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Thomas CE, Georgeson P, Qu C, Steinfelder RS, Buchanan DD, Song M, Harrison TA, Um CY, Hullar MA, Jenkins MA, Guelpen BV, Lynch BM, Melaku YA, Huyghe JR, Aglago EK, Berndt SI, Boardman LA, Campbell PT, Cao Y, Chan AT, Drew DA, Figueiredo JC, French AJ, Giannakis M, Goode EL, Gruber SB, Gsur A, Gunter MJ, Hoffmeister M, Hsu L, Huang WY, Moreno V, Murphy N, Newcomb PA, Newton CC, Nowak JA, Obón-Santacana M, Ogino S, Sun W, Toland AE, Trinh QM, Ugai T, Zaidi SH, Peters U, Phipps AI. Epidemiologic Factors in Relation to Colorectal Cancer Risk and Survival by Genotoxic Colibactin Mutational Signature. Cancer Epidemiol Biomarkers Prev 2024; 33:534-546. [PMID: 38252034 PMCID: PMC10990777 DOI: 10.1158/1055-9965.epi-23-0600] [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: 05/24/2023] [Revised: 08/31/2023] [Accepted: 01/18/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND The genotoxin colibactin causes a tumor single-base substitution (SBS) mutational signature, SBS88. It is unknown whether epidemiologic factors' association with colorectal cancer risk and survival differs by SBS88. METHODS Within the Genetic Epidemiology of Colorectal Cancer Consortium and Colon Cancer Family Registry, we measured SBS88 in 4,308 microsatellite stable/microsatellite instability low tumors. Associations of epidemiologic factors with colorectal cancer risk by SBS88 were assessed using multinomial regression (N = 4,308 cases, 14,192 controls; cohort-only cases N = 1,911), and with colorectal cancer-specific survival using Cox proportional hazards regression (N = 3,465 cases). RESULTS 392 (9%) tumors were SBS88 positive. Among all cases, the highest quartile of fruit intake was associated with lower risk of SBS88-positive colorectal cancer than SBS88-negative colorectal cancer [odds ratio (OR) = 0.53, 95% confidence interval (CI) 0.37-0.76; OR = 0.75, 95% CI 0.66-0.85, respectively, Pheterogeneity = 0.047]. Among cohort studies, associations of body mass index (BMI), alcohol, and fruit intake with colorectal cancer risk differed by SBS88. BMI ≥30 kg/m2 was associated with worse colorectal cancer-specific survival among those SBS88-positive [hazard ratio (HR) = 3.40, 95% CI 1.47-7.84], but not among those SBS88-negative (HR = 0.97, 95% CI 0.78-1.21, Pheterogeneity = 0.066). CONCLUSIONS Most epidemiologic factors did not differ by SBS88 for colorectal cancer risk or survival. Higher BMI may be associated with worse colorectal cancer-specific survival among those SBS88-positive; however, validation is needed in samples with whole-genome or whole-exome sequencing available. IMPACT This study highlights the importance of identification of tumor phenotypes related to colorectal cancer and understanding potential heterogeneity for risk and survival.
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Affiliation(s)
- Claire E Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Australia
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Robert S Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Australia
- Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Caroline Y Um
- Department of Population Science, American Cancer Society, Atlanta, Georgia
| | - Meredith A Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Brigid M Lynch
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Yohannes Adama Melaku
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- FHMRI Sleep, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Elom K Aglago
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa A Boardman
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, Missouri, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew T Chan
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - David A Drew
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amy J French
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen B Gruber
- Department of Medical Oncology & Therapeutics Research and Center for Precision Medicine, City of Hope National Medical Center, Duarte CA, USA
| | - Andrea Gsur
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Victor Moreno
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat,08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Christina C Newton
- Department of Population Science, American Cancer Society, Atlanta, Georgia
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat,08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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Georgeson P, Steinfelder RS, Harrison TA, Pope BJ, Zaidi SH, Qu C, Lin Y, Joo JE, Mahmood K, Clendenning M, Walker R, Aglago EK, Berndt SI, Brenner H, Campbell PT, Cao Y, Chan AT, Chang-Claude J, Dimou N, Doheny KF, Drew DA, Figueiredo JC, French AJ, Gallinger S, Giannakis M, Giles GG, Goode EL, Gruber SB, Gsur A, Gunter MJ, Harlid S, Hoffmeister M, Hsu L, Huang WY, Huyghe JR, Manson JE, Moreno V, Murphy N, Nassir R, Newton CC, Nowak JA, Obón-Santacana M, Ogino S, Pai RK, Papadimitrou N, Potter JD, Schoen RE, Song M, Sun W, Toland AE, Trinh QM, Tsilidis K, Ugai T, Um CY, Macrae FA, Rosty C, Hudson TJ, Winship IM, Phipps AI, Jenkins MA, Peters U, Buchanan DD. Genotoxic colibactin mutational signature in colorectal cancer is associated with clinicopathological features, specific genomic alterations and better survival. medRxiv 2024:2023.03.10.23287127. [PMID: 37090539 PMCID: PMC10120801 DOI: 10.1101/2023.03.10.23287127] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Background and Aims The microbiome has long been suspected of a role in colorectal cancer (CRC) tumorigenesis. The mutational signature SBS88 mechanistically links CRC development with the strain of Escherichia coli harboring the pks island that produces the genotoxin colibactin, but the genomic, pathological and survival characteristics associated with SBS88-positive tumors are unknown. Methods SBS88-positive CRCs were identified from targeted sequencing data from 5,292 CRCs from 17 studies and tested for their association with clinico-pathological features, oncogenic pathways, genomic characteristics and survival. Results In total, 7.5% (398/5,292) of the CRCs were SBS88-positive, of which 98.7% (392/398) were microsatellite stable/microsatellite instability low (MSS/MSI-L), compared with 80% (3916/4894) of SBS88 negative tumors (p=1.5x10-28). Analysis of MSS/MSI-L CRCs demonstrated that SBS88 positive CRCs were associated with the distal colon (OR=1.84, 95% CI=1.40-2.42, p=1x10-5) and rectum (OR=1.90, 95% CI=1.44-2.51, p=6x10-6) tumor sites compared with the proximal colon. The top seven recurrent somatic mutations associated with SBS88-positive CRCs demonstrated mutational contexts associated with colibactin-induced DNA damage, the strongest of which was the APC:c.835-8A>G mutation (OR=65.5, 95%CI=39.0-110.0, p=3x10-80). Large copy number alterations (CNAs) including CNA loss on 14q and gains on 13q, 16q and 20p were significantly enriched in SBS88-positive CRCs. SBS88-positive CRCs were associated with better CRC-specific survival (p=0.007; hazard ratio of 0.69, 95% CI=0.52-0.90) when stratified by age, sex, study, and by stage. Conclusion SBS88-positivity, a biomarker of colibactin-induced DNA damage, can identify a novel subtype of CRC characterized by recurrent somatic mutations, copy number alterations and better survival. These findings provide new insights for treatment and prevention strategies for this subtype of CRC.
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Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
| | - Robert S. Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Syed H. Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
| | - Elom K Aglago
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - 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
| | - Peter T. Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, Missouri, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Niki Dimou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Kimberly F. Doheny
- Center for Inherited Disease Research (CIDR), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David A. Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - 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, California, USA
| | - Amy J. French
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Ellen L Goode
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Stephen B Gruber
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte CA, USA
| | - Andrea Gsur
- Center for Cancer Research, Medical University Vienna, Vienna, Austria
| | - Marc J. Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - JoAnn E. Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Victor Moreno
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rami Nassir
- Department of Pathology, College of Medicine, Umm Al-Qura University, Saudi Arabia
| | | | - Jonathan A. Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, Massachusetts, USA
| | - Rish K. Pai
- Department of Pathology and Laboratory Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Nikos Papadimitrou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Robert E. Schoen
- Departments of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Mingyang Song
- Departments of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Amanda E. Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Quang M. Trinh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kostas Tsilidis
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caroline Y Um
- Department of Population Science, American Cancer Society, Atlanta, Georgia, USA
| | - Finlay A. Macrae
- Parkville Familial Cancer Centre, and Dept of Colorectal Medicine and Genetics The Royal Melbourne Hospital
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
- Envoi Specialist Pathologists, Brisbane, Australia
- University of Queensland, Brisbane, Australia
| | | | - Ingrid M. Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Amanda I. Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010 Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3010 Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia
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3
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Murphy N, Newton CC, Song M, Papadimitriou N, Hoffmeister M, Phipps AI, Harrison TA, Newcomb PA, Aglago EK, Berndt SI, Brenner H, Buchanan DD, Cao Y, Chan AT, Chen X, Cheng I, Chang-Claude J, Dimou N, Drew D, Farris AB, French AJ, Gallinger S, Georgeson P, Giannakis M, Giles GG, Gruber SB, Harlid S, Hsu L, Huang WY, Jenkins MA, Laskar RS, Le Marchand L, Limburg P, Lin Y, Mandic M, Nowak JA, Obón-Santacana M, Ogino S, Qu C, Sakoda LC, Schoen RE, Southey MC, Stadler ZK, Steinfelder RS, Sun W, Thibodeau SN, Toland AE, Trinh QM, Tsilidis KK, Ugai T, Van Guelpen B, Wang X, Woods MO, Zaidi SH, Gunter MJ, Peters U, Campbell PT. Body mass index and molecular subtypes of colorectal cancer. J Natl Cancer Inst 2023; 115:165-173. [PMID: 36445035 PMCID: PMC9905970 DOI: 10.1093/jnci/djac215] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/23/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Obesity is an established risk factor for colorectal cancer (CRC), but the evidence for the association is inconsistent across molecular subtypes of the disease. METHODS We pooled data on body mass index (BMI), tumor microsatellite instability status, CpG island methylator phenotype status, BRAF and KRAS mutations, and Jass classification types for 11 872 CRC cases and 11 013 controls from 11 observational studies. We used multinomial logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for covariables. RESULTS Higher BMI was associated with increased CRC risk (OR per 5 kg/m2 = 1.18, 95% CI = 1.15 to 1.22). The positive association was stronger for men than women but similar across tumor subtypes defined by individual molecular markers. In analyses by Jass type, higher BMI was associated with elevated CRC risk for types 1-4 cases but not for type 5 CRC cases (considered familial-like/Lynch syndrome microsatellite instability-H, CpG island methylator phenotype-low or negative, BRAF-wild type, KRAS-wild type, OR = 1.04, 95% CI = 0.90 to 1.20). This pattern of associations for BMI and Jass types was consistent by sex and design of contributing studies (cohort or case-control). CONCLUSIONS In contrast to previous reports with fewer study participants, we found limited evidence of heterogeneity for the association between BMI and CRC risk according to molecular subtype, suggesting that obesity influences nearly all major pathways involved in colorectal carcinogenesis. The null association observed for the Jass type 5 suggests that BMI is not a risk factor for the development of CRC for individuals with Lynch syndrome.
