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Chen Z, Guo X, Tao R, Huyghe JR, Law PJ, Fernandez-Rozadilla C, Ping J, Jia G, Long J, Li C, Shen Q, Xie Y, Timofeeva MN, Thomas M, Schmit SL, Díez-Obrero V, Devall M, Moratalla-Navarro F, Fernandez-Tajes J, Palles C, Sherwood K, Briggs SEW, Svinti V, Donnelly K, Farrington SM, Blackmur J, Vaughan-Shaw PG, Shu XO, Lu Y, Broderick P, Studd J, Harrison TA, Conti DV, Schumacher FR, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper JL, Jenkins MA, Win AK, Pai RK, Figueiredo JC, Haile RW, Gallinger S, Woods MO, Newcomb PA, Duggan D, Cheadle JP, Kaplan R, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin JP, Jousilahti P, Knekt P, Aaltonen LA, Rissanen H, Pukkala E, Eriksson JG, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Männistö S, Albanes D, Weinstein SJ, Ruiz-Narvaez E, Palmer JR, Buchanan DD, Platz EA, Visvanathan K, Ulrich CM, Siegel E, Brezina S, Gsur A, Campbell PT, Chang-Claude J, Hoffmeister M, Brenner H, Slattery ML, Potter JD, Tsilidis KK, Schulze MB, Gunter MJ, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Bishop DT, Giles GG, Southey MC, Idos GE, McDonnell KJ, Abu-Ful Z, Greenson JK, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku TO, van Guelpen B, Hudson TJ, Hampel H, Pearlman R, Berndt SI, Hayes RB, Martinez ME, Thomas SS, Pharoah PDP, Larsson SC, Yen Y, Lenz HJ, White E, Li L, Doheny KF, Pugh E, Shelford T, Chan AT, Cruz-Correa M, Lindblom A, Hunter DJ, Joshi AD, Schafmayer C, Scacheri PC, Kundaje A, Schoen RE, Hampe J, Stadler ZK, Vodicka P, Vodickova L, Vymetalkova V, Edlund CK, Gauderman WJ, Shibata D, Toland A, Markowitz S, Kim A, Chanock SJ, van Duijnhoven F, Feskens EJM, Sakoda LC, Gago-Dominguez M, Wolk A, Pardini B, FitzGerald LM, Lee SC, Ogino S, Bien SA, Kooperberg C, Li CI, Lin Y, Prentice R, Qu C, Bézieau S, Yamaji T, Sawada N, Iwasaki M, Le Marchand L, Wu AH, Qu C, McNeil CE, Coetzee G, Hayward C, Deary IJ, Harris SE, Theodoratou E, Reid S, Walker M, Ooi LY, Lau KS, Zhao H, Hsu L, Cai Q, Dunlop MG, Gruber SB, Houlston RS, Moreno V, Casey G, Peters U, Tomlinson I, Zheng W. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nat Commun 2024; 15:3557. [PMID: 38670944 PMCID: PMC11053150 DOI: 10.1038/s41467-024-47399-x] [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: 10/16/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, 37232, TN, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Ceres Fernandez-Rozadilla
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Genomic Medicine Group, Instituto de Investigacion Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chao Li
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quanhu Shen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Maria N Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Virginia Díez-Obrero
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Matthew Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Ferran Moratalla-Navarro
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Juan Fernandez-Tajes
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah E W Briggs
- Department of Public Health, Richard Doll Building, University of Oxford, Oxford, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Blackmur
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter G Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James Studd
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick R Schumacher
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gad Rennert
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Vicente Martín-Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Biomedicine Institute, University of León, León, Spain
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Aesun Shin
- Cancer Research Institute, Seoul National University, Seoul, South Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Rish K Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Cedars-Sinai Cancer Research Center for Health Equity, Los Angeles, CA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Michael O Woods
- Division of Biomedical Sciences, Memorial University of Newfoundland, St. John, ON, Canada
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - David Duggan
- City of Hope National Medical Center, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Richard Kaplan
- MRC Clinical Trials Unit, Medical Research Council, Cardiff, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | | | - Pekka Jousilahti
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paul Knekt
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Harri Rissanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eero Pukkala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, University of Helsinki, Helsinki, Finland
- Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Ulrika Hänninen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie R Palmer
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Erin Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Gregory E Idos
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin J McDonnell
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Zomoroda Abu-Ful
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Joel K Greenson
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Katerina Shulman
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit Health Services, Personalized Genomic Service, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yu-Ru Su
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Robert Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | | | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Marie Elena Martinez
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
- Population Sciences, Disparities and Community Engagement, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Yen
- Taipei Medical University, Taipei, Taiwan
| | - Heinz-Josef Lenz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew T Chan
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marcia Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Zsofia K Stadler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amanda Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Sanford Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Andre Kim
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franzel van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Public Foundation of Genomic Medicine, Servicio Galego de Saude, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Barbara Pardini
- Candiolo Cancer Institute FPO-IRCCS, Candiolo, (TO), Italy
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo, (TO), Italy
| | - Liesel M FitzGerald
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Soo Chin Lee
- National University Cancer Institute, Singapore, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | | | - Anna H Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stuart Reid
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Li Yin Ooi
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stephen B Gruber
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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2
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Schmit SL, Tsai YY, Bonner JD, Sanz-Pamplona R, Joshi AD, Ugai T, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Qu C, Kast WM, Da Silva DM, Glickman JN, Chan AT, Giannakis M, Nowak JA, Rennert HS, Robins HS, Ogino S, Greenson JK, Moreno V, Rennert G, Gruber SB. Germline genetic regulation of the colorectal tumor immune microenvironment. BMC Genomics 2024; 25:409. [PMID: 38664626 PMCID: PMC11046907 DOI: 10.1186/s12864-024-10295-1] [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: 05/01/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC). METHODS Germline DNA samples were genotyped and imputed using genome-wide arrays. Tumor DNA samples were extracted from paraffin blocks, and T cell receptor clonality and abundance were quantified by immunoSEQ (Adaptive Biotechnologies, Seattle, WA). Tumor infiltrating lymphocytes per high powered field (TILs/hpf) were scored by a gastrointestinal pathologist. Regression models were used to evaluate the associations between each variant and the three T-cell features, adjusting for sex, age, genotyping platform, and global ancestry. Three independent datasets were used for replication. RESULTS We identified a SNP (rs4918567) near RBM20 associated with clonality at a genome-wide significant threshold of 5 × 10- 8, with a consistent direction of association in both discovery and replication datasets. Expression quantitative trait (eQTL) analyses and in silico functional annotation for these loci provided insights into potential functional roles, including a statistically significant eQTL between the T allele at rs4918567 and higher expression of ADRA2A (P = 0.012) in healthy colon mucosa. CONCLUSIONS Our study suggests that germline genetic variation is associated with the quantity and diversity of adaptive immune responses in CRC. Further studies are warranted to replicate these findings in additional samples and to investigate functional genomic mechanisms.
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Affiliation(s)
- Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA.
| | - Ya-Yu Tsai
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joseph D Bonner
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sidney S Lindsey
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Marilena Melas
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kevin J McDonnell
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Gregory E Idos
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Christopher P Walker
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Chenxu Qu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - W Martin Kast
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Diane M Da Silva
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hedy S Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | | | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Tokyo Medical and Dental University (Institute of Science Tokyo), Tokyo, Japan
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gad Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - Stephen B Gruber
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA.
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3
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Tsai YY, Qu C, Bonner JD, Sanz-Pamplona R, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Tsang KK, Da Silva DM, Moratalla-Navarro F, Maoz A, Rennert HS, Kast WM, Greenson JK, Moreno V, Rennert G, Gruber SB, Schmit SL. Heterozygote advantage at HLA class I and II loci and reduced risk of colorectal cancer. Front Immunol 2023; 14:1268117. [PMID: 37942321 PMCID: PMC10627840 DOI: 10.3389/fimmu.2023.1268117] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023] Open
Abstract
Objective Reduced diversity at Human Leukocyte Antigen (HLA) loci may adversely affect the host's ability to recognize tumor neoantigens and subsequently increase disease burden. We hypothesized that increased heterozygosity at HLA loci is associated with a reduced risk of developing colorectal cancer (CRC). Methods We imputed HLA class I and II four-digit alleles using genotype data from a population-based study of 5,406 cases and 4,635 controls from the Molecular Epidemiology of Colorectal Cancer Study (MECC). Heterozygosity at each HLA locus and the number of heterozygous genotypes at HLA class -I (A, B, and C) and HLA class -II loci (DQB1, DRB1, and DPB1) were quantified. Logistic regression analysis was used to estimate the risk of CRC associated with HLA heterozygosity. Individuals with homozygous genotypes for all loci served as the reference category, and the analyses were adjusted for sex, age, genotyping platform, and ancestry. Further, we investigated associations between HLA diversity and tumor-associated T cell repertoire features, as measured by tumor infiltrating lymphocytes (TILs; N=2,839) and immunosequencing (N=2,357). Results Individuals with all heterozygous genotypes at all three class I genes had a reduced odds of CRC (OR: 0.74; 95% CI: 0.56-0.97, p= 0.031). A similar association was observed for class II loci, with an OR of 0.75 (95% CI: 0.60-0.95, p= 0.016). For class-I and class-II combined, individuals with all heterozygous genotypes had significantly lower odds of developing CRC (OR: 0.66, 95% CI: 0.49-0.87, p= 0.004) than those with 0 or one heterozygous genotype. HLA class I and/or II diversity was associated with higher T cell receptor (TCR) abundance and lower TCR clonality, but results were not statistically significant. Conclusion Our findings support a heterozygote advantage for the HLA class-I and -II loci, indicating an important role for HLA genetic variability in the etiology of CRC.
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Affiliation(s)
- Ya-Yu Tsai
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Chenxu Qu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Joseph D. Bonner
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Hospital Universitario Lozano Blesa, Aragon Health Research Institute (IISA), ARAID Foundation, Aragon Government, Zaragoza, Spain
| | - Sidney S. Lindsey
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Marilena Melas
- Molecular Diagnostics, New York Genome Center, New York, NY, United States
| | - Kevin J. McDonnell
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Gregory E. Idos
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Christopher P. Walker
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Kevin K. Tsang
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Diane M. Da Silva
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Ferran Moratalla-Navarro
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Asaf Maoz
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Hedy S. Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - W. Martin Kast
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Joel K. Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Gad Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - Stephen B. Gruber
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Stephanie L. Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, United States
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4
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Fernandez-Rozadilla C, Timofeeva M, Chen Z, Law P, Thomas M, Schmit S, Díez-Obrero V, Hsu L, Fernandez-Tajes J, Palles C, Sherwood K, Briggs S, Svinti V, Donnelly K, Farrington S, Blackmur J, Vaughan-Shaw P, Shu XO, Long J, Cai Q, Guo X, Lu Y, Broderick P, Studd J, Huyghe J, Harrison T, Conti D, Dampier C, Devall M, Schumacher F, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Moratalla-Navarro F, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper J, Jenkins M, Win AK, Pai R, Figueiredo J, Haile R, Gallinger S, Woods M, Newcomb P, Duggan D, Cheadle J, Kaplan R, Maughan T, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin LP, Jousilahti P, Knekt P, Aaltonen L, Rissanen H, Pukkala E, Eriksson J, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Zanke B, Männistö S, Albanes D, Weinstein S, Ruiz-Narvaez E, Palmer J, Buchanan D, Platz E, Visvanathan K, Ulrich C, Siegel E, Brezina S, Gsur A, Campbell P, Chang-Claude J, Hoffmeister M, Brenner H, Slattery M, Potter J, Tsilidis K, Schulze M, Gunter M, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Stern M, Pardamean B, Bishop T, Giles G, Southey M, Idos G, McDonnell K, Abu-Ful Z, Greenson J, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku T, van Guelpen B, Hudson T, Hampel H, Pearlman R, Berndt S, Hayes R, Martinez ME, Thomas S, Corley D, Pharoah P, Larsson S, Yen Y, Lenz HJ, White E, Li L, Doheny K, Pugh E, Shelford T, Chan A, Cruz-Correa M, Lindblom A, Hunter D, Joshi A, Schafmayer C, Scacheri P, Kundaje A, Nickerson D, Schoen R, Hampe J, Stadler Z, Vodicka P, Vodickova L, Vymetalkova V, Papadopoulos N, Edlund C, Gauderman W, Thomas D, Shibata D, Toland A, Markowitz S, Kim A, Chanock S, van Duijnhoven F, Feskens E, Sakoda L, Gago-Dominguez M, Wolk A, Naccarati A, Pardini B, FitzGerald L, Lee SC, Ogino S, Bien S, Kooperberg C, Li C, Lin Y, Prentice R, Qu C, Bézieau S, Tangen C, Mardis E, Yamaji T, Sawada N, Iwasaki M, Haiman C, Le Marchand L, Wu A, Qu C, McNeil C, Coetzee G, Hayward C, Deary I, Harris S, Theodoratou E, Reid S, Walker M, Ooi LY, Moreno V, Casey G, Gruber S, Tomlinson I, Zheng W, Dunlop M, Houlston R, Peters U. Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nat Genet 2023; 55:519-520. [PMID: 36782065 DOI: 10.1038/s41588-023-01334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Affiliation(s)
- Ceres Fernandez-Rozadilla
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Genomic Medicine Group, Instituto de Investigacion Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Virginia Díez-Obrero
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Juan Fernandez-Tajes
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah Briggs
- Department of Public Health, Richard Doll Building, University of Oxford, Oxford, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Blackmur
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James Studd
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Jeroen Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher Dampier
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Mathew Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Fredrick Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Vicente Martín-Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Biomedicine Institute, University of León, León, Spain
| | - Ferran Moratalla-Navarro
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - John Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jane Figueiredo
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Haile
- Division of Oncology, Department of Medicine, Cedars-Sinai Cancer Research Center for Health Equity, Los Angeles, CA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Michael Woods
- Division of Biomedical Sciences, Memorial University of Newfoundland, St. John, Ontario, Canada
| | - Polly Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - David Duggan
- City of Hope National Medical Center, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jeremy Cheadle
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Medical Research Council, Cardiff, UK
| | - Timothy Maughan
- MRC Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | | | - Pekka Jousilahti
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paul Knekt
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lauri Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Harri Rissanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Johan Eriksson
- Folkhälsan Research Centre, University of Helsinki, Helsinki, Finland
- Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Ulrika Hänninen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Brent Zanke
- Department of Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Daniel Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Elizabeth Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cornelia Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Erin Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Peter Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Martha Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - John Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Konstantinos Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Matthias Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Marc Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mariana Stern
- Department of Population and Public Health Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Bens Pardamean
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Indonesia
| | - Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gregory Idos
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin McDonnell
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Zomoroda Abu-Ful
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Joel Greenson
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Katerina Shulman
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Clalit Health Services, Personalized Genomic Service, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yu-Ru Su
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Robert Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Temitope Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Thomas Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Marie Elena Martinez
- Population Sciences, Disparities and Community Engagement, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Sushma Thomas
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Douglas Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Department of Gastroenterology, Kaiser Permanente Medical Center, San Francisco, CA, USA
| | - Paul Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susanna Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Yen
- Taipei Medical University, Taipei, Taiwan
| | - Heinz-Josef Lenz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kimberly Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marcia Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - David Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Amit Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Deborah Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Robert Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Zsofia Stadler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Nickolas Papadopoulos
- Department of Oncology Ludwig Center at the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chistopher Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - William Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Duncan Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amanda Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Sanford Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Andre Kim
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franzel van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Edith Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - Lori Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Public Foundation of Genomic Medicine, Servicio Galego de Saude, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
- Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
- Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
| | - Liesel FitzGerald
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Soo Chin Lee
- National University Cancer Institute, Singapore, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Catherine Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine Mardis
- Department of Pediatrics, Nationwide Children's Hospital, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Christopher Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | | | - Anna Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline McNeil
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stuart Reid
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Li Yin Ooi
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephen Gruber
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK.
