (p=0.044) and disease free (p=0.046) survival. DISCUSSION BRAF mutant tumours may attain part of their chemoresistance from abnormal TFAP2E methylation, which has not previously been described.
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Affiliation(s)
- Andrew D Beggs
- Translational Surgical Biology Laboratory, School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Mark P Dilworth
- Translational Surgical Biology Laboratory, School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Enric Domingo
- Molecular & Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rachel Midgley
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - Ian P M Tomlinson
- Molecular & Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gary W Middleton
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
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19
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Church DN, Stelloo E, Nout RA, Valtcheva N, Depreeuw J, ter Haar N, Noske A, Amant F, Tomlinson IPM, Wild PJ, Lambrechts D, Jürgenliemk-Schulz IM, Jobsen JJ, Smit VTHBM, Creutzberg CL, Bosse T. Prognostic significance of POLE proofreading mutations in endometrial cancer. J Natl Cancer Inst 2015; 107:402. [PMID: 25505230 PMCID: PMC4301706 DOI: 10.1093/jnci/dju402] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [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: 07/31/2014] [Revised: 09/26/2014] [Accepted: 10/29/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Current risk stratification in endometrial cancer (EC) results in frequent over- and underuse of adjuvant therapy, and may be improved by novel biomarkers. We examined whether POLE proofreading mutations, recently reported in about 7% of ECs, predict prognosis. METHODS We performed targeted POLE sequencing in ECs from the PORTEC-1 and -2 trials (n = 788), and analyzed clinical outcome according to POLE status. We combined these results with those from three additional series (n = 628) by meta-analysis to generate multivariable-adjusted, pooled hazard ratios (HRs) for recurrence-free survival (RFS) and cancer-specific survival (CSS) of POLE-mutant ECs. All statistical tests were two-sided. RESULTS POLE mutations were detected in 48 of 788 (6.1%) ECs from PORTEC-1 and-2 and were associated with high tumor grade (P < .001). Women with POLE-mutant ECs had fewer recurrences (6.2% vs 14.1%) and EC deaths (2.3% vs 9.7%), though, in the total PORTEC cohort, differences in RFS and CSS were not statistically significant (multivariable-adjusted HR = 0.43, 95% CI = 0.13 to 1.37, P = .15; HR = 0.19, 95% CI = 0.03 to 1.44, P = .11 respectively). However, of 109 grade 3 tumors, 0 of 15 POLE-mutant ECs recurred, compared with 29 of 94 (30.9%) POLE wild-type cancers; reflected in statistically significantly greater RFS (multivariable-adjusted HR = 0.11, 95% CI = 0.001 to 0.84, P = .03). In the additional series, there were no EC-related events in any of 33 POLE-mutant ECs, resulting in a multivariable-adjusted, pooled HR of 0.33 for RFS (95% CI = 0.12 to 0.91, P = .03) and 0.26 for CSS (95% CI = 0.06 to 1.08, P = .06). CONCLUSION POLE proofreading mutations predict favorable EC prognosis, independently of other clinicopathological variables, with the greatest effect seen in high-grade tumors. This novel biomarker may help to reduce overtreatment in EC.
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Affiliation(s)
- David N Church
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Ellen Stelloo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Remi A Nout
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Nadejda Valtcheva
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Jeroen Depreeuw
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Natalja ter Haar
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Aurelia Noske
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Frederic Amant
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Ian P M Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ).
| | - Peter J Wild
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Diether Lambrechts
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Ina M Jürgenliemk-Schulz
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Jan J Jobsen
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Vincent T H B M Smit
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Carien L Creutzberg
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Tjalling Bosse
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
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Kämpjärvi K, Park MJ, Mehine M, Kim NH, Clark AD, Bützow R, Böhling T, Böhm J, Mecklin JP, Järvinen H, Tomlinson IPM, van der Spuy ZM, Sjöberg J, Boyer TG, Vahteristo P. Mutations in Exon 1 highlight the role of MED12 in uterine leiomyomas. Hum Mutat 2014; 35:1136-41. [PMID: 24980722 DOI: 10.1002/humu.22612] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/17/2014] [Indexed: 01/05/2023]
Abstract
Mediator regulates transcription by connecting gene-specific transcription factors to the RNA polymerase II initiation complex. We recently discovered by exome sequencing that specific exon 2 mutations in mediator complex subunit 12 (MED12) are extremely common in uterine leiomyomas. Subsequent screening studies have focused on this mutational hot spot, and mutations have been detected in uterine leiomyosarcomas, extrauterine leiomyomas and leiomyosarcomas, endometrial polyps, and colorectal cancers. All mutations have been missense changes or in-frame insertions/deletions. Here, we have analyzed 611 samples representing all above-mentioned tumor types for possible exon 1 mutations. Five mutations were observed, all of which were in-frame insertion/deletions in uterine leiomyomas. Transcriptome-wide expression data revealed that MED12 exon 1 and exon 2 mutations lead to the same unique global gene expression pattern with RAD51B being the most upregulated gene. Immunoprecipitation and kinase activity assays showed that both exon 1 and exon 2 mutations disrupt the interaction between MED12 and Cyclin C and CDK8/19 and abolish the mediator-associated CDK kinase activity. These results further emphasize the role of MED12 in uterine leiomyomas, show that exon 1 and exon 2 exert their tumorigenic effect in similar manner, and stress that exon 1 should be included in subsequent MED12 screenings.
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Affiliation(s)
- Kati Kämpjärvi
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
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21
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Mouradov D, Sloggett C, Jorissen RN, Love CG, Li S, Burgess AW, Arango D, Strausberg RL, Buchanan D, Wormald S, O'Connor L, Wilding JL, Bicknell D, Tomlinson IPM, Bodmer WF, Mariadason JM, Sieber OM. Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer. Cancer Res 2014; 74:3238-47. [PMID: 24755471 DOI: 10.1158/0008-5472.can-14-0013] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human colorectal cancer cell lines are used widely to investigate tumor biology, experimental therapy, and biomarkers. However, to what extent these established cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we profiled 70 colorectal cancer cell lines for mutations and DNA copy number by whole-exome sequencing and SNP microarray analyses, respectively. Gene expression was defined using RNA-Seq. Cell line data were compared with those published for primary colorectal cancers in The Cancer Genome Atlas. Notably, we found that exome mutation and DNA copy-number spectra in colorectal cancer cell lines closely resembled those seen in primary colorectal tumors. Similarities included the presence of two hypermutation phenotypes, as defined by signatures for defective DNA mismatch repair and DNA polymerase ε proofreading deficiency, along with concordant mutation profiles in the broadly altered WNT, MAPK, PI3K, TGFβ, and p53 pathways. Furthermore, we documented mutations enriched in genes involved in chromatin remodeling (ARID1A, CHD6, and SRCAP) and histone methylation or acetylation (ASH1L, EP300, EP400, MLL2, MLL3, PRDM2, and TRRAP). Chromosomal instability was prevalent in nonhypermutated cases, with similar patterns of chromosomal gains and losses. Although paired cell lines derived from the same tumor exhibited considerable mutation and DNA copy-number differences, in silico simulations suggest that these differences mainly reflected a preexisting heterogeneity in the tumor cells. In conclusion, our results establish that human colorectal cancer lines are representative of the main subtypes of primary tumors at the genomic level, further validating their utility as tools to investigate colorectal cancer biology and drug responses.
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Affiliation(s)
- Dmitri Mouradov
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Clare Sloggett
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Robert N Jorissen
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Christopher G Love
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Shan Li
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Antony W Burgess
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Diego Arango
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Robert L Strausberg
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Daniel Buchanan
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Samuel Wormald
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Liam O'Connor
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Jennifer L Wilding
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - David Bicknell
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Ian P M Tomlinson
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Walter F Bodmer
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - John M Mariadason
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Oliver M Sieber
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
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22
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Domingo E, Church DN, Sieber O, Ramamoorthy R, Yanagisawa Y, Johnstone E, Davidson B, Kerr DJ, Tomlinson IPM, Midgley R. Evaluation of PIK3CA mutation as a predictor of benefit from nonsteroidal anti-inflammatory drug therapy in colorectal cancer. J Clin Oncol 2013; 31:4297-305. [PMID: 24062397 DOI: 10.1200/jco.2013.50.0322] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) protect against colorectal cancer (CRC) and are associated with reduced disease recurrence and improved outcome after primary treatment. However, toxicities of NSAIDs have limited their use as antineoplastic therapy. Recent data have suggested that the benefit of aspirin after CRC diagnosis is limited to patients with PIK3CA-mutant cancers. We sought to determine the predictive utility of PIK3CA mutation for benefit from both cyclooxygenase-2 inhibition and aspirin. METHODS We performed molecular analysis of tumors from 896 participants in the Vioxx in Colorectal Cancer Therapy: Definition of Optimal Regime (VICTOR) trial, a large randomized trial comparing rofecoxib with placebo after primary CRC resection. We compared relapse-free survival and overall survival between rofecoxib therapy and placebo and between the use and nonuse of low-dose aspirin, according to tumor PIK3CA mutation status. RESULTS We found no evidence of a greater benefit from rofecoxib treatment compared with placebo in patients whose tumors had PIK3CA mutations (multivariate adjusted hazard ratio [HR], 1.2; 95% CI, 0.53 to 2.72; P = .66; (P)INTERACTION = .47) compared with patients with PIK3CA wild-type cancers (HR, 0.87; 95% CI, 0.64 to 1.16; P = .34). In contrast, regular aspirin use after CRC diagnosis was associated with a reduced rate of CRC recurrence in patients with PIK3CA-mutant cancers (HR, 0.11; 95% CI, 0.001 to 0.832; P = .027; (P)INTERACTION = .024) but not in patients lacking tumor PIK3CA mutation (HR, 0.92; 95% CI, 0.60 to 1.42; P = .71). CONCLUSION Although tumor PIK3CA mutation does not predict benefit from rofecoxib treatment, it merits further evaluation as a predictive biomarker for aspirin therapy. Our findings are concordant with recent data and support the prospective investigation of adjuvant aspirin in PIK3CA-mutant CRC.