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Affiliation(s)
- Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Christina C Newton
- Population Science Department, American Cancer Society (ACS), Atlanta, GA, USA
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- 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
| | - Nikos Papadimitriou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elom K Aglago
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Alvin J. Siteman Cancer Center, St Louis, MO, USA
| | - Andrew T Chan
- 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
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Niki Dimou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - David Drew
- 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
| | - Alton B Farris
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Amy J French
- Division of Laboratory Genetics, Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Stephen B Gruber
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- 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
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Ruhina S Laskar
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Epidemiology Program, Honolulu, HI, USA
| | | | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marko Mandic
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johnathan A Nowak
- Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mereia Obón-Santacana
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Melissa C Southey
- Department of Clinical Pathology, The 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
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert S Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer 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
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Xiaoliang Wang
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
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4
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Hamed AA, Kunz DJ, El-Hamamy I, Trinh QM, Subedar OD, Richards LM, Foltz W, Bullivant G, Ware M, Vladoiu MC, Zhang J, Raj AM, Pugh TJ, Taylor MD, Teichmann SA, Stein LD, Simons BD, Dirks PB. A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours. Nat Commun 2022; 13:4178. [PMID: 35853870 PMCID: PMC9296666 DOI: 10.1038/s41467-022-31408-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 10/26/2021] [Accepted: 06/16/2022] [Indexed: 01/01/2023] Open
Abstract
Human cerebral cancers are known to contain cell types resembling the varying stages of neural development. However, the basis of this association remains unclear. Here, we map the development of mouse cerebrum across the developmental time-course, from embryonic day 12.5 to postnatal day 365, performing single-cell transcriptomics on >100,000 cells. By comparing this reference atlas to single-cell data from >100 glial tumours of the adult and paediatric human cerebrum, we find that tumour cells have an expression signature that overlaps with temporally restricted, embryonic radial glial precursors (RGPs) and their immediate sublineages. Further, we demonstrate that prenatal transformation of RGPs in a genetic mouse model gives rise to adult cerebral tumours that show an embryonic/juvenile RGP identity. Together, these findings implicate the acquisition of embryonic-like states in the genesis of adult glioma, providing insight into the origins of human glioma, and identifying specific developmental cell types for therapeutic targeting.
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Affiliation(s)
- Akram A Hamed
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daniel J Kunz
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK.,Cavendish Laboratory, Department of Physics, JJ Thomson Avenue, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ibrahim El-Hamamy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Omar D Subedar
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Laura M Richards
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Warren Foltz
- STTARR Innovation Centre, Department of Radiation Oncology, University Health Network, Toronto, ON, Canada
| | - Garrett Bullivant
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthaeus Ware
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Maria C Vladoiu
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jiao Zhang
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Antony M Raj
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Neurosurgery, University of Toronto, Toronto, ON, Canada.,Department of Surgery and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sarah A Teichmann
- Cavendish Laboratory, Department of Physics, JJ Thomson Avenue, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Ontario Institute for Cancer Research, Toronto, ON, Canada.
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, JJ Thomson Avenue, Cambridge, UK. .,Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, UK. .,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Peter B Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada. .,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada. .,Division of Neurosurgery, University of Toronto, Toronto, ON, Canada.
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5
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Barfield R, Qu C, Steinfelder RS, Zeng C, Harrison TA, Brezina S, Buchanan DD, Campbell PT, Casey G, Gallinger S, Giannakis M, Gruber SB, Gsur A, Hsu L, Huyghe JR, Moreno V, Newcomb PA, Ogino S, Phipps AI, Slattery ML, Thibodeau SN, Trinh QM, Toland AE, Hudson TJ, Sun W, Zaidi SH, Peters U. Association between germline variants and somatic mutations in colorectal cancer. Sci Rep 2022; 12:10207. [PMID: 35715570 PMCID: PMC9205954 DOI: 10.1038/s41598-022-14408-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 06/07/2022] [Indexed: 01/11/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with evidence of distinct tumor types that develop through different somatically altered pathways. To better understand the impact of the host genome on somatically mutated genes and pathways, we assessed associations of germline variations with somatic events via two complementary approaches. We first analyzed the association between individual germline genetic variants and the presence of non-silent somatic mutations in genes in 1375 CRC cases with genome-wide SNPs data and a tumor sequencing panel targeting 205 genes. In the second analysis, we tested if germline variants located within previously identified regions of somatic allelic imbalance were associated with overall CRC risk using summary statistics from a recent large scale GWAS (n≃125 k CRC cases and controls). The first analysis revealed that a variant (rs78963230) located within a CNA region associated with TLR3 was also associated with a non-silent mutation within gene FBXW7. In the secondary analysis, the variant rs2302274 located in CDX1/PDGFRB frequently gained/lost in colorectal tumors was associated with overall CRC risk (OR = 0.96, p = 7.50e-7). In summary, we demonstrate that an integrative analysis of somatic and germline variation can lead to new insights about CRC.
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Affiliation(s)
- Richard Barfield
- grid.26009.3d0000 0004 1936 7961Department of Biostatistics and Bioinformatics, Duke University, 11028A Hock Plaza, 2424 Erwin Road Suite 1106, Durham, NC 27705 USA
| | - Conghui Qu
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Robert S. Steinfelder
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Chenjie Zeng
- grid.280128.10000 0001 2233 9230National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Tabitha A. Harrison
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Stefanie Brezina
- grid.22937.3d0000 0000 9259 8492Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Daniel D. Buchanan
- grid.1008.90000 0001 2179 088XColorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1008.90000 0001 2179 088XUniversity of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010 Australia ,grid.416153.40000 0004 0624 1200Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, VIC Australia
| | - Peter T. Campbell
- grid.251993.50000000121791997Department of Epidemiology and Population Science, Albert Einstein College of Medicine, Bronx, NY USA
| | - Graham Casey
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Steven Gallinger
- grid.250674.20000 0004 0626 6184Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
| | - Marios Giannakis
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA ,grid.66859.340000 0004 0546 1623The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stephen B. Gruber
- grid.42505.360000 0001 2156 6853Department of Medical Oncology and Therapeuytic, University of Southern California, Los Angeles, CA USA
| | - Andrea Gsur
- grid.22937.3d0000 0000 9259 8492Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Li Hsu
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Jeroen R. Huyghe
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Victor Moreno
- grid.418701.b0000 0001 2097 8389Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain ,grid.466571.70000 0004 1756 6246CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain ,grid.5841.80000 0004 1937 0247Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain ,grid.418284.30000 0004 0427 2257ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Polly A. Newcomb
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657School of Public Health, University of Washington, Seattle, WA USA
| | - Shuji Ogino
- grid.66859.340000 0004 0546 1623The Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XProgram in MPE Molecular Pathological Epidemiology, 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 ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Amanda I. Phipps
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,Department of Epidemiology, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave N, Mail Stop M4-B402, Seattle, WA 98109 USA
| | - Martha L. Slattery
- grid.223827.e0000 0001 2193 0096Department of Internal Medicine, University of Utah, Salt Lake City, UT USA
| | - Stephen N. Thibodeau
- grid.66875.3a0000 0004 0459 167XDivision of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Quang M. Trinh
- grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Amanda E. Toland
- grid.261331.40000 0001 2285 7943Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH USA
| | - Thomas J. Hudson
- grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Wei Sun
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA USA ,grid.410711.20000 0001 1034 1720Department of Biostatistics, University of North Carolina, Chapel Hill, NC USA
| | - Syed H. Zaidi
- grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Ulrike Peters
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,Department of Epidemiology, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave N, Mail Stop M4-B402, Seattle, WA 98109 USA
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6
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Georgeson P, Harrison TA, Pope BJ, Zaidi SH, Qu C, Steinfelder RS, Lin Y, Joo JE, Mahmood K, Clendenning M, Walker R, Amitay EL, Berndt SI, Brenner H, Campbell PT, Cao Y, Chan AT, Chang-Claude J, Doheny KF, Drew DA, Figueiredo JC, French AJ, Gallinger S, Giannakis M, Giles GG, Gsur A, Gunter MJ, Hoffmeister M, Hsu L, Huang WY, Limburg P, Manson JE, Moreno V, Nassir R, Nowak JA, Obón-Santacana M, Ogino S, Phipps AI, Potter JD, Schoen RE, Sun W, Toland AE, Trinh QM, Ugai T, Macrae FA, Rosty C, Hudson TJ, Jenkins MA, Thibodeau SN, Winship IM, Peters U, Buchanan DD. Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures. Nat Commun 2022; 13:3254. [PMID: 35668106 PMCID: PMC9170691 DOI: 10.1038/s41467-022-30916-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023] Open
Abstract
Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.