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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Schmit S, Tsai YY, Nair KG, Barot SV, Xiang S, Kamath SD, Melas M, Walker CP, Srivastava R, Chan TAT, Bonner JD, McDonnell K, Idos G, Greenson JK, Rennert HS, Rennert G, Gruber SB, Khorana AA, Liska D. Differences in tumor-associated T cell receptor repertoires between young-onset and average-onset colorectal cancer. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
207 Background: The incidence of colorectal cancer (CRC) among individuals younger than age 50 (young-onset CRC; YOCRC) has increased, yet the etiology and molecular mechanisms underlying this alarming rise remain unclear. Some studies suggest that YOCRCs have more aggressive biology. Here, we compare tumor-associated T cell repertoires between patients with YOCRC and average-onset CRC (AOCRC). A robust, focused T cell response is a positive prognostic indicator; therefore, we hypothesized that YOCRCs demonstrate lower T cell abundance and greater T cell diversity than AOCRCs. Methods: The discovery cohort included 242 patients with histologically confirmed Stage I-IV CRC who underwent surgical resection at Cleveland Clinic from 2000 to 2020 and consented to a biorepository. YOCRC was defined as < 50 years at diagnosis (N = 126), and AOCRC as > 60 years (N = 116). DNA was extracted from frozen tumors, and T Cell Receptor (TCR) abundance and clonality were measured using immunoSEQ (Adaptive Biotechnologies). Following quality control, logistic regression models were used to evaluate the associations between TCR repertoire features and age of onset, adjusting for sex, race, tumor location, and stage. Findings were replicated in 152 YOCRC and 1,984 AOCRC cases from the Molecular Epidemiology of Colorectal Cancer Study with adjustment for sex, Jewish ethnicity, tumor location, and stage. Results: YOCRC patients were more likely to have left-sided tumors and be diagnosed at advanced stages in both cohorts. In the discovery cohort, YOCRC tumors had significantly lower TCR clonality (higher T cell diversity) compared to AOCRC tumors in a multivariable model adjusting for sex, race, tumor location and stage (OR: 0.38, 95% Confidence Interval (CI): 0.25-0.56, p < 0.0001). This association was also observed in the replication cohort (OR: 0.74, 95% CI: 0.62-0.89, p = 0.0013). In the replication cohort, further adjustment for microsatellite instability status did not substantially change the association (OR: 0.73, 95% CI: 0.61-0.88 p = 0.0012). When restricting to microsatellite stable tumors, clonality remained statistically significant in both the discovery and replication cohorts. No significant difference in TCR abundance was observed between YOCRC and AOCRC in either cohort. Conclusions: Higher T cell repertoire diversity, indicating a less focused intratumoral T cell response, is more frequently observed in YOCRC. Further studies are warranted to investigate the role of T cell diversity in the etiology and outcomes of YOCRC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Gregory Idos
- City of Hope National Comprehensive Cancer Center, Duarte, CA
| | | | - Hedy S Rennert
- CHS National Israeli Cancer Control Center, Haifa, Israel
| | - Gad Rennert
- Clalit National Cancer Control Center, Haifa, Israel
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Fernandez-Rozadilla C, Timofeeva M, Chen Z, Law P, Thomas M, Schmit S, Díez-Obrero V, Hsu L, Fernandez-Tajes J, Palles C, Sherwood K, Briggs S, Svinti V, Donnelly K, Farrington S, Blackmur J, Vaughan-Shaw P, Shu XO, Long J, Cai Q, Guo X, Lu Y, Broderick P, Studd J, Huyghe J, Harrison T, Conti D, Dampier C, Devall M, Schumacher F, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Moratalla-Navarro F, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper J, Jenkins M, Win AK, Pai R, Figueiredo J, Haile R, Gallinger S, Woods M, Newcomb P, Duggan D, Cheadle J, Kaplan R, Maughan T, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin LP, Jousilahti P, Knekt P, Aaltonen L, Rissanen H, Pukkala E, Eriksson J, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Zanke B, Männistö S, Albanes D, Weinstein S, Ruiz-Narvaez E, Palmer J, Buchanan D, Platz E, Visvanathan K, Ulrich C, Siegel E, Brezina S, Gsur A, Campbell P, Chang-Claude J, Hoffmeister M, Brenner H, Slattery M, Potter J, Tsilidis K, Schulze M, Gunter M, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Stern M, Pardamean B, Bishop T, Giles G, Southey M, Idos G, McDonnell K, Abu-Ful Z, Greenson J, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku T, van Guelpen B, Hudson T, Hampel H, Pearlman R, Berndt S, Hayes R, Martinez ME, Thomas S, Corley D, Pharoah P, Larsson S, Yen Y, Lenz HJ, White E, Li L, Doheny K, Pugh E, Shelford T, Chan A, Cruz-Correa M, Lindblom A, Hunter D, Joshi A, Schafmayer C, Scacheri P, Kundaje A, Nickerson D, Schoen R, Hampe J, Stadler Z, Vodicka P, Vodickova L, Vymetalkova V, Papadopoulos N, Edlund C, Gauderman W, Thomas D, Shibata D, Toland A, Markowitz S, Kim A, Chanock S, van Duijnhoven F, Feskens E, Sakoda L, Gago-Dominguez M, Wolk A, Naccarati A, Pardini B, FitzGerald L, Lee SC, Ogino S, Bien S, Kooperberg C, Li C, Lin Y, Prentice R, Qu C, Bézieau S, Tangen C, Mardis E, Yamaji T, Sawada N, Iwasaki M, Haiman C, Le Marchand L, Wu A, Qu C, McNeil C, Coetzee G, Hayward C, Deary I, Harris S, Theodoratou E, Reid S, Walker M, Ooi LY, Moreno V, Casey G, Gruber S, Tomlinson I, Zheng W, Dunlop M, Houlston R, Peters U. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nat Genet 2023; 55:89-99. [PMID: 36539618 PMCID: PMC10094749 DOI: 10.1038/s41588-022-01222-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [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: 11/24/2021] [Accepted: 10/09/2022] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.
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Affiliation(s)
- Ceres Fernandez-Rozadilla
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Genomic Medicine Group, Instituto de Investigacion Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Virginia Díez-Obrero
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Juan Fernandez-Tajes
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah Briggs
- Department of Public Health, Richard Doll Building, University of Oxford, Oxford, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Blackmur
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James Studd
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Jeroen Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher Dampier
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Mathew Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Fredrick Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Vicente Martín-Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Biomedicine Institute, University of León, León, Spain
| | - Ferran Moratalla-Navarro
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - John Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jane Figueiredo
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Haile
- Division of Oncology, Department of Medicine, Cedars-Sinai Cancer Research Center for Health Equity, Los Angeles, CA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Michael Woods
- Division of Biomedical Sciences, Memorial University of Newfoundland, St. John, Ontario, Canada
| | - Polly Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - David Duggan
- City of Hope National Medical Center, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jeremy Cheadle
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Medical Research Council, Cardiff, UK
| | - Timothy Maughan
- MRC Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | | | - Pekka Jousilahti
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paul Knekt
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lauri Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Harri Rissanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Johan Eriksson
- Folkhälsan Research Centre, University of Helsinki, Helsinki, Finland
- Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Ulrika Hänninen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Brent Zanke
- Department of Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Daniel Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Elizabeth Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cornelia Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Erin Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Peter Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Martha Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - John Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Konstantinos Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Matthias Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Marc Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mariana Stern
- Department of Population and Public Health Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Bens Pardamean
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Indonesia
| | - Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gregory Idos
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin McDonnell
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Zomoroda Abu-Ful
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Joel Greenson
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Katerina Shulman
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Clalit Health Services, Personalized Genomic Service, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yu-Ru Su
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Robert Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Temitope Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Thomas Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Marie Elena Martinez
- Population Sciences, Disparities and Community Engagement, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Sushma Thomas
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Douglas Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Department of Gastroenterology, Kaiser Permanente Medical Center, San Francisco, CA, USA
| | - Paul Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susanna Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Yen
- Taipei Medical University, Taipei, Taiwan
| | - Heinz-Josef Lenz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kimberly Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marcia Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - David Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Amit Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Deborah Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Robert Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Zsofia Stadler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Nickolas Papadopoulos
- Department of Oncology Ludwig Center at the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chistopher Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - William Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Duncan Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amanda Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Sanford Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Andre Kim
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franzel van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Edith Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - Lori Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Public Foundation of Genomic Medicine, Servicio Galego de Saude, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
- Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
- Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
| | - Liesel FitzGerald
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Soo Chin Lee
- National University Cancer Institute, Singapore, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Catherine Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine Mardis
- Department of Pediatrics, Nationwide Children's Hospital, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Christopher Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | | | - Anna Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline McNeil
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stuart Reid
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Li Yin Ooi
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephen Gruber
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK.
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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7
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Melas M, Geiger H, Srinivasa ST, Guha S, Felice V, Fielding L, Thomas-Wilson A, Wilson A, MacDonald T, Smith R, Manohar J, Primiano M, Elemento O, Sharaf R, Wrzeszczynski KO, Jobanputra V. 102. Elucidating the genomic landscape of Prostate Adenocarcinoma through whole genome and transcriptome sequencing. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Wrzeszczynski KO, Geiger H, Srinivasa ST, Melas M, Shah V, Felice V, Suarez L, Hegedus E, Phadke S, Guha S, Manaa D, Robinson D, Fielding L, Jobanputra V. Abstract 757: Clinical interpretation and utility of whole genome and whole transcriptome sequencing for precision oncology. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
The New York Genome Center CLIA laboratory has been providing New York State approved molecular diagnostic whole genome and whole transcriptome sequencing (WGTS) since October 2018. Indications for testing are cancers (solid tumors or hematological malignancies) where a mutational profile from multiple genes would be informative for disease stratification, prognosis, treatment options or alternative treatments or clinical trials. Germline analysis for ACMG designated cancer predisposition variants also is performed for consented patients. To date we have provided clinical next generation sequencing (NGS) genomic profile reports for 139 oncological cases from 31 different cancer types including GBM (41 cases), Pancreas (17), CRC (15), Lung (8) and others. The clinical interpretation of WGTS data of molecular tumor markers from NGS encompasses automated variant calling tools with human interpretation. The final mostly manual review of data is intensive, involving highly trained scientists engaged in substantial literature review and interpretation for each case alongside pathologists, molecular geneticists, and treating oncologists. We first present the technical challenges of validating a WGTS oncological diagnostic assay for appropriate clinical grade accuracy and sensitivity acceptable for patient care. We then present case studies illustrating the varying degree of tumor profiling and analysis outlining the current clinical utility and challenges of precision oncology medicine and therapeutic associations from sequencing of cancer patient tumors. We conclude with a previously unreported summary of therapeutic actionability derived from WGTS for all cancer cases sequenced at NYGC. We show that 28% percent of all samples in our cohort contain a tier 1 variant but additional second line therapies (or off-label drugs) can be considered for over 75% of WGTS sequenced cancer patients. Our case studies being in both solid tumor and hematological cancers illustrate the variability in sequencing data and the individual patient specificities in each interpretation of clinical findings. We show how NGS sequencing can offer multiple treatment outcomes when combining all genomic aberrations (copy number, structural variants and SNV/indels) found in a subtype of prostate cancer. We present hematological malignancies that show how certain DNA mutations point to RNA aberrations leading to therapeutic associations. In pancreatic cancer we present how a unique alteration in BRAF can lead to second line treatment with clinical benefit. We therefore demonstrate that more complete NGS assays those examining both the whole genome and transcriptome have added value in precision oncology practice enabling to find second-line treatment options or alternative therapeutic options when primary approaches fail or are not identified following a targeted sequencing approach.