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Affiliation(s)
- Enric Domingo
- Enric Domingo, David N. Church, Rajarajan Ramamoorthy, and Ian P.M. Tomlinson, The Wellcome Trust Centre for Human Genetics, University of Oxford; David N. Church, David J. Kerr, and Rachel Midgley, Oxford Cancer Centre, Churchill Hospital; Yoko Yanagisawa, Elaine Johnstone, David J. Kerr, and Rachel Midgley, University of Oxford, Oxford; Rajarajan Ramamoorthy and Brian Davidson, University College London, Royal Free Hospital, London, United Kingdom; and Oliver Sieber, Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
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23
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Beggs AD, Domingo E, Abulafi M, Hodgson SV, Tomlinson IPM. A study of genomic instability in early preneoplastic colonic lesions. Oncogene 2013; 32:5333-7. [PMID: 23246972 PMCID: PMC3898108 DOI: 10.1038/onc.2012.584] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/15/2012] [Accepted: 10/28/2012] [Indexed: 12/16/2022]
Abstract
It is difficult to explain the differential rates of progression of premalignant colonic lesions and differences in behaviour of morphologically similar lesions. Heterogeneity for microsatellite instability (MSI) and promoter methylation in driving these phenomena forward may explain this; however, no previous analysis has examined this in detail at the gland level, the smallest unit of colorectal premalignant lesions. We aimed to carry out an analysis of gland level genomic instability for MSI and promoter methylation. MSI occurred significantly more frequently (20%) in colonic glands than has previously been observed in whole colorectal polyps. Significant promoter methylation was seen in MLH1, PMS2, MLH3 and MSH3 as well as significant heterogeneity for both MSI and promoter methylation. Methylation and MSI may have a significant role in driving forward colorectal carcinogenesis, although in the case of MSI, this association is less clear as it occurs significantly more frequently than previously thought, and may simply be a passenger in the adenoma-carcinoma sequence. Promoter methylation in MLH1, MLH3, MSH3 and PMS2 was also found to be significantly associated with MSI and should be investigated further. A total of 273 colorectal glands (126 hyperplastic, 147 adenomatous) were isolated via laser capture microdissection (targeted at regions of MLH1 loss) from 93 colonic polyps and tested for MSI, and promoter methylation of the DNA mismatch repair genes MLH1, MSH2, MLH3, MSH6, PMS2, MGMT and MLH3 via methylation specific multiplex ligation-dependent probe amplification. Logistic regression modelling was then used to identify significant associations between promoter methylation and gland histological type and MSI status.
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Affiliation(s)
- A D Beggs
- Molecular and Population Genetics Laboratory and NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Surgery, Croydon University Hospital, Croydon, UK
| | - E Domingo
- Molecular and Population Genetics Laboratory and NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M Abulafi
- Department of Surgery, Croydon University Hospital, Croydon, UK
| | - S V Hodgson
- Department of Medical Genetics, St George's University of London, Cranmer Terrace, Tooting, London, UK
| | - I P M Tomlinson
- Molecular and Population Genetics Laboratory and NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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24
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Mouradov D, Domingo E, Gibbs P, Jorissen RN, Li S, Soo PY, Lipton L, Desai J, Danielsen HE, Oukrif D, Novelli M, Yau C, Holmes CC, Jones IT, McLaughlin S, Molloy P, Hawkins NJ, Ward R, Midgely R, Kerr D, Tomlinson IPM, Sieber OM. Survival in stage II/III colorectal cancer is independently predicted by chromosomal and microsatellite instability, but not by specific driver mutations. Am J Gastroenterol 2013; 108:1785-93. [PMID: 24042191 DOI: 10.1038/ajg.2013.292] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 08/05/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Microsatellite instability (MSI) is an established marker of good prognosis in colorectal cancer (CRC). Chromosomal instability (CIN) is strongly negatively associated with MSI and has been shown to be a marker of poor prognosis in a small number of studies. However, a substantial group of "double-negative" (MSI-/CIN-) CRCs exists. The prognosis of these patients is unclear. Furthermore, MSI and CIN are each associated with specific molecular changes, such as mutations in KRAS and BRAF, that have been associated with prognosis. It is not known which of MSI, CIN, and the specific gene mutations are primary predictors of survival. METHODS We evaluated the prognostic value (disease-free survival, DFS) of CIN, MSI, mutations in KRAS, NRAS, BRAF, PIK3CA, FBXW7, and TP53, and chromosome 18q loss-of-heterozygosity (LOH) in 822 patients from the VICTOR trial of stage II/III CRC. We followed up promising associations in an Australian community-based cohort (N=375). RESULTS In the VICTOR patients, no specific mutation was associated with DFS, but individually MSI and CIN showed significant associations after adjusting for stage, age, gender, tumor location, and therapy. A combined analysis of the VICTOR and community-based cohorts showed that MSI and CIN were independent predictors of DFS (for MSI, hazard ratio (HR)=0.58, 95% confidence interval (CI) 0.36-0.93, and P=0.021; for CIN, HR=1.54, 95% CI 1.14-2.08, and P=0.005), and joint CIN/MSI testing significantly improved the prognostic prediction of MSI alone (P=0.028). Higher levels of CIN were monotonically associated with progressively poorer DFS, and a semi-quantitative measure of CIN was a better predictor of outcome than a simple CIN+/- variable. All measures of CIN predicted DFS better than the recently described Watanabe LOH ratio. CONCLUSIONS MSI and CIN are independent predictors of DFS for stage II/III CRC. Prognostic molecular tests for CRC relapse should currently use MSI and a quantitative measure of CIN rather than specific gene mutations.
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Affiliation(s)
- Dmitri Mouradov
- 1] Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Parkville, Victoria, Australia [2] Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
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25
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Christie M, Jorissen RN, Mouradov D, Sakthianandeswaren A, Li S, Day F, Tsui C, Lipton L, Desai J, Jones IT, McLaughlin S, Ward RL, Hawkins NJ, Ruszkiewicz AR, Moore J, Burgess AW, Busam D, Zhao Q, Strausberg RL, Simpson AJ, Tomlinson IPM, Gibbs P, Sieber OM. Different APC genotypes in proximal and distal sporadic colorectal cancers suggest distinct WNT/β-catenin signalling thresholds for tumourigenesis. Oncogene 2013; 32:4675-82. [PMID: 23085758 PMCID: PMC3787794 DOI: 10.1038/onc.2012.486] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/20/2012] [Accepted: 09/04/2012] [Indexed: 01/05/2023]
Abstract
Biallelic protein-truncating mutations in the adenomatous polyposis coli (APC) gene are prevalent in sporadic colorectal cancer (CRC). Mutations may not be fully inactivating, instead producing WNT/β-catenin signalling levels 'just-right' for tumourigenesis. However, the spectrum of optimal APC genotypes accounting for both hits, and the influence of clinicopathological features on genotype selection remain undefined. We analysed 630 sporadic CRCs for APC mutations and loss of heterozygosity (LOH) using sequencing and single-nucleotide polymorphism microarrays, respectively. Truncating APC mutations and/or LOH were detected in 75% of CRCs. Most truncating mutations occurred within a mutation cluster region (MCR; codons 1282-1581) leaving 1-3 intact 20 amino-acid repeats (20AARs) and abolishing all Ser-Ala-Met-Pro (SAMP) repeats. Cancers commonly had one MCR mutation plus either LOH or another mutation 5' to the MCR. LOH was associated with mutations leaving 1 intact 20AAR. MCR mutations leaving 1 vs 2-3 intact 20AARs were associated with 5' mutations disrupting or leaving intact the armadillo-repeat domain, respectively. Cancers with three hits had an over-representation of mutations upstream of codon 184, in the alternatively spliced region of exon 9, and 3' to the MCR. Microsatellite unstable cancers showed hyper-mutation at MCR mono- and di-nucleotide repeats, leaving 2-3 intact 20AARs. Proximal and distal cancers exhibited different preferred APC genotypes, leaving a total of 2 or 3 and 0 to 2 intact 20AARs, respectively. In conclusion, APC genotypes in sporadic CRCs demonstrate 'fine-tuned' interdependence of hits by type and location, consistent with selection for particular residual levels of WNT/β-catenin signalling, with different 'optimal' thresholds for proximal and distal cancers.