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Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert S Steinfelder
- 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
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Efrat L Amitay
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - 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
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew T 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 MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 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
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Drew
- 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
| | - 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
| | - Amy J French
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- 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
| | - Paul Limburg
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rami Nassir
- Department of Pathology, College of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, 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
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wei Sun
- 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
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Finlay A Macrae
- Parkville Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, Australia
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | | | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia.
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia.
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7
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Wright AJ, Orlic-Milacic M, Rothfels K, Weiser J, Trinh QM, Jassal B, Haw RA, Stein LD. Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. Database (Oxford) 2022; 2022:6555052. [PMID: 35348650 PMCID: PMC9216552 DOI: 10.1093/database/baac009] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 02/15/2022] [Indexed: 11/14/2022]
Abstract
Abstract Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturbations, we compared predictions of perturbation effects based on Reactome pathways against published empirical observations. Ten cancer-relevant Reactome pathways, representing diverse biological processes such as signal transduction, cell division, DNA repair and transcriptional regulation, were selected for testing. For each pathway, root input nodes and key pathway outputs were defined. We then used pathway-diagram-derived logic graphs to predict, either by inspection by biocurators or using a novel algorithm MP-BioPath, the effects of bidirectional perturbations (upregulation/activation or downregulation/inhibition) of single root inputs on the status of key outputs. These predictions were then compared to published empirical tests. In total, 4968 test cases were analyzed across 10 pathways, of which 847 were supported by published empirical findings. Out of the 847 test cases, curators’ predictions agreed with the experimental evidence in 670 and disagreed in 177 cases, resulting in ∼81% overall accuracy. MP-BioPath predictions agreed with experimental evidence for 625 and disagreed for 222 test cases, resulting in ∼75% overall accuracy. The expected accuracy of random guessing was 33%. Per-pathway accuracy did not correlate with the number of pathway edges nor the number of pathway nodes but varied across pathways, ranging from 56% (curator)/44% (MP-BioPath) for ‘Mitotic G1 phase and G1/S transition’ to 100% (curator)/94% (MP-BioPath) for ‘RAF/MAP kinase cascade’. This study highlights the potential of pathway databases such as Reactome in modeling genetic perturbations, promoting standardization of experimental pathway activity readout and supporting hypothesis-driven research by revealing relationships between pathway inputs and outputs that have not yet been directly experimentally tested. Database URL www.reactome.org
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Affiliation(s)
- Adam J Wright
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Marija Orlic-Milacic
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Karen Rothfels
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Joel Weiser
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Quang M Trinh
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Bijay Jassal
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Robin A Haw
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Lincoln D Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, Room 4396, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A1, Canada
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8
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Borozan I, Zaidi SH, Harrison TA, Phipps AI, Zheng J, Lee S, Trinh QM, Steinfelder RS, Adams J, Banbury BL, Berndt SI, Brezina S, Buchanan DD, Bullman S, Cao Y, Farris AB, Figueiredo JC, Giannakis M, Heisler LE, Hopper JL, Lin Y, Luo X, Nishihara R, Mardis ER, Papadopoulos N, Qu C, Reid EEG, Thibodeau SN, Harlid S, Um CY, Hsu L, Gsur A, Campbell PT, Gallinger S, Newcomb PA, Ogino S, Sun W, Hudson TJ, Ferretti V, Peters U. Molecular and Pathology Features of Colorectal Tumors and Patient Outcomes Are Associated with Fusobacterium nucleatum and Its Subspecies animalis. Cancer Epidemiol Biomarkers Prev 2022; 31:210-220. [PMID: 34737207 PMCID: PMC8755593 DOI: 10.1158/1055-9965.epi-21-0463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/11/2021] [Revised: 06/27/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Fusobacterium nucleatum (F. nucleatum) activates oncogenic signaling pathways and induces inflammation to promote colorectal carcinogenesis. METHODS We characterized F. nucleatum and its subspecies in colorectal tumors and examined associations with tumor characteristics and colorectal cancer-specific survival. We conducted deep sequencing of nusA, nusG, and bacterial 16s rRNA genes in tumors from 1,994 patients with colorectal cancer and assessed associations between F. nucleatum presence and clinical characteristics, colorectal cancer-specific mortality, and somatic mutations. RESULTS F. nucleatum, which was present in 10.3% of tumors, was detected in a higher proportion of right-sided and advanced-stage tumors, particularly subspecies animalis. Presence of F. nucleatum was associated with higher colorectal cancer-specific mortality (HR, 1.97; P = 0.0004). This association was restricted to nonhypermutated, microsatellite-stable tumors (HR, 2.13; P = 0.0002) and those who received chemotherapy [HR, 1.92; confidence interval (CI), 1.07-3.45; P = 0.029). Only F. nucleatum subspecies animalis, the main subspecies detected (65.8%), was associated with colorectal cancer-specific mortality (HR, 2.16; P = 0.0016), subspecies vincentii and nucleatum were not (HR, 1.07; P = 0.86). Additional adjustment for tumor stage suggests that the effect of F. nucleatum on mortality is partly driven by a stage shift. Presence of F. nucleatum was associated with microsatellite instable tumors, tumors with POLE exonuclease domain mutations, and ERBB3 mutations, and suggestively associated with TP53 mutations. CONCLUSIONS F. nucleatum, and particularly subspecies animalis, was associated with a higher colorectal cancer-specific mortality and specific somatic mutated genes. IMPACT Our findings identify the F. nucleatum subspecies animalis as negatively impacting colorectal cancer mortality, which may occur through a stage shift and its effect on chemoresistance.
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Affiliation(s)
- Ivan Borozan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Jiayin Zheng
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Stephen Lee
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert S Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Jeremy Adams
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Familial Cancer Clinic, Genetic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine in St. Louis, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St Louis, Missouri
| | - Alton B Farris
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - John L Hopper
- The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Xuemei Luo
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Reiko Nishihara
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Emma E G Reid
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sophia Harlid
- Oncology, Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Caroline Y Um
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, University of Toronto, Toronto, Ontario, Canada
- General Surgery, Surgery and Critical Care Program, University Health Network Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
- Cancer Immunology Program, Dana-Farber/Harvard Cancer Center, Boston, Massachusetts
- Cancer Epidemiology Program, Dana-Farber/Harvard Cancer Center, Boston, Massachusetts
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vincent Ferretti
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, Washington.
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
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9
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Harrison TA, Zaidi SH, Qu C, Phipps AI, Steinfelder RS, Trinh QM, Berndt SI, Buchanan DD, Campbell PT, Chan AT, Doheny KF, Drew DA, Figueiredo JC, Gallinger SJ, Giannakis M, Gsur A, Gunter MJ, Hoffmeister M, Huang WY, Limburg PJ, Moreno V, Newcomb PA, Ogino S, Prentice RL, Shelford T, Sun W, Thibodeau SN, Hsu L, Peters U. Abstract LB090: Associations of somatically mutated genes and pathways with colorectal cancer specific survival in 4,500 colorectal cancer patients. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb090] [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) is a heterogenous disease that develops through somatic mutations in driver genes, leading to activation of diverse neoplastic pathways. To systematically examine if somatically mutated genes and pathways impact survival, we sequenced tumor and normal DNA samples for 4,512 CRC cases using a targeted panel. We performed Cox regression to estimate hazard ratios (HR) and 95% confidence intervals (CIs) for associations of disease-specific (DS)-survival with somatically mutated genes and pathways, adjusting for age and sex, and stratifying baseline hazards by study population. We assessed statistical significance using Bonferroni p-value thresholds to account for multiple testing of 214 genes (2.34x10-4) and 6 key CRC pathways (8.3x10-3). We limited analyses to non-silent mutations.
We observed that DS-survival was significantly more favorable among individuals with hypermutated (HM) tumors, primarily consisting of microsatellite unstable and POLE-mutated tumors, as compared to those with non-hypermutated (NHM) tumors (HR=0.4, 95% CI: 0.3-0.5, p=1.2x10-17). BRAF V600E mutations were associated with poorer survival (HR=2.0, 95% CI: 1.6-2.5, p=1.6x10-10). This association was more pronounced among NHM tumors (HR=2.3, 95% CI: 1.8-2.9, p=4.3x10-12). We identified suggestive associations (p-values < 5.0x10-3 in overall or stratified analyses) between DS-survival and mutations in B2M, TP53, and SMAD4. Mutations in B2M may provide more favorable prognosis for survival (HR=0.5, 95% CI: 0.3-0.8, p=4.4x10-3), with similar effect sizes in HM and NHM tumors. Poorer survival may be associated with mutations in TP53 (HR=1.2, 95% CI:1.2-1.4, p=9.3x10-4) and SMAD4 (HR=1.3, 95% CI:1.1-1.6, p=3.2x10-3) in NHM tumors.
We further observed statistically significant associations between survival and three mutated pathways: TP53/ATM (HR=1.2, 95% CI:1.1-1.4, p=9.0x10-4), receptor tyrosine kinases (RTK) and RAS (HR=1.3, 95% CI:1.1-1.5, p=4.5x10-5), and TGF-beta (HR=1.3, 95% CI:1.1-1.5, p=2.9x10-4). Findings for TP53/ATM and RTK/RAS were primarily due to mutations in one gene within each pathway (TP53 and BRAF, respectively). However, the TGF-beta pathway finding, which was more pronounced in NHM tumors, included two genes with p-values less than 0.05 (SMAD4 p=3.2x10-3 and TGFBR2 p=0.01).