Citation Format: Kazimierz O. Wrzeszczynski, Heather Geiger, Sowmya T. Srinivasa, Marilena Melas, Valisha Shah, Vanessa Felice, Luisa Suarez, Endre Hegedus, Shruti Phadke, Saurav Guha, Dina Manaa, Dino Robinson, Lena Fielding, Vaidehi Jobanputra. Clinical interpretation and utility of whole genome and whole transcriptome sequencing for precision oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 757.
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Affiliation(s)
| | - Heather Geiger
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | | | - Marilena Melas
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Valisha Shah
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Vanessa Felice
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Luisa Suarez
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Endre Hegedus
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Shruti Phadke
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Saurav Guha
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Dina Manaa
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Dino Robinson
- 1The New York Genome Center Clinical Laboratory, New York, NY
| | - Lena Fielding
- 1The New York Genome Center Clinical Laboratory, New York, NY
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9
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Tsai YY, Qu C, Bonner JD, Sanz-Pamplona R, Lindsey S, Melas M, McDonnell KJ, Idos GE, Walker CP, Tsang KK, Da Silva DM, Moratalla F, Maoz A, Rennert HS, Kast WM, Greenson JK, Moreno V, Rennert G, Gruber SB, Schmit SL. Abstract 5874: Heterozygote advantage at HLA class I and II loci and colorectal cancer risk. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Diversity in Human Leukocyte Antigen (HLA) genes has been associated with risk of several diseases, including Non-Hodgkin’s lymphoma and ulcerative colitis. Reduced diversity at HLA loci may adversely affect the host’s ability to recognize foreign antigens and tumor neoantigens, and subsequently, increase disease burden. To better understand the role of inherited HLA diversity in colorectal cancer (CRC) risk, we utilized data from a population-based study of 10,347 participants (5,574 CRC cases and 4,773 healthy controls) from the Molecular Epidemiology of Colorectal Cancer Study (MECC). Germline DNA samples were genotyped using genome-wide arrays, and HLA Class I and II four-digit resolution alleles were imputed using SNP2HLA and a reference panel of 5,225 individuals from the Type 1 Diabetes Genetics Consortium. Heterozygosity and homozygosity at each HLA locus and the number of homozygous genotypes at class I loci (A, B, C) and class II loci (DQB1, DRB1, DPB1) were quantified. To examine the joint effect of Class I and Class II loci, we combined the total number of homozygotes for all loci and categorized into 3 groups: heterozygotes at all loci, 1 to 4 homozygotes, or 5 or more homozygotes. Logistic regression was used to estimate the risk of CRC associated with HLA locus homozygosity. Individuals with heterozygous genotypes for all loci served as the reference category, and analyses were adjusted for sex, age, genotyping platform, and global ancestry. Individuals with homozygous genotypes at all 3 Class I genes had an increased risk of CRC when compared to those with heterozygous genotypes at all Class I loci (OR: 1.34; 95% CI: 1.02-1.76, P = 0.033; Ptrend = 0.039). A similar association was observed for Class II loci, with an OR of 1.32 (95% CI: 1.05-1.65, P = 0.015; Ptrend = 0.157). For HLA Class I and II combined, individuals with five or more homozygous genotypes at HLA class I or II loci were at higher risk for developing CRC (OR: 1.84, 95% CI: 1.24-2.73, P = 0.0023; Ptrend = 0.015), when compared to those with all heterozygous genotypes. Our findings support a heterozygote advantage at HLA class I and II loci as a protective factor for CRC. This indicates an important role for HLA genetic variability in the etiology of CRC potentially operating through a mechanism of decreased diversity of tumor neoantigens that can be displayed to the adaptive immune system.
Citation Format: Ya-Yu Tsai, Chenxu Qu, Joseph D. Bonner, Rebeca Sanz-Pamplona, Sidney Lindsey, Marilena Melas, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, Kevin K. Tsang, Diane M. Da Silva, Ferran Moratalla, Asaf Maoz, Hedy S. Rennert, W. Martin Kast, Joel K. Greenson, Victor Moreno, Gad Rennert, Stephen B. Gruber, Stephanie L. Schmit. Heterozygote advantage at HLA class I and II loci and colorectal cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5874.
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Affiliation(s)
| | - Chenxu Qu
- 2USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Rebeca Sanz-Pamplona
- 4Hospitalet de Llobregat; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | | | | | | | | | | | | | | | - Ferran Moratalla
- 4Hospitalet de Llobregat; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Asaf Maoz
- 6Dana-Farber Cancer Institute; Harvard Medical School, Boston, MA
| | - Hedy S. Rennert
- 7Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - W. Martin Kast
- 2USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Victor Moreno
- 4Hospitalet de Llobregat; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Gad Rennert
- 7Clalit Health Services National Cancer Control Center, Haifa, Israel
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10
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Melas M, Shatara M, Schieffer KM, Lee K, Varga EA, Leraas KM, Rodriguez DP, Abdelbaki MS, Osorio DS, Finlay JL, Boué DR, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE. 26. Co-occurrence of rosette-forming glioneuronal tumors with Noonan Syndrome. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2021.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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11
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Melas M, Kautto EA, Franklin SJ, Mori M, McBride KL, Mosher TM, Pfau RB, Hernandez-Gonzalez ME, McGrath SD, Magrini VJ, White P, Samora JB, Koboldt DC, Wilson RK. Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly. Hum Mutat 2021; 43:189-199. [PMID: 34859533 DOI: 10.1002/humu.24304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/26/2021] [Revised: 09/24/2021] [Accepted: 11/20/2021] [Indexed: 12/11/2022]
Abstract
Synpolydactyly 1, also called syndactyly type II (SDTY2), is a genetic limb malformation characterized by polydactyly with syndactyly involving the webbing of the third and fourth fingers, and the fourth and fifth toes. It is caused by heterozygous alterations in HOXD13 with incomplete penetrance and phenotypic variability. In our study, a five-generation family with an SPD phenotype was enrolled in our Rare Disease Genomics Protocol. A comprehensive examination of three generations using Illumina short-read whole-genome sequencing (WGS) did not identify any causative variants. Subsequent WGS using Pacific Biosciences (PacBio) long-read HiFi Circular Consensus Sequencing (CCS) revealed a heterozygous 27-bp duplication in the polyalanine tract of HOXD13. Sanger sequencing of all available family members confirmed that the variant segregates with affected individuals. Reanalysis of an unrelated family with a similar SPD phenotype uncovered a 21-bp (7-alanine) duplication in the same region of HOXD13. Although ExpansionHunter identified these events in most individuals in a retrospective analysis, low sequence coverage due to high GC content in the HOXD13 polyalanine tract makes detection of these events challenging. Our findings highlight the value of long-read WGS in elucidating the molecular etiology of congenital limb malformation disorders.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Esko A Kautto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Samuel J Franklin
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mari Mori
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Theresa Mihalic Mosher
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vincent J Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Julie Balch Samora
- Department of Orthopedic Surgery, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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12
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Melas M, Mathew MT, Mori M, Jayaraman V, Wilson SA, Martin C, Jacobson-Kelly AE, Kelly BJ, Magrini V, Mardis ER, Cottrell CE, Lee K. Somatic Variation as an Incidental Finding in the Pediatric Next Generation Sequencing Era. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006135. [PMID: 34716204 PMCID: PMC8751410 DOI: 10.1101/mcs.a006135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
The methodologic approach used in next-generation sequencing (NGS) affords a high depth of coverage in genomic analysis. Inherent in the nature of genomic testing, there exists potential for identifying genomic findings that are incidental or secondary to the indication for clinical testing, with the frequency dependent on the breadth of analysis and the tissue sample under study. The interpretation and management of clinically meaningful incidental genomic findings is a pressing issue particularly in the pediatric population. Our study describes a 16-mo-old male who presented with profound global delays, brain abnormality, progressive microcephaly, and growth deficiency, as well as metopic craniosynostosis. Clinical exome sequencing (ES) trio analysis revealed the presence of two variants in the proband. The first was a de novo variant in the PPP2R1A gene (c.773G > A, p.Arg258His), which is associated with autosomal dominant (AD) intellectual disability, accounting for the proband's clinical phenotype. The second was a recurrent hotspot variant in the CBL gene (c.1111T > C, p.Tyr371His), which was present at a variant allele fraction of 11%, consistent with somatic variation in the peripheral blood sample. Germline pathogenic variants in CBL are associated with AD Noonan syndrome–like disorder with or without juvenile myelomonocytic leukemia. Molecular analyses using a different tissue source, buccal epithelial cells, suggest that the CBL alteration may represent a clonal population of cells restricted to leukocytes. This report highlights the laboratory methodologic and interpretative processes and clinical considerations in the setting of acquired variation detected during clinical ES in a pediatric patient.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Mariam T Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State Univ; Dept of Pediatrics, The Ohio State University
| | - Mari Mori
- Dept of Pediatrics, The Ohio State University; Genetic and Genomic Medicine, Nationwide Children's Hospital
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Sarah A Wilson
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | | | - Amanda E Jacobson-Kelly
- Dept of Pediatrics, The Ohio State University; Division of Hematology/Oncology/BMT, Nationwide Children's Hospital
| | - Ben J Kelly
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pediatrics, The Ohio State University
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pediatrics, The Ohio State University
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State University; Dept of Pediatrics, The Ohio State University
| | - Kristy Lee
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State University; Dept of Pediatrics, The Ohio State University
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13
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Gruber SB, Bonner JD, Lindsey SS, Tsai YY, Sanz-Pamplona R, Alonso MH, Melas M, Rennert HS, McDonnell KJ, Idos GE, Walker CP, Kast WM, Da Silva D, Robins HS, Greenson JK, Moreno V, Schmit SL, Rennert G. Abstract 2737: Clinical and epidemiologic predictors of clonal immune responses in colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
The quantity and quality of immune responses in colorectal cancers (CRC) are widely variable and have important clinical, therapeutic, and prognostic implications. We studied clinical and epidemiologic factors that might influence T-cell quantity and clonality within colorectal adenocarcinomas to better understand the drivers of diverse immune responses. Incident cases of CRC from the Molecular Epidemiology of Colorectal Cancer Study (MECC) were interviewed, and 6,006 cases had complete epidemiologic data. Archived tumor blocks were retrieved from 3,865 (64.4%) cases, and all were reviewed by a single expert pathologist who quantified TILS/hpf. Sufficient tissue for macrodissection and measurement of TCR abundance and clonality using the immunoSEQ assay (Adaptive Biotechnologies) was available and completed for 2,750 cases. Logistic regression, negative binomial regression and linear regression models were used to evaluate potential associations between clinical and epidemiologic variables for: TILS/hpf, TCR abundance, and T-cell clonality. The stage distribution was representative of cancer incidence in the population, and the MSI-H phenotype was observed in 14.2% of cases. Clinical, pathologic, and epidemiologic variables including aspirin, alcohol, diet, hormone use, physical activity, smoking, and statins were assessed in relation to immune measures. Among other findings, >5 years of statins (p<0.001) and daily aspirin (p=0.037) were each strongly associated with T-cell clonality. Our study suggests that important parameters of the adaptive immune response may be mediated by modifiable factors. Mechanisms regulating immune responses in CRC may have implications for chemoprevention as well as immunotherapy.
Citation Format: Stephen B. Gruber, Joseph D. Bonner, Sidney S. Lindsey, Ya-Yu Tsai, Rebeca Sanz-Pamplona, M. Henar Alonso, Marilena Melas, Hedy S. Rennert, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, W. Martin Kast, Diane Da Silva, Harlan S. Robins, Joel K. Greenson, Victor Moreno, Stephanie L. Schmit, Gad Rennert. Clinical and epidemiologic predictors of clonal immune responses in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2737.
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Affiliation(s)
- Stephen B. Gruber
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Joseph D. Bonner
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Sidney S. Lindsey
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Ya-Yu Tsai
- 2Cleveland Clinic Foundation, Cleveland, OH, Cleveland, OH
| | - Rebeca Sanz-Pamplona
- 3Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - M. Henar Alonso
- 3Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Hedy S. Rennert
- 5Carmel Medical Center and Faculty of Medicine, Technion-Israel Institute of Technology, Clalit National Cancer Control Center, Haifa, Israel
| | - Kevin J. McDonnell
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Gregory E. Idos
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | | | - W. Martin Kast
- 6Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Diane Da Silva
- 6Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | - Victor Moreno
- 3Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Gad Rennert
- 5Carmel Medical Center and Faculty of Medicine, Technion-Israel Institute of Technology, Clalit National Cancer Control Center, Haifa, Israel
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Schmit SL, Tsai YY, Bonner J, Sanz-Pamplona R, Joshi AD, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Kast WM, Da Silva D, Ugai T, Rennert HS, Robins HS, Greenson JK, Ogino S, Moreno V, Rennert G, Gruber SB. Abstract 824: Germline genetic regulation of the adaptive immune response in colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Adaptive immune responses in the tumor microenvironment of colorectal cancer (CRC) play an important role in prognosis. However, the contributions of germline genetic variations to the strength and diversity of T cell responses in CRC are unclear. We conducted a genome-wide association study to examine the relationships between germline genetic variants and measures of the T cell repertoire in colorectal tumors. Germline DNA samples from 5,581 CRC cases recruited into the Molecular Epidemiology of Colorectal Cancer Study (MECC) were genotyped in batches using four different platforms. Genotype data were imputed to the Haplotype Reference Consortium panel separately by genotyping platform. Tumor DNA samples were extracted from paraffin blocks, and tumor infiltrating lymphocytes per high powered field (TILs/hpf) were quantified by a single gastrointestinal pathologist. TCR abundance and clonality within individual CRCs were measured using the immunoSEQ assay (Adaptive Biotechnologies). Appropriate quality control steps and data transformations were applied to fit downstream statistical modeling assumptions. After standard quality control on both imputed genotypes and transformed immune metrics, 2,876 (TILs/hpf) and 2,395 (TCR abundance and clonality) cases with approximately 9 million imputed genetic variants were included in the discovery phase. Logistic or linear regression models were used to evaluate the associations between allelic dosage of each variant and each immune-related outcome, adjusting for sex, age at diagnosis, genotyping platform, and principal components for global ancestry. Three independent datasets were available to replicate our findings using similar quality control measures and regression models: Colonomics (N=96; TILs/hpf, TCR abundance, clonality), the CRC Genetics Study (N=162; TCR abundance, clonality), and the Harvard Cohorts (N=505; TILs/hpf; in progress). The discovery phase identified 5 independent genetic variants associated with TILs/hpf, 15 associated with TCR abundance, and 19 associated with clonality at p<5X10E-06. Replication analyses as well as expression quantitative trait analyses and in silico functional annotation are underway for the loci of interest. Our study suggests that germline genetic variation is associated with the quantity and quality of adaptive immune responses in CRC.