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Affiliation(s)
- M Christie
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - R N Jorissen
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - D Mouradov
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - A Sakthianandeswaren
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - S Li
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - F Day
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - C Tsui
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - L Lipton
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - J Desai
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - I T Jones
- Department of Colorectal Surgery, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - S McLaughlin
- Department of Colorectal Surgery, Western Hospital, Footscray, Victoria, Australia
| | - R L Ward
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - N J Hawkins
- Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - A R Ruszkiewicz
- Pathology Department, Institute of Medical and Veterinary Science, Adelaide, South Australia, Australia
| | - J Moore
- Department of Colorectal Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - A W Burgess
- Epithelial Biology Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - D Busam
- J Craig Venter Institute, Rockville, MD, USA
| | - Q Zhao
- J Craig Venter Institute, Rockville, MD, USA
| | - R L Strausberg
- Department of Neurosurgery, Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Ludwig Institute for Cancer Research Ltd, New York, NY, USA
| | - A J Simpson
- Department of Neurosurgery, Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Ludwig Institute for Cancer Research Ltd, New York, NY, USA
| | - I P M Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, OX, UK
| | - P Gibbs
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - O M Sieber
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
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Church DN, Briggs SEW, Palles C, Domingo E, Kearsey SJ, Grimes JM, Gorman M, Martin L, Howarth KM, Hodgson SV, Kaur K, Taylor J, Tomlinson IPM. DNA polymerase ε and δ exonuclease domain mutations in endometrial cancer. Hum Mol Genet 2013; 22:2820-8. [PMID: 23528559 PMCID: PMC3690967 DOI: 10.1093/hmg/ddt131] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [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: 01/22/2013] [Revised: 03/19/2013] [Indexed: 12/31/2022] Open
Abstract
Accurate duplication of DNA prior to cell division is essential to suppress mutagenesis and tumour development. The high fidelity of eukaryotic DNA replication is due to a combination of accurate incorporation of nucleotides into the nascent DNA strand by DNA polymerases, the recognition and removal of mispaired nucleotides (proofreading) by the exonuclease activity of DNA polymerases δ and ε, and post-replication surveillance and repair of newly synthesized DNA by the mismatch repair (MMR) apparatus. While the contribution of defective MMR to neoplasia is well recognized, evidence that faulty DNA polymerase activity is important in cancer development has been limited. We have recently shown that germline POLE and POLD1 exonuclease domain mutations (EDMs) predispose to colorectal cancer (CRC) and, in the latter case, to endometrial cancer (EC). Somatic POLE mutations also occur in 5-10% of sporadic CRCs and underlie a hypermutator, microsatellite-stable molecular phenotype. We hypothesized that sporadic ECs might also acquire somatic POLE and/or POLD1 mutations. Here, we have found that missense POLE EDMs with good evidence of pathogenic effects are present in 7% of a set of 173 endometrial cancers, although POLD1 EDMs are uncommon. The POLE mutations localized to highly conserved residues and were strongly predicted to affect proofreading. Consistent with this, POLE-mutant tumours were hypermutated, with a high frequency of base substitutions, and an especially large relative excess of G:C>T:A transversions. All POLE EDM tumours were microsatellite stable, suggesting that defects in either DNA proofreading or MMR provide alternative mechanisms to achieve genomic instability and tumourigenesis.
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Affiliation(s)
- David N Church
- Molecular and Population Genetics Laboratory, University of Oxford, Roosevelt Drive, Oxford OX3 7BN.
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27
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Willis L, Graham TA, Alarcón T, Alison MR, Tomlinson IPM, Page KM. What can be learnt about disease progression in breast cancer dormancy from relapse data? PLoS One 2013; 8:e62320. [PMID: 23671591 PMCID: PMC3646031 DOI: 10.1371/journal.pone.0062320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 01/09/2013] [Accepted: 03/20/2013] [Indexed: 02/07/2023] Open
Abstract
Breast cancer patients have an anomalously high rate of relapse many years–up to 25 years–after apparently curative surgery removed the primary tumour. Disease progression during the intervening years between resection and relapse is poorly understood. There is evidence that the disease persists as dangerous, tiny metastases that remain at a growth restricted, clinically undetectable size until a transforming event restarts growth. This is the starting point for our study, where patients who have metastases that are all tiny and growth-restricted are said to have cancer dormancy. Can long-term follow-up relapse data from breast cancer patients be used to extract knowledge about the progression of the undetected disease? Here, we evaluate whether this is the case by introducing and analysing four simple mathematical models of cancer dormancy. These models extend the common assumption that a random transforming event, such as a mutation, can restart growth of a tiny, growth-restricted metastasis; thereafter, cancer dormancy progresses to detectable metastasis. We find that physiopathological details, such as the number of random transforming events that metastases must undergo to escape from growth restriction, cannot be extracted from relapse data. This result is unsurprising. However, the same analysis suggested a natural question that does have a surprising answer: why are interesting trends in long-term relapse data not more commonly observed? Further, our models indicate that (a) therapies which induce growth restriction among metastases but do not prevent increases in metastases' tumourigenicity may introduce a time post-surgery when more patients are prone to relapse; and (b), if a number of facts about disease progression are first established, how relapse data might be used to estimate clinically relevant variables, such as the likely numbers of undetected growth-restricted metastases. This work is a necessary, early step in building a quantitative mechanistic understanding of cancer dormancy.
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Affiliation(s)
- Lisa Willis
- Centre for Mathematics and Physics in the Life Sciences and EXperimental Biology, University College London, London, United Kingdom.
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28
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Beggs AD, Jones A, Shepherd N, Arnaout A, Finlayson C, Abulafi AM, Morton DG, Matthews GM, Hodgson SV, Tomlinson IPM. Loss of expression and promoter methylation of SLIT2 are associated with sessile serrated adenoma formation. PLoS Genet 2013; 9:e1003488. [PMID: 23671423 PMCID: PMC3649993 DOI: 10.1371/journal.pgen.1003488] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 10/16/2012] [Accepted: 03/11/2013] [Indexed: 12/22/2022] Open
Abstract
Serrated adenomas form a distinct subtype of colorectal pre-malignant lesions that may progress to malignancy along a different molecular pathway than the conventional adenoma-carcinoma pathway. Previous studies have hypothesised that BRAF mutation and promoter hypermethylation plays a role, but the evidence for this is not robust. We aimed to carry out a whole-genome loss of heterozygosity analysis, followed by targeted promoter methylation and expression analysis to identify potential pathways in serrated adenomas. An initial panel of 9 sessile serrated adenomas (SSA) and one TSA were analysed using Illumina Goldengate HumanLinkage panel arrays to ascertain regions of loss of heterozygosity. This was verified via molecular inversion probe analysis and microsatellite analysis of a further 32 samples. Methylation analysis of genes of interest was carried out using methylation specific PCR (verified by pyrosequencing) and immunohistochemistry used to correlate loss of expression of genes of interest. All experiments used adenoma samples and normal tissue samples as control. SSA samples were found on whole-genome analysis to have consistent loss of heterozygosity at 4p15.1-4p15.31, which was not found in the sole TSA, adenomas, or normal tissues. Genes of interest in this region were PDCH7 and SLIT2, and combined MSP/IHC analysis of these genes revealed significant loss of SLIT2 expression associated with promoter methylation of SLIT2. Loss of expression of SLIT2 by promoter hypermethylation and loss of heterozygosity events is significantly associated with serrated adenoma development, and SLIT2 may represent a epimutated tumour suppressor gene according to the Knudson "two hit" hypothesis.
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Affiliation(s)
- Andrew D Beggs
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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29
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Beggs AD, Jones A, El-Bahrawy M, El-Bahwary M, Abulafi M, Hodgson SV, Tomlinson IPM. Whole-genome methylation analysis of benign and malignant colorectal tumours. J Pathol 2013; 229:697-704. [PMID: 23096130 PMCID: PMC3619233 DOI: 10.1002/path.4132] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 10/02/2012] [Accepted: 10/10/2012] [Indexed: 12/19/2022]
Abstract
Changes in DNA methylation, whether hypo- or hypermethylation, have been shown to be associated with the progression of colorectal cancer. Methylation changes substantially in the progression from normal mucosa to adenoma and to carcinoma. This phenomenon has not been studied extensively and studies have been restricted to individual CpG islands, rather than taking a whole-genome approach. We aimed to study genome-wide methylation changes in colorectal cancer. We obtained 10 fresh-frozen normal tissue-cancer sample pairs, and five fresh-frozen adenoma samples. These were run on the lllumina HumanMethylation27 whole-genome methylation analysis system. Differential methylation between normal tissue, adenoma and carcinoma was analysed using Bayesian regression modelling, gene set enrichment analysis (GSEA) and hierarchical clustering (HC). The highest-rated individual gene for differential methylation in carcinomas versus normal tissue and adenomas versus normal tissue was GRASP (padjusted = 1.59 × 10(-5) , BF = 12.62, padjusted = 1.68 × 10(-6) , BF = 14.53). The highest-rated gene when comparing carcinomas versus adenomas was ATM (padjusted = 2.0 × 10(-4) , BF = 10.17). Hierarchical clustering demonstrated poor clustering by the CIMP criteria for methylation. GSEA demonstrated methylation changes in the Netrin-DCC and SLIT-ROBO pathways. Widespread changes in DNA methylation are seen in the transition from adenoma to carcinoma. The finding that GRASP, which encodes the general receptor for phosphoinositide 1-associated scaffold protein, was differentially methylated in colorectal cancer is interesting. This may be a potential biomarker for colorectal cancer.
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Affiliation(s)
- Andrew D Beggs
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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30
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Leedham SJ, Rodenas-Cuadrado P, Howarth K, Lewis A, Mallappa S, Segditsas S, Davis H, Jeffery R, Rodriguez-Justo M, Keshav S, Travis SPL, Graham TA, East J, Clark S, Tomlinson IPM. A basal gradient of Wnt and stem-cell number influences regional tumour distribution in human and mouse intestinal tracts. Gut 2013; 62:83-93. [PMID: 22287596 PMCID: PMC3551213 DOI: 10.1136/gutjnl-2011-301601] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/15/2011] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Wnt signalling is critical for normal intestinal development and homeostasis. Wnt dysregulation occurs in almost all human and murine intestinal tumours and an optimal but not excessive level of Wnt activation is considered favourable for tumourigenesis. The authors assessed effects of pan-intestinal Wnt activation on tissue homeostasis, taking into account underlying physiological Wnt activity and stem-cell number in each region of the bowel. DESIGN The authors generated mice that expressed temporally controlled, stabilised β-catenin along the crypt-villus axis throughout the intestines. Physiological Wnt target gene activity was assessed in different regions of normal mouse and human tissue. Human intestinal tumour mutation spectra were analysed. RESULTS In the mouse, β-catenin stabilisation resulted in a graduated neoplastic response, ranging from dysplastic transformation of the entire epithelium in the proximal small bowel to slightly enlarged crypts of non-dysplastic morphology in the colorectum. In contrast, stem and proliferating cell numbers were increased in all intestinal regions. In the normal mouse and human intestines, stem-cell and Wnt gradients were non-identical, but higher in the small bowel than large bowel in both species. There was also variation in the expression of some Wnt modulators. Human tumour analysis confirmed that different APC mutation spectra are selected in different regions of the bowel. CONCLUSIONS There are variable gradients in stem-cell number, physiological Wnt activity and response to pathologically increased Wnt signalling along the crypt-villus axis and throughout the length of the intestinal tract. The authors propose that this variation influences regional mutation spectra, tumour susceptibility and lesion distribution in mice and humans.