Despite our large sample size, relatively few somatically mutated genes were significantly associated with DS-survival. It may be that pathway-level testing affords more power for analyses and that larger sample sizes are needed. It is of interest that non-silent mutations in B2M, whose product is a component of the class I major histocompatibility complex, was associated with improved DS-survival, though our finding was not statistically significant after multiple testing correction so further exploration and replication is needed.
Citation Format: Tabitha A. Harrison, Syed H. Zaidi, Conghui Qu, Amanda I. Phipps, Robert S. Steinfelder, Quang M. Trinh, Sonja I. Berndt, Daniel D. Buchanan, Peter T. Campbell, Andrew T. Chan, Kim F. Doheny, David A. Drew, Jane C. Figueiredo, Steven J. Gallinger, Marios Giannakis, Andrea Gsur, Marc J. Gunter, Michael Hoffmeister, Wen-Yi Huang, Paul J. Limburg, Victor Moreno, Polly A. Newcomb, Shuji Ogino, Ross L. Prentice, Tameka Shelford, Wei Sun, Stephen N. Thibodeau, Li Hsu, Ulrike Peters. Associations of somatically mutated genes and pathways with colorectal cancer specific survival in 4,500 colorectal cancer patients [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 LB090.
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Affiliation(s)
| | - Syed H. Zaidi
- 2Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Conghui Qu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Quang M. Trinh
- 2Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | - Andrea Gsur
- 12Medical University of Vienna, Vienna, Austria
| | - Marc J. Gunter
- 13International Agency for Research on Cancer, Lyon, France
| | | | | | | | | | | | | | | | | | - Wei Sun
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Li Hsu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ulrike Peters
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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10
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Bayani J, Trinh QM, Quintayo MA, Crozier C, Hopkins M, Qiao J, Cheung A, Mainprize J, Morris Q, Spears M, Yaffe M, Stein L, Bartlett JM. Abstract 3131: Tumour spatial heterogeneity in breast cancer and the impact on clinical management. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-3131] [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
We recognize that many cancers are highly complex mixtures of sub-populations of cells, which are also influenced by their microenvironment. This heterogeneity explains in part, why the majority of current therapeutic approaches for cancer work best when multiple agents are combined. Therefore, in an era of targeted therapeutics it becomes critical to understand the complexity of tumors both at diagnosis and over the course of therapy, including measures of heterogeneity. Here we present genomic, transcriptomic and in situ proteomic profiling of a cohort of breast cancer (BCa) lumpectomies to reveal the extent of heterogeneity in pathologically defined unifocal and multifocal cancers. Integration of molecular profiling, phylogenetic analyses and radiomics has the potential to significantly improve BCa clinical management and stratification to targeted therapies that are already available in the clinic. In this study, lumpectomies with imaging data were processed as whole mounts with serial blocks reviewed. Tissue cores were taken from at least three different regions through the lumpectomy for nucleic acid extraction and tissue microarray (TMA) construction, focusing on morphologic/histological differences in addition to the spatial orientation of the sampled region within the lumpectomy. Targeted sequencing using the Oncomine Comprehensive Assay v3 (OCAv3); transcriptional profiling using the NanoString Breast Cancer 360 Panel; in situ profiling by multiplex fluorescence immunohistochemistry (MxIF) and Digital Spatial Profiling (see abstract Spears et al) were performed. From this cohort of 60 patients, we present a subset of patients demonstrating integration of the molecular profiling to reveal the phylogenetic relationship between the multiple samplings and the impact on clinical decision making in BCa. Briefly, we identified differences in the molecular subtypes between the different sample regions from the same unifocal cancer as well as differences in the predicted responses to anti-PDL1 therapy by transcriptional profiling; while targeted sequencing of driver mutations suggested the likelihood of an ancestral tumor cell giving rise to the lesions in pathologically defined multifocal cancers. However it was evident that genes and pathways found to be aberrant in these different lesions from the same cancer could impact the response to standard BCa treatment, or the selection of targeted therapies. In situ proteomics demonstrated differences in the expression of standard BCa markers ER, PgR, HER2 and Ki67 in addition to immune markers in the tumor and tumor microenvironment. While there are clinically validated transcriptional risk test available for BCa, we have demonstrated that transcriptomics or genomics alone is insufficient for a rational stratification of patients to currently available targeted therapies; therefore supporting the need for an integrative approach.
Citation Format: Jane Bayani, Quang M. Trinh, Mary Anne Quintayo, Cheryl Crozier, Megan Hopkins, Jingping Qiao, Alison Cheung, James Mainprize, Quaid Morris, Melanie Spears, Martin Yaffe, Lincoln Stein, John M. Bartlett. Tumour spatial heterogeneity in breast cancer and the impact on clinical management [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 3131.
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Affiliation(s)
- Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Quang M. Trinh
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Cheryl Crozier
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jingping Qiao
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alison Cheung
- 2Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | | | - Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Martin Yaffe
- 2Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Lincoln Stein
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M. Bartlett
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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11
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Bayani J, Trinh QM, Quintayo MA, Crozier C, Hopkins M, Qiao J, Cheung A, Mainprize JG, Morris Q, Spears M, Yaffe MJ, Stein LD, Bartlett JM. Abstract PO-002: Revealing tumour spatial heterogeneity in breast cancer and the impact on clinical management. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-002] [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
Many cancers are highly complex mixtures of many sub-populations of cells, also influenced by their microenvironment. This heterogeneity explains, in part, why the majority of current therapeutic approaches for cancer work best when multiple agents are combined. Therefore, in an era of targeted therapeutics it becomes critical to understand the complexity of tumours both at diagnosis and over the course of therapy, including measures of heterogeneity. Here we present genomic, transcriptomic and in situ proteomic profiling of a cohort of breast cancer (BCa) lumpectomies with associated imaging data to reveal the extent of heterogeneity in pathologically defined unifocal and multifocal cancers. Integration of molecular profiling, phylogenetic analyses and radiomics has the potential to significantly improve BCa clinical management and stratification to targeted therapies that are already available in the clinic. In this study, lumpectomies were processed as whole mounts with serial blocks reviewed. Tissue cores were taken from at least three different regions throughout the lumpectomy for nucleic acid extraction and tissue microarray (TMA) construction, focusing on morphologic/histological differences in addition to the spatial orientation of the sampled region within the lumpectomy. Targeted sequencing using the Oncomine Comprehensive Assay v3 (OCAv3); transcriptional profiling using the NanoString Breast Cancer 360 Panel; and in situ profiling by multiplex fluorescence immunohistochemistry (MxIF) performed (see abstract Cheung et al). From this cohort of 60 patients, we present a subset of patients demonstrating integration of the molecular profiling to reveal the phylogenetic relationship between the multiple samplings and the potential impact on clinical decision making in BCa. We identified differences in the molecular subtypes between the different sample regions from the same unifocal cancer as well as differences in the predicted responses to anti-PDL1 therapy by transcriptional profiling. Targeted sequencing of driver mutations suggested the likelihood of an ancestral tumour cell giving rise to the lesions in pathologically defined multifocal cancers; however it was evident that genes and pathways found to be aberrant in these different lesions from the same cancer could impact the response to standard BCa treatment, or the selection of targeted therapies. In situ proteomics demonstrated differences in the expression of standard BCa markers ER, PgR, HER2 and Ki67, in addition to immune markers in the tumour and its microenvironment. While there are clinically validated transcriptional risk tests available for BCa, we have demonstrated that transcriptomics or genomics alone is insufficient for a rational stratification of patients to currently available targeted therapies, therefore, supporting the need for an integrative approach.
Citation Format: Jane Bayani, Quang M. Trinh, Mary Anne Quintayo, Cheryl Crozier, Megan Hopkins, Jingping Qiao, Alison Cheung, James G Mainprize, Quaid Morris, Melanie Spears, Martin J. Yaffe, Lincoln D. Stein, John M.S. Bartlett. Revealing tumour spatial heterogeneity in breast cancer and the impact on clinical management [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-002.