Citation Format: Stephanie L. Schmit, Ya-Yu Tsai, Joseph Bonner, Rebeca Sanz-Pamplona, Amit D. Joshi, Sidney S. Lindsey, Marilena Melas, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, W. Martin Kast, Diane Da Silva, Tomotaka Ugai, Hedy S. Rennert, Harlan S. Robins, Joel K. Greenson, Shuji Ogino, Victor Moreno, Gad Rennert, Stephen B. Gruber. Germline genetic regulation of the adaptive immune response in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 824.
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Affiliation(s)
| | | | | | | | - Amit D. Joshi
- 4Massachusetts General Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | | | | | | | - W. Martin Kast
- 6University of Southern California; Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Tomotaka Ugai
- 8Brigham and Women's Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Hedy S. Rennert
- 9Clalit Health Services National Cancer Control Center, Haifa, Israel
| | | | | | - Shuji Ogino
- 12Brigham and Women's Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health; Dana-Farber Cancer Institute, Boston, MA
| | | | - Gad Rennert
- 9Clalit Health Services National Cancer Control Center, Haifa, Israel
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15
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Bonner J, Schmit SL, Lindsey SS, Tsai YY, Sanz-Pamplona R, Alonso MH, Melas M, Rennert HS, McDonnell KJ, Idos G, Walker CP, Kast WM, Da Silva D, Robins HS, Greenson JK, Moreno V, Rennert G, Gruber SB. Abstract 835: T-cell abundance, clonality and disease specific survival in colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Immune responses to colorectal cancer (CRC) are important prognostic factors as measured by either tumor infiltrating lymphocytes per high powered field or the presence of Crohn's like lymphoid reaction. New technologies to quantify specific features of immune responses include immunoSeq (Adaptive Biotechnologies), which accurately quantifies T-cell receptor (TCR) abundance and T-cell receptor clonality. Here we measured the independent contributions of TCR abundance and TCR clonality to 5-year CRC-specific survival in the Molecular Epidemiology of Colorectal Cancer (MECC) study. The MECC study consented, interviewed, and followed 6,006 incident cases of CRC diagnosed between March 31, 1998 and July 1, 2017 (median follow-up time = 6.9 years). Archived paraffin blocks were retrieved, and 2,750 cases had sufficient tissue and adequate DNA extraction to perform the immunoSeq assay. Analyses were restricted to 1,625 samples with more than 100 T-cells to permit accurate quantification of TCR abundance and TCR clonality as measured by Simpson Clonality Index. TCR abundance was log2 transformed for analyses, and Simpson Clonality Index was log2-transformed and z-scale normalized separately by assay version. In unadjusted models, dichotomized log2 transformed TCR abundance (Hazard Ratio (HR) = 0.57, 95% confidence interval (CI) 0.47-0.71, p=9.77E-08) and dichotomized TCR clonality (HR = 0.77, 95% CI 0.63-0.94, p=0.01) were each statistically significantly associated with 5-year CRC-specific survival. In a model with adjustment for age, sex, microsatellite instability, stage and assay version, both dichotomized log2 transformed TCR abundance (HR = 0.61, 95% CI, 0.49-0.75, p=3.03E-06), and dichotomized TCR clonality (HR = 0.81, 95% CI, 0.66-0.99, p=0.048) were associated with improved 5-year disease-specific survival.
Conclusion: TCR abundance and TCR clonality are independent prognostic indicators in CRC.
Citation Format: Joseph Bonner, Sephanie L. Schmit, Sidney S. Lindsey, Ya-Yu Tsai, Rebeca Sanz-Pamplona, M. Henar Alonso, Marilena Melas, Hedy S. Rennert, Kevin J. McDonnell, Gregory Idos, Christopher P. Walker, W. Martin Kast, Diane Da Silva, Harlan S. Robins, Joel K. Greenson, Victor Moreno, Gad Rennert, Stephen B. Gruber. T-cell abundance, clonality and disease specific survival in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 835.
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Affiliation(s)
| | | | | | - Ya-Yu Tsai
- 2Cleveland Clinic Foundation, Cleveland, OH
| | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Rennert
- 5Technion-Israel Institute of Technology, Haifa, Israel
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16
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Kamal Y, Dwan D, Hoehn HJ, Sanz-Pamplona R, Alonso MH, Moreno V, Cheng C, Schell MJ, Kim Y, Felder SI, Rennert HS, Melas M, Lazaris C, Bonner JD, Siegel EM, Shibata D, Rennert G, Gruber SB, Frost HR, Amos CI, Schmit SL. Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse. Oncoimmunology 2021; 10:1862529. [PMID: 33763292 PMCID: PMC7951964 DOI: 10.1080/2162402x.2020.1862529] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/20/2019] [Accepted: 12/01/2020] [Indexed: 01/10/2023] Open
Abstract
A substantial fraction of patients with stage I-III colorectal adenocarcinoma (CRC) experience disease relapse after surgery with curative intent. However, biomarkers for predicting the likelihood of CRC relapse have not been fully explored. Therefore, we assessed the association between tumor infiltration by a broad array of innate and adaptive immune cell types and CRC relapse risk. We implemented a discovery-validation design including a discovery dataset from Moffitt Cancer Center (MCC; Tampa, FL) and three independent validation datasets: (1) GSE41258 (2) the Molecular Epidemiology of Colorectal Cancer (MECC) study, and (3) GSE39582. Infiltration by 22 immune cell types was inferred from tumor gene expression data, and the association between immune infiltration by each cell type and relapse-free survival was assessed using Cox proportional hazards regression. Within each of the four independent cohorts, CD4+ memory activated T cell (HR: 0.93, 95% CI: 0.90-0.96; FDR = 0.0001) infiltration was associated with longer time to disease relapse, independent of stage, microsatellite instability, and adjuvant therapy. Based on our meta-analysis across the four datasets, 10 innate and adaptive immune cell types associated with disease relapse of which 2 were internally validated using multiplex immunofluorescence. Moreover, immune cell type infiltration was a better predictors of disease relapse than Consensus Molecular Subtype (CMS) and other expression-based biomarkers (Immune-AICMCC:238.1-238.9; CMS-AICMCC: 241.0). These data suggest that transcriptome-derived immune profiles are prognostic indicators of CRC relapse and quantification of both innate and adaptive immune cell types may serve as candidate biomarkers for predicting prognosis and guiding frequency and modality of disease surveillance.
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Affiliation(s)
- Yasmin Kamal
- Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Dennis Dwan
- Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Hannah J. Hoehn
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rebeca Sanz-Pamplona
- Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - M. Henar Alonso
- Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Victor Moreno
- Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Chao Cheng
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Michael J. Schell
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Columbus, OH, USA
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Columbus, OH, USA
| | - Seth I. Felder
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute
| | - Hedy S. Rennert
- Department of Community Medicine & Epidemiology, Lady Davis Carmel Medical Center, Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Lady Davis Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Marilena Melas
- Department of Medical Oncology and Therapeutics Research, Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
- Nationwide Children’s Hospital, Columbus, OH, USA
| | - Charalampos Lazaris
- Department of Medical Oncology and Therapeutics Research, Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph D. Bonner
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Erin M. Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Gad Rennert
- Department of Community Medicine & Epidemiology, Lady Davis Carmel Medical Center, Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Lady Davis Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Stephen B. Gruber
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - H. Robert Frost
- Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Christopher I. Amos
- Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie L. Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute
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Ciccone MA, Adams CL, Bowen C, Thakur T, Ricker C, Culver JO, Maoz A, Melas M, Idos GE, Jeyasekharan AD, Matsuo K, Roman LD, Gruber SB, McDonnell KJ. Inhibition of poly(ADP-ribose) polymerase induces synthetic lethality in BRIP1 deficient ovarian epithelial cells. Gynecol Oncol 2020; 159:869-876. [PMID: 33032822 PMCID: PMC9893519 DOI: 10.1016/j.ygyno.2020.09.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/08/2020] [Accepted: 09/23/2020] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Pathogenic variations in the homologous recombination (HR) gene, BRCA1 interacting protein C-terminal helicase 1 (BRIP1) increase the risk for ovarian cancer. PARP inhibitors (PARPi) exert a synthetic lethal effect in BRCA-mutated ovarian cancers. Effective HR requires cooperation between BRCA1 and BRIP1; therefore, BRIP1-incompetancy may predict vulnerability to synthetic lethality. Here we investigated the response of ovarian epithelial cells with defective BRIP1 function to PARPi, and compared these cells to those lacking BRCA1 activity. METHODS We engineered Chinese Hamster ovarian (CHO) epithelial cells to express deficient BRIP1 or BRCA1, and exposed them to olaparib with or without carboplatin or cisplatin. We assessed cellular proliferation and survival; we calculated inhibitory concentrations and combination and reduction drug indices. RESULTS BRIP1 and BRCA1 inactivation impedes HR activity, decreases cellular proliferation and compromises DNA damage recovery. Platinum agent exposure impairs cellular survival. Olaparib exposure alone decreases cell viability in BRCA1-deficient cells, although has no effect on BRIP1-deficient cells. Combining carboplatin or cisplatin with olaparib synergistically attenuates cellular survival, consistent with synthetic lethality. CONCLUSIONS BRIP1-deficient ovarian epithelial cells exhibit defective HR, resulting in synthetic lethality when exposed to a platinum agent/PARPi combination. PARPi alone had no effect; this lack of effect may result from distinguishing molecular properties of BRIP1and/or consequences of genomic background. Our study identifies altered BRIP1 as a target for precision medicine-based therapies for ovarian cancers. This investigation supports consideration of the use of a platinum agent/PARPi combination in ovarian cancers depending upon genetic profile and genomic background.