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Affiliation(s)
- Simon J Leedham
- Molecular and Population Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN, UK.
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Mäkinen N, Heinonen HR, Moore S, Tomlinson IPM, van der Spuy ZM, Aaltonen LA. MED12 exon 2 mutations are common in uterine leiomyomas from South African patients. Oncotarget 2012; 2:966-9. [PMID: 22182697 PMCID: PMC3282101 DOI: 10.18632/oncotarget.370] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Uterine leiomyomas, or fibroids, are extremely common tumors. Regardless of their benign nature, fibroids can cause considerable morbidity. Women with African ancestry have a threefold increased risk of developing uterine leiomyomas with a greater symptom severity when compared to white women. Recently, we demonstrated that exon 2 of the MED12 gene is somatically altered in up to 70 per cent of uterine leiomyomas in a series of Finnish (Caucasian) patients. To validate these results in other populations, we sequenced a set of 28 uterine leiomyomas for MED12 exon 2 mutations from 18 different Black African or Coloured South African patients. We observed 14 mutation positive lesions (50%). When corrected by tumor size, these results are very similar to those derived in the Finnish material. This study confirms a major role of MED12 in the genesis of leiomyomas, regardless of ethnicity.
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Affiliation(s)
- Netta Mäkinen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
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Tomlinson IPM, Houlston RS, Montgomery GW, Sieber OM, Dunlop MG. Investigation of the effects of DNA repair gene polymorphisms on the risk of colorectal cancer. Mutagenesis 2012; 27:219-23. [PMID: 22294770 DOI: 10.1093/mutage/ger070] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite their prime candidate status, polymorphisms near genes involved in DNA repair or in other functions related to genome stability have been conspicuously under-represented in the significant associations reported from genome-wide association studies (GWAS) of cancer susceptibility. In this study, we assessed a set of single-nucleotide polymorphisms (SNPs) near 157 DNA repair genes in three colorectal cancer (CRC) GWAS. Although no individual SNP showed evidence of association, the set of SNPs as a whole was associated with colorectal cancer risk. When candidate SNPs were examined, our data did not support most of the previously reported associations with CRC susceptibility, an exception being an effect of the MLH1 promoter SNP -93G>A (rs1800734). Rare variants in CHEK2 (I157T and possibly del1100C) also appear to be associated with CRC risk. Overall, the absence to date of disease-associated DNA repair SNPs in cancer GWAS may be explained by a combination of the following: (i) many loci with individually very small effects on risk; (ii) rare alleles of moderate effect and (iii) subgroups of CRC, such as those with microsatellite instability, associated with specific variants. It will be particularly intriguing to determine whether any GWAS across cancer types identify DNA variants that predispose to cancers of more than one site.
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Affiliation(s)
- Ian P M Tomlinson
- Molecular and Population Genetics Laboratory and Oxford NIHR Comprehensive Biomedical Research Centre, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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33
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Enciso-Mora V, Hosking FJ, Sheridan E, Kinsey SE, Lightfoot T, Roman E, Irving JAE, Tomlinson IPM, Allan JM, Taylor M, Greaves M, Houlston RS. Common genetic variation contributes significantly to the risk of childhood B-cell precursor acute lymphoblastic leukemia. Leukemia 2012; 26:2212-5. [PMID: 22456626 DOI: 10.1038/leu.2012.89] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent genome-wide association studies (GWAS) have provided the first unambiguous evidence that common genetic variation influences the risk of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), identifying risk single-nucleotide polymorphisms (SNPs) localizing to 7p12.2, 9p21.3, 10q21.2 and 14q11.2. The testing of SNPs individually for an association in GWA studies necessitates the imposition of a very stringent P-value to address the issue of multiple testing. While this reduces false positives, real associations may be missed and therefore any estimate of the total heritability will be negatively biased. Using GWAS data on 823 BCP-ALL cases by considering all typed SNPs simultaneously, we have calculated that 24% of the total variation in BCP-ALL risk is accounted for common genetic variation (95% confidence interval 6-42%). Our findings provide support for a polygenic basis for susceptibility to BCP-ALL and have wider implications for future searches for novel disease-causing risk variants.
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Affiliation(s)
- V Enciso-Mora
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
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Jones AM, Beggs AD, Carvajal-Carmona L, Farrington S, Tenesa A, Walker M, Howarth K, Ballereau S, Hodgson SV, Zauber A, Bertagnolli M, Midgley R, Campbell H, Kerr D, Dunlop MG, Tomlinson IPM. TERC polymorphisms are associated both with susceptibility to colorectal cancer and with longer telomeres. Gut 2012; 61:248-54. [PMID: 21708826 PMCID: PMC3245900 DOI: 10.1136/gut.2011.239772] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND AIMS Shorter telomeres have been associated with increased risk of malignancy, including colorectal cancer (CRC). Telomere length is heritable and may be an intermediate phenotype linked to genetic susceptibility to CRC. METHODS In a large sample, the study investigated whether candidate single nucleotide polymorphisms (SNP) in 'telomere biology' genes were associated with telomere length in leucocytes. SNP associated with an increased risk of CRC were searched for separately. RESULTS Carriers of the common allele at SNP rs10936599, near the telomerase RNA component (TERC) locus, had significantly longer telomeres. It was independently found that the same rs10936599 allele was associated with increased risk of both CRC and colorectal adenomas. Neither telomere length nor CRC risk was associated with variation near telomerase reverse transcriptase or other telomere biology genes. In silico analysis showed that SNP rs2293607 was strongly correlated with rs10936599, mapped within TERC transcripts, had a predicted effect on messenger RNA folding and lay at a reported transcription factor binding site. TERC mRNA were expressed, differing only at the alleles of rs2293607, in CRC cell line HCT116. The long-telomere/CRC-risk allele was associated with higher levels of TERC mRNA and the formation of longer telomeres. CONCLUSIONS Common genetic variation at TERC is associated with both longer telomeres and an increased risk of CRC, a potential mechanism being reduced levels of cell senescence or death. This finding is somewhat paradoxical, given retrospective studies reporting that CRC cases have shorter telomeres than controls. One possibility is that that association actually results from poorer survival in patients with longer telomeres.
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Affiliation(s)
- A M Jones
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A D Beggs
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L Carvajal-Carmona
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - S Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, UK
| | - A Tenesa
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, UK
| | - M Walker
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, UK
| | - K Howarth
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - S Ballereau
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, UK
| | - S V Hodgson
- Department of Clinical Genetics, St George's Hospital Medical School, London, UK
| | - A Zauber
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - M Bertagnolli
- Brigham and Women's Hospital, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - R Midgley
- Department of Clinical Pharmacology, University of Oxford, Oxford, UK
| | - H Campbell
- Public Health Sciences, University of Edinburgh, Edinburgh, UK
| | - D Kerr
- Department of Clinical Pharmacology, University of Oxford, Oxford, UK
| | - M G Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, UK
| | - I P M Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Spain SL, Carvajal-Carmona LG, Howarth KM, Jones AM, Su Z, Cazier JB, Williams J, Aaltonen LA, Pharoah P, Kerr DJ, Cheadle J, Li L, Casey G, Vodicka P, Sieber O, Lipton L, Gibbs P, Martin NG, Montgomery GW, Young J, Baird PN, Morreau H, van Wezel T, Ruiz-Ponte C, Fernandez-Rozadilla C, Carracedo A, Castells A, Castellvi-Bel S, Dunlop M, Houlston RS, Tomlinson IPM. Refinement of the associations between risk of colorectal cancer and polymorphisms on chromosomes 1q41 and 12q13.13. Hum Mol Genet 2011; 21:934-46. [PMID: 22076443 PMCID: PMC3263985 DOI: 10.1093/hmg/ddr523] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In genome-wide association studies (GWASs) of colorectal cancer, we have identified two genomic regions in which pairs of tagging-single nucleotide polymorphisms (tagSNPs) are associated with disease; these comprise chromosomes 1q41 (rs6691170, rs6687758) and 12q13.13 (rs7163702, rs11169552). We investigated these regions further, aiming to determine whether they contain more than one independent association signal and/or to identify the SNPs most strongly associated with disease. Genotyping of additional sample sets at the original tagSNPs showed that, for both regions, the two tagSNPs were unlikely to identify a single haplotype on which the functional variation lay. Conversely, one of the pair of SNPs did not fully capture the association signal in each region. We therefore undertook more detailed analyses, using imputation, logistic regression, genealogical analysis using the GENECLUSTER program and haplotype analysis. In the 1q41 region, the SNP rs11118883 emerged as a strong candidate based on all these analyses, sufficient to account for the signals at both rs6691170 and rs6687758. rs11118883 lies within a region with strong evidence of transcriptional regulatory activity and has been associated with expression of PDGFRB mRNA. For 12q13.13, a complex situation was found: SNP rs7972465 showed stronger association than either rs11169552 or rs7136702, and GENECLUSTER found no good evidence for a two-SNP model. However, logistic regression and haplotype analyses supported a two-SNP model, in which a signal at the SNP rs706793 was added to that at rs11169552. Post-GWAS fine-mapping studies are challenging, but the use of multiple tools can assist in identifying candidate functional variants in at least some cases.