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Affiliation(s)
- Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Quang M. Trinh
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | | | - Cheryl Crozier
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Jingping Qiao
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Alison Cheung
- 2Sunnybrook Research Institute, Toronto, ON, Canada,
| | | | - Quaid Morris
- 3Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
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Bayani J, Trinh QM, Quintayo MA, Crozier C, Lungu I, Dion D, Felipe-Lima J, Pruneri G, Bergh J, Warnberg F, Viale G, Stein LD, Bartlett JMS. Abstract P3-08-22: The mutational landscape of cancer driver genes in matched primary ductal carcinoma in situ and recurrent ductal carcinoma in situ or recurrent invasive cancers. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p3-08-22] [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
Due to breast screening, ductal carcinoma in situ (DCIS) accounts for approximately 25% of all newly diagnosed breast neoplasms. Believed to be a precursor to invasive carcinoma, a significant number of patients diagnosed with DCIS are effectively managed by surgery alone or in conjunction with radiotherapy and endocrine therapy. In general, there is an 8-11% relative risk for a subsequent invasive carcinoma over a period of 10 year, with 98% breast cancer-specific survival after 10 years of follow up. Although mastectomy, breast conserving surgery, and radiotherapy can reduce the risk of recurrence, there are ongoing lifetime consequences of treatment. Thus, there is a clinical need to identify those patients who are at risk of an invasive recurrence from those who might not recur or experience a subsequent DCIS recurrence. In this study, 60 patients with pure primary DCIS, treated with only with breast conserving therapy, across three different clinical outcome groups were examined: patients who did not experience a recurrence within 5 years (n=20); patients who experienced a recurrent DCIS within 5 years (n=20); and patients that recurred with an invasive cancer within 5 years (n=20). Pure primary DCIS lesions, as well as the matched DCIS recurrence or invasive recurrence, were macrodissected from formalin fixed paraffin embedded tissues and subjected to nucleic acid extraction. All samples were profiled using Thermo Fisher Scientific’s validated targeted sequencing panel, the Oncomine Comprehensive Assay v3.0 (OCAv3.0). This assay is comprised of common cancer driver genes shown to be prognostic and predictive to targeted therapies in use or in late-phase clinical trials, and is currently being used in the NCI-MATCH trial (NCT02465060). While the OCA panel and accompanying Oncomine Knowledgebase Reporter provides information regarding the targeted treatments linked to known actionable mutations, this study utilized all somatic mutations and copy number changes to reveal the genomic landscape of DCIS and their matched recurrences across these pan-cancer driver genes Amongst all primary DCIS samples across the three different clinical outcome groups, PIK3CA, was frequently found to be affected by SNV and Indels (32.8%) in addition to TP53 (26.2%), NF1 (21.3%), CREBBP (16.4%), ATM (14.8%), PALB2 (14.8%). DNA repair genes, including CHEK1, RAD50, RAD51B, MRE11A, BRCA1 and BRCA2, were found to be frequently subject to mutation in these primary DCIS samples ranging from 5%-15%. Similarly, copy number gains were frequently detected in HER2 (26.2%), CDK12 (18%), FGFR1 (4.9%), GNAS (4.9%), MYC, CCNE1, AR, RAD51C and RNF43 (1.6% each), and loses at H3F3A and KNSTRN (each 1.6%). Matched primary DCIS and their recurrent DCIS or invasive lesions exhibited similar changes with invasive cancers suggesting that in some cases, the primary DCIS gives rise to the invasive cancer. We will present the preliminary findings mapping the mutational and copy-number landscape of primary DCIS and matched recurrences to identify putative genomic changes defining these clinical outcome groups and to investigate the genomic progression of DCIS to invasive carcinoma.
Citation Format: Jane Bayani, Quang M Trinh, Mary Anne Quintayo, Cheryl Crozier, Ilinca Lungu, Dan Dion, Joema Felipe-Lima, Giancarlo Pruneri, Jonas Bergh, Fredrik Warnberg, Giuseppe Viale, Lincoln D Stein, John MS Bartlett. The mutational landscape of cancer driver genes in matched primary ductal carcinoma in situ and recurrent ductal carcinoma in situ or recurrent invasive cancers [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-08-22.
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Affiliation(s)
- Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Quang M Trinh
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Cheryl Crozier
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ilinca Lungu
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dan Dion
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
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Bayani J, Poncet C, Crozier C, Trinh QM, Hopkins M, Uwimana AL, Piper T, Cunningham C, Sobol M, Aebi S, Benstead K, Bogler O, Lago LD, Hilbers F, Hedenfalk I, Korde L, Linderholm B, Martens J, Middleton L, Murray M, Kelly C, Nilsson C, Nowaczyk M, Peeters S, Peric A, Porter P, Schröder C, Rubio IT, Ruddy KJ, van Asperen C, Weyngaert DVD, van Deurzen CHM, van Leeuwen-Stok E, Vermeij J, Winer E, Stein LD, Giordano SH, Cardoso F, Bartlett JMS. Abstract P4-10-03: The genomic landscape of male breast cancers using the oncomine comprehensive assay for actionable mutations. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-10-03] [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
Introduction: Male breast cancer (BCa) is a rare disease accounting for less than 1% of all breast cancers (BC) and 1% of all cancers in males. The clinical management is largely extrapolated from female BCa. Few studies have examined the genomic landscape of male BCas, with six male BCas included in The Cancer Genome Atlas (TCGA). Familial studies of male BCas have shown genomic changes similar to female BCa, while a larger targeted sequencing study of 59 male breast cancers identified recurrent mutations affecting PIK3CA and GATA3. To date, there is still limited information regarding the genomic landscape of male BCas; particularly in the context of identifying targeted treatments. To reveal genomic changes that characterize male BCas in the context of known cancer driver genes linked to prognosis and targeted agents, we performed a targeted sequencing study on 248 male BCas from the International Male Breast Cancer Program. Methods: 248 primary M0, ER+ve, HER2-ve male BCas enrolled in the Part 1 (retrospective joint analysis) International Male Breast Cancer Program of 1483 patients diagnosed between 1990-2010 (Cardoso et al. Annals of Oncology, 2018) were processed for nucleic acid extraction from formalin-fixed paraffin embedded (FFPE) tissues. Using the Thermo Fisher Scientific Oncomine Comprehensive Assay v3 (OCAv3), a validated targeted sequencing panel currently used in the NCI-MATCH trial (NCT02465060), we evaluated mutational and copy number variations (CNVs) of genes that are prognostic or predictive to targeted therapies currently in use in the clinic or late-stage clinical trials. The OCAv3 DNA pan-cancer panel assays 115 genes for determining mutational status (48 full coding and 67 hotspot) as well as copy-number assessment in 43 genes. The OCAv3 uses Ampliseq-based technology linked to the Oncomine NGS workflow to identify actionable mutations and CNVs Results: Of the 248 samples assayed, 216 passed strict quality control parameters (87.1%). Using the Oncomine NGS workflow, actionable mutations at ≥5% variant allele frequency (VAF) were most frequently identified in PIK3CA (29.2%), BRCA2 (11.1%), NF1 (11.6%), indels in TP53 (10.6%), ATR (5.6%), ATRX (5.1%), indel BRCA2 (5.1%), TP53 point mutations (4.6%), MET (4.6%), ATM (4.6%), NOTCH2 (4.6%), CHEK1 (4.2%), FANCI (4.2%), PTEN (3.2%) with a number of additional genes identified at lower frequencies. Gene amplifications were most frequently detected in MYC (24.5%), FGFR1 (14.8%), CCND1 (12%), FGF3 (9.7%), FGF19 (9.7%), MDM2 (6.5%), CDK4 (1.4%), FGFR3, MDM4, ERBB2 (0.9% each), and FLT3, AR, MYCL, CDK6, IGF1R, FGFR4, KRAS, AKT3 and ESR1 (0.5% each). Although the results here describe the mutations and copy-number changes deemed to be actionable, further analysis of all non-actionable somatic mutations and CNVs will be presented and compared to female BCas previously assayed using the same panel. Conclusion: In this targeted sequencing study of the largest series of male BCas to our knowledge, we have revealed that PIK3CA continues to be a frequently altered gene in both male and female BCas. However, there is an enrichment of mutations in genes related to DNA repair in male BCs. Interestingly, while MYC is commonly amplified in female BCa, a higher frequency of amplified cases were seen in male BCas, in contrast to female BCas. Together with our previously generated transcriptional profiling data in this data set, we believe that both common and unique biological processes comprising male and female BCas will ultimately improve their clinical management and move towards the goal of precision medicine.
This work has been funded by the Breast Cancer Research Foundation (BCRF).
Citation Format: Jane Bayani, Coralie Poncet, Cheryl Crozier, Quang M Trinh, Megan Hopkins, Aime Lambert Uwimana, Tammy Piper, Carrie Cunningham, Monika Sobol, Stefan Aebi, Kim Benstead, Oliver Bogler, Lissandra Dal Lago, Florentine Hilbers, Ingrid Hedenfalk, Larissa Korde, Barbro Linderholm, John Martens, Lavinia Middleton, Melissa Murray, Catherine Kelly, Cecilia Nilsson, Monika Nowaczyk, Stephanie Peeters, Aleksandra Peric, Peggy Porter, Carolien Schröder, Isabel T Rubio, Kathryn J Ruddy, Christi van Asperen, Danielle Van Den Weyngaert, Carolien HM van Deurzen, Elise van Leeuwen-Stok, Joanna Vermeij, Eric Winer, Lincoln D Stein, Sharon H Giordano, Fatima Cardoso, John MS Bartlett. The genomic landscape of male breast cancers using the oncomine comprehensive assay for actionable mutations [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-03.
