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Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O’Farrell AC, Modave E, Lambrechts D, ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nat Genet 2021; 53:86-99. [PMID: 33414553 PMCID: PMC7808565 DOI: 10.1038/s41588-020-00750-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 11/18/2020] [Indexed: 02/03/2023]
Abstract
Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multiregion samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.
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Grants
- NC/T001267/1 National Centre for the Replacement, Refinement and Reduction of Animals in Research
- P30 CA016672 NCI NIH HHS
- 29567 Cancer Research UK
- U54 CA233223 NCI NIH HHS
- P30 CA034196 NCI NIH HHS
- P01 CA114046 NCI NIH HHS
- T32 HG008962 NHGRI NIH HHS
- HHSN261201400008C NCI NIH HHS
- P30 CA091842 NCI NIH HHS
- U24 CA224067 NCI NIH HHS
- P50 CA196510 NCI NIH HHS
- U54 CA224070 NCI NIH HHS
- HHSN261200800001C CCR NIH HHS
- U54 CA224076 NCI NIH HHS
- U54 CA224065 NCI NIH HHS
- U54 CA233306 NCI NIH HHS
- P30 CA010815 NCI NIH HHS
- U24 CA204781 NCI NIH HHS
- U54 CA224083 NCI NIH HHS
- HHSN261201500003C NCI NIH HHS
- R50 CA211199 NCI NIH HHS
- P30 CA125123 NCI NIH HHS
- P50 CA070907 NCI NIH HHS
- HHSN261201500003I NCI NIH HHS
- HHSN261200800001E NCI NIH HHS
- P30 CA042014 NCI NIH HHS
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- KWF Kankerbestrijding (Dutch Cancer Society)
- Oncode Institute
- Fondazione AIRC under 5 per Mille 2018 - ID. 21091 EU H2020 Research and Innovation Programme, grant agreement no. 731105 European Research Council Consolidator Grant 724748
- EU H2020 Research and Innovation Programme, grant Agreement No. 754923
- EU H2020 Research and Innovation Programme, grant agreement no. 731105 ISCIII - Miguel Servet program CP14/00228 GHD-Pink/FERO Foundation grant
- Fondazione Piemontese per la Ricerca sul Cancro-ONLUS 5 per mille Ministero della Salute 2015
- Korean Health Industry Development Institute HI13C2148
- Korean Health Industry Development Institute HI13C2148 The First Affiliated Hospital of Xi’an Jiaotong University Ewha Womans University Research Grant
- CPRIT RP170691
- SCU | Ignatian Center for Jesuit Education, Santa Clara University
- Breast Cancer Research Foundation (BCRF)
- Fashion Footwear Charitable Foundation of New York The Foundation for Barnes-Jewish Hospital’s Cancer Frontier Fund
- My First AIRC Grant 19047
- Fondazione AIRC under 5 per Mille 2018 - ID. 21091 AIRC Investigator Grants 18532 and 20697 AIRC/CRUK/FC AECC Accelerator Award 22795 Fondazione Piemontese per la Ricerca sul Cancro-ONLUS 5 per mille Ministero della Salute 2015, 2014, 2016 EU H2020 Research and Innovation Programme, grant Agreement No. 754923 EU H2020 Research and Innovation Programme, grant agreement no. 731105
- Science Foundation Ireland (SFI)
- EU H2020 Research and Innovation Programme, grant agreement no. 731105 EU H2020 Research and Innovation Programme, grant Agreement No. 754923 Irish Health Research Board grant ILP-POR-2019-066
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
- EU H2020 Research and Innovation Programme, grant agreement no. 731105 European Research Council (ERC) Synergy project CombatCancer Oncode Institute
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Affiliation(s)
- Xing Yi Woo
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Jessica Giordano
- grid.7605.40000 0001 2336 6580Department of Oncology, University of Turin, Turin, Italy ,grid.419555.90000 0004 1759 7675Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Anuj Srivastava
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Zi-Ming Zhao
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Michael W. Lloyd
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Roebi de Bruijn
- grid.430814.aNetherlands Cancer Institute, Amsterdam, the Netherlands
| | - Yun-Suhk Suh
- grid.31501.360000 0004 0470 5905College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Rajesh Patidar
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Li Chen
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Sandra Scherer
- grid.223827.e0000 0001 2193 0096Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Matthew H. Bailey
- grid.223827.e0000 0001 2193 0096Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Chieh-Hsiang Yang
- grid.223827.e0000 0001 2193 0096Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Emilio Cortes-Sanchez
- grid.223827.e0000 0001 2193 0096Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Yuanxin Xi
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jing Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | | | | | - Vito W. Rebecca
