Patient-derived xenografts (PDXs) have become a prominent cancer model system, as they are presumed to faithfully represent the genomic features of primary tumors. Here we monitored the dynamics of copy number alterations (CNAs) in 1,110 PDX samples across 24 cancer types. We observed rapid accumulation of CNAs during PDX passaging, often due to selection of preexisting minor clones. CNA acquisition in PDXs was correlated with the tissue-specific levels of aneuploidy and genetic heterogeneity observed in primary tumors. However, the particular CNAs acquired during PDX passaging differed from those acquired during tumor evolution in patients. Several CNAs recurrently observed in primary tumors gradually disappeared in PDXs, indicating that events undergoing positive selection in humans can become dispensable during propagation in mice. Notably, the genomic stability of PDXs was associated with their response to chemotherapy and targeted drugs. These findings have major implications for PDX-based modeling of human cancer.
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Gene Expression Omnibus
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We thank L. Franke for assistance with functional genomic mRNA profiling; A. Bass, K. Ligon, A.J. Aguirre and J. Lorch for providing the clinical samples for cell line derivation; A. Tubelli for assistance with figure preparation; M. Meyerson, A.J. Cherniack, A. Taylor, A. Pearson and Z. Tothova for helpful discussions; and W.J. Gibson for copy number data. U.B.-D. is supported by a Human Frontiers Science Program postdoctoral fellowship, R.B. received support from the US National Institutes of Health (R01 CA188228) and the Gray Matters Brain Cancer Foundation, and T.R.G. received support from the Howard Hughes Medical Institute.
The authors declare no competing financial interests.
Supplementary Figures 1–14, Supplementary Tables 1–6 and Supplementary Note (PDF 4534 kb)
CNA profiles of PDX samples. (XLSX 26968 kb)
Model-acquired CNAs in PDX samples. (XLSX 1425 kb)
CNA profiles of CLDX samples. (XLSX 15919 kb)
Model-acquired CNAs in CLDX samples. (XLSX 791 kb)
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Ben-David, U., Ha, G., Tseng, YY. et al. Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet 49, 1567–1575 (2017). https://doi.org/10.1038/ng.3967
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