Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts
Authors/Creators
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Woo, Xing Yi
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Giordano, Jessica
- Srivastava, Anuj
- Zhao, Zi-Ming
- Lloyd, Michael W.
- de Bruijn, Roebi
- Suh, Yun-Suhk
- Patidar, Rajesh
- Chen, Li
- Scherer, Sandra
- Bailey, Matthew H.
- Yang, Chieh-Hsiang
- Cortes-Sanchez, Emilio
- Xi, Yuanxin
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Wang, Jing
- Wickramasinghe, Jayamanna
- Kossenkov, Andrew V.
- Rebecca, Vito W.
- Sun, Hua
- Mashl, R. Jay
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Davies, Sherri R.
- Jeon, Ryan
- Frech, Christian
- Randjelovic, Jelena
- Rosains, Jacqueline
- Galimi, Francesco
- Bertotti, Andrea
- Lafferty, Adam
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O'Farrell, Alice C.1
- Modave, Elodie
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Lambrechts, Diether2
- ter Brugge, Petra
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Serra, Violeta
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Marangoni, Elisabetta
- El Botty, Rania
- Kim, Hyunsoo
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Kim, Jong-Il
- Yang, Han-Kwang
- Lee, Charles
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Dean II, Dennis A.
- Davis-Dusenbery, Brandi
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Evrard, Yvonne A.
- Doroshow, James H.
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Welm, Alana L.
- Welm, Bryan E.
- Lewis, Michael T.
- Fang, Bingliang
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Roth, Jack A.
- Meric-Bernstam, Funda
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Herlyn, Meenhard
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Davies, Michael A.
- Ding, Li
- Li, Shunqiang
- Govindan, Ramaswamy
- Isella, Claudio
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Moscow, Jeffrey A.
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Trusolino, Livio3
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Byrne, Annette T.1
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Jonkers, Jos
- Bult, Carol J.
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Medico, Enzo3
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Chuang, Jeffrey H.
- PDXNET Consortium4
- EurOPDX Consortium5
- 1. RCSI
- 2. VIB
- 3. UNITO
- 4. PDXNET Consortium
- 5. EurOPDX Consortium
Description
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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s41588-020-00750-6.pdf
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Additional details
Funding
- European Commission
- COLOSSUS - Advancing a Precision Medicine Paradigm in metastatic Colorectal Cancer: Systems based patient stratification solutions 754923
- European Commission
- EDIReX - EurOPDX Distributed Infrastructure for Research on patient-derived cancer Xenografts 731105
- European Commission
- BEAT - The functional interaction of EGFR and beta-catenin signalling in colorectal cancer: Genetics, mechanisms, and therapeutic potential. 724748