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Affiliation(s)
- Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Coralie Poncet
- 2European Organization for Research and Treatment of Cancer (EORTC) Headquarters, Brussels, Belgium
| | - Cheryl Crozier
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Quang M Trinh
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Aime Lambert Uwimana
- 2European Organization for Research and Treatment of Cancer (EORTC) Headquarters, Brussels, Belgium
| | - Tammy Piper
- 3University of Edinburgh, Edinburgh, United Kingdom
| | | | - Monika Sobol
- 3University of Edinburgh, Edinburgh, United Kingdom
| | - Stefan Aebi
- 4Swiss Group for Clinical Cancer Research (SAKK), Bern, Swaziland
| | - Kim Benstead
- 5Cheltenham General Hospital, Gloucestershire, United Kingdom
| | - Oliver Bogler
- 6University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - John Martens
- 12Erasmus Medical Center Rotterdam, Rotterdam, Netherlands
| | | | | | - Catherine Kelly
- 14All Ireland Cooperative Oncology Research Group (ICORG), Dublin, Ireland
| | | | | | | | - Aleksandra Peric
- 2European Organization for Research and Treatment of Cancer (EORTC) Headquarters, Brussels, Belgium
| | - Peggy Porter
- 18Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Isabel T Rubio
- 20Hospital Universitario Vall d´Hebron, Barcelona, Spain
| | | | | | | | | | | | - Joanna Vermeij
- 25Department of Medical Oncology, ZNA, Jan Palfijn, Belgium
| | - Eric Winer
- 26Dana-Farber Cancer Institute,, Boston, MA
| | | | | | - Fatima Cardoso
- 27Champalimaud Clinical Center/Champalimaud Foundation, Lisbond, Portugal
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Bayani J, Kornaga EN, Crozier C, Jang GH, Bathurst L, Kalatskaya I, Trinh QM, Yao CQ, Livingstone J, Boutros PC, Spears M, McPherson JD, Stein LD, Rea D, Bartlett JM. Identification of Distinct Prognostic Groups: Implications for Patient Selection to Targeted Therapies Among Anti-Endocrine Therapy–Resistant Early Breast Cancers. JCO Precis Oncol 2019; 3:1-13. [DOI: 10.1200/po.18.00373] [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
PURPOSE Hormone receptor–positive breast cancer remains an ongoing therapeutic challenge, despite optimal anti-endocrine therapies. In this study, we assessed the prognostic ability of genomic signatures to identify patients at risk for recurrence after endocrine therapy. Analysis was performed on the basis of an a priori hypothesis related to molecular pathways, which might predict response to existing targeted therapies. PATIENTS AND METHODS A subset of patients from the Tamoxifen Versus Exemestane Adjuvant Multinational trial ( ClinicalTrials.gov identifiers: NCT00279448 and NCT00032136, and NCT00036270) pathology cohort were analyzed to determine the prognostic ability of mutational and copy number aberration biomarkers that represent the cyclin D/cyclin-dependent kinase (CCND/CDK), fibroblast growth factor receptor/fibroblast growth factor (FGFR/FGF), and phosphatidylinositol 3-kinase/protein kinase B (PI3K/ATK) pathways to inform the potential choice of additional therapies to standard endocrine treatment. Copy number analysis and targeted sequencing was performed. Pathways were identified as aberrant if there were copy number aberrations and/or mutations in any of the predetermined pathway genes: CCND1/CCND2/CCND3/CDK4/CDK6, FGFR1/FGFR2/FGFR2/FGFR4, and AKT1/AKT2/PIK3CA/PTEN. RESULTS The 390 of 420 samples that passed quality control were analyzed for distant metastasis–free survival between groups. Patients with no changes in the CCND/CDK pathway experienced a better distant metastasis–free survival (hazard ratio, 1.94; 95% CI, 1.45 to 2.61; P < .001) than those who possessed aberrations. In the FGFR/FGF and PI3K/AKT pathways, a similar outcome was observed (hazard ratio, 1.43 [95% CI, 1.07 to 1.92; P = .017] and 1.34 [95% CI, 1.00 to 1.81; P = .053], respectively). CONCLUSION We show that aberrations of genes in these pathways are independently linked to a higher risk of relapse after endocrine treatment. Improvement of the clinical management of early breast cancers could be made by identifying those for whom current endocrine therapies are sufficient, thus reducing unnecessary treatment, and secondly, by identifying those who are at high risk for recurrence and linking molecular features that drive these cancers to treatment with targeted therapies.
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Affiliation(s)
- Jane Bayani
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Elizabeth N. Kornaga
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Cheryl Crozier
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lauren Bathurst
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Irina Kalatskaya
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- EMD Serono Research and Development Institute, Billerica, MA
| | - Quang M. Trinh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Cindy Q. Yao
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Paul C. Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Melanie Spears
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | | | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Daniel Rea
- University of Birmingham, Birmingham, United Kingdom
| | - John M.S. Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
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Spears M, Kalatskaya I, Trinh QM, Liao L, Chong TM, Crozier C, Dion D, Heisler L, Timms L, Stein LD, Pritchard KI, Levine MN, Shepherd L, Twelves CJ, Bartlett JMS. Abstract P2-10-04: Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-10-04] [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 The use of chemotherapies such as anthracyclines and taxanes have improved overall and disease free survival in breast cancer. For all patients, anthracyclines can have significant toxicities including cardiotoxicity and leukemia. It is therefore essential to select the subset of patients who will receive the optimal overall benefit from anthracycline therapy and to identify molecular pathways driving resistance. To fully understand the impact of mutations in the context of current breast cancer therapy, requires a comprehensive mapping of key molecular events in the context of treatment. We sequenced 101 genes, that were prioritized based on not only gene frequency, but also taking into account the importance of amino acid substitution, type of mutation and network connectivity, in 692 primary tumours to both identify driver genes and pathway cassettes and to understand their clinical significance in response to anthracycline treatment.
Methods We performed targeted sequencing in patients from the BR9601 (n=374) and CCTG MA.5 (n=703) clinical trials. The BR9601 and MA.5 clinical trials examined the effectiveness of combination chemotherapy consisting of CMF (cyclophosphamide, methotrexate and 5-fluorouracil) with or without epirubicin. DNA was extracted, samples were sequenced using AmpliSeq Technology adapted to Illumina and somatic mutations were called using a novel mutation calling pipeline (ISOWN). A priori analyses were performed using distant recurrence free survival (DRFS) as the primary endpoint.
Results: In 692 successfully analysed samples 509 (73.6%) samples exhibited at least one single nucleotide mutation (range 0-54). 94/101 genes were mutated in at least one patient. Only variants in PIK3CA, TP53, CDH1, TLE6, MLL3 and USH2A were detected in 5% or more of samples. TSC22D1, RB1 and ZNF565 were associated with increased risk of distant relapse in multivariate analyses corrected for clinic-pathological variables. No single genes were predictive of anthracycline treatment compared to CMF in multivariate analyses corrected for clinic-pathological variables. Signaling cassettes/modules were designed based on the pathway database, Reactome. Within the signaling cassettes one module was predictive of anthracycline failure. Patients with one or more mutations in this module had an increased risk of distant relapse (HR 0.52, 95% CI 0.29-0.95, p=0.034) when treated with an anthracycline containing chemotherapy regimen compared to CMF (HR 1.34 95% CI 1.05-1.72, p=0.019).
Conclusions: We successfully performed a signaling pathway-based targeted sequencing analysis within predefined signaling modules. We identified a single signaling cassette linked to anthracycline resistance in early breast cancer. However, further work to validate this study in a separate clinical trial is warranted.
Citation Format: Spears M, Kalatskaya I, Trinh QM, Liao L, Chong TM, Crozier C, Dion D, Heisler L, Timms L, Stein LD, Pritchard KI, Levine MN, Shepherd L, Twelves CJ, Bartlett JMS. Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-10-04.
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Affiliation(s)
- M Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - I Kalatskaya
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - QM Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - TM Chong
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - C Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - D Dion
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Heisler
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Timms
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - LD Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - KI Pritchard
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - MN Levine
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Shepherd
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - CJ Twelves
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - JMS Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
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Kalatskaya I, Trinh QM, Spears M, McPherson JD, Bartlett JMS, Stein L. ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. Genome Med 2017; 9:59. [PMID: 28659176 PMCID: PMC5490163 DOI: 10.1186/s13073-017-0446-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 01/09/2017] [Accepted: 06/06/2017] [Indexed: 12/31/2022] Open
Abstract
Background A key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a variety of common scenarios in which matched normal tissue is not available for comparison. Results In this work, we describe an algorithm to distinguish somatic single nucleotide variants (SNVs) in next-generation sequencing data from germline polymorphisms in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded tissues; we tested our algorithm with both deep targeted and whole-exome sequencing data. Our algorithm correctly classified between 95 and 98% of somatic mutations with F1-measure ranges from 75.9 to 98.6% depending on the tumor type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues). Conclusions In this work, we describe the development, implementation, and validation of ISOWN, an accurate algorithm for predicting somatic mutations in cancer tissues in the absence of matching normal tissues. ISOWN is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0446-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina Kalatskaya
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Quang M Trinh
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, California, USA
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Lincoln Stein
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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17
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Bartlett J, Kalatskaya I, Yousif F, Bayani J, Trinh QM, Heisler L, Timms L, Lee S, Buchner N, Milacic M, Rothfels K, Crozier C, Drake C, Hasenburg A, Kieback DG, Rea D, McPherson J, Boutros PC, Stein LD. Targeted sequencing in a phase III trial of luminal breast cancer: Identification of novel targets. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.505] [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
505 Background: The International Cancer Genome Consortium and The Cancer Genome Atlas have had a global transformative impact on our understanding of cancer. These programs have mapped the genomic landscape of common and rare tumors setting the scene for a comprehensive change in the approach to cancer diagnosis and treatment. However, the task remains incomplete until these mutational events are linked to clinical outcomes in the context of current therapeutic intervention to drive future stratified medicine approaches. Methods: We performed targeted sequencing in patients from the Tamoxifen Exemestane Adjuvant Multicentre trial. DNA was extracted and a 101 gene panel analysed using a novel mutation calling pipeline. Both a priori and machine learning analyses were performed using distant recurrence free survival as the primary endpoint. Results: In 1,491 successfully analyzed samples 1,070 (71.76%) samples exhibited at least one single nucleotide mutation (range 0-94, 1.828+/-0.133, mean+/-s.e.). 98/101 genes were mutated in at least one patient. Only variants in PIK3CA, TP53, MLL3, CDH1 were detected in 5% or more of samples. Twenty genes were associated with increased risk of recurrence in multivariate analyses corrected for clinic-pathological variables, 50% of these genes were involved in transcriptional regulation or RNA/protein processing. In a multivariate analysis, two combined signalling modules were independently prognostic for residual risk following hormone therapy (HRvalidation 3.10 95%CI 1.78-5.40 and HRvalidation 2.70 95%CI 1.57-4.64). Conclusions: We successfully performed a signalling pathway-based targeted sequencing analysis within predefined signalling modules. In supervised and unsupervised analyses we identified multiple signalling cassettes linked to poor outcome in patients with ER+ve breast cancers treated with modern endocrine therapy in the context of a phase III clinical trial. These results identify novel candidates as targets to treat endocrine refractory breast cancers.