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Affiliation(s)
- Marcia A. Ciccone
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA,Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA,Corresponding Author: Marcia A. Ciccone, 2020 Zonal Ave, IRD 520, Los Angeles, CA, 90033, phone: (323) 409-3416, Fax: (323) 226-2734,
| | - Crystal L. Adams
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA,Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charles Bowen
- Department of Clinical Cancer Prevention, Division of Cancer Prevention and Population Sciences, MD Anderson Cancer Center, Houston, TX, USA
| | - Teena Thakur
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Charité Ricker
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA,Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julie O. Culver
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Asaf Maoz
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Gregory E. Idos
- Department of Internal Medicine, Division of Gastroenterology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA,Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | | | - Koji Matsuo
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA,Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lynda D. Roman
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA,Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen B. Gruber
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, and Beckman Research Institute, Duarte, CA, USA,Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, and Beckman Research Institute, Duarte, CA, USA,Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
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18
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Sanz-Pamplona R, Melas M, Maoz A, Schmit SL, Rennert H, Lejbkowicz F, Greenson JK, Sanjuan X, Lopez-Zambrano M, Alonso MH, Qu C, McDonnell KJ, Idos GE, Vignali M, Emerson R, Fields P, Guinó E, Santos C, Salazar R, Robins HS, Rennert G, Gruber SB, Moreno V. Lymphocytic infiltration in stage II microsatellite stable colorectal tumors: A retrospective prognosis biomarker analysis. PLoS Med 2020; 17:e1003292. [PMID: 32970670 PMCID: PMC7514069 DOI: 10.1371/journal.pmed.1003292] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Identifying stage II patients with colorectal cancer (CRC) at higher risk of progression is a clinical priority in order to optimize the advantages of adjuvant chemotherapy while avoiding unnecessary toxicity. Recently, the intensity and the quality of the host immune response in the tumor microenvironment have been reported to have an important role in tumorigenesis and an inverse association with tumor progression. This association is well established in microsatellite instable CRC. In this work, we aim to assess the usefulness of measures of T-cell infiltration as prognostic biomarkers in 640 stage II, CRC tumors, 582 of them confirmed microsatellite stable. METHODS AND FINDINGS We measured both the quantity and clonality index of T cells by means of T-cell receptor (TCR) immunosequencing in a discovery dataset (95 patients with colon cancer diagnosed at stage II and microsatellite stable, median age 67, 30% women) and replicated the results in 3 additional series of stage II patients from 2 countries. Series 1 and 2 were recruited in Barcelona, Spain and included 112 fresh frozen (FF, median age 69, 44% women) and 163 formalin-fixed paraffin-embedded (FFPE, median age 67, 39% women) samples, respectively. Series 3 included 270 FFPE samples from patients recruited in Haifa, Northern Israel, as part of a large case-control study of CRC (median age 73, 46% women). Median follow-up time was 81.1 months. Cox regression models were fitted to evaluate the prognostic value of T-cell abundance and Simpson clonality of TCR variants adjusting by sex, age, tumor location, and stage (IIA and IIB). In the discovery dataset, higher TCR abundance was associated with better prognosis (hazard ratio [HR] for ≥Q1 = 0.25, 95% CI 0.10-0.63, P = 0.003). A functional analysis of gene expression on these tumors revealed enrichment in pathways related to immune response. Higher values of clonality index (lower diversity) were not associated with worse disease-free survival, though the HR for ≥Q3 was 2.32 (95% CI 0.90-5.97, P = 0.08). These results were replicated in an independent FF dataset (TCR abundance: HR = 0.30, 95% CI 0.12-0.72, P = 0.007; clonality: HR = 3.32, 95% CI 1.38-7.94, P = 0.007). Also, the association with prognosis was tested in 2 independent FFPE datasets. The same association was observed with TCR abundance (HR = 0.41, 95% CI 0.18-0.93, P = 0.03 and HR = 0.56, 95% CI 0.31-1, P = 0.042, respectively, for each FFPE dataset). However, the clonality index was associated with prognosis only in the FFPE dataset from Israel (HR = 2.45, 95% CI 1.39-4.32, P = 0.002). Finally, a combined analysis combining all microsatellite stable (MSS) samples demonstrated a clear prognosis value both for TCR abundance (HR = 0.39, 95% CI 0.26-0.57, P = 1.3e-06) and the clonality index (HR = 2.13, 95% CI 1.44-3.15, P = 0.0002). These associations were also observed when variables were considered continuous in the models (HR per log2 of TCR abundance = 0.85, 95% CI 0.78-0.93, P = 0.0002; HR per log2 or clonality index = 1.16, 95% CI 1.03-1.31, P = 0.016). LIMITATIONS This is a retrospective study, and samples had been preserved with different methods. Validation series lack complete information about microsatellite instability (MSI) status and pathology assessment. The Molecular Epidemiology of Colorectal Cancer (MECC) study had information about overall survival instead of progression-free survival. CONCLUSION Results from this study demonstrate that tumor lymphocytes, assessed by TCR repertoire quantification based on a sequencing method, are an independent prognostic factor in microsatellite stable stage II CRC.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Marilena Melas
- Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Asaf Maoz
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Stephanie L. Schmit
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Hedy Rennert
- Carmel Medical Center, and Technion, Haifa, Israel
| | | | - Joel K. Greenson
- University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Xavier Sanjuan
- University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Maria Lopez-Zambrano
- University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M. Henar Alonso
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Chenxu Qu
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Kevin J. McDonnell
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Gregory E. Idos
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Marissa Vignali
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Ryan Emerson
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Paul Fields
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Elisabet Guinó
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Cristina Santos
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Ramon Salazar
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, Washington, United States of America
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Gad Rennert
- Carmel Medical Center, and Technion, Haifa, Israel
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Stephen B. Gruber
- City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- * E-mail: (VM); (SBG); (GR); (HSR)
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19
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Melas M, Subbiah S, Saadat S, Rajurkar S, McDonnell KJ. The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations. J Clin Med 2020; 9:E2125. [PMID: 32640668 PMCID: PMC7408957 DOI: 10.3390/jcm9072125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. The active engagement of community oncology practices with academic partners helps with meeting these challenges; community/academic alliances result in improved cancer patient care and provider efficacy. Here, we review the community oncology and academic medical center alliance. We examine how practitioners may leverage academic center precision medicine-based cancer genetics and genomics programs to advance their patients' needs. We highlight a number of project initiatives at the City of Hope Comprehensive Cancer Center that seek to optimize community oncology and academic cancer center precision medicine interactions.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Glendora, CA 91741, USA;
| | - Siamak Saadat
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Colton, CA 92324, USA;
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Upland, CA 91786, USA;
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
- Center for Precision Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
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Melas M, Mathew M, Jayaraman V, Martin C, Mori M, Jacobson-Kelly AE, Cottrell C, Lee K. 35. Mosaicism as incidental finding in the pediatric next generation sequencing era. Cancer Genet 2020. [DOI: 10.1016/j.cancergen.2020.04.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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McDonnell K, Kulkarni A, Woodhouse M, Smith SA, Hong C, Melas M, Heller K, Lazaris C, Sturgeon D, Ricker C, Solomon I, Culver J, Lowstuter K, Morales Pichardo J, Jones V, Idos G, Bonner JD, Gruber SB. Advancing precision medicine in clinical oncology: Whole exome paired tumor-normal DNA and RNA sequencing at a single-institution cancer center. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14006 Background: Next generation sequencing (NGS) allows for reliable, comprehensive and cost-effective identification of clinically actionable genetic and genomic alterations. The increasing adoption of NGS in clinical oncology has increased our ability to identify germline alterations predisposing to cancer development as well as somatic changes enabling prescription of individualized cancer treatment and enhanced clinical trial participation. Here we summarize implementation of an NGS-based precision medicine initiative involving oncology patients from a single institution cancer center. Methods: IRB-approved NGS matched whole exome (WES) germline and solid tumor somatic tumor sequencing together with somatic tumor RNA sequencing (RNA-seq) were performed using germline DNA extracted from peripheral blood lymphocytes and nucleic acids for tumor DNA and RNA sequencing obtained from formalin-fixed, paraffin-embedded tumor specimens. Results of sequencing and analyses were presented to a multi-disciplinary tumor board to establish recommendations for management of germline pathogenic variation, therapeutic drug matching, clinical trials eligibility and molecularly informed patient prognosis. Results: A total of 1,005 patients completed sequencing. Germline and somatic WES exceeded 100X and 250X mean target coverage, respectively; somatic RNA-seq exceeded 200 million mean reads. Patients ranged in age from 17 to 90 years. The study cohort comprised comparable numbers of female (51%) and male (49%) patients. Ethnicities and races were broadly represented with 22% of participants identifying as Hispanic, 14% as Asian, 4% as Black, 55% as Non-Hispanic White and 5% as other. The most common solid tumor histological classification was colorectal (18%), followed by breast (16%), prostate (7%), head and neck (7%), sarcoma (7%), ovarian (5%), melanoma (4%) and lung (3%). Bioinformatic analyses and precision medicine tumor board review established that 12% of patients harbored a germline pathogenic variant and 43% carried clinically actionable genetic/genomic alterations; a majority of patients met molecular requirements for participation in a clinical trial. Conclusions: This study confirms the feasibility and utility of clinical NGS and precision medicine tumor board review in clinical oncology to identify germline genetic pathology, deliver personalized cancer therapeutics, increase clinical trial enrollment and clarify diagnosis and prognosis.
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Affiliation(s)
| | | | | | | | | | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | | | | | | | | | | | - Julie Culver
- USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | - Gregory Idos
- City of Hope National Medical Center, Duarte, CA
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Gruber SB, Bonner JD, Lejbkowicz F, Schmit S, Rennert H, Greenson JK, Pinchev M, Melas M, Moreno V, Tomsho LP, Capella G, Braun D, Smith SA, McDonnell K, Idos G, Rennert G. Cancer risk and overall survival in APC I1307K carriers. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.1592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1592 Background: The germline variant APC I1307K is one of the most commonly identified pathogenic variants on germline genetic testing panels. The purpose of the Molecular Epidemiology of Colorectal Cancer study was to quantify the risk of colorectal cancer among carriers, characterize the clinical, pathologic, and molecular features of colorectal cancers arising in patients with APC I1307K, and to describe the overall and disease-specific survival of carriers with colorectal cancer. Here, the final results of the Molecular Epidemiology of Colorectal Cancer Study are reported with respect to APC I1307K. Methods: We consented 6,006 incident, pathologically confirmed cases of colorectal adenocarcinoma and 5,023 age, sex, and ethnicity matched controls without colorectal cancer between March 31, 1998 and July 1, 2017 within a geographically defined area of Northern Israel. Comprehensive, in-person epidemiologic interviews were conducted for cases and controls, with uniform histopathologic review, detailed molecular analysis, medical record review and clinical follow-up for up to 21 years. Results: The demographic and clinical features of incident colorectal cancer cases matched the population distribution of colorectal cancer in Israel. APC I1307K was identified in 429 (7.1%) of cases and 201 (4.0%) of controls. The estimated relative risk of colorectal cancer among carriers was 1.89 (95% confidence interval, 1.59 - 2.24), p < 0.0001. The prevalence and odds ratios differed by ethnic group. Homozygous carriers were at especially high risk, with an odds ratio of 3.90 (95% confidence interval 1.11–13.71). APC I1307K carriers were significantly less likely to have microsatellite instable tumors (p = 0.04). Overall survival of APC I1307K carriers was not significantly different than survival of non-carriers, after adjustment for age, stage, sex, ethnicity, and microsatellite instability. Conclusions: APC I1307K is an actionable germline mutation that confers meaningful lifetime risk of colorectal cancer in heterozygous and homozygous carriers. APC I1307K is not an independent prognostic factor for overall survival or disease specific survival and is not associated with the MSI phenotype. Cumulative lifetime risk estimates inform genetic counseling and provide data for policies regarding the timing and frequency of screening and other preventive strategies.
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Affiliation(s)
| | | | | | | | | | | | - Mila Pinchev
- CHS National Israeli Cancer Control Center, Haifa, Israel
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Victor Moreno
- IDIBELL, Catalan Institute of Oncology, Barcelona, Spain
| | | | - Gabriel Capella
- Programa de Càncer Hereditari–Institut Català d’Oncologia, Barcelona, Spain
| | | | | | | | - Gregory Idos
- City of Hope National Medical Center, Duarte, CA
| | - Gad Rennert
- CHS National Israeli Cancer Control Center, Haifa, Israel
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Melas M, Lazaris C, Schmit SL, Maoz A, Pamplona RS, Qu C, Greenson JK, Kuick R, Lejbkowicz F, Rennert HS, Walker CP, Bowen CM, Silva DMD, Kast WM, Idos GE, McDonnell KJ, Moreno V, Rennert G, Gruber SB. Abstract 2332: Tumor infiltrating lymphocytes, immunoSeq, and CMS classification in the molecular epidemiology of colorectal cancer study. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Background: Tumor infiltrating lymphocytes (TILs) are prognostic and predictive biomarkers in colorectal cancer and are associated with improved prognosis and response to immunotherapy. While TILs are routinely assessed by pathologists, a standardized technique (immunoSEQ, Adaptive Biotechnologies) that leverages targeted next-generation sequencing can also be used to quantify and characterize the T-cell receptor (TCR) repertoire of individual colorectal cancers. In a large, population-based study of incident colorectal cancer, the host immune responses were measured by an expert pathologist and ImmunoSEQ to understand the relationships between TILs, TCRs/cell and specific subgroups of colorectal cancer. Methods: Incident cases of adenocarcinoma of the colon or rectum from the Molecular Epidemiology of Colorectal Cancer (MECC) study included 1,000 cancers that were uniformly evaluated for TILs and other histopathologic features by one pathologist. FFPE-derived DNA from microdissected tumor tissue was extracted and sequenced using ImmunoSEQ analysis for the same 1,000 individuals. A resulting quantitative metric from this assay includes TCRs/cell, a measure of rearranged T cell quantity relative to all nucleated cells in a tumor sample. Gene expression in snap-frozen tissue available from 342/1,000 MECC colorectal cancers was measured with Affymetrix Human Genome U133 Arrays (U133A and U133 Plus2.0) as previously described. CMS classification was performed using the R package 3.5.1, CMS classifier, randomForest 4.6-14. Multivariate analysis assessed CMS by age, gender, TILs/HPF, TCRs/cell, MSI status, BRAF and KRAS mutational status. Results: TILs/HPF and TCRs/cell were significantly correlated among all 1000 cases (r=0.5, p<0.001). Among the 342 cases with available expression profiles, CMS1 constituted 12.0% of all CRC, with CMS2 (41.8%), CMS3 (8.5%), and CMS4 (13.7%) and unclassified (24%) representing the remaining distribution. There were statistically significant differences in the molecular and histopathologic features of colorectal cancers by CMS subgroups. MSI-H tumors were most frequently observed within CMS1 cancers (56.6% of CMS1 were MSI-H), with lower representation among CMS2 (1.5%), CMS3 (10%), CMS4 (3.5%), and unclassified CRC (9.5%) (p<0.0001). In addition, BRAF positive tumors were more frequently observed within the CMS1 group (12.2%, p =0.0065) and KRAS positive tumors within the CMS3 group (31%, p<0.0001). Consistent with prior reports, TILs/HPF were significantly higher in the CMS1 group (mean=7.7, p<0.0001). Similar statistically significant trends were observed across classes for TCRs/cell (mean=0.16, p=0.04). Conclusions: Subtypes of CRC have distinct histopathologic and molecular features that can be distinguished by expression profiles and immunoSEQ.
Citation Format: Marilena Melas, Charalampos Lazaris, Stephanie L. Schmit, Asaf Maoz, Rebeca Sanz Pamplona, Chenxu Qu, Joel K. Greenson, Rork Kuick, Flavio Lejbkowicz, Hedy S. Rennert, Christopher P. Walker, Chase M. Bowen, Diane M. Da Silva, W. Martin Kast, Gregory E. Idos, Kevin J. McDonnell, Victor Moreno, Gad Rennert, Stephen B. Gruber. Tumor infiltrating lymphocytes, immunoSeq, and CMS classification in the molecular epidemiology of colorectal cancer study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2332.