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Affiliation(s)
- Sarah L Spain
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK
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36
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Frezza C, Zheng L, Folger O, Rajagopalan KN, MacKenzie ED, Jerby L, Micaroni M, Chaneton B, Adam J, Hedley A, Kalna G, Tomlinson IPM, Pollard PJ, Watson DG, Deberardinis RJ, Shlomi T, Ruppin E, Gottlieb E. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature 2011; 477:225-8. [PMID: 21849978 DOI: 10.1038/nature10363] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 07/11/2011] [Indexed: 02/07/2023]
Abstract
Fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle (TCA cycle) that catalyses the hydration of fumarate into malate. Germline mutations of FH are responsible for hereditary leiomyomatosis and renal-cell cancer (HLRCC). It has previously been demonstrated that the absence of FH leads to the accumulation of fumarate, which activates hypoxia-inducible factors (HIFs) at normal oxygen tensions. However, so far no mechanism that explains the ability of cells to survive without a functional TCA cycle has been provided. Here we use newly characterized genetically modified kidney mouse cells in which Fh1 has been deleted, and apply a newly developed computer model of the metabolism of these cells to predict and experimentally validate a linear metabolic pathway beginning with glutamine uptake and ending with bilirubin excretion from Fh1-deficient cells. This pathway, which involves the biosynthesis and degradation of haem, enables Fh1-deficient cells to use the accumulated TCA cycle metabolites and permits partial mitochondrial NADH production. We predicted and confirmed that targeting this pathway would render Fh1-deficient cells non-viable, while sparing wild-type Fh1-containing cells. This work goes beyond identifying a metabolic pathway that is induced in Fh1-deficient cells to demonstrate that inhibition of haem oxygenation is synthetically lethal when combined with Fh1 deficiency, providing a new potential target for treating HLRCC patients.
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Affiliation(s)
- Christian Frezza
- Cancer Research UK, Beatson Institute for Cancer Research, Switchback Road, Glasgow G61 1BD, UK
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Tomlinson IPM, Carvajal-Carmona LG, Dobbins SE, Tenesa A, Jones AM, Howarth K, Palles C, Broderick P, Jaeger EEM, Farrington S, Lewis A, Prendergast JGD, Pittman AM, Theodoratou E, Olver B, Walker M, Penegar S, Barclay E, Whiffin N, Martin L, Ballereau S, Lloyd A, Gorman M, Lubbe S, Howie B, Marchini J, Ruiz-Ponte C, Fernandez-Rozadilla C, Castells A, Carracedo A, Castellvi-Bel S, Duggan D, Conti D, Cazier JB, Campbell H, Sieber O, Lipton L, Gibbs P, Martin NG, Montgomery GW, Young J, Baird PN, Gallinger S, Newcomb P, Hopper J, Jenkins MA, Aaltonen LA, Kerr DJ, Cheadle J, Pharoah P, Casey G, Houlston RS, Dunlop MG. Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. PLoS Genet 2011; 7:e1002105. [PMID: 21655089 PMCID: PMC3107194 DOI: 10.1371/journal.pgen.1002105] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [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: 03/05/2011] [Accepted: 04/08/2011] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified 14 tagging single nucleotide polymorphisms (tagSNPs) that are associated with the risk of colorectal cancer (CRC), and several of these tagSNPs are near bone morphogenetic protein (BMP) pathway loci. The penalty of multiple testing implicit in GWAS increases the attraction of complementary approaches for disease gene discovery, including candidate gene- or pathway-based analyses. The strongest candidate loci for additional predisposition SNPs are arguably those already known both to have functional relevance and to be involved in disease risk. To investigate this proposition, we searched for novel CRC susceptibility variants close to the BMP pathway genes GREM1 (15q13.3), BMP4 (14q22.2), and BMP2 (20p12.3) using sample sets totalling 24,910 CRC cases and 26,275 controls. We identified new, independent CRC predisposition SNPs close to BMP4 (rs1957636, P = 3.93×10(-10)) and BMP2 (rs4813802, P = 4.65×10(-11)). Near GREM1, we found using fine-mapping that the previously-identified association between tagSNP rs4779584 and CRC actually resulted from two independent signals represented by rs16969681 (P = 5.33×10(-8)) and rs11632715 (P = 2.30×10(-10)). As low-penetrance predisposition variants become harder to identify-owing to small effect sizes and/or low risk allele frequencies-approaches based on informed candidate gene selection may become increasingly attractive. Our data emphasise that genetic fine-mapping studies can deconvolute associations that have arisen owing to independent correlation of a tagSNP with more than one functional SNP, thus explaining some of the apparently missing heritability of common diseases.
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Affiliation(s)
- Ian P. M. Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (IPMT); (RSH); (MGD)
| | | | - Sara E. Dobbins
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Albert Tenesa
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Angela M. Jones
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kimberley Howarth
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter Broderick
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Emma E. M. Jaeger
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Susan Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Annabelle Lewis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James G. D. Prendergast
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Alan M. Pittman
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | | | - Bianca Olver
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Marion Walker
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Steven Penegar
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicola Whiffin
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Stephane Ballereau
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Amy Lloyd
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Steven Lubbe
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | | | | | | | - Bryan Howie
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jonathan Marchini
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Ceres Fernandez-Rozadilla
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia, Spain
| | - Angel Carracedo
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Sergi Castellvi-Bel
- Department of Gastroenterology, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia, Spain
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jean-Baptiste Cazier
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Harry Campbell
- Public Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver Sieber
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Lara Lipton
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Peter Gibbs
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Nicholas G. Martin
- Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia
| | - Grant W. Montgomery
- Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia
| | - Joanne Young
- Familial Cancer Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Polly Newcomb
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John Hopper
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Australia
| | - Mark A. Jenkins
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Australia
| | - Lauri A. Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - David J. Kerr
- Department of Clinical Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Jeremy Cheadle
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Paul Pharoah
- Cancer Research UK Laboratories, Strangeways Research Laboratory, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Richard S. Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
- * E-mail: (IPMT); (RSH); (MGD)
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
- * E-mail: (IPMT); (RSH); (MGD)
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Sakthianandeswaren A, Christie M, D'Andreti C, Tsui C, Jorissen RN, Li S, Fleming NI, Gibbs P, Lipton L, Malaterre J, Ramsay RG, Phesse TJ, Ernst M, Jeffery RE, Poulsom R, Leedham SJ, Segditsas S, Tomlinson IPM, Bernhard OK, Simpson RJ, Walker F, Faux MC, Church N, Catimel B, Flanagan DJ, Vincan E, Sieber OM. PHLDA1 Expression Marks the Putative Epithelial Stem Cells and Contributes to Intestinal Tumorigenesis. Cancer Res 2011; 71:3709-19. [DOI: 10.1158/0008-5472.can-10-2342] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lee AJX, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IPM, Howell M, Kschischo M, Swanton C. Chromosomal instability confers intrinsic multidrug resistance. Cancer Res 2011; 71:1858-70. [PMID: 21363922 DOI: 10.1158/0008-5472.can-10-3604] [Citation(s) in RCA: 333] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aneuploidy is associated with poor prognosis in solid tumors. Spontaneous chromosome missegregation events in aneuploid cells promote chromosomal instability (CIN) that may contribute to the acquisition of multidrug resistance in vitro and heighten risk for tumor relapse in animal models. Identification of distinct therapeutic agents that target tumor karyotypic complexity has important clinical implications. To identify distinct therapeutic approaches to specifically limit the growth of CIN tumors, we focused on a panel of colorectal cancer (CRC) cell lines, previously classified as either chromosomally unstable (CIN(+)) or diploid/near-diploid (CIN(-)), and treated them individually with a library of kinase inhibitors targeting components of signal transduction, cell cycle, and transmembrane receptor signaling pathways. CIN(+) cell lines displayed significant intrinsic multidrug resistance compared with CIN(-) cancer cell lines, and this seemed to be independent of somatic mutation status and proliferation rate. Confirming the association of CIN rather than ploidy status with multidrug resistance, tetraploid isogenic cells that had arisen from diploid cell lines displayed lower drug sensitivity than their diploid parental cells only with increasing chromosomal heterogeneity and isogenic cell line models of CIN(+) displayed multidrug resistance relative to their CIN(-) parental cancer cell line derivatives. In a meta-analysis of CRC outcome following cytotoxic treatment, CIN(+) predicted worse progression-free or disease-free survival relative to patients with CIN(-) disease. Our results suggest that stratifying tumor responses according to CIN status should be considered within the context of clinical trials to minimize the confounding effects of tumor CIN status on drug sensitivity.
