title: 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.
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.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
authors.forename: Peilin
authors.initials: P
authors.lastname: Jia
authors.forename: Hailing
authors.initials: H
authors.lastname: Jin
authors.forename: Catherine B
authors.initials: CB
authors.lastname: Meador
authors.forename: Junfeng
authors.initials: J
authors.lastname: Xia
authors.forename: Kadoaki
authors.initials: K
authors.lastname: Ohashi
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.forename: Valentina
authors.initials: V
authors.lastname: Pirazzoli
authors.forename: Kimberly B
authors.initials: KB
authors.lastname: Dahlman
authors.forename: Katerina
authors.initials: K
authors.lastname: Politi
authors.forename: Franziska
authors.initials: F
authors.lastname: Michor
authors.forename: Zhongming
authors.initials: Z
authors.lastname: Zhao
authors.forename: William
authors.initials: W
authors.lastname: Pao
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D066246:ErbB Receptors / Q000037:antagonists & inhibitors*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D008175:Lung Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D017422:Sequence Analysis, DNA
chemical_list: D000970:Antineoplastic Agents; D047428:Protein Kinase Inhibitors; C512478:EGFR protein, human; D066246:ErbB Receptors