Mechanisms Of Crizotinib Resistance Research Articles

Disease progression patterns and molecular resistance mechanisms to crizotinib of lung adenocarcinoma harboring ROS1 rearrangements

This retrospective study investigated the association between the pattern of disease progression and molecular mechanism of acquired resistance in a large cohort of 49 patients with ROS1-rearranged advanced non-small-cell lung cancer treated with first-line crizotinib. We found that treatment-emergent ROS1 point mutations were the major molecular mechanism of crizotinib resistance, particularly for patients who developed extracranial-only disease progression. Our findings highlight the importance of rebiopsy and gene testing for subsequent-line therapeutic management.

LINC01001 Promotes Progression of Crizotinib-Resistant NSCLC by Modulating IGF2BP2/MYC Axis.

Background: Crizotinib is a microtubule-related protein-4-anaplastic lymphoma kinase (EML4-ALK) multi-target tyrosine kinase inhibitor applied in the treatment of ALK-rearranged NSCLC. However, the specific molecular mechanism underlying its therapeutic effect remains unclear. Therefore, the purpose of this research is to explore the mechanism by which crizotinib targets NSCLC with ALK-rearrangement, mainly whether it is related to LINC01001 in regulating NSCLC progression via IGF2BP2/MYC axis. Methods: RT-qPCR is conducted to evaluate the mRNA levels of LINC01001, IGF2BP2 and MYC in A549/R and H1299/R cells. CCK-8 and EdU assays are performed to assess the viability and proliferation of A549/R and H1299/R cells. Western blot is conducted to measure the levels of PCNA and Ki-67 proteins in A549/R and H1299/R cells. FACs and TUNEL are performed to detect apoptosis of A549/R and H1299/R cells. Immunohistochemical staining is performed to assess the levels of Ki67 in crizotinib-resistant NSCLC tissue. Bioinformatics analysis of multiple CLIP (crosslinking-immunoprecipitation) data found potential binding sites between LINC01001 and IGF2BP2, IGF2BP2 and MYC, that are confirmed by RIP assay and RNA pulldown assay. Results: Our findings illustrated that LINC01001 is highly expressed in crizotinib-resistant NSCLC cells and associated with poor overall survival of NSCLC patients. Inhibition of LINC01001 depresses crizotinib resistance of NSCLC cells. LINC01001 interacts with IGF2BP2, and inhibition of IGF2BP2 depresses crizotinib resistance of NSCLC cells. IGF2BP2 interacts with the mRNA of MYC, and LINC01001 overexpression increases crizotinib resistance of NSCLC via MYC. Conclusion: LINC01001 promotes the progression of crizotinib-resistant NSCLC by modulating the IGF2BP2/MYC axis. Our research clarifies the specific mechanism of crizotinib-resistance in NSCLC treatment.

Genomic and clinical characteristics of MET exon14 alterations in a large cohort of Chinese cancer patients revealed distinct features and a novel resistance mechanism for crizotinib

Background: Alterations in MET exon 14 (METex14) and its flanking intronic regions have been identified in a variety of cancers. Patients with METex14 alterations often benefit from MET inhibitors such as crizotinib. Given the unique mutation profiles of Chinese lung cancer patients, it is necessary to investigate the prevalence of METex14 alterations in a large cohort of cancer patients.Patients and methods: Cases carrying METex14 alterations were screened from 26,391 Chinese cancer patients by next-generation sequencing (NGS), and the clinicopathologic and molecular characteristics were reviewed.Results: Compared to Western population (~3%), the frequency of METex14 alterations is much lower in Chinese cancer patients (0.7%, n=184) and lung cancer patients (1.1%, n=175). Seventy-eight distinct METex14 alterations, including several novel alteration types were detected. Concurrent MET copy gain and non-exon14 MET mutations were also found. EGFR copy gain (11%) and mutations (8%), KRAS (5%) and PIK3CA (5%), appeared in a mutually exclusive pattern. Female patients contain much less TP53 mutations than male patients (65% vs. 24%, FDR = 0.01). Co-amplification of CDK4 and MDM2, CDK6 and EGFR were identified, which indicated cell cycle dysregulation and EGFR alteration are important co-occurring features in patients with METex 14 alteration. Of 9 tissue specimens having PD-L1 immunohistochemistry (IHC) results, 5 of them (55.5%) were found PD-L1 positive, which is comparable to other types of tumor. In 14 crizotinib-treated patients, the median progression free survival (mPFS) was 7 months. Upon resistance to crizotinib, two patients acquired secondary mutations in MET and one patient acquired BRAF p.K601E that can be a novel resistance mechanism.Conclusion: Chinese cancer patients have a relatively lower frequency of METex14 alterations compared to Western patients. Patients with METex14 alterations showed distinct molecular characteristics and the representative case study showed responses to MET tyrosine kinase inhibitor (TKI).