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Affiliation(s)
- Alvin J X Lee
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
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Niittymäki I, Tuupanen S, Li Y, Järvinen H, Mecklin JP, Tomlinson IPM, Houlston RS, Karhu A, Aaltonen LA. Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci. BMC Med Genet 2011; 12:23. [PMID: 21314996 PMCID: PMC3045878 DOI: 10.1186/1471-2350-12-23] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 02/14/2011] [Indexed: 01/20/2023]
Abstract
BACKGROUND Common single-nucleotide polymorphisms (SNPs) in ten chromosomal loci have been shown to predispose to colorectal cancer (CRC) in genome-wide association studies. A plausible biological mechanism of CRC susceptibility associated with genetic variation has so far only been proposed for three loci, each pointing to variants that affect gene expression through distant regulatory elements. In this study, we aimed to gain insight into the molecular basis of seven low-penetrance CRC loci tagged by rs4779584 at 15q13, rs10795668 at 10p14, rs3802842 at 11q23, rs4444235 at 14q22, rs9929218 at 16q22, rs10411210 at 19q13, and rs961253 at 20p12. METHODS Possible somatic gain of the risk allele or loss of the protective allele was studied by analyzing allelic imbalance in tumour and corresponding normal tissue samples of heterozygous patients. Functional variants were searched from in silico predicted enhancer elements locating inside the CRC-associating linkage-disequilibrium regions. RESULTS No allelic imbalance targeting the SNPs was observed at any of the seven loci. Altogether, 12 SNPs that were predicted to disrupt potential transcription factor binding sequences were genotyped in the same population-based case-control series as the seven tagging SNPs originally. None showed association with CRC. CONCLUSIONS The results of the allelic imbalance analysis suggest that the seven CRC risk variants are not somatically selected for in the neoplastic progression. The bioinformatic approach was unable to pinpoint cancer-causing variants at any of the seven loci. While it is possible that many of the predisposition loci for CRC are involved in control of gene expression by targeting transcription factor binding sites, also other possibilities, such as regulatory RNAs, should be considered.
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Affiliation(s)
- Iina Niittymäki
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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Tie J, Lipton L, Desai J, Gibbs P, Jorissen RN, Christie M, Drummond KJ, Thomson BNJ, Usatoff V, Evans PM, Pick AW, Knight S, Carne PWG, Berry R, Polglase A, McMurrick P, Zhao Q, Busam D, Strausberg RL, Domingo E, Tomlinson IPM, Midgley R, Kerr D, Sieber OM. KRAS mutation is associated with lung metastasis in patients with curatively resected colorectal cancer. Clin Cancer Res 2011; 17:1122-30. [PMID: 21239505 DOI: 10.1158/1078-0432.ccr-10-1720] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Oncogene mutations contribute to colorectal cancer development. We searched for differences in oncogene mutation profiles between colorectal cancer metastases from different sites and evaluated these as markers for site of relapse. EXPERIMENTAL DESIGN One hundred colorectal cancer metastases were screened for mutations in 19 oncogenes, and further 61 metastases and 87 matched primary cancers were analyzed for genes with identified mutations. Mutation prevalence was compared between (a) metastases from liver (n = 65), lung (n = 50), and brain (n = 46), (b) metastases and matched primary cancers, and (c) metastases and an independent cohort of primary cancers (n = 604). Mutations differing between metastasis sites were evaluated as markers for site of relapse in 859 patients from the VICTOR trial. RESULTS In colorectal cancer metastases, mutations were detected in 4 of 19 oncogenes: BRAF (3.1%), KRAS (48.4%), NRAS (6.2%), and PIK3CA (16.1%). KRAS mutation prevalence was significantly higher in lung (62.0%) and brain (56.5%) than in liver metastases (32.3%; P = 0.003). Mutation status was highly concordant between primary cancer and metastasis from the same individual. Compared with independent primary cancers, KRAS mutations were more common in lung and brain metastases (P < 0.005), but similar in liver metastases. Correspondingly, KRAS mutation was associated with lung relapse (HR = 2.1; 95% CI, 1.2 to 3.5, P = 0.007) but not liver relapse in patients from the VICTOR trial. CONCLUSIONS KRAS mutation seems to be associated with metastasis in specific sites, lung and brain, in colorectal cancer patients. Our data highlight the potential of somatic mutations for informing surveillance strategies.
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Affiliation(s)
- Jeanne Tie
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Parkville, Melbourne, Australia
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Venkatachalam R, Ligtenberg MJL, Hoogerbrugge N, Schackert HK, Görgens H, Hahn MM, Kamping EJ, Vreede L, Hoenselaar E, van der Looij E, Goossens M, Churchman M, Carvajal-Carmona L, Tomlinson IPM, de Bruijn DRH, Van Kessel AG, Kuiper RP. Germline epigenetic silencing of the tumor suppressor gene PTPRJ in early-onset familial colorectal cancer. Gastroenterology 2010; 139:2221-4. [PMID: 21036128 DOI: 10.1053/j.gastro.2010.08.063] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 08/26/2010] [Indexed: 01/05/2023]
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Elliott KS, Zeggini E, McCarthy MI, Gudmundsson J, Sulem P, Stacey SN, Thorlacius S, Amundadottir L, Grönberg H, Xu J, Gaborieau V, Eeles RA, Neal DE, Donovan JL, Hamdy FC, Muir K, Hwang SJ, Spitz MR, Zanke B, Carvajal-Carmona L, Brown KM, Hayward NK, Macgregor S, Tomlinson IPM, Lemire M, Amos CI, Murabito JM, Isaacs WB, Easton DF, Brennan P, Barkardottir RB, Gudbjartsson DF, Rafnar T, Hunter DJ, Chanock SJ, Stefansson K, Ioannidis JPA. Evaluation of association of HNF1B variants with diverse cancers: collaborative analysis of data from 19 genome-wide association studies. PLoS One 2010; 5:e10858. [PMID: 20526366 PMCID: PMC2878330 DOI: 10.1371/journal.pone.0010858] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [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: 04/08/2010] [Accepted: 04/28/2010] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide association studies have found type 2 diabetes-associated variants in the HNF1B gene to exhibit reciprocal associations with prostate cancer risk. We aimed to identify whether these variants may have an effect on cancer risk in general versus a specific effect on prostate cancer only. METHODOLOGY/PRINCIPAL FINDINGS In a collaborative analysis, we collected data from GWAS of cancer phenotypes for the frequently reported variants of HNF1B, rs4430796 and rs7501939, which are in linkage disequilibrium (r(2) = 0.76, HapMap CEU). Overall, the analysis included 16 datasets on rs4430796 with 19,640 cancer cases and 21,929 controls; and 21 datasets on rs7501939 with 26,923 cases and 49,085 controls. Malignancies other than prostate cancer included colorectal, breast, lung and pancreatic cancers, and melanoma. Meta-analysis showed large between-dataset heterogeneity that was driven by different effects in prostate cancer and other cancers. The per-T2D-risk-allele odds ratios (95% confidence intervals) for rs4430796 were 0.79 (0.76, 0.83)] per G allele for prostate cancer (p<10(-15) for both); and 1.03 (0.99, 1.07) for all other cancers. Similarly for rs7501939 the per-T2D-risk-allele odds ratios (95% confidence intervals) were 0.80 (0.77, 0.83) per T allele for prostate cancer (p<10(-15) for both); and 1.00 (0.97, 1.04) for all other cancers. No malignancy other than prostate cancer had a nominally statistically significant association. CONCLUSIONS/SIGNIFICANCE The examined HNF1B variants have a highly specific effect on prostate cancer risk with no apparent association with any of the other studied cancer types.
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Affiliation(s)
- Katherine S. Elliott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eleftheria Zeggini
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Applied Statistical Genetics, Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Valerie Gaborieau
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Rosalind A. Eeles
- Oncogenetics Team, The Institute of Cancer Research, Sutton, United Kingdom
| | - David E. Neal
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jenny L. Donovan
- Department of Social Medicine, University of Bristol, Bristol, United Kingdom
| | - Freddie C. Hamdy
- Nuffield Department of Surgery, University of Oxford, Oxford, United Kingdom
| | - Kenneth Muir
- Health Sciences Research Institute, University of Warwick, Coventry, United Kingdom
| | - Shih-Jen Hwang
- Framingham Study, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Margaret R. Spitz
- Department of Epidemiology, M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Brent Zanke
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
- Ottawa Health Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Luis Carvajal-Carmona
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kevin M. Brown
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | | | - Nicholas K. Hayward
- Queensland Institute of Medical Research, Royal Brisbane Hospital, Brisbane, Queensland, Australia
| | - Stuart Macgregor
- Queensland Institute of Medical Research, Royal Brisbane Hospital, Brisbane, Queensland, Australia
| | - Ian P. M. Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Christopher I. Amos
- Department of Epidemiology, M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Joanne M. Murabito
- Section of General Internal Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - William B. Isaacs
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Douglas F. Easton
- Cancer Research UK Genetic Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Rosa B. Barkardottir
- Department of Pathology, Landspitali-University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | | | - David J. Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | | | - John P. A. Ioannidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine and Biomedical Research Institute, Foundation for Research and Technology-Hellas, Ioannina, Greece
- Center for Genetic Epidemiology and Modelling, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Willis L, Alarcón T, Elia G, Jones JL, Wright NA, Tomlinson IPM, Graham TA, Page KM. Breast cancer dormancy can be maintained by small numbers of micrometastases. Cancer Res 2010; 70:4310-7. [PMID: 20501854 DOI: 10.1158/0008-5472.can-09-3144] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Late relapse of breast cancer can occur more than 25 years after primary diagnosis. During the intervening years between initial treatment and relapse, occult cancers are maintained in an apparent state of dormancy that is poorly understood. In this study, we applied a probabilistic mathematical model to long-term follow-up studies of postresection patients to investigate the factors involved in mediating breast cancer dormancy. Our results suggest that long-term dormancy is maintained most often by just one growth-restricted dangerous micrometastasis. Analysis of the empirical data by Approximate Bayesian Computation indicated that patients in dormancy have between 1 and 5 micrometastases at 10 years postresection, when they escape growth restriction with a half-life of <69 years and are >0.4 mm in diameter. Before resection, primary tumors seed at most an average of 6 dangerous micrometastases that escape from growth restriction with a half-life of at least 12 years. Our findings suggest that effective preventive treatments will need to eliminate these small numbers of micrometastases, which may be preangiogenic and nonvascularized until they switch to growth due to one oncogenic mutation or tumor suppressor gene inactivation. In summary, breast cancer dormancy seems to be maintained by small numbers of sizeable micrometastases that escape from growth restriction with a half-life exceeding 12 years.