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Affiliation(s)
- John Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Fouad Yousif
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jane Bayani
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Shawna Lee
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Marija Milacic
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Karen Rothfels
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Cheryl Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Camilla Drake
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | - Daniel Rea
- Cancer Research UK Institute for Cancer Studies, Birmingham, United Kingdom
| | - John McPherson
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
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18
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Bayani J, Kornaga E, Crozier C, Jang GH, Kalatskaya I, Trinh QM, Yao CQ, Livingstone J, Hasenburg A, Kieback DG, Markopoulos C, Dirix L, Boutros PC, Spears M, Stein LD, Rea D, Bartlett J. Copy-number and targeted sequencing analyses to identify distinct prognostic groups: Implications for patient selection to targeted therapies amongst anti-endocrine therapy resistant early breast cancers. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
524 Background: Hormone receptor positive breast cancer is a therapeutic challenge. Despite optimal anti-endocrine therapies, most breast cancer deaths follow a diagnosis of early luminal cancer. To understand the impact of multiple aberrations in the context of current therapy, we assessed the prognostic ability of genomic signatures as a putative stratification tool to targeted therapies. Methods: This a priori study is based on molecular pathways which might predict response to targeted therapies. DNA from 420 patients from the phase III TEAM pathology cohort were used. Patients with a distant recurrence within 5 years were matched by clinical variables to those disease-free at follow up. Copy number analysis was performed using the Affymetrix Oncoscan Assay. Targeted sequencing was performed in a subset of samples for genes based on signaling cassettes mined from the ICGC. Pathways were identified as aberrant if there were copy number variations (CNVs) and/or mutations in any of the pre-determined pathway genes: 1) CCND1/CCND2/CCND3/CDK4/CDK6; 2) FGFR1/FGFR2/FGFR2/FGFR4; and 3) AKT1/AKT2/PIK3CA/PTEN. Kaplan-Meier and log-rank analyses were used for DFS between groups. Hazard ratios were calculated using the Cox proportional hazard models adjusted for age, tumour size, grade, lymph node and HER2 status. Results: 390/420 samples passed informatics QC filters. For the CCND/CDK pathway, patients with no CNV changes experienced a better DFS (HR = 1.7, 95% CI 1.3-2.3, p < 0.001). For the FGFR/FGF pathway, a similar outcome is seen among patients without CNVs (HR = 1.5, 95% CI 1.1-2.0; p = 0.005). For AKT/PIK3CA, a decrease in DFS was seen in those with aberrations (HR = 1.4, 95% CI 1.0-1.8, p = 0.03). Conclusions: We demonstrated that CNVs of genes within CDK4/CCND, PIK3CA/AKT and FGFR pathways are independently linked to high risk of relapse following endocrine treatment, with implications for identifying those patients who are at high-risk for recurrence despite optimal anti-endocrine therapy and linking molecular features driving these cancers to targeted therapies.
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Affiliation(s)
- Jane Bayani
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Cheryl Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | | | - Luc Dirix
- Sint-Augustinus Hospital Oncology Center, Medical Oncology, Antwerpen, Belgium
| | | | | | | | - Daniel Rea
- Cancer Research UK Institute for Cancer Studies, Birmingham, United Kingdom
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19
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Wang D, Pham NA, Tong J, Sakashita S, Allo G, Kim L, Yanagawa N, Raghavan V, Wei Y, To C, Trinh QM, Starmans MHW, Chan-Seng-Yue MA, Chadwick D, Li L, Zhu CQ, Liu N, Li M, Lee S, Ignatchenko V, Strumpf D, Taylor P, Moghal N, Liu G, Boutros PC, Kislinger T, Pintilie M, Jurisica I, Shepherd FA, McPherson JD, Muthuswamy L, Moran MF, Tsao MS. Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors. Int J Cancer 2016; 140:662-673. [PMID: 27750381 DOI: 10.1002/ijc.30472] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 05/15/2016] [Accepted: 09/29/2016] [Indexed: 01/10/2023]
Abstract
Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice. Subsequent passages were in NOD SCID mice. A subset of matched patient and PDX tumors and non-neoplastic lung tissues were profiled by whole exome sequencing, single nucleotide polymorphism (SNP) and methylation arrays, and phosphotyrosine (pY)-proteome by mass spectrometry. The data were compared to published NSCLC datasets of NSCLC primary and cell lines. 127 stable PDXs were established from 441 lung carcinomas representing all major histological subtypes: 52 adenocarcinomas, 62 squamous cell carcinomas, one adeno-squamous carcinoma, five sarcomatoid carcinomas, five large cell neuroendocrine carcinomas, and two small cell lung cancers. Somatic mutations, gene copy number and expression profiles, and pY-proteome landscape of 36 PDXs showed greater similarity with patient tumors than with established cell lines. Novel somatic mutations on cancer associated genes were identified but only in PDXs, likely due to selective clonal growth in the PDXs that allows detection of these low allelic frequency mutations. The results provide the strongest evidence yet that PDXs established from lung cancers closely mimic the characteristics of patient primary tumors.
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Affiliation(s)
- Dennis Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK, S1O 2HQ
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jiefei Tong
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ghassan Allo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Naoki Yanagawa
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yuhong Wei
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Christine To
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Quang M Trinh
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | | | | | - Dianne Chadwick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lei Li
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ni Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sharon Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Dan Strumpf
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul Taylor
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Paul C Boutros
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - John D McPherson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Lakshmi Muthuswamy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael F Moran
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada.,Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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20
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Trinh QM, Nguyen HL, Do TN, Nguyen VN, Nguyen BH, Nguyen TVA, Sintchenko V, Marais BJ. Tuberculosis and HIV co-infection in Vietnam. Int J Infect Dis 2016; 46:56-60. [PMID: 27044521 DOI: 10.1016/j.ijid.2016.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 03/24/2016] [Accepted: 03/24/2016] [Indexed: 10/22/2022] Open
Abstract
UNLABELLED Tuberculosis (TB) and human immunodeficiency virus (HIV) infection are leading causes of disease and death in Vietnam, but TB/HIV disease trends and the profile of co-infected patients are poorly described. METHODS We examined national TB and HIV notification data to provide a geographic overview and describe relevant disease trends within Vietnam. We also compared the demographic and clinical profiles of TB patients with and without HIV infection. RESULTS During the past 10 years (2005-2014) cumulative HIV case numbers and deaths increased to 298,151 and 71,332 respectively, but access to antiretroviral therapy (ART) improved and new infections and deaths declined. From 2011-2014 routine HIV testing of TB patients increased from 58.9% to 72.5% and of all TB patients diagnosed with HIV in 2014, 2,803 (72.4%) received ART. The number of multidrug resistant (MDR)-TB cases enrolled for treatment increased almost 3-fold (578 to 1,532) from 2011-2014. The rate of HIV co-infection in MDR and non-MDR TB cases (51/1,532; 3.3% vs 3,774/100,555; 3.8%; OR 0.77, 95% CI 0.7-1.2) was similar in 2014. CONCLUSIONS The care of TB/HIV co-infected patients have shown sustained improvement in Vietnam. Rising numbers of MDR-TB cases is a concern, but this is not "driven" by HIV co-infection.
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Affiliation(s)
- Q M Trinh
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia; NSW Mycobacterium Reference Laboratory, Centre for Infectious Disease and Microbiology - Public Health, ICPMR, Westmead Hospital, Sydney, Australia; Vietnam National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
| | - H L Nguyen
- Vietnam Administration of HIV/AIDS Control, Hanoi, Vietnam
| | - T N Do
- Vietnam Administration of HIV/AIDS Control, Hanoi, Vietnam
| | - V N Nguyen
- Vietnam National TB Program, Hanoi, Vietnam
| | - B H Nguyen
- Vietnam National TB Program, Hanoi, Vietnam; International Union Against Tuberculosis and Lung Diseases, Paris, France
| | - T V A Nguyen
- Vietnam National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - V Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia; NSW Mycobacterium Reference Laboratory, Centre for Infectious Disease and Microbiology - Public Health, ICPMR, Westmead Hospital, Sydney, Australia
| | - B J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia
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21
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Trinh QM, Nguyen HL, Nguyen VN, Nguyen TVA, Sintchenko V, Marais BJ. Tuberculosis and HIV co-infection-focus on the Asia-Pacific region. Int J Infect Dis 2016; 32:170-8. [PMID: 25809776 DOI: 10.1016/j.ijid.2014.11.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 11/12/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB) is the leading opportunistic disease and cause of death in patients with HIV infection. In 2013 there were 1.1 million new TB/HIV co-infected cases globally, accounting for 12% of incident TB cases and 360,000 deaths. The Asia-Pacific region, which contributes more than a half of all TB cases worldwide, traditionally reports low TB/HIV co-infection rates. However, routine testing of TB patients for HIV infection is not universally implemented and the estimated prevalence of HIV in new TB cases increased to 6.3% in 2013. Although HIV infection rates have not seen the rapid rise observed in Sub-Saharan Africa, indications are that rates are increasing among specific high-risk groups. This paper reviews the risks of TB exposure and progression to disease, including the risk of TB recurrence, in this vulnerable population. There is urgency to scale up interventions such as intensified TB case-finding, isoniazid preventive therapy, and TB infection control, as well as HIV testing and improved access to antiretroviral treatment. Increased awareness and concerted action is required to reduce TB/HIV co-infection rates in the Asia-Pacific region and to improve the outcomes of people living with HIV.
