Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance
- Peilin Jia1,
- Hailing Jin2,
- Catherine B. Meador2,
- Junfeng Xia1,
- Kadoaki Ohashi2,
- Lin Liu3,4,
- Valentina Pirazzoli5,6,
- Kimberly B. Dahlman7,
- Katerina Politi5,6,8,
- Franziska Michor3,4,
- Zhongming Zhao1,7,9 and
- William Pao2,7,9
- 1Department of Biomedical Informatics,
- 2Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA;
- 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;
- 4Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02215, USA;
- 5Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
- 6Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
- 7Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA;
- 8Department of Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
Abstract
Somatic mutations in kinase genes are associated with sensitivity of solid tumors to kinase inhibitors, but patients with metastatic cancer eventually develop disease progression. In EGFR mutant lung cancer, modeling of acquired resistance (AR) with drug-sensitive cell lines has identified clinically relevant EGFR tyrosine kinase inhibitor (TKI) resistance mechanisms such as the second-site mutation, EGFR T790M, amplification of the gene encoding an alternative kinase, MET, and epithelial–mesenchymal transition (EMT). The full spectrum of DNA changes associated with AR remains unknown. We used next-generation sequencing to characterize mutational changes associated with four populations of EGFR mutant drug-sensitive and five matched drug-resistant cell lines. Comparing resistant cells with parental counterparts, 18–91 coding SNVs/indels were predicted to be acquired and 1–27 were lost; few SNVs/indels were shared across resistant lines. Comparison of two related parental lines revealed no unique coding SNVs/indels, suggesting that changes in the resistant lines were due to drug selection. Surprisingly, we observed more CNV changes across all resistant lines, and the line with EMT displayed significantly higher levels of CNV changes than the other lines with AR. These results demonstrate a framework for studying the evolution of AR and provide the first genome-wide spectrum of mutations associated with the development of cellular drug resistance in an oncogene-addicted cancer. Collectively, the data suggest that CNV changes may play a larger role than previously appreciated in the acquisition of drug resistance and highlight that resistance may be heterogeneous in the context of different tumor cell backgrounds.
Footnotes
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↵9 Corresponding authors
E-mail william.pao{at}vanderbilt.edu
E-mail zhongming.zhao{at}vanderbilt.edu
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.152322.112.
- Received November 20, 2012.
- Accepted May 30, 2013.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
