Resistance Mechanisms to Targeted Therapies in ROS1+ and ALK+ Non–small Cell Lung Cancer

Abstract

Despite initial benefit from tyrosine kinase inhibitors (TKIs), patients with advanced non-small cell lung cancer (NSCLC) harboring (ALK) and (ROS1) gene fusions ultimately progress. Here, we report on the potential resistance mechanisms in a series of patients with ALK and ROS1 NSCLC progressing on different types and/or lines of -targeted therapy. We used a combination of next-generation sequencing (NGS), multiplex mutation assay, direct DNA sequencing, RT-PCR, and FISH to identify fusion variants/partners and copy-number gain (CNG), kinase domain mutations (KDM), and copy-number variations (CNVs) in other cancer-related genes. We performed testing on 12 and 43 patients. One of 12 ROS1 (8%) and 15 of 43 (35%) ALK patients harbored KDM. In the ROS1 cohort, we identified and β-catenin mutations and HER2-mediated bypass signaling as non-ROS1-dominant resistance mechanisms. In the ALK cohort, we identified a novel gene fusion, a fusion, 2 , and 3 mutations, as well as mutations in , and In addition, we identified CNV in multiple proto-oncogenes genes including and others. We identified a putative TKI resistance mechanism in six of 12 (50%) ROS1 patients and 37 of 43 (86%) ALK patients. Our data suggest that a focus on KDMs will miss most resistance mechanisms; broader gene testing strategies and functional validation is warranted to devise new therapeutic strategies for drug resistance. .

Clinical Utility of Cell-Free DNA for the Detection of ALK Fusions and Genomic Mechanisms of ALK Inhibitor Resistance in Non–Small Cell Lung Cancer

“…This result is similar to other studies reporting between 44 and 56% of patients with kinase domain mutations. 10,27,37,38 Notably, seven of the 16 (43.8%) patients with resistance mutations in ALK demonstrated more than one mutation. This contrasts with a recently published series of ALK positive patients who underwent tissue-based NGS after progression on second generation ALKi in which 6/48 (12%) patient specimens contained compound mutations.…”

“…Recently reported cohorts of ALK positive patients have identified similar percentages of resistance mechanisms (including kinase domain mutations, alternative oncogenic mutations, and copy number gains) in patients who have progressed on at least one type of ALKi therapy. 10,37,38 …”

Patterns of Metastatic Spread and Mechanisms of Resistance to Crizotinib in ROS1-Positive Non–Small-Cell Lung Cancer

“…16,43–45 Thus far, insights into the mechanisms of resistance to crizotinib among ROS1 -positive patients have been quite limited and generally consist of isolated case reports, small series and preclinical evaluations. 16–19,46 To date, seven different ROS1 resistance mutations have been described. 16–19,46 In addition, up-regulation of bypass signaling pathways (e.g., EGFR, RAS, and KIT) have also been reported.…”

“…16–19,46 To date, seven different ROS1 resistance mutations have been described. 16–19,46 In addition, up-regulation of bypass signaling pathways (e.g., EGFR, RAS, and KIT) have also been reported. 20–22,47 …”

Recent Advances in Targeting ROS1 in Lung Cancer

“…This mutation affects the key electrostatic interaction between the D2033 residue and the piperidine moiety of crizotinib and also affects the neighboring residues at the surface of the ATP-binding pocket (64). As demonstrated in Figure 4A, additional mutations reported in clinical samples include: S1986Y/F (a mutation affecting the αC helix of the kinase domain which causes steric interference with drug binding; analogous to ALK C1156Y) (42, 65), L2026M (a ‘gatekeeper’ mutation in the ATP-binding pocket which hinders drug binding; analogous to ALK L1196M) (66), and L1951R (a solvent front mutation; no known analogous mutation in ALK) (66). The L1951R resistance mutation also emerged in an N -ethyl- N -nitrosourea (ENU) mutagenesis screen with CD74-ROS1 -transformed Ba/F3 cells (67).…”