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

In ∼30% of patients with EGFR-mutant lung adenocarcinomas whose disease progresses on EGFR inhibitors, the basis for acquired resistance remains unclear. We have integrated transposon mutagenesis screening in an EGFR-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 MET, 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 YES1 exhibited resistance to all three generations of EGFR inhibitors and sensitivity to pharmacologic and siRNA-mediated inhibition of YES1. Analysis of clinical genomic sequencing data from cases of acquired resistance to EGFR inhibitors revealed amplification of YES1 in five cases, four of which lacked any other known mechanisms of resistance. Preinhibitor samples, available for two of the five patients, lacked YES1 amplification. None of 136 postinhibitor samples had detectable amplification of other Src family kinases (SRC and FYN). YES1 amplification was also found in 2 of 17 samples from ALK fusion-positive lung cancer patients who had progressed on ALK TKIs. Taken together, our findings identify acquired amplification of YES1 as a recurrent and targetable mechanism of resistance to EGFR inhibition in EGFR-mutant lung cancers and demonstrate the utility of transposon mutagenesis in discovering clinically relevant mechanisms of drug resistance.

News: Scientists Pinpoint a New Cause of Resistance to EGFR-Targeting Drugs @ MSKCC – Thursday, June 7, 2018


Other Contributors

  1. Pang-Dian Fana,b
  2. Giuseppe Narzisic,
  3. Anitha D. Jayaprakashd
  4. Elisa Venturinie
  5. Nicolas Robinec,
  6. Peter Smibertd,
  7. Soren Germerf,
  8. Helena A. Yug,
  9. Emmet J. Jordang
  10. Paul K. Paikg,
  11. Yelena Y. Janjigiang,
  12. Jamie E. Chaftg,
  13. Lu Wanga
  14. Achim A. Jungblutha,
  15. Sumit Middhaa,
  16. Lee Spraggona,b
  17. Huan Qiaoh,
  18. Christine M. Lovlyh,
  19. Mark G. Krisg,
  20. Gregory J. Rielyg,
  21. Katerina Politii,
  22. Harold Varmusj and
  23. Marc Ladanyia,b

aDepartment of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065;

bHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;

cComputational Biology, New York Genome Center, New York, NY 10013;

dTechnology Innovation Lab, New York Genome Center, New York, NY 10013;

eProject Management, New York Genome Center, New York, NY 10013;

fSequencing Operations, New York Genome Center, New York, NY 10013;

gDivision of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065;

hVanderbilt–Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN37232;

iDepartment of Pathology and the Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520;

jCancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065