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Affiliation(s)
- Q M Trinh
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia; Centre for Infectious Disease and Microbiology - Public Health, ICPMR, Westmead Hospital, Sydney, Australia; Tuberculosis Laboratory, Vietnam National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
| | - H L Nguyen
- Vietnam Administration of HIV/AIDS Control, Hanoi, Vietnam
| | - V N Nguyen
- Vietnam National Lung Hospital, Hanoi, Vietnam
| | - T V A Nguyen
- Tuberculosis Laboratory, Vietnam National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - V Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia; Centre for Infectious Disease and Microbiology - Public Health, ICPMR, Westmead Hospital, Sydney, Australia
| | - B J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia
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22
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Shlush LI, Zandi S, Mitchell A, Chen WC, Brandwein JM, Gupta V, Kennedy JA, Schimmer AD, Schuh AC, Yee KW, McLeod JL, Doedens M, Medeiros JJF, Marke R, Kim HJ, Lee K, McPherson JD, Hudson TJ, Brown AMK, Yousif F, Trinh QM, Stein LD, Minden MD, Wang JCY, Dick JE. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature 2014; 506:328-33. [PMID: 24522528 PMCID: PMC4991939 DOI: 10.1038/nature13038] [Citation(s) in RCA: 1080] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/20/2014] [Indexed: 12/17/2022]
Abstract
In acute myeloid leukemia (AML), the cell of origin, nature and biological consequences of initiating lesions and order of subsequent mutations remain poorly understood, as AML is typically diagnosed without observation of a pre-leukemic phase. Here, highly purified hematopoietic stem cells (HSC), progenitor and mature cell fractions from the blood of AML patients were found to contain recurrent DNMT3a mutations (DNMT3amut) at high allele frequency, but without coincident NPM1 mutations (NPM1c) present in AML blasts. DNMT3amut-bearing HSC exhibited multilineage repopulation advantage over non-mutated HSC in xenografts, establishing their identity as pre-leukemic-HSC (preL-HSC). preL-HSC were found in remission samples indicating that they survive chemotherapy. Thus DNMT3amut arises early in AML evolution, likely in HSC, leading to a clonally expanded pool of preL-HSC from which AML evolves. Our findings provide a paradigm for the detection and treatment of pre-leukemic clones before the acquisition of additional genetic lesions engenders greater therapeutic resistance.
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Affiliation(s)
- Liran I Shlush
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2]
| | - Sasan Zandi
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2]
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Weihsu Claire Chen
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Joseph M Brandwein
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada
| | - Vikas Gupta
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Aaron D Schimmer
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada [4] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Andre C Schuh
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada
| | - Karen W Yee
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada
| | - Jessica L McLeod
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Monica Doedens
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Rene Marke
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Radboud University, Nijmegen Medical Centre, Nijmegen 6500 HB, The Netherlands
| | - Hyeoung Joon Kim
- Chonnam National University Hwasun Hospital, Genome Research Center for Hematopoietic Diseases, Gwangju 519-809, South Korea
| | - Kwon Lee
- Chonnam National University Hwasun Hospital, Genome Research Center for Hematopoietic Diseases, Gwangju 519-809, South Korea
| | - John D McPherson
- 1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada [2] Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Thomas J Hudson
- 1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada [2] Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Andrew M K Brown
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Lincoln D Stein
- 1] Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mark D Minden
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada [4] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Jean C Y Wang
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada [3] Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada
| | - John E Dick
- 1] Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Peltekova VD, Lemire M, Qazi AM, Zaidi SHE, Trinh QM, Bielecki R, Rogers M, Hodgson L, Wang M, D'Souza DJA, Zandi S, Chong T, Kwan JYY, Kozak K, De Borja R, Timms L, Rangrej J, Volar M, Chan-Seng-Yue M, Beck T, Ash C, Lee S, Wang J, Boutros PC, Stein LD, Dick JE, Gryfe R, McPherson JD, Zanke BW, Pollett A, Gallinger S, Hudson TJ. Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. Int J Cancer 2013; 134:2330-41. [PMID: 24154973 PMCID: PMC3949167 DOI: 10.1002/ijc.28557] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 09/05/2013] [Accepted: 09/27/2013] [Indexed: 12/19/2022]
Abstract
A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case–control studies worldwide. In order to identify biologic factors at this locus that are related to the etiopathology of CRC, we used microarray-based target selection methods, coupled to next-generation sequencing, to study 103 kb at the 11q23 locus. We genotyped 369 putative variants from 1,030 patients with CRC (cases) and 1,061 individuals without CRC (controls) from the Ontario Familial Colorectal Cancer Registry. Two previously uncharacterized genes, COLCA1 and COLCA2, were found to be co-regulated genes that are transcribed from opposite strands. Expression levels of COLCA1 and COLCA2 transcripts correlate with rs3802842 genotypes. In colon tissues, COLCA1 co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages, dendritic cells and differentiated myeloid-derived cell lines. COLCA2 is present in the cytoplasm of normal epithelial, immune and other cell lineages, as well as tumor cells. Tissue microarray analysis demonstrates the association of rs3802842 with lymphocyte density in the lamina propria (p = 0.014) and levels of COLCA1 in the lamina propria (p = 0.00016) and COLCA2 (tumor cells, p = 0.0041 and lamina propria, p = 6 × 10–5). In conclusion, genetic, expression and immunohistochemical data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. Histologic analyses indicate the involvement of immune pathways.
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Trinh QM, Jen FYA, Zhou Z, Chu KM, Perry MD, Kephart ET, Contrino S, Ruzanov P, Stein LD. Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. BMC Genomics 2013; 14:494. [PMID: 23875683 PMCID: PMC3734164 DOI: 10.1186/1471-2164-14-494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/16/2013] [Indexed: 01/20/2023] Open
Abstract
Background Funded by the National Institutes of Health (NIH), the aim of the Model Organism ENCyclopedia of DNA Elements (modENCODE) project is to provide the biological research community with a comprehensive encyclopedia of functional genomic elements for both model organisms C. elegans (worm) and D. melanogaster (fly). With a total size of just under 10 terabytes of data collected and released to the public, one of the challenges faced by researchers is to extract biologically meaningful knowledge from this large data set. While the basic quality control, pre-processing, and analysis of the data has already been performed by members of the modENCODE consortium, many researchers will wish to reinterpret the data set using modifications and enhancements of the original protocols, or combine modENCODE data with other data sets. Unfortunately this can be a time consuming and logistically challenging proposition. Results In recognition of this challenge, the modENCODE DCC has released uniform computing resources for analyzing modENCODE data on Galaxy (https://github.com/modENCODE-DCC/Galaxy), on the public Amazon Cloud (http://aws.amazon.com), and on the private Bionimbus Cloud for genomic research (http://www.bionimbus.org). In particular, we have released Galaxy workflows for interpreting ChIP-seq data which use the same quality control (QC) and peak calling standards adopted by the modENCODE and ENCODE communities. For convenience of use, we have created Amazon and Bionimbus Cloud machine images containing Galaxy along with all the modENCODE data, software and other dependencies. Conclusions Using these resources provides a framework for running consistent and reproducible analyses on modENCODE data, ultimately allowing researchers to use more of their time using modENCODE data, and less time moving it around.
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Affiliation(s)
- Quang M Trinh
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON, M5G 0A3, Canada
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Grant RC, Al-Sukhni W, Borgida AE, Holter S, Kanji ZS, McPherson T, Whelan E, Serra S, Trinh QM, Peltekova V, Stein LD, McPherson JD, Gallinger S. Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer. Hum Genomics 2013; 7:11. [PMID: 23561644 PMCID: PMC3639869 DOI: 10.1186/1479-7364-7-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/18/2013] [Indexed: 12/20/2022] Open
Abstract
We sequenced 11 germline exomes from five families with familial pancreatic cancer (FPC). One proband had a germline nonsense variant in ATM with somatic loss of the variant allele. Another proband had a nonsense variant in PALB2 with somatic loss of the variant allele. Both variants were absent in a relative with FPC. These findings question the causal mechanisms of ATM and PALB2 in these families and highlight challenges in identifying the causes of familial cancer syndromes using exome sequencing.
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Affiliation(s)
- Robert C Grant
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, Canada
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Soh J, Turinsky AL, Trinh QM, Chang J, Sabhaney A, Dong X, Gordon PM, Janzen RP, Hau D, Xia J, Wishart DS, Sensen CW. Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping. Int J Nanomedicine 2009; 4:79-89. [PMID: 19421373 PMCID: PMC2720741 DOI: 10.2147/ijn.s4375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data and pharmacokinetic data, respectively, we demonstrate how existing knowledge bases for molecular data can be semantically mapped onto a standardized anatomical context of human body. Our data mapping methodology uses ontological representations of heterogeneous biomedical datasets and an ontology reasoner to create complex semantic descriptions of biomedical processes. This framework provides a means to systematically combine an increasing amount of biomedical imaging and numerical data into spatiotemporally coherent graphical representations. Our work enables medical researchers with different expertise to simulate complex phenomena visually and to develop insights through the use of shared data, thus paving the way for pathological inference, developmental pattern discovery and biomedical hypothesis testing.
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Affiliation(s)
- Jung Soh
- Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, AB, Canada
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