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Affiliation(s)
- Marilena Melas
- 1USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | - Asaf Maoz
- 3Boston University School of Medicine, Boston, MA
| | | | - Chenxu Qu
- 1USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | | | | | - Chase M. Bowen
- 1USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - W. Martin Kast
- 1USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | - Gad Rennert
- 6Carmel Medical Center and Technion, Haifa, Israel
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24
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Bien SA, Su YR, Conti DV, Harrison TA, Qu C, Guo X, Lu Y, Albanes D, Auer PL, Banbury BL, Berndt SI, Bézieau S, Brenner H, Buchanan DD, Caan BJ, Campbell PT, Carlson CS, Chan AT, Chang-Claude J, Chen S, Connolly CM, Easton DF, Feskens EJM, Gallinger S, Giles GG, Gunter MJ, Hampe J, Huyghe JR, Hoffmeister M, Hudson TJ, Jacobs EJ, Jenkins MA, Kampman E, Kang HM, Kühn T, Küry S, Lejbkowicz F, Le Marchand L, Milne RL, Li L, Li CI, Lindblom A, Lindor NM, Martín V, McNeil CE, Melas M, Moreno V, Newcomb PA, Offit K, Pharaoh PDP, Potter JD, Qu C, Riboli E, Rennert G, Sala N, Schafmayer C, Scacheri PC, Schmit SL, Severi G, Slattery ML, Smith JD, Trichopoulou A, Tumino R, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abeçasis GR, Casey G, Nickerson DA, Gruber SB, Hsu L, Zheng W, Peters U. Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer. Hum Genet 2019; 138:789-791. [PMID: 31254090 DOI: 10.1007/s00439-019-02030-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Every author has erroneously been assigned to the affiliation "62". The affiliation 62 belongs to the author Graham Casey.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - David V Conti
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Tabitha A Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Xingyi Guo
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Yingchang Lu
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53205, USA
| | - Barbara L Banbury
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Stéphane Bézieau
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France.,Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia.,Colorectal Oncogenomics Group, Department of Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, 94612, USA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Genetic Tumour Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, 20246, Hamburg, Germany
| | - Sai Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Charles M Connolly
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care School of Clinical Medicine, University of Cambridge, Cambridge, England, 01223, UK
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, 1X5, Canada
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia.,Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
| | - Marc J Gunter
- Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, 01307, Dresden, Germany
| | - Jeroen R Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,AbbVie Inc, 1500 Seaport Blvd, Redwood City, CA, 94063, USA
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
| | - Flavio Lejbkowicz
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel.,Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
| | - Loic Le Marchand
- University of Hawai'i Cancer Center, Honolulu, Hawaii, 96813, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia.,Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
| | - Li Li
- Department of Family Medicine and Community Health, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital Solna, 171 77, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, 171 77, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
| | - Vicente Martín
- Research Group on Gene-Environment Interactions and Health, (GIIGAS). Institute of Biomedicine (IBIOMED), University of León, León, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain.,Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08028, Barcelona, Spain.,University of Barcelona, 08007, Barcelona, Spain
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Paul D P Pharaoh
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB2 1TN, UK
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel.,Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, 24118, Kiel, Germany
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA.,Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Joshua D Smith
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, 13 Kaisareias & Alexandroupoleos, 115 27, Athens, Greece.,WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 115 27, Athens, Greece
| | - Rosario Tumino
- Affiliation Cancer Registry, Department of Prevention, Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy
| | - Cornelia M Ulrich
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | | | | | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet Solna, 17177, Stockholm, Sweden.,Department of Surgical Sciences, Uppsala University, 75121, Uppsala, Sweden
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, Saint John's, NL, A1B 3V6, Canada
| | - Anna H Wu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Goncalo R Abeçasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Graham Casey
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Deborah A Nickerson
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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25
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Bien SA, Su YR, Conti DV, Harrison TA, Qu C, Guo X, Lu Y, Albanes D, Auer PL, Banbury BL, Berndt SI, Bézieau S, Brenner H, Buchanan DD, Caan BJ, Campbell PT, Carlson CS, Chan AT, Chang-Claude J, Chen S, Connolly CM, Easton DF, Feskens EJM, Gallinger S, Giles GG, Gunter MJ, Hampe J, Huyghe JR, Hoffmeister M, Hudson TJ, Jacobs EJ, Jenkins MA, Kampman E, Kang HM, Kühn T, Küry S, Lejbkowicz F, Le Marchand L, Milne RL, Li L, Li CI, Lindblom A, Lindor NM, Martín V, McNeil CE, Melas M, Moreno V, Newcomb PA, Offit K, Pharaoh PDP, Potter JD, Qu C, Riboli E, Rennert G, Sala N, Schafmayer C, Scacheri PC, Schmit SL, Severi G, Slattery ML, Smith JD, Trichopoulou A, Tumino R, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Casey G, Nickerson DA, Gruber SB, Hsu L, Zheng W, Peters U. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer. Hum Genet 2019; 138:307-326. [PMID: 30820706 PMCID: PMC6483948 DOI: 10.1007/s00439-019-01989-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10- 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10- 4, replication P = 6.7 × 10- 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David V Conti
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tabitha A Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Xingyi Guo
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Yingchang Lu
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53205, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Barbara L Banbury
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stéphane Bézieau
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Colorectal Oncogenomics Group, Department of Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, 94612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Genetic Tumour Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, 20246, Hamburg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sai Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Charles M Connolly
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care School of Clinical Medicine, University of Cambridge, Cambridge, England, 01223, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, 1X5, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marc J Gunter
- Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, 01307, Dresden, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeroen R Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- AbbVie Inc, 1500 Seaport Blvd, Redwood City, CA, 94063, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sébastien Küry
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Flavio Lejbkowicz
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Loic Le Marchand
- University of Hawai'i Cancer Center, Honolulu, Hawaii, 96813, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Li
- Department of Family Medicine and Community Health, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital Solna, 171 77, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, 171 77, Stockholm, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Vicente Martín
- Biomedicine Institute (IBIOMED), University of León, León, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08028, Barcelona, Spain
- University of Barcelona, 08007, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul D P Pharaoh
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB2 1TN, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, 24118, Kiel, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Joshua D Smith
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, 13 Kaisareias & Alexandroupoleos, 115 27, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 115 27, Athens, Greece
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Rosario Tumino
- Affiliation Cancer Registry, Department of Prevention, Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Cornelia M Ulrich
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Fränzel J B van Duijnhoven
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bethany Van Guelpen
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet Solna, 17177, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, 75121, Uppsala, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, Saint John's, NL, A1B 3V6, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Anna H Wu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham Casey
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Deborah A Nickerson
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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Schmit SL, Edlund CK, Schumacher FR, Gong J, Harrison TA, Huyghe JR, Qu C, Melas M, Van Den Berg DJ, Wang H, Tring S, Plummer SJ, Albanes D, Alonso MH, Amos CI, Anton K, Aragaki AK, Arndt V, Barry EL, Berndt SI, Bezieau S, Bien S, Bloomer A, Boehm J, Boutron-Ruault MC, Brenner H, Brezina S, Buchanan DD, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castelao JE, Chan AT, Chang-Claude J, Chanock SJ, Cheng I, Cheng YW, Chin LS, Church JM, Church T, Coetzee GA, Cotterchio M, Cruz Correa M, Curtis KR, Duggan D, Easton DF, English D, Feskens EJM, Fischer R, FitzGerald LM, Fortini BK, Fritsche LG, Fuchs CS, Gago-Dominguez M, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Giovannucci EL, Gogarten SM, Gonzalez-Villalpando C, Gonzalez-Villalpando EM, Grady WM, Greenson JK, Gsur A, Gunter M, Haiman CA, Hampe J, Harlid S, Harju JF, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Huang SC, Huerta JM, Hudson TJ, Hunter DJ, Idos GE, Iwasaki M, Jackson RD, Jacobs EJ, Jee SH, Jenkins MA, Jia WH, Jiao S, Joshi AD, Kolonel LN, Kono S, Kooperberg C, Krogh V, Kuehn T, Küry S, LaCroix A, Laurie CA, Lejbkowicz F, Lemire M, Lenz HJ, Levine D, Li CI, Li L, Lieb W, Lin Y, Lindor NM, Liu YR, Loupakis F, Lu Y, Luh F, Ma J, Mancao C, Manion FJ, Markowitz SD, Martin V, Matsuda K, Matsuo K, McDonnell KJ, McNeil CE, Milne R, Molina AJ, Mukherjee B, Murphy N, Newcomb PA, Offit K, Omichessan H, Palli D, Cotoré JPP, Pérez-Mayoral J, Pharoah PD, Potter JD, Qu C, Raskin L, Rennert G, Rennert HS, Riggs BM, Schafmayer C, Schoen RE, Sellers TA, Seminara D, Severi G, Shi W, Shibata D, Shu XO, Siegel EM, Slattery ML, Southey M, Stadler ZK, Stern MC, Stintzing S, Taverna D, Thibodeau SN, Thomas DC, Trichopoulou A, Tsugane S, Ulrich CM, van Duijnhoven FJB, van Guelpan B, Vijai J, Virtamo J, Weinstein SJ, White E, Win AK, Wolk A, Woods M, Wu AH, Wu K, Xiang YB, Yen Y, Zanke BW, Zeng YX, Zhang B, Zubair N, Kweon SS, Figueiredo JC, Zheng W, Marchand LL, Lindblom A, Moreno V, Peters U, Casey G, Hsu L, Conti DV, Gruber SB. Novel Common Genetic Susceptibility Loci for Colorectal Cancer. J Natl Cancer Inst 2019; 111:146-157. [PMID: 29917119 PMCID: PMC6555904 DOI: 10.1093/jnci/djy099] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [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: 12/27/2017] [Revised: 03/09/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. METHODS We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. RESULTS The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. CONCLUSIONS This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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Affiliation(s)
- Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | | | | | | | | | - Chenxu Qu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Public Health Sciences Division
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | - Hansong Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Stephanie Tring
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- National Cancer Center, Tokyo, Japan
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Sarah J Plummer
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - M Henar Alonso
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Barcelona, Barcelona, Spain
| | | | | | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research
| | - Elizabeth L Barry
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Stephanie Bien
- Centre Hospitalier Universitaire Hotel-Dieu, Nantes, France
| | - Amanda Bloomer
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Marie-Christine Boutron-Ruault
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research
- German Cancer Consortium
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefanie Brezina
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), Nantes, France
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Colorectal Oncogenomics Group, Department of Pathology (DDB) and Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | | | - Jose E Castelao
- Genetic Oncology Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Complejo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo (Pontevedra) Spain
| | - Andrew T Chan
- Division of Gastroenterology
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology
- Harvard Medical School, Boston, MA
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA
| | - Ya-Wen Cheng
- Ph.D. Program of Cancer Research and Drug Discovery
| | - Lee Soo Chin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - James M Church
- Department of Colorectal Surgery, Cleveland Clinic, Cleveland, OH
| | - Timothy Church
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN
| | | | | | | | | | - David Duggan
- Genetic Basis of Human Disease Division, Translational Genomics Research Institute, Phoenix, AZ
| | | | - Dallas English
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, the Netherlands
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Liesel M FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Sør-Trøndelag, Norway
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brookline, MA
- Department of Medicine, Brigham and Women’s Institute, Brookline, MA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | | | - Steven J Gallinger
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edward L Giovannucci
- Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Institute, Brookline, MA
| | | | - Clicerio Gonzalez-Villalpando
- Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Cuernavaca, Morelos, Mexico
| | | | - William M Grady
- Department of Medicine, Division of Gastroenterology, School of Medicine
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Andrea Gsur
- Medical University of Vienna, Department of Medicine I, Institute of Cancer Research, Vienna, Austria
| | - Marc Gunter
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | | | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - John F Harju
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY
| | - Philipp Hofer
- Medical University of Vienna, Department of Medicine I, Institute of Cancer Research, Vienna, Austria
| | | | - John L Hopper
- Centre for MEGA Epidemiology, The University of Melbourne, Carlton, Victoria, Australia
| | - Shu-Chen Huang
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Jose Maria Huerta
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
| | - Thomas J Hudson
- AbbVie, Redwood City, CA
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences
| | | | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yatsen University, Guangzhou, China
| | | | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI
| | - Suminori Kono
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), Nantes, France
| | | | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Sébastien Küry
- Department of Preventive Medicine, Kyushu University, Fukuoka, Japan
| | | | | | - Flavio Lejbkowicz
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- School of Medicine, Taipei Medical University, Taipei, Taiwan
- Sino-American Cancer Foundation, Temple City, CA
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Heinz-Josef Lenz
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Department of Medicine, University of Southern California, Los Angeles, CA
| | | | - Christopher I Li
- Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Li Li
- Department of Family Medicine and Community Health, Mary Ann Swetland Center for Environmental Health, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ
- Unit of Oncology, Department of Clinical and Experimental Oncology, Instituto Oncologico Veneto, IRCCS Padua, Italy
| | | | | | - Yingchang Lu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Frank Luh
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
| | - Jing Ma
- Harvard School of Public Health, Boston, MA
| | | | - Frank J Manion
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH
| | - Vicente Martin
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Japan
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Chikusa-Ku Nagoya, Japan
| | - Kevin J McDonnell
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Caroline E McNeil
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Roger Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Antonio J Molina
