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Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 2018; 173:321-337.e10. [PMID: 29625050 PMCID: PMC6070353 DOI: 10.1016/j.cell.2018.03.035] [Citation(s) in RCA: 1724] [Impact Index Per Article: 287.3] [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: 11/17/2017] [Revised: 02/28/2018] [Accepted: 03/15/2018] [Indexed: 02/08/2023]
Abstract
Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFβ signaling, p53 and β-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these pathways, and 57% percent of tumors had at least one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy.
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Affiliation(s)
- Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Mina
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Joshua Armenia
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Augustin Luna
- cBio Center, Dana-Farber Cancer Institute, Boston, MA; Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Konnor C La
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - David L Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | | | - Sadegh Saghafinia
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Foysal Daian
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qingsong Gao
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Matthew H Bailey
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Wen-Wei Liang
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Steven M Foltz
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | | | - Li Ding
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cyriac Kandoth
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Istemi Bahceci
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Leonard Dervishi
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Ugur Dogrusoz
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Wanding Zhou
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids Michigan, 49503, USA
| | - Hui Shen
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids Michigan, 49503, USA
| | - Peter W Laird
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids Michigan, 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Chen Wang
- Department of Health Sciences Research and Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology and Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Trever G Bivona
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94143, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine & Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, Texas 77030, USA
| | - Gary D Hammer
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, Endocrine Oncology Program, University of Michigan, Ann Arbor, Michigan, MI 48105, USA
| | - Thomas Giordano
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI; Department of Internal Medicine, Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI; Comprehensive Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Grant McArthur
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Chenfei Huang
- Dept. of Otolaryngology, Baylor College of Medicine, USA
| | - Aaron D Tward
- University of California, San Francisco Department of Otolaryngology-Head and Neck Surgery. 2233 Post Street, San Francisco, CA, 94143, USA
| | | | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, CA 94143, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute, Boston, MA; Department of Cell Biology, Harvard Medical School, Boston, MA.
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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