MET gene amplification is a mechanism of resistance to entrectinib in ROS1+ NSCLC

Abstract

Background: ROS1 tyrosine kinase inhibitors (TKIs) have demonstrated significant clinical benefit for ROS1+ NSCLC patients. However, TKI resistance inevitably develops through ROS1 kinase domain (KD) modification or another kinase driving bypass signaling. While multiple TKIs have been designed to target ROS1 KD mutations, less is known about bypass signaling in TKI-resistant ROS1+ lung cancers. Methods: Utilizing a primary, patient-derived TPM3-ROS1 cell line (CUTO28), we derived an entrectinib-resistant line (CUTO28-ER). We evaluated proliferation and signaling responses to TKIs, and utilized RNA sequencing, whole exome sequencing, and fluorescence in situ hybridization to detect transcriptional, mutational, and copy number alterations, respectively. We substantiated in vitro findings using a CD74-ROS1 NSCLC patient's tumor samples. Last, we analyzed circulating tumor DNA (ctDNA) from ROS1+ NSCLC patients in the STARTRK-2 entrectinib trial to determine the prevalence of MET amplification. Results: CUTO28-ER cells did not exhibit ROS1 KD mutations. MET TKIs inhibited proliferation and downstream signaling and MET transcription was elevated in CUTO28-ER cells. CUTO28-ER cells displayed extrachromosomal (ecDNA) MET amplification without MET activating mutations, exon 14 skipping, or fusions. The CD74-ROS1 patient samples illustrated MET amplification while receiving ROS1 TKI. Finally, two of 105 (1.9%) entrectinib-resistant ROS1+ NSCLC STARTRK-2 patients with ctDNA analysis at enrollment and disease progression displayed MET amplification. Conclusions: Treatment with ROS1-selective inhibitors may lead to MET-mediated resistance. The discovery of ecDNA MET amplification is noteworthy, as ecDNA is associated with more aggressive cancers. Following progression on ROS1-selective inhibitors, MET gene testing and treatments targeting MET should be explored to overcome MET-driven resistance.

Efficacy of Crizotinib After Entrectinib Resistance Due to MET Polysomy in ROS1-Rearranged NSCLC: A Case Report

“… 2 KRAS G12C mutation, KRAS amplification, FGF3 amplification, MET amplification, and the ROS1 mutations G2032R and F2004C/I have been identified as mechanisms of resistance to entrecinib. 3 , 4 , 5 , 6 Our report suggests that crizotinib could be an effective option for patients with MET amplification or polysomy, even after disease progression during entrectinib treatment.…”

TKI Type Switching Overcomes ROS1 L2086F in ROS1 Fusion-Positive Cancers

“…The CUTO-28 cell line is a patient-derived cell line harboring a TPM3-ROS1 fusion, authenticated by short tandem repeat (STR) analysis by the Barbara Davis Center Molecular Biology Service Center at the University of Colorado 16 .…”

Pre-clinical modelling of ROS1+ non-small cell lung cancer

“…Inevitably, the majority of patients will experience disease progression due to the appearance of tumor resistance mechanisms. A first group of observed strategies consist in bypassing the ROS1-mediated signaling by acquiring a wide range of mutations such as MET amplification, KRAS G12C , BRAF V600E [25,26], activation of signaling pathways like EGFR, RAS, and KIT or histological transformation to small cell lung cancer [27][28][29]. The second group of events consist in point mutations located in the ROS1 kinase domain which modify the conformation of its active site, preventing drug binding without impairing the capacity to phosphorylate the downstream targets.…”