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Research Group on Gene-Environment Interactions and Health, University of León, León, Spain
| | | | - Neil Murphy
- Nutrition and Metabolism Section, IARC, Lyon, CEDEX 08, France
| | | | - Kenneth Offit
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hanane Omichessan
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Jesus P Paredes Cotoré
- Department of Surgery, Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Galego de Saúde (SERGAS), Santiago De Compostela, Spain
| | | | - Paul D Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Conghui Qu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Public Health Sciences Division
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
- Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Bridget M Riggs
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Daniela Seminara
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gianluca Severi
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Human Genetics Foundation (HuGeF), Torino, Italy
| | - Wei Shi
- Department of Surgery, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Erin M Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Melissa Southey
- Colorectal Oncogenomics Group, Department of Pathology (DDB) and Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Zsofia K Stadler
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical Center, New York, NY
| | - Mariana C Stern
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Sebastian Stintzing
- Department of Hematology and Oncology University of Munich (LMU), Munich, Germany
| | | | | | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | - Shoichiro Tsugane
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- National Cancer Center, Tokyo, Japan
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | | | | | - Joseph Vijai
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Michael Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Kana Wu
- Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Yun Yen
- Ph.D. Program of Cancer Research and Drug Discovery
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, Duarte, CA
| | - Brent W Zanke
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- The University of Ottawa, Ottawa, Ontario, Canada
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yatsen University, Guangzhou, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology and Southwest Hospital Clinical Research Center, Third Military Medical University, Chongqing, China
| | | | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
- South Korea Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Victor Moreno
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Barcelona, Barcelona, Spain
| | - Ulrike Peters
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Li Hsu
- Public Health Sciences Division
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Department of Medicine, University of Southern California, Los Angeles, CA
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Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, Conti DV, Qu C, Jeon J, Edlund CK, Greenside P, Wainberg M, Schumacher FR, Smith JD, Levine DM, Nelson SC, Sinnott-Armstrong NA, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Bamia C, Banbury BL, Baron JA, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Chirlaque MD, Cho SH, Connolly CM, Cross AJ, Cuk K, Curtis KR, de la Chapelle A, Doheny KF, Duggan D, Easton DF, Elias SG, Elliott F, English DR, Feskens EJM, Figueiredo JC, Fischer R, FitzGerald LM, Forman D, Gala M, Gallinger S, Gauderman WJ, Giles GG, Gillanders E, Gong J, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hampel H, Harlid S, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Hunter DJ, Ibañez-Sanz G, Idos GE, Ingersoll R, Jackson RD, Jacobs EJ, Jenkins MA, Joshi AD, Joshu CE, Keku TO, Key TJ, Kim HR, Kobayashi E, Kolonel LN, Kooperberg C, Kühn T, Küry S, Kweon SS, Larsson SC, Laurie CA, Le Marchand L, Leal SM, Lee SC, Lejbkowicz F, Lemire M, Li CI, Li L, Lieb W, Lin Y, Lindblom A, Lindor NM, Ling H, Louie TL, Männistö S, Markowitz SD, Martín V, Masala G, McNeil CE, Melas M, Milne RL, Moreno L, Murphy N, Myte R, Naccarati A, Newcomb PA, Offit K, Ogino S, Onland-Moret NC, Pardini B, Parfrey PS, Pearlman R, Perduca V, Pharoah PDP, Pinchev M, Platz EA, Prentice RL, Pugh E, Raskin L, Rennert G, Rennert HS, Riboli E, Rodríguez-Barranco M, Romm J, Sakoda LC, Schafmayer C, Schoen RE, Seminara D, Shah M, Shelford T, Shin MH, Shulman K, Sieri S, Slattery ML, Southey MC, Stadler ZK, Stegmaier C, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Thomas SS, Toland AE, Trichopoulou A, Ulrich CM, Van Den Berg DJ, van Duijnhoven FJB, Van Guelpen B, van Kranen H, Vijai J, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Win AK, Wolf CR, Wolk A, Woods MO, Wu AH, Zaidi SH, Zanke BW, Zhang Q, Zheng W, Scacheri PC, Potter JD, Bassik MC, Kundaje A, Casey G, Moreno V, Abecasis GR, Nickerson DA, Gruber SB, Hsu L, Peters U. Discovery of common and rare genetic risk variants for colorectal cancer. Nat Genet 2019; 51:76-87. [PMID: 30510241 PMCID: PMC6358437 DOI: 10.1038/s41588-018-0286-6] [Citation(s) in RCA: 293] [Impact Index Per Article: 58.6] [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: 05/11/2018] [Accepted: 10/22/2018] [Indexed: 12/17/2022]
Abstract
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jihyoun Jeon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peyton Greenside
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Michael Wainberg
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, 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, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Bamia
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, CA, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Sergi Castellví-Bel
- Gastroenterology Department, 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, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria-Dolores Chirlaque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - Charles M Connolly
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Faye Elliott
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
| | - Liesel M FitzGerald
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - David Forman
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John S Grove
- University of Hawaii Cancer Research Center, Honolulu, HI, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Philipp Hofer
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Gemma Ibañez-Sanz
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roxann Ingersoll
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca D Jackson
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Emiko Kobayashi
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Li Li
- Center for Community Health Integration and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Hua Ling
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Vicente Martín
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute of Cancer Research, Prevention and Clinical Network - ISPRO, Florence, Italy
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, 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, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robin Myte
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Patrick S Parfrey
- The Clinical Epidemiology Unit, Memorial University Medical School, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- CESP (Inserm U1018), Facultés de Medicine Université Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Miguel Rodríguez-Barranco
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain
| | - Jane Romm
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Tameka Shelford
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
| | | | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sushma S Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - David J Van Den Berg
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Henk van Kranen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aung Ko Win
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - C Roland Wolf
- School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Brent W Zanke
- Division of Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Qing Zhang
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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Pierce CM, Hong BY, Hoehn HJ, Gomez MF, Melas M, McDonnell K, Kim Y, Sodergren E, Weinstock G, Rennert HS, Giordano T, Greenson J, Rennert G, Gruber SB, Schmit SL. Abstract 4746: Microbes in the tumor microenvironment: Bacterial influences on host immunity in colorectal cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
Abstract
Mounting evidence suggests that a prominent T cell response in the colorectal cancer (CRC) tumor microenvironment is a valuable prognostic indicator, independent of stage at diagnosis. However, the strength and quality of host immune responses are highly variable across patients, and the factors that influence this variability are not well understood. The unique microbial communities present in the CRC tumor microenvironment may contribute to the modulation of local host immune responses, but prior investigations have been limited and focused on candidate microbes. Here, we investigated the association between the CRC tumor bacterial microbiome and the quantity and clonality of the T cell infiltrate. This investigation included 51 CRC from the Molecular Epidemiology of Colorectal Cancer (MECC) study, a population-based case-control study in northern Israel. Genomic DNA was extracted from fresh frozen tumors using microbiome-optimized techniques and sequenced using a PCR amplicon-mediated workflow on the Illumina MiSeq. Sequences from the V1-V3 hypervariable regions of the bacterial 16S rRNA gene region were clustered into operational taxonomic units (OTUs), a proxy for species, and taxonomic identification was determined using the Ribosomal Database Project. In addition, T cell repertoires were measured using the DNA-based immunoSEQ assay (Adaptive Biotechnologies), and T cell fraction (i.e. proportion of rearranged T cells relative to all nucleated cells) and clonality (i.e. T cell receptor diversity) were calculated. Bacterial sequencing was successful in 48 (94%) of samples, with a total of 868 OTUs identified. Klebsiella and Escherichia/Shigella were the most prevalent genera, detected in approximately 90% of tumors, followed by Propionibacterium, Pelomonas, and Veillonella, with each detected in approximately 50% of tumors. Fusobacterium, a genus of oral anaerobic bacteria believed to accelerate tumor progression and enable immune evasion in CRC, was detected in 20% of tumors. When present, Bacteroides and Fusobacterium were the most abundant, comprising 10-15% of all bacteria within each tumor, on average. ImmunoSEQ analysis identified a mean productive T cell fraction of 0.08 (SD: 0.16) and a mean productive clonality of 0.14 (SD: 0.06). Analysis of molecular variance (AMOVA) of the Theta YC measure of dissimilarity showed a statistically significant difference in bacterial community structure (i.e. composition and relative abundance) between samples in the highest versus lower three quartiles of T cell fraction (P=0.03) and clonality (P=0.01). These preliminary findings suggest a potential relationship between microbial community structure and the quantity and diversity of the CRC T cell infiltrate. Additional analyses are underway to better understand this association as well as the independent contributions of the microbiome to CRC prognosis.
Citation Format: Christine M. Pierce, Bo-young Hong, Hannah J. Hoehn, Maria F. Gomez, Marilena Melas, Kevin McDonnell, Youngchul Kim, Erica Sodergren, George Weinstock, Hedy S. Rennert, Thomas Giordano, Joel Greenson, Gad Rennert, Stephen B. Gruber, Stephanie L. Schmit. Microbes in the tumor microenvironment: Bacterial influences on host immunity in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4746.
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Affiliation(s)
| | - Bo-young Hong
- 2The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | | | - Marilena Melas
- 3University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Kevin McDonnell
- 3University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Erica Sodergren
- 2The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Hedy S. Rennert
- 4Clalit National Israeli Cancer Control Center, Haifa, Israel
| | | | - Joel Greenson
- 5University of Michigan School of Medicine, Ann Arbor, MI
| | - Gad Rennert
- 4Clalit National Israeli Cancer Control Center, Haifa, Israel
| | - Stephen B. Gruber
- 3University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
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Gruber SB, Schmit S, Melas M, Qu C, Heinemann V, Stintzing S, Falcone A, Loupakis F, Mancao C, Cao S, Cremolini C, Conti DV, Zhang W, Lenz HJ. Genetic variation in TET3 and survival in metastatic colorectal cancer (mCRC) from FIRE-3, TRIBE, and MAVERICC clinical trials. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Marilena Melas
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | - Alfredo Falcone
- Department of Translational Research and New Technologies in Medicine and Surgery, Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Istituto Toscano Tumori, Pisa, Italy
| | | | | | - Shu Cao
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA
| | | | - David V Conti
- USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Wu Zhang
- USC Keck School of Medicine, Los Angeles, CA
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Irabor DO, Melas M, Gruber SB, Shi C, Raskin L. Abstract A17: Molecular and clinicopathological features of native Nigerian colorectal cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.newfront17-a17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Colorectal cancer (CRC) needs no introduction in Africa; once a rare cancer type, it is now the 3rd or 4th most common cancer. However, there are significant differences in the incidence rates, tumor biology, and clinical behavior in comparison to other populations. While the total incidence rates are about one-tenth of those in the developed world, Nigerian CRC occurs at a younger age and rapidly metastasizes. Molecular pathology and genetics of African CRC have not been comprehensively studied. In addition to better understanding of the biology of African CRC, analysis of genetic and molecular biomarkers, including microsatellite instability (MSI), is aimed at improving CRC diagnosis, treatment, and prognosis in Africa. We obtained 83 CRC paraffin-embedded blocks from the University of Ibadan and private pathology laboratories in Ibadan collected in the period from 2007 to 2014. Median age of the cases was 56±14.6 years with equal number of males and females. More than 60% of the patients had stage III and IV CRC. The majority were adenocarcinomas (76%) with a relatively high prevalence of mucinous adenocarcinoma (10%) and signet ring carcinoma (4%). Of all patients, 66% had rectal cancer. Poorly differentiated tumors were observed in 34% of all cases. We found a high prevalence of MSI CRC (43%, 15/35) in the tested Nigerian samples. There were no significant differences in clinicopathological features, including tumor location, between MSI and microsatellite stable (MSS) CRC. Our results are in line with our previous report that found a high prevalence (41%) of MSI CRC in Ghanaian patients. These findings raise important questions about the role of genetic and environmental factors in CRC development in West Africa.
Citation Format: David O. Irabor, Marilena Melas, Stephen B. Gruber, Chanjuan Shi, Leon Raskin. Molecular and clinicopathological features of native Nigerian colorectal cancer [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr A17.
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Lowstuter K, Espenschied CR, Sturgeon D, Ricker C, Karam R, LaDuca H, Culver JO, Dolinsky JS, Chao E, Sturgeon J, Speare V, Ma Y, Kingham K, Melas M, Idos GE, McDonnell KJ, Gruber SB. Unexpected CDH1 Mutations Identified on Multigene Panels Pose Clinical Management Challenges. JCO Precis Oncol 2017; 1:1-12. [DOI: 10.1200/po.16.00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Mutations in the CDH1 gene confer up to an 80% lifetime risk of diffuse gastric cancer and up to a 60% lifetime risk of lobular breast cancer. Testing for CDH1 mutations is recommended for individuals who meet the International Gastric Cancer Linkage Consortium (IGCLC) guidelines. However, the interpretation of unexpected CDH1 mutations identified in patients who do not meet IGCLC criteria or do not have phenotypes suggestive of hereditary diffuse gastric cancer is clinically challenging. This study aims to describe phenotypes of CDH1 mutation carriers identified through multigene panel testing (MGPT) and to offer informed recommendations for medical management. Patients and Methods This cross-sectional prevalence study included all patients who underwent MGPT between March 2012 and September 2014 from a commercial laboratory (n = 26,936) and an academic medical center cancer genetics clinic (n = 318) to estimate CDH1 mutation prevalence and associated clinical phenotypes. CDH1 mutation carriers were classified as IGCLC positive (met criteria), IGCLC partial phenotype, and IGCLC negative. Results In the laboratory cohort, 16 (0.06%) of 26,936 patients were identified as having a pathogenic CDH1 mutation. In the clinic cohort, four (1.26%) of 318 had a pathogenic CDH1 mutation. Overall, 65% of mutation carriers did not meet the revised testing criteria published in 2015. All three CDH1 mutation carriers who had risk-reducing gastrectomy had pathologic evidence of diffuse gastric cancer despite not having met IGCLC criteria. Conclusion The majority of CDH1 mutations identified on MGPT are unexpected and found in individuals who do not fit the accepted diagnostic testing criteria. These test results alter the medical management of CDH1-positive patients and families and provide opportunities for early detection and risk reduction.