- grid.251075.40000 0001 1956 6678The Wistar Institute, Philadelphia, PA USA
| | - Hua Sun
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - R. Jay Mashl
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Sherri R. Davies
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Ryan Jeon
- grid.492568.4Seven Bridges Genomics, Charlestown, MA USA
| | | | | | | | - Francesco Galimi
- grid.7605.40000 0001 2336 6580Department of Oncology, University of Turin, Turin, Italy ,grid.419555.90000 0004 1759 7675Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Andrea Bertotti
- grid.7605.40000 0001 2336 6580Department of Oncology, University of Turin, Turin, Italy ,grid.419555.90000 0004 1759 7675Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Adam Lafferty
- grid.4912.e0000 0004 0488 7120Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alice C. O’Farrell
- grid.4912.e0000 0004 0488 7120Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Elodie Modave
- grid.5596.f0000 0001 0668 7884Center for Cancer Biology, VIB, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- grid.5596.f0000 0001 0668 7884Center for Cancer Biology, VIB, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Petra ter Brugge
- grid.430814.aNetherlands Cancer Institute, Amsterdam, the Netherlands
| | - Violeta Serra
- grid.411083.f0000 0001 0675 8654Vall d´Hebron Institute of Oncology, Barcelona, Spain
| | - Elisabetta Marangoni
- grid.418596.70000 0004 0639 6384Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Rania El Botty
- grid.418596.70000 0004 0639 6384Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Hyunsoo Kim
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Jong-Il Kim
- grid.31501.360000 0004 0470 5905College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han-Kwang Yang
- grid.31501.360000 0004 0470 5905College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Charles Lee
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA ,grid.452438.cPrecision Medicine Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China ,grid.255649.90000 0001 2171 7754Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Dennis A. Dean
- grid.492568.4Seven Bridges Genomics, Charlestown, MA USA
| | | | - Yvonne A. Evrard
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - James H. Doroshow
- grid.48336.3a0000 0004 1936 8075Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD USA
| | - Alana L. Welm
- grid.223827.e0000 0001 2193 0096Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Bryan E. Welm
- grid.223827.e0000 0001 2193 0096Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA ,grid.223827.e0000 0001 2193 0096Department of Surgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Michael T. Lewis
- grid.39382.330000 0001 2160 926XLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Bingliang Fang
- grid.240145.60000 0001 2291 4776Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jack A. Roth
- grid.240145.60000 0001 2291 4776Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Funda Meric-Bernstam
- grid.240145.60000 0001 2291 4776Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Meenhard Herlyn
- grid.251075.40000 0001 1956 6678The Wistar Institute, Philadelphia, PA USA
| | - Michael A. Davies
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Li Ding
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Shunqiang Li
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Ramaswamy Govindan
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Claudio Isella
- grid.7605.40000 0001 2336 6580Department of Oncology, University of Turin, Turin, Italy ,grid.419555.90000 0004 1759 7675Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Jeffrey A. Moscow
- grid.48336.3a0000 0004 1936 8075Investigational Drug Branch, National Cancer Institute, Bethesda, MD USA
| | - Livio Trusolino
- grid.7605.40000 0001 2336 6580Department of Oncology, University of Turin, Turin, Italy ,grid.419555.90000 0004 1759 7675Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Annette T. Byrne
- grid.4912.e0000 0004 0488 7120Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jos Jonkers
- grid.430814.aNetherlands Cancer Institute, Amsterdam, the Netherlands
| | - Carol J. Bult
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Enzo Medico
- grid.7605.40000 0001 2336 6580Department of Oncology, University of Turin, Turin, Italy ,grid.419555.90000 0004 1759 7675Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Jeffrey H. Chuang
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
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