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Affiliation(s)
- Lisa Willis
- CoMPLEX, University College London, London, United Kingdom.
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Niittymäki I, Kaasinen E, Tuupanen S, Karhu A, Järvinen H, Mecklin JP, Tomlinson IPM, Di Bernardo MC, Houlston RS, Aaltonen LA. Low-penetrance susceptibility variants in familial colorectal cancer. Cancer Epidemiol Biomarkers Prev 2010; 19:1478-83. [PMID: 20501757 DOI: 10.1158/1055-9965.epi-09-1320] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genomewide association studies have identified 10 low-penetrance loci that confer modestly increased risk for colorectal cancer (CRC). Although they underlie a significant proportion of CRC in the general population, their impact on the familial risk for CRC has yet to be formally enumerated. The aim of this study was to examine the combined contribution of the 10 variants, rs6983267, rs4779584, rs4939827, rs16892766, rs10795668, rs3802842, rs4444235, rs9929218, rs10411210, and rs961253, on familial CRC. METHODS The population-based series of CRC samples included in this study consisted of 97 familial cases and 691 sporadic cases. Genotypes in the 10 loci and clinical data, including family history of cancer verified from the Finnish Cancer Registry, were available. The overall number of risk alleles (0-20) was determined, and its association with familial CRC was analyzed. Excess familial risk was estimated using cancer incidence data from the first-degree relatives of the cases. RESULTS A linear association between the number of risk alleles and familial CRC was observed (P = 0.006). With each risk-allele addition, the odds of having an affected first-degree relative increased by 1.16 (95% confidence interval, 1.04-1.30). The 10 low-penetrance loci collectively explain approximately 9% of the variance in familial risk for CRC. CONCLUSIONS This study provides evidence to support the previous indirect estimations that these low-penetrance variants account for a relatively small proportion of the familial aggregation of CRC. IMPACT Our results emphasize the need to characterize the remaining molecular basis of familial CRC, which should eventually yield in individualized targeting of preventive interventions.
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Affiliation(s)
- Iina Niittymäki
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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Elsaba TMA, Martinez-Pomares L, Robins AR, Crook S, Seth R, Jackson D, McCart A, Silver AR, Tomlinson IPM, Ilyas M. The stem cell marker CD133 associates with enhanced colony formation and cell motility in colorectal cancer. PLoS One 2010; 5:e10714. [PMID: 20502714 PMCID: PMC2873293 DOI: 10.1371/journal.pone.0010714] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 04/27/2010] [Indexed: 01/28/2023] Open
Abstract
CD133 is a membrane molecule that has been, controversially, reported as a CSC marker in colorectal cancer (CRC). In this study, we sought to clarify the expression and role of CD133 in CRC. Initially the size of the CD133-expressing (CD133+) population in eight well-described CRC cell lines was measured by flow cytometry and was found to range from 0% to >95%. The cell line HT29 has a CD133+ population of >95% and was chosen for functional evaluation of CD133 after gene knockdown by RNA interference. A time course assay showed that CD133 inhibition had no significant effect on cell proliferation or apoptosis. However, CD133 knockdown did result in greater susceptibility to staurosporine-induced apoptosis (p = 0.01) and reduction in cell motility (p<0.04). Since gene knockdown may cause "off-target" effects, the cell line SW480 (which has a CD133+ population of 40%) was sorted into pure CD133+ and CD133- populations to allow functional comparison of isogenic populations separated only by CD133 expression. In concordance with the knockdown experiments, a time course assay showed no significant proliferative differences between the CD133+/CD133- populations. Also greater resistance to staurosporine-induced apoptosis (p = 0.008), greater cell motility (p = 0.03) and greater colony forming efficiency was seen in the CD133+ population than the CD133- population in both 2D and 3D culture (p<0.0001 and p<0.003 respectively). Finally, the plasticity of CD133 expression in tumour cells was tested. Quantitative PCR analysis showed there was transcriptional repression in the CD133- population of SW480. Prolonged culture of a pure CD133- population resulted in re-emergence of CD133+ cells. We conclude that CD133 expression in CRCs is associated with some features attributable to stemness and that there is plasticity of CD133 expression. Further studies are necessary to delineate the mechanistic basis of these features.
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Affiliation(s)
- Tarek M. A. Elsaba
- Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
- Department of Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Luisa Martinez-Pomares
- Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Adrian R. Robins
- Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Simon Crook
- Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Rashmi Seth
- Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Darryl Jackson
- Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Amy McCart
- Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Andrew R. Silver
- Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Ian P. M. Tomlinson
- Molecular and Population Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mohammad Ilyas
- Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre–Biological Research Unit, Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail:
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Ahmed MAH, Jackson D, Seth R, Robins A, Lobo DN, Tomlinson IPM, Ilyas M. CD24 is upregulated in inflammatory bowel disease and stimulates cell motility and colony formation. Inflamm Bowel Dis 2010; 16:795-803. [PMID: 19998456 DOI: 10.1002/ibd.21134] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND We investigated whether CD24 (reportedly a stem cell marker and adhesion molecule) was expressed in regenerative mucosa in inflammatory bowel disease (IBD) and whether it could be functionally relevant. METHODS CD24 expression was examined in 10 cases of IBD and the relationship of CD24 with Wnt signaling was tested using dominant negative (DN)-TCF4 expression. For functional evaluation, CD24 was 1) cloned and forcibly expressed in HCT116 (which expresses very low levels of CD24) and 2) knocked-down by RNA interference in HT29 (which expresses high levels of CD24). The effect of altered CD24 expression on proliferation/apoptosis, staurosporine-induced apoptosis, colony formation in soft agar, migration, and invasion was examined. RESULTS CD24 was not expressed in normal tissue, while 10/10 cases of IBD showed CD24 upregulation. Inhibition of Wnt signaling with DN-TCF4 caused CD24 downregulation. Forced expression of CD24 did not influence cell proliferation, apoptosis, or staurosporine-induced apoptosis but it did significantly enhance colony forming efficiency (P < 0.01). Furthermore, there was increased transwell migration (P < 0.001) and invasion (P < 0.03) and there was increased cell migration in wounding assays. Conversely, knockdown of CD24 reduced transwell migration (P < 0.01) and invasion (P < 0.01) and reduced cell motility in wounding assays. CD24 knockdown did not influence proliferation, apoptosis resistance, or staurosporine-induced apoptosis. CONCLUSIONS This is the first study to report upregulation of CD24 in regenerating tissue in IBD. This may be regulated by Wnt signaling and can confer enhanced colony forming ability and enhanced cell motility-features that may be important in tissue healing in the colon.
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Affiliation(s)
- Mohamed A H Ahmed
- Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre Campus, University of Nottingham, UK.
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Thirlwell C, Will OCC, Domingo E, Graham TA, McDonald SAC, Oukrif D, Jeffrey R, Gorman M, Rodriguez-Justo M, Chin-Aleong J, Clark SK, Novelli MR, Jankowski JA, Wright NA, Tomlinson IPM, Leedham SJ. Clonality assessment and clonal ordering of individual neoplastic crypts shows polyclonality of colorectal adenomas. Gastroenterology 2010; 138:1441-54, 1454.e1-7. [PMID: 20102718 DOI: 10.1053/j.gastro.2010.01.033] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 11/24/2009] [Accepted: 01/07/2010] [Indexed: 01/28/2023]
Abstract
BACKGROUND & AIMS According to the somatic mutation theory, monoclonal colorectal lesions arise from sequential mutations in the progeny of a single stem cell. However, studies in a sex chromosome mixoploid mosaic (XO/XY) patient indicated that colorectal adenomas were polyclonal. We assessed adenoma clonality on an individual crypt basis and completed a genetic dependency analysis in carcinomas-in-adenomas to assess mutation order and timing. METHODS Polyp samples were analyzed from the XO/XY individual, patients with familial adenomatous polyposis and attenuated familial adenomatous polyposis, patients with small sporadic adenomas, and patients with sporadic carcinoma-in-adenomas. Clonality was analyzed using X/Y chromosome fluorescence in situ hybridization, analysis of 5q loss of heterozygosity in XO/XY tissue, and sequencing of adenomatous polyposis coli. Individual crypts and different phenotypic areas of carcinoma-in-adenoma lesions were analyzed for mutations in adenomatous polyposis coli, p53, and K-RAS; loss of heterozygosity at 5q, 17p, and 18q; and aneuploidy. Phylogenetic trees were constructed. RESULTS All familial adenomatous polyposis-associated adenomas and some sporadic lesions had polyclonal genetic defects. Some independent clones appeared to be maintained in advanced adenomas. No clear obligate order of genetic events was established. Top-down growth of dysplastic tissue into neighboring crypts was a possible mechanism of clonal competition. CONCLUSIONS Human colorectal microadenomas are polyclonal and may arise from a combination of host genetic features, mucosal exposures, and active crypt interactions. Analyses of tumor phylogenies show that most lesions undergo intermittent genetic homogenization, but heterotypic mutation patterns indicate that independent clonal evolution can occur throughout adenoma development. Based on observations of clonal ordering the requirement and timing of genetic events during neoplastic progression may be more variable than previously thought.
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49
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Tomlinson IPM, Dunlop M, Campbell H, Zanke B, Gallinger S, Hudson T, Koessler T, Pharoah PD, Niittymäkix I, Tuupanenx S, Aaltonen LA, Hemminki K, Lindblom A, Försti A, Sieber O, Lipton L, van Wezel T, Morreau H, Wijnen JT, Devilee P, Matsuda K, Nakamura Y, Castellví-Bel S, Ruiz-Ponte C, Castells A, Carracedo A, Ho JWC, Sham P, Hofstra RMW, Vodicka P, Brenner H, Hampe J, Schafmayer C, Tepel J, Schreiber S, Völzke H, Lerch MM, Schmidt CA, Buch S, Moreno V, Villanueva CM, Peterlongo P, Radice P, Echeverry MM, Velez A, Carvajal-Carmona L, Scott R, Penegar S, Broderick P, Tenesa A, Houlston RS. COGENT (COlorectal cancer GENeTics): an international consortium to study the role of polymorphic variation on the risk of colorectal cancer. Br J Cancer 2010; 102:447-54. [PMID: 19920828 PMCID: PMC2816642 DOI: 10.1038/sj.bjc.6605338] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 09/03/2009] [Accepted: 09/03/2009] [Indexed: 12/24/2022] Open
Abstract
It is now recognised that a part of the inherited risk of colorectal cancer (CRC) can be explained by the co-inheritance of low-penetrance genetic variants. The accumulated experience to date in identifying these variants has served to highlight difficulties in conducting statistically and methodologically rigorous studies and follow-up analyses. The COGENT (COlorectal cancer GENeTics) consortium includes 20 research groups in Europe, Australia, the Americas, China and Japan. The overarching goal of COGENT is to identify and characterise low-penetrance susceptibility variants for CRC through association-based analyses. In this study, we review the rationale for identifying low-penetrance variants for CRC and our proposed strategy for establishing COGENT.
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Affiliation(s)
- I P M Tomlinson
- Molecular and Population Genetics, Nuffield Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - M Dunlop
- Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC-HGU, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - H Campbell
- Public Health Sciences, University of Edinburgh, Edinburgh EH89AG, UK
| | - B Zanke
- The Ontario Institute for Cancer Research, The MaRS Center, 101 College St, Suite 800, Toronto, Ontario, Canada M5G 1L7
- The University of Ottawa Faculty of Medicine, 101 Smythe Rd, Ottawa, Ontario, Canada K1H 8L6
- Cancer Care Ontario, 620 University Ave., Toronto, Ontario, Canada M5G 2L7
| | - S Gallinger
- Cancer Care Ontario, 620 University Ave., Toronto, Ontario, Canada M5G 2L7
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital and University of Toronto, 600 University Ave., Toronto, Ontario, Canada M5G 1X5
| | - T Hudson
- The Ontario Institute for Cancer Research, The MaRS Center, 101 College St, Suite 800, Toronto, Ontario, Canada M5G 1L7
| | - T Koessler
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - P D Pharoah
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - I Niittymäkix
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum 9, University of Helsinki, Helsinki, Finland
| | - S Tuupanenx
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum 9, University of Helsinki, Helsinki, Finland
| | - L A Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum 9, University of Helsinki, Helsinki, Finland
| | - K Hemminki
- German Cancer Research Center, Heidelberg, Germany
| | - A Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, CMM02, Stockholm S17176, Sweden
| | - A Försti
- Department of Molecular Medicine and Surgery, Karolinska Institutet, CMM02, Stockholm S17176, Sweden
| | - O Sieber
- LCCI Biomarker Laboratory, Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, VIC 3050, Australia
| | - L Lipton
- LCCI Biomarker Laboratory, Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, VIC 3050, Australia
| | - T van Wezel
- Department of Pathology, Leiden University Medical Center, ZA LEIDEN 2333, The Netherlands
| | - H Morreau
- Department of Pathology, Leiden University Medical Center, ZA LEIDEN 2333, The Netherlands
| | - J T Wijnen
- Departments of Human and Clinical Genetics, Leiden University Medical Center, ZA LEIDEN 2333, The Netherlands
| | - P Devilee
- Departments of Human and Clinical Genetics, Leiden University Medical Center, ZA LEIDEN 2333, The Netherlands
| | - K Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Y Nakamura
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Castellví-Bel
- Department of Gastroenterology, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), IDIBAPS, University of Barcelona, Barcelona, Catalonia, Spain
| | - C Ruiz-Ponte
- Fundacion Publica Galega de Medicina Xenomica (FPGMX), CIBERER, Genomic Medicine Group-University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - A Castells
- Department of Gastroenterology, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), IDIBAPS, University of Barcelona, Barcelona, Catalonia, Spain
| | - A Carracedo
- Fundacion Publica Galega de Medicina Xenomica (FPGMX), CIBERER, Genomic Medicine Group-University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - J W C Ho
- The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - P Sham
- The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - R M W Hofstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, P.O. Box 30.0001, Groningen 9700 RB, the Netherlands
| | - P Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, 14200 Prague 4, Czech Republic
| | - H Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - J Hampe
- Department of General Internal Medicine, University Hospital, Schleswig-Holstein, Campus Kiel, Schittenhelmstraße 12, Kiel 24105, Germany
| | - C Schafmayer
- POPGEN Biobank, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse 12, Kiel 24105, Germany
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 3, Kiel 24105, Germany
| | - J Tepel
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 3, Kiel 24105, Germany
| | - S Schreiber
- Department of General Internal Medicine, University Hospital, Schleswig-Holstein, Campus Kiel, Schittenhelmstraße 12, Kiel 24105, Germany
| | - H Völzke
- Institut für Community Medicine, University Hospital Greifswald, Walther-Rathenau-Strasse 48, Greifswald 17487, Germany
| | - M M Lerch
- Klinik für Innere Medizin A University Hospital Greifswald, Friedrich-Loeffler-Strasse 23a, Greifswald 17487, Germany
| | - C A Schmidt
- Klinik für Innere Medizin C, University Hospital Greifswald, Ferdinand-Sauerbruch-Strasse, Greifswald 17487, Germany
| | - S Buch
- Department of General Internal Medicine, University Hospital, Schleswig-Holstein, Campus Kiel, Schittenhelmstraße 12, Kiel 24105, Germany
| | - V Moreno
- IDIBELL-Catalan Institute of Oncology and University of Barcelona, Av Gran Via 199, L’Hospitalet, Barcelona 08907, Spain
| | - C M Villanueva
- Centre for Research in Environmental Epidemiology (CREAL), Municipal Institute of Medical Research (IMIM-Hospital del Mar) and CIBER Epidemiología y Salud Pública (CIBERESP), Doctor Aiguader, Barcelona 88 E-08003, Spain
| | - P Peterlongo
- Fondazione IRCCS Istituto Nazionale Tumori, and Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - P Radice
- Fondazione IRCCS Istituto Nazionale Tumori, and Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - M M Echeverry
- Departamento de Biología, Universidad del Tolima, Barrio Altos de Santa Helena, Ibague, Tolima, Colombia
| | - A Velez
- Departamento de Patología, Hospital Pablo Tobon Uribe, Calle 78 B No. 69-240, Medellín, Colombia
| | - L Carvajal-Carmona
- Molecular and Population Genetics, Nuffield Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Departamento de Biología, Universidad del Tolima, Barrio Altos de Santa Helena, Ibague, Tolima, Colombia
| | - R Scott
- Faculty of Health, School of Biomedical Sciences, University of Newcastle, NSW, Australia
| | - S Penegar
- Section of Cancer Genetics, Institute of Cancer Research, 15 Cotswold Rd, Sutton, Surrey SM2 5NG, UK
| | - P Broderick
- Section of Cancer Genetics, Institute of Cancer Research, 15 Cotswold Rd, Sutton, Surrey SM2 5NG, UK
| | - A Tenesa
- Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC-HGU, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - R S Houlston
- Section of Cancer Genetics, Institute of Cancer Research, 15 Cotswold Rd, Sutton, Surrey SM2 5NG, UK
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Jorissen RN, Lipton L, Gibbs P, Chapman M, Desai J, Jones IT, Yeatman TJ, East P, Tomlinson IPM, Verspaget HW, Aaltonen LA, Kruhøffer M, Orntoft TF, Andersen CL, Sieber OM. DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2009; 14:8061-9. [PMID: 19088021 DOI: 10.1158/1078-0432.ccr-08-1431] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE About 15% of colorectal cancers harbor microsatellite instability (MSI). MSI-associated gene expression changes have been identified in colorectal cancers, but little overlap exists between signatures hindering an assessment of overall consistency. Little is known about the causes and downstream effects of differential gene expression. EXPERIMENTAL DESIGN DNA microarray data on 89 MSI and 140 microsatellite-stable (MSS) colorectal cancers from this study and 58 MSI and 77 MSS cases from three published reports were randomly divided into test and training sets. MSI-associated gene expression changes were assessed for cross-study consistency using training samples and validated as MSI classifier using test samples. Differences in biological pathways were identified by functional category analysis. Causation of differential gene expression was investigated by comparison to DNA copy-number data. RESULTS MSI-associated gene expression changes in colorectal cancers were found to be highly consistent across multiple studies of primary tumors and cancer cell lines from patients of different ethnicities (P < 0.001). Clustering based on consistent changes separated additional test cases by MSI status, and classification of individual samples predicted MSI status with a sensitivity of 96% and specificity of 85%. Genes associated with immune response were up-regulated in MSI cancers, whereas genes associated with cell-cell adhesion, ion binding, and regulation of metabolism were down-regulated. Differential gene expression was shown to reflect systematic differences in DNA copy-number aberrations between MSI and MSS tumors (P < 0.001). CONCLUSIONS Our results show cross-study consistency of MSI-associated gene expression changes in colorectal cancers. DNA copy-number alterations partly cause the differences in gene expression between MSI and MSS cancers.
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Affiliation(s)
- Robert N Jorissen
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Parkville, Victoria, Australia
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