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Affiliation(s)
- Katrina Lowstuter
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Carin R. Espenschied
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Duveen Sturgeon
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Charité Ricker
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Rachid Karam
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Holly LaDuca
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Julie O. Culver
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Jill S. Dolinsky
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Elizabeth Chao
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Julia Sturgeon
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Virginia Speare
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Yanling Ma
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Kerry Kingham
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Marilena Melas
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Gregory E. Idos
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Kevin J. McDonnell
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Stephen B. Gruber
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
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Irabor DO, Oluwasola OA, Ogunbiyi OJ, Ogun OG, Okolo CA, Melas M, Gruber SB, Shi C, Raskin L. Microsatellite Instability Is Common in Colorectal Cancer in Native Nigerians. Anticancer Res 2017; 37:2649-2654. [PMID: 28476840 DOI: 10.21873/anticanres.11612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 03/14/2017] [Revised: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is the fifth most common cancer in Africa, with significant differences in incidence, biology and clinical behavior from other populations. MATERIALS AND METHODS We studied prevalence and clinicopathological features of microsatellite instability (MSI) and young onset CRC in 83 archival samples from the University of Ibadan, Nigeria. RESULTS Nigerian cases of CRC were MSI-high in 43% and MSI-high CRC had significantly lower histological heterogeneity than microsatellite-stable CRC (20% vs. 55% respectively, p=0.046). Presence of signet ring cell differentiation (10-50% of tumor) was significantly higher in younger patients with CRC (<50 years) (odds ratio(OR)=5.93, 95% confidence interval(CI)=1.17-29.95, p=0.038). Poor differentiation (34%), invasive growth (96%), and high prevalence of mucinous (10%) and signet ring cell adenocarcinomas (4%) were among distinct features of Nigerian patients with CRC. CONCLUSION MSI-high CRC is more common in West Africa and more detailed molecular and genetic analysis is warranted as CRC incidence and mortality continue to increase in the Sub-Saharan Africa.
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Affiliation(s)
- David O Irabor
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Olufemi J Ogunbiyi
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olabiyi G Ogun
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clement A Okolo
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, U.S.A
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, U.S.A.,Department of Preventive Medicine, University of Southern California, Los Angeles, CA, U.S.A
| | - Chanjuan Shi
- Department of Pathology, Microbiology and Immunology, School of Medicine, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, U.S.A
| | - Leon Raskin
- Division of Epidemiology, School of Medicine, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, U.S.A.
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Melas M, McDonnell KJ, Edlund CK, Tash SJ, Sturgeon DY, Qu C, Lazaris C, Gruber PJ, Glover TW, Emanuel BS, Gruber SB. Abstract 491: Elucidating de novo PATRR-mediated t(3;8) balanced translocation and clear cell renal cell carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Palindromic AT-Rich Repeat (PATRR) - mediated translocations entail exchange across chromosomes at sites enriched in palindromic repeats of the nucleotides adenine (A) and thymine (T). Their precise embryologic origin and associated pathobiology with clear cell renal cell carcinoma (ccRCC) remain incompletely described. In the present study we document an individual with familial non-VHL ccRCC (7 primary renal tumors) who harbors a germline de novo PATRR mediated balanced translocation involving chromosomes 3 and 8 [t(3;8)] validated by spectral karyotyping (SKY).
Using translocation specific PCR and DNA sequencing we determined the chromosome 3 breakpoint to be located in an AT-rich palindromic sequence in the third intron of the FHIT gene (chr3p14.2) and the chromosome 8 breakpoint in the first intron of the TRC8 gene (chr8q24.1). Genotyping analysis, using a high density custom exomechip array by Illumina, revealed a loss of the entire aberrant chromosome 8 carrying the 3p segment [der(8)] in all renal tumors tested. We also determined that the [46, XY, t(3;8), (p14.2, q24.1)] translocation was paternally derived by performing a genotypic assessment of the regions that differ between the parental alleles and then establishing which haplotypes are associated with the translocation. The somatic mutational landscape was assessed by Whole Exome sequencing of the renal tumors and the proband’s germline DNA. No germline or somatic deleterious mutations were detected in VHL gene suggesting that the ccRCC phenotype is not associated with Von Hippel-Lindau disease.
Furthermore, we measured the transcriptomic profiles of the renal tumors and matched normal tissues employing barcoded probe hybridization technology (NanoString) and RNASeq to fully characterize differential gene expression and define gene ontology networks that are dysregulated. Most significantly, no difference in expression of the VHL gene was detected between tumors and normal counterparts. Aberrant regulation was detected in members of WNT signaling pathway, TGF-beta and MAPK pathways, in addition to NOTCH signaling pathway genes and members of the VEGF family. In summary, in this study we employed advanced genomic and transcriptomic techniques, to delineate the embryologic origin and deleterious biological consequences of the PATRR-mediated t(3;8) balanced translocation associated with clear cell renal cell carcinoma.
Citation Format: Marilena Melas, Kevin J. McDonnell, Christopher K. Edlund, Sarah J. Tash, Duveen Y. Sturgeon, Chenxu Qu, Charalampos Lazaris, Peter J. Gruber, Thomas W. Glover, Beverly S. Emanuel, Stephen B. Gruber. Elucidating de novo PATRR-mediated t(3;8) balanced translocation and clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 491. doi:10.1158/1538-7445.AM2017-491
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Affiliation(s)
- Marilena Melas
- 1USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Kevin J. McDonnell
- 1USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Christopher K. Edlund
- 1USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Sarah J. Tash
- 2Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Duveen Y. Sturgeon
- 1USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Chenxu Qu
- 1USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Charalampos Lazaris
- 3Laura & Isaac Perlmutter Cancer Center and Helen L. & Martin S. Kimmel Center for Stem Cell Biology School of Medicine, New York, NY
| | - Peter J. Gruber
- 4Division of Cardiothoracic Surgery, Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Thomas W. Glover
- 5Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
| | - Beverly S. Emanuel
- 2Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Stephen B. Gruber
- 1USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
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Maoz A, Greenson JK, Melas M, Emerson RO, Vignali M, Robins H, Qu C, Schmit S, Pinchev M, McDonnell KJ, Rennert G, Gruber SB. Similar T-cell repertoires of tumor infiltrating lymphocytes and Crohn’s-like lymphoid reaction in colorectal cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e15133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15133 Background: Tumor infiltrating lymphocytes (TILs) and Crohn’s-like Lymphoid Reaction (CLR) are independently associated with improved survival in colorectal cancer (CRC). Whereas TILs are localized within tumors, CLR are extra-tumoral lymphocytic aggregates. The origins and relationships of the T-cell repertoire of TILs and the T cells within CLR of the colorectal cancer tumor microenvironment are unknown. Methods: Expert pathology review identified and circled areas of invasive adenocarcinoma and areas containing CLR from 13 CRC patients for macrodissection from formalin fixed paraffin embedded (FFPE) slides. DNA was extracted from matched tumor and CLR areas for multiplex PCR sequencing of the CDR3 region of the T-cell receptor beta chain (TCRβ), using the immunoSEQ platform. This approach permits 1) estimating the T-cell content of each sample, 2) measuring the clonality of the T-cell repertoire as a measure of diversity, and 3) quantifying the overlap and similarity of T-cell repertoires across samples. Results: The T-cell content (Spearman’s rs = 0.56, p = 0.046) and clonality (Spearman’s rs = 0.66, p = 0.014) were highly correlated among matched tumor and CLR samples. The ten most frequently identified TIL clones were found at similar frequencies in matched CLR enriched tissues. Comparisons of all the clones detected in tumor and matched CLR tissue demonstrated substantial similarity of these immune repertoires, with an average of 186 shared clones between samples. This degree of similarity was significantly greater than published reports of the similarity of the T-cell repertoire of colorectal tumors and adjacent normal tissue (p = 1.1e-5). Conclusions: The T-cell repertoire of CLR is highly similar to the tumor infiltrating T-cell repertoire, providing supporting evidence for the hypothesis that tumor-specific antigen presentation and lymphocyte maturation occur within CLR.
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Affiliation(s)
- Asaf Maoz
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Marilena Melas
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | - Chenxu Qu
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Mila Pinchev
- CHS National Israeli Cancer Control Center, Haifa, Israel
| | - Kevin J McDonnell
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Gad Rennert
- CHS National Israeli Cancer Control Center, Haifa, Israel
| | - Stephen B. Gruber
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
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Sunga AY, Ricker C, Espenschied CR, Castillo D, Melas M, Herzog J, Bannon S, Cruz-Correa M, Lynch P, Solomon I, Gruber SB, Weitzel JN. Spectrum of mismatch repair gene mutations and clinical presentation of Hispanic individuals with Lynch syndrome. Cancer Genet 2017; 212-213:1-7. [PMID: 28449805 PMCID: PMC8800930 DOI: 10.1016/j.cancergen.2017.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 04/19/2016] [Revised: 01/13/2017] [Accepted: 01/15/2017] [Indexed: 12/21/2022]
Abstract
Lynch syndrome (LS), the most common hereditary colorectal cancer syndrome, is caused by mismatch repair (MMR) gene mutations. However, data about MMR mutations in Hispanics are limited. This study aims to describe the spectrum of MMR mutations in Hispanics with LS and explore ancestral origins. This case series involved an IRB-approved retrospective chart review of self-identified Hispanic patients (n = 397) seen for genetic cancer risk assessment at four collaborating academic institutions in California, Texas, and Puerto Rico who were evaluated by MMR genotyping and/or tumor analysis. A literature review was conducted for all mutations identified. Of those who underwent clinical genetic testing (n = 176), 71 had MMR gene mutations. Nine mutations were observed more than once. One third (3/9) of recurrent mutations and two additional mutations (seen only once) were previously reported in Spain, confirming the influence of Spanish ancestry on MMR mutations in Hispanic populations. The recurrent mutations identified (n = 9) included both previously reported mutations as well as unique mutations not in the literature. This is the largest report of Hispanic MMR mutations in North America; however, a larger sample and haplotype analyses are needed to better understand recurrent MMR mutations in Hispanic populations.
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Affiliation(s)
- Annette Y Sunga
- Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Charité Ricker
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Carin R Espenschied
- Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Danielle Castillo
- Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Josef Herzog
- Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Sarah Bannon
- Clinical Cancer Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marcia Cruz-Correa
- Clinical Cancer Genetics, University of Puerto Rico Comprehensive Cancer Center, Rio Piedras 00935, Puerto Rico
| | - Patrick Lynch
- Clinical Cancer Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ilana Solomon
- Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Jeffrey N Weitzel
- Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA.
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Ciccone M, Ricker C, Culver J, Maoz A, Melas M, Idos G, Gruber S, McDonnell K. Inactivation of the Tumor Suppressor BRCA1 Interacting Protein C-terminal Helicase 1 (BRIP1) Gene Confers Increased Susceptibility to Platinum Antineoplastic Agents and Augments the Synergistic Response to Poly (ADP-ribose) Polymerase (PARP) Inhibition in Ovarian Epithelial Cells. Gynecol Oncol 2016. [DOI: 10.1016/j.ygyno.2016.08.246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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McDonnell KJ, Gallanis GT, Heller KA, Melas M, Idos GE, Culver JO, Martin SE, Peng DH, Gruber SB. A novel BAP1 mutation is associated with melanocytic neoplasms and thyroid cancer. Cancer Genet 2015; 209:75-81. [PMID: 26774355 DOI: 10.1016/j.cancergen.2015.12.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/11/2015] [Accepted: 12/12/2015] [Indexed: 12/28/2022]
Abstract
Germline mutations in the tumor suppressor gene, BRCA-1 associated protein (BAP1), underlie a tumor predisposition syndrome characterized by increased risk for numerous cancers including uveal melanoma, melanocytic tumors and mesothelioma, among others. In the present study we report the identification of a novel germline BAP1 mutation, c.1777C>T, which produces a truncated BAP1 protein product and segregates with cancer. Family members with this mutation demonstrated a primary clinical phenotype of autosomal dominant, early-onset melanocytic neoplasms with immunohistochemistry (IHC) of these tumors demonstrating lack of BAP1 protein expression. In addition, family members harboring the BAP1 c.1777C>T germline mutation developed other neoplastic disease including thyroid cancer. IHC analysis of the thyroid cancer, as well, demonstrated loss of BAP1 protein expression. Our investigation identifies a new BAP1 mutation, further highlights the relevance of BAP1 as a clinically important tumor suppressor gene, and broadens the range of cancers associated with BAP1 inactivation. Further study will be required to understand the full scope of BAP1-associated neoplastic disease.
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Affiliation(s)
- Kevin J McDonnell
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Gregory T Gallanis
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kathleen A Heller
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Gregory E Idos
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Julie O Culver
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sue-Ellen Martin
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA; Keck School of Medicine, Department of Pathology, University of Southern California, Los Angeles, CA, USA
| | - David H Peng
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA; Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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Grivas PD, Melas M, Papavassiliou AG. The biological complexity of urothelial carcinoma: Insights into carcinogenesis, targets and biomarkers of response to therapeutic approaches. Semin Cancer Biol 2015; 35:125-32. [DOI: 10.1016/j.semcancer.2015.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/08/2023]
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Melas M, Luu HN, Rennert G, Lejbkowicz F, Gruber SB, Wiesner GL, Raskin L. Abstract 2745: Exome sequencing analysis of 41 patients with Familial Colorectal Cancer Type X (FCCTX). Epidemiology 2015. [DOI: 10.1158/1538-7445.am2015-2745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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