Acquired BRAF Rearrangements Induce Secondary Resistance to EGFR therapy in EGFR-Mutated Lung Cancers

Morana Vojnic, Daisuke Kubota, Christopher Kurzatkowski, Michael Offin, Ken Suzawa, Ryma Benayed, Adam J. Schoenfeld, Andrew J. Plodkowski, John T. Poirier, Charles M. Rudin, Mark G. Kris, Neal X. Rosen, Helena A. Yu, Gregory J. Riely, Maria E. Arcila, Romel Somwar, Marc Ladanyi

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Introduction: Multiple genetic mechanisms have been identified in EGFR-mutant lung cancers as mediators of acquired resistance (AR) to EGFR tyrosine kinase inhibitors (TKIs), but many cases still lack a known mechanism. Methods: To identify novel mechanisms of AR, we performed targeted large panel sequencing of samples from 374 consecutive patients with metastatic EGFR-mutant lung cancer, including 174 post-TKI samples, of which 38 also had a matched pre-TKI sample. Alterations hypothesized to confer AR were introduced into drug-sensitive EGFR-mutant lung cancer cell lines (H1975, HCC827, and PC9) by using clustered regularly interspaced short palindromic repeats/Cas9 genome editing. MSK-LX138cl, a cell line with EGFR exon 19 deletion (ex19del) and praja ring finger ubiquitin ligase 2 gene (PJA2)/BRAF fusion, was generated from an EGFR TKI–resistant patient sample. Results: We identified four patients (2.3%) with a BRAF fusion (three with acylglycerol kinase gene (AGK)/BRAF and one with PJA2/BRAF) in samples obtained at AR to EGFR TKI therapy (two posterlotinib samples and two posterlotinib and postosimertinib samples). Pre-TKI samples were available for two of four patients and both were negative for BRAF fusion. Induction of AGK/BRAF fusion in H1975 (L858R + T790M), PC9 (ex19del) and HCC827 (ex19del) cells increased phosphorylation of BRAF, MEK1/2, ERK1/2, and signal transducer and activator of transcription 3 and conferred resistance to growth inhibition by osimertinib. MEK inhibition with trametinib synergized with osimertinib to block growth. Alternately, a pan-RAF inhibitor as a single agent blocked growth of all cell lines with mutant EGFR and BRAF fusion. Conclusion: BRAF fusion is a mechanism of AR to EGFR TKI therapy in approximately 2% of patients. Combined inhibition of EGFR and MEK (with osimertinib and trametinib) or BRAF (with a pan-RAF inhibitor) are potential therapeutic strategies that should be explored.

Original languageEnglish
Pages (from-to)802-815
Number of pages14
JournalJournal of Thoracic Oncology
Volume14
Issue number5
DOIs
Publication statusPublished - May 2019
Externally publishedYes

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Protein-Tyrosine Kinases
Lung Neoplasms
acylglycerol kinase
Exons
Mitogen-Activated Protein Kinase Kinases
Cell Line
Therapeutics
Clustered Regularly Interspaced Short Palindromic Repeats
Growth
STAT3 Transcription Factor
Gene Fusion
Ligases
Ubiquitin
Genes
Fingers
Phosphorylation
Pharmaceutical Preparations
osimertinib
trametinib

Keywords

  • Acquired resistance
  • BRAF fusion
  • CRISPR-Cas9
  • EGFR
  • Lung adenocarcinoma
  • Osimertinib

ASJC Scopus subject areas

  • Oncology
  • Pulmonary and Respiratory Medicine

Cite this

Acquired BRAF Rearrangements Induce Secondary Resistance to EGFR therapy in EGFR-Mutated Lung Cancers. / Vojnic, Morana; Kubota, Daisuke; Kurzatkowski, Christopher; Offin, Michael; Suzawa, Ken; Benayed, Ryma; Schoenfeld, Adam J.; Plodkowski, Andrew J.; Poirier, John T.; Rudin, Charles M.; Kris, Mark G.; Rosen, Neal X.; Yu, Helena A.; Riely, Gregory J.; Arcila, Maria E.; Somwar, Romel; Ladanyi, Marc.

In: Journal of Thoracic Oncology, Vol. 14, No. 5, 05.2019, p. 802-815.

Research output: Contribution to journalArticle

Vojnic, M, Kubota, D, Kurzatkowski, C, Offin, M, Suzawa, K, Benayed, R, Schoenfeld, AJ, Plodkowski, AJ, Poirier, JT, Rudin, CM, Kris, MG, Rosen, NX, Yu, HA, Riely, GJ, Arcila, ME, Somwar, R & Ladanyi, M 2019, 'Acquired BRAF Rearrangements Induce Secondary Resistance to EGFR therapy in EGFR-Mutated Lung Cancers', Journal of Thoracic Oncology, vol. 14, no. 5, pp. 802-815. https://doi.org/10.1016/j.jtho.2018.12.038
Vojnic, Morana ; Kubota, Daisuke ; Kurzatkowski, Christopher ; Offin, Michael ; Suzawa, Ken ; Benayed, Ryma ; Schoenfeld, Adam J. ; Plodkowski, Andrew J. ; Poirier, John T. ; Rudin, Charles M. ; Kris, Mark G. ; Rosen, Neal X. ; Yu, Helena A. ; Riely, Gregory J. ; Arcila, Maria E. ; Somwar, Romel ; Ladanyi, Marc. / Acquired BRAF Rearrangements Induce Secondary Resistance to EGFR therapy in EGFR-Mutated Lung Cancers. In: Journal of Thoracic Oncology. 2019 ; Vol. 14, No. 5. pp. 802-815.
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abstract = "Introduction: Multiple genetic mechanisms have been identified in EGFR-mutant lung cancers as mediators of acquired resistance (AR) to EGFR tyrosine kinase inhibitors (TKIs), but many cases still lack a known mechanism. Methods: To identify novel mechanisms of AR, we performed targeted large panel sequencing of samples from 374 consecutive patients with metastatic EGFR-mutant lung cancer, including 174 post-TKI samples, of which 38 also had a matched pre-TKI sample. Alterations hypothesized to confer AR were introduced into drug-sensitive EGFR-mutant lung cancer cell lines (H1975, HCC827, and PC9) by using clustered regularly interspaced short palindromic repeats/Cas9 genome editing. MSK-LX138cl, a cell line with EGFR exon 19 deletion (ex19del) and praja ring finger ubiquitin ligase 2 gene (PJA2)/BRAF fusion, was generated from an EGFR TKI–resistant patient sample. Results: We identified four patients (2.3{\%}) with a BRAF fusion (three with acylglycerol kinase gene (AGK)/BRAF and one with PJA2/BRAF) in samples obtained at AR to EGFR TKI therapy (two posterlotinib samples and two posterlotinib and postosimertinib samples). Pre-TKI samples were available for two of four patients and both were negative for BRAF fusion. Induction of AGK/BRAF fusion in H1975 (L858R + T790M), PC9 (ex19del) and HCC827 (ex19del) cells increased phosphorylation of BRAF, MEK1/2, ERK1/2, and signal transducer and activator of transcription 3 and conferred resistance to growth inhibition by osimertinib. MEK inhibition with trametinib synergized with osimertinib to block growth. Alternately, a pan-RAF inhibitor as a single agent blocked growth of all cell lines with mutant EGFR and BRAF fusion. Conclusion: BRAF fusion is a mechanism of AR to EGFR TKI therapy in approximately 2{\%} of patients. Combined inhibition of EGFR and MEK (with osimertinib and trametinib) or BRAF (with a pan-RAF inhibitor) are potential therapeutic strategies that should be explored.",
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T1 - Acquired BRAF Rearrangements Induce Secondary Resistance to EGFR therapy in EGFR-Mutated Lung Cancers

AU - Vojnic, Morana

AU - Kubota, Daisuke

AU - Kurzatkowski, Christopher

AU - Offin, Michael

AU - Suzawa, Ken

AU - Benayed, Ryma

AU - Schoenfeld, Adam J.

AU - Plodkowski, Andrew J.

AU - Poirier, John T.

AU - Rudin, Charles M.

AU - Kris, Mark G.

AU - Rosen, Neal X.

AU - Yu, Helena A.

AU - Riely, Gregory J.

AU - Arcila, Maria E.

AU - Somwar, Romel

AU - Ladanyi, Marc

PY - 2019/5

Y1 - 2019/5

N2 - Introduction: Multiple genetic mechanisms have been identified in EGFR-mutant lung cancers as mediators of acquired resistance (AR) to EGFR tyrosine kinase inhibitors (TKIs), but many cases still lack a known mechanism. Methods: To identify novel mechanisms of AR, we performed targeted large panel sequencing of samples from 374 consecutive patients with metastatic EGFR-mutant lung cancer, including 174 post-TKI samples, of which 38 also had a matched pre-TKI sample. Alterations hypothesized to confer AR were introduced into drug-sensitive EGFR-mutant lung cancer cell lines (H1975, HCC827, and PC9) by using clustered regularly interspaced short palindromic repeats/Cas9 genome editing. MSK-LX138cl, a cell line with EGFR exon 19 deletion (ex19del) and praja ring finger ubiquitin ligase 2 gene (PJA2)/BRAF fusion, was generated from an EGFR TKI–resistant patient sample. Results: We identified four patients (2.3%) with a BRAF fusion (three with acylglycerol kinase gene (AGK)/BRAF and one with PJA2/BRAF) in samples obtained at AR to EGFR TKI therapy (two posterlotinib samples and two posterlotinib and postosimertinib samples). Pre-TKI samples were available for two of four patients and both were negative for BRAF fusion. Induction of AGK/BRAF fusion in H1975 (L858R + T790M), PC9 (ex19del) and HCC827 (ex19del) cells increased phosphorylation of BRAF, MEK1/2, ERK1/2, and signal transducer and activator of transcription 3 and conferred resistance to growth inhibition by osimertinib. MEK inhibition with trametinib synergized with osimertinib to block growth. Alternately, a pan-RAF inhibitor as a single agent blocked growth of all cell lines with mutant EGFR and BRAF fusion. Conclusion: BRAF fusion is a mechanism of AR to EGFR TKI therapy in approximately 2% of patients. Combined inhibition of EGFR and MEK (with osimertinib and trametinib) or BRAF (with a pan-RAF inhibitor) are potential therapeutic strategies that should be explored.

AB - Introduction: Multiple genetic mechanisms have been identified in EGFR-mutant lung cancers as mediators of acquired resistance (AR) to EGFR tyrosine kinase inhibitors (TKIs), but many cases still lack a known mechanism. Methods: To identify novel mechanisms of AR, we performed targeted large panel sequencing of samples from 374 consecutive patients with metastatic EGFR-mutant lung cancer, including 174 post-TKI samples, of which 38 also had a matched pre-TKI sample. Alterations hypothesized to confer AR were introduced into drug-sensitive EGFR-mutant lung cancer cell lines (H1975, HCC827, and PC9) by using clustered regularly interspaced short palindromic repeats/Cas9 genome editing. MSK-LX138cl, a cell line with EGFR exon 19 deletion (ex19del) and praja ring finger ubiquitin ligase 2 gene (PJA2)/BRAF fusion, was generated from an EGFR TKI–resistant patient sample. Results: We identified four patients (2.3%) with a BRAF fusion (three with acylglycerol kinase gene (AGK)/BRAF and one with PJA2/BRAF) in samples obtained at AR to EGFR TKI therapy (two posterlotinib samples and two posterlotinib and postosimertinib samples). Pre-TKI samples were available for two of four patients and both were negative for BRAF fusion. Induction of AGK/BRAF fusion in H1975 (L858R + T790M), PC9 (ex19del) and HCC827 (ex19del) cells increased phosphorylation of BRAF, MEK1/2, ERK1/2, and signal transducer and activator of transcription 3 and conferred resistance to growth inhibition by osimertinib. MEK inhibition with trametinib synergized with osimertinib to block growth. Alternately, a pan-RAF inhibitor as a single agent blocked growth of all cell lines with mutant EGFR and BRAF fusion. Conclusion: BRAF fusion is a mechanism of AR to EGFR TKI therapy in approximately 2% of patients. Combined inhibition of EGFR and MEK (with osimertinib and trametinib) or BRAF (with a pan-RAF inhibitor) are potential therapeutic strategies that should be explored.

KW - Acquired resistance

KW - BRAF fusion

KW - CRISPR-Cas9

KW - EGFR

KW - Lung adenocarcinoma

KW - Osimertinib

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