Abstract PO-50: Phophatases modulate resistance to ALK inhibitors in anaplastic large-cell lymphoma

Abstract Introduction: Anaplastic large-cell lymphomas (ALCL) frequently carry oncogenic fusions involving the anaplastic lymphoma kinase (ALK) gene. The ALK fusions activate several signaling pathways, promoting cell growth, migration, and survival. Chemotherapy is the standard treatment for ALCL patients, but about 30% of patients relapse. Targeting ALK using tyrosine kinase inhibitors (TKIs) has shown promising results, and the FDA recently granted breakthrough therapy designation to crizotinib for use in patients with relapsed/refractory ALK+ ALCL. However, resistance to crizotinib develops in ALK+ ALCL patients secondary to ALK mutations or unknown mechanisms. In this study, we aimed at elucidating unknown bypass mechanisms of crizotinib resistance in ALK+ ALCL. Methods: We used Genome-wide CRISPR-Cas9 Knockout Screening (GeCKO.v2) to identify candidate genes that contribute to resistance to crizotinib. Four different ALCL cell lines were infected with Lenti-GeCKO libraries. After treatment with crizotinib for 14 days to select for resistant cells, next-generation sequencing was performed on crizotinib-resistant cells to identify candidate resistance genes. Top candidates were selected for validation assays and further analyses. Results: Genomic loss-of-function screens identified two phosphatases, PTPN1 and PTPN2, in all ALCL cell lines as consistent top hits driving resistance to crizotinib. Functional validation of these candidate genes showed that single loss of either PTPN1 or PTPN2 generates immediate resistance to crizotinib and other ALK TKIs such as alectinib and lorlatinib. Consistently, RNA-seq in patients who developed resistance to crizotinib showed downregulation of PTPN1 or PTPN2 expression. By multiple assays, we demonstrate that PTPN1 and PTPN2 are phosphatases that de-phosphorylate ALK, thereby regulating its overall phosphorylation levels and activity. In addition, we found that PTPN1, but not PTPN2, is also a phosphatase of SHP2, a key mediator of oncogenic ALK signaling. Downstream signaling analysis showed that deletion of PTPN1 or PTPN2 induces resistance to crizotinib by hyperactivating the MAPK and JAK/STAT pathways. A treatment that combined crizotinib and a recently developed SHP2 inhibitor (SHP099) completely blocked the sustained MAPK activation and reverted crizotinib resistance in vitro and in vivo. Conclusions: We discovered that PTPN1 and PTPN2 are ALK phosphatases that control sensitivity to ALK TKIs in ALCL. Combined inhibition of SHP2 is a potential therapeutic approach to overcome resistance to ALK TKIs in ALCL. Citation Format: Elif Atabay, Qi Wang, Taek-Chin Cheong, Nina Prokoph, Chiara Ambrogio, Ines Mota, Achille Pich, Enrico Patrucco, Claudia Voena, Roberto Chiarle. Phophatases modulate resistance to ALK inhibitors in anaplastic large-cell lymphoma [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-50.

398P Real-world mechanism of crizotinib-resistance in MET exon 14 skipping mutations non-small-cell lung cancer using next generation sequencing: A multicenter study

398P Real-world mechanism of crizotinib-resistance in MET exon 14 skipping mutations non-small-cell lung cancer using next generation sequencing: A multicenter study

Clinical activity of brigatinib in ROS1-rearranged non-small cell lung cancer.

Brigatinib is a potent ROS1 inhibitor. The existing data on its clinical activity in ROS1-rearranged non-small cell lung cancer (NSCLC) are limited to four cases. Six patients with ROS1-rearranged advanced NSCLC treated with brigatinib were identified through search of the internal databases of four participating cancer centers. Four additional patients were selected by PubMed and Google Scholar search. The objective response rate (ORR), progression-free survival (PFS) (RECIST v.1.1), duration of treatment (DOT), and safety were assessed. Of eight patients evaluable for response assessment (crizotinib naive-1, crizotinib resistant -7), three patients demonstrated a partial response (ORR-37%). One crizotinib-naive patient had an ongoing response at 21.6months. Of seven crizotinib-resistant patients, two patients demonstrated a partial response (ORR-29%), and one patient (14%) had stable disease. PFS, available in four crizotinib-resistant patients, was 7.6 + , 2.9, 2.0, and 0.4months. In crizotinib-resistant patients, DOT was 9.7 + , 7.7 + , 7.6 + , 4.0, 2.0, 1.1, 0.4months, and was not reported in two patients. Genomic profiling in one responder revealed no ROS1 alteration, suggesting that the response was attributable to "off-target" brigatinib activity. In two patients with progressive disease, genomic profiling demonstrated a cMET exon 14 mutation + KRAS G12A mutation in one case, and a persisting ROS1-CD74 fusion + TP53 K139N, FGFR2 E250G, ATM G2695D, and NF1 R2258Q mutations in the other. No grade 3-5 toxicity was observed. Brigatinib demonstrated modest activity in crizotinib-resistant ROS1-rearranged NSCLC. Its intracranial and systemic activity should be assessed in correlation with the underlying molecular mechanism of crizotinib resistance.

Abstract C084: Crizotinib resistance mechanisms and potential therapeutic strategies to overcome the resistance in ROS1-rearranged non-small cell lung cancer

Abstract ROS1 rearrangement was observed in about 1 % of NSCLC patients and in several other cancers such as cholangiocarcinoma, glioblastoma, or colorectal cancer. To date, crizotinib, an ALK/ROS1 inhibitor was approved and widely used for the treatment of ROS1 rearranged NSCLC. However, the tumor relapses within a few years due to the emergence of crizotinib resistance by the secondary mutations in ROS1 kinase domain (e.g. G2032R) or other unidentified mechanisms. In this study, we explored crizotinib resistance mechanisms using ENU mutagenesis screening and the analysis of crizotinib resistant patient’s pleural effusion. We found several secondary mutations in ROS1 kinase domain including previously reported mutations. From a crizotinib resistant patient’s specimen, no secondary mutation in ROS1 was observed. By establishing a cell line from the specimen, we performed kinase inhibitor screening combined with crizotinib, and found that a combination of crizotinib with dasatinib or a few other tyrosine kinase inhibitors can suppress the growth. These results suggested that a bypass pathway mediated resistance through Src family kinase conferred resistance in this crizotinib resistant case. For overcoming the secondary ROS1 mutations mediated crizotinib resistance, we characterized several ROS1 inhibitors including a new selective ROS1/NTRK inhibitor DS-6051b in preclinical models of ROS1-rarranged cancers by newly establishing cell lines from TKI naïve ROS1 fusion positive NSCLC patients, or developing resistant mutation harboring HCC78 (SCL34A2-ROS1) or Ba/F3-CD74-ROS1 cell line models. Using these preclinical models, we demonstrated that DS-6051b induced dramatic growth inhibition of both wild type and G2032R mutant ROS1–rearranged cancers in vitro and in vivo, suggesting that DS-6051b might be effective in treating wildtype and crizotinib resistant mutant ROS1-rearranged lung cancer. This study revealed that potential resistance mechanisms in ROS1-rearranged NSCLC are similar to those identified in ALK rearranged NSCLC, and next-generation ROS1 inhibitor provides future promising therapeutic strategies to overcome the secondary mutation mediated resistance. Citation Format: Ryohei Katayama, Bo Gong, Makoto Nishio, Naoya Fujita. Crizotinib resistance mechanisms and potential therapeutic strategies to overcome the resistance in ROS1-rearranged non-small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C084. doi:10.1158/1535-7163.TARG-19-C084

Identifying Novel Mechanisms of Resistance to Tyrosine Kinase Inhibitors in Anaplastic Large Cell Lymphoma

INTRODUCTION: Anaplastic large cell lymphomas (ALCL) frequently carry oncogenic fusion proteins as a consequence of chromosomal translocations of the anaplastic lymphoma kinase (ALK) gene. The fusion protein resulting from the translocation between dimerization domain of nucleophosmin (NPM) and intracellular tyrosine kinase domain of ALK activates several signaling pathways, promoting cell growth, transformation, migration, and survival of the cells. Chemotherapy has been used as a standard treatment approach for ALCL patients, yet about 30% of patients relapse. A more specific treatment method is based on targeting ALK tyrosine kinase using tyrosine kinase inhibitors (TKIs). Crizotinib is an ALK TKI that is approved for the treatment of ALK-rearranged lung cancer and has received Breakthrough Therapy designation for lymphoma because of its high activity in chemo refractory ALCL. However, as for lung cancer, also ALCL patient develop crizotinib resistance due to ALK mutations or unknown mechanisms. In this study, we aimed at elucidating unknown by-pass mechanisms of crizotinib resistance in ALCL. METHODS: We used Genome-wide CRISPR-Cas9 Knockout Screening (GeCKO) to identify candidate genes that contribute to resistance to crizotinib. Four different ALCL cell lines were infected with Lenti-GeCKO libraries. After treatment with crizotinib for 14 days, DNA isolation and next generation sequencing was performed on crizotinib resistant cells to identify candidate genes depleted by the GeCKO screening. Top candidates were selected for validation assays and further analyses. RESULTS: We identified two phosphatases, PTPN1 and PTPN2, in different ALCL cell lines as consistent top hits. Functional validation of these candidate genes showed that single loss of either PTPN1 or PTPN2 generate immediate resistance to crizotinib in ALCL cell lines. Analysis of downstream pathways showed that while loss of PTPN1 activates primarily the MAPK pathway, loss of PTPN2 promotes persistent STAT3 and MAPK activation in ALK inhibited cells. Remarkably, in PTPN1 knockout cells we observed hyperactivation of SHP2, an oncogenic phosphatase that positively regulates the RAS-MAPK pathway. On the other hand, over-expression of PTPN1 and PTPN2 partially inhibited SHP2 phosphorylation. A treatment that combined crizotinib and the recently developed SHP2 inhibitor completely blocked the sustained ERK phosphorylation and reverted the crizotinib resistance observed in PTPN1 and PTPN2 deficient lymphoma cells. CONCLUSIONS: GeCKO library screen identified PTPN1 and PTPN2 as specific genes that mediate crizotinib resistance in ALCL cell lines. Loss of PTPN1 and PTPN2 drives resistance by activating MAPK and/or JAK-STAT pathway. Combined inhibition of SHP2 is a potent therapeutic approach to overcome resistance to crizotinib in ALCL cells. Disclosures Gambacorti-Passerini: Bristol-Meyers Squibb: Consultancy; Pfizer: Honoraria, Research Funding.

P1.14-07 Genomic Profiling of Liquid Biopsies During 2nd/3rd Generation ALK Inhibitor Therapy to Identify Novel Mechanisms of Resistance

Second- and third-generation ALK inhibitors each have diverse mechanisms of resistance. Only a fraction of resistance is due to secondary mutations of the ALK gene. Altered bypass tracts are likely the case in some other instances. Genomic alterations of other genes and pathways may be a third mechanism of resistance. Repeat liquid biopsies during the course of patients’ treatments can provide a minimally invasive method for sampling cancer-specific genomic information that leads to improved treatment selection. In the Lung Cancer Clinic of the Princess Margaret Cancer Centre, serial plasma samples were collected from six lung cancer patients with ALK rearrangement at multiple serial clinic visits pre- and post- progression on next-generation ALK inhibitors. We focused on next generation agents, as there has been previous focus on crizotinib resistance mechanisms already. Cell-free DNA (cfDNA) was extracted (median: 50 ng; range: 20-2760 ng) and profiled using a next-generation sequencing (NGS) platform with Geneseeq Prime 425-gene panel at a mean coverage depth of 4747X (and a deduplicated mean coverage depth of 2160X). Somatic alterations from plasma cfDNA were detected in all six patients at various time points with three patients having detectable ALK alterations. Systemic progression (2/2 patients) correlated well with the ability of liquid biopsies to detect somatic mutations, while central nervous system (CNS)-predominant progression did not (4/4 patients). One patient, after disease progression on ceritinib, alectinib and brigatinib, exhibited variable allele fractions (AFs) of ALK G1202R mutation in cfDNA. The levels of G1202R decreased and ultimately became undetectable, corresponding to the patient’s clinical response to lorlatinib. In a patient who exhibited significant systemic progression, a massive increase in mutation AFs and many newly acquired mutations were detected in the cfDNA, including NOTCH1, DICER1, BRCA2, TP53, CDKN2A, ERBB3, and FAT1mutations. However, the increase in the number of co-mutations was not related to increases in the amount of extracted cfDNA. Broad panel-based NGS of plasma cfDNA enabled noninvasive detection of systemic (but not CNS-predominant) progression during second and subsequent generation ALK inhibitor treatment, and can identify known