<i>YES1</i> amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics.

Abstract

In ∼30% of patients with <i>EGFR</i>-mutant lung adenocarcinomas whose disease progresses on EGFR inhibitors, the basis for acquired resistance remains unclear. We have integrated transposon mutagenesis screening in an <i>EGFR</i>-mutant cell line and clinical genomic sequencing in cases of acquired resistance to identify mechanisms of resistance to EGFR inhibitors. The most prominent candidate genes identified by insertions in or near the genes during the screen were <i>MET</i>, a gene whose amplification is known to mediate resistance to EGFR inhibitors, and the gene encoding the Src family kinase YES1. Cell clones with transposon insertions that activated expression of <i>YES1</i> exhibited resistance to all three generations of EGFR inhibitors and sensitivity to pharmacologic and siRNA-mediated inhibition of <i>YES1</i> Analysis of clinical genomic sequencing data from cases of acquired resistance to EGFR inhibitors revealed amplification of <i>YES1</i> in five cases, four of which lacked any other known mechanisms of resistance. Preinhibitor samples, available for two of the five patients, lacked <i>YES1</i> amplification. None of 136 postinhibitor samples had detectable amplification of other Src family kinases (<i>SRC</i> and <i>FYN</i>). <i>YES1</i> amplification was also found in 2 of 17 samples from <i>ALK</i> fusion-positive lung cancer patients who had progressed on ALK TKIs. Taken together, our findings identify acquired amplification of <i>YES1</i> as a recurrent and targetable mechanism of resistance to EGFR inhibition in <i>EGFR</i>-mutant lung cancers and demonstrate the utility of transposon mutagenesis in discovering clinically relevant mechanisms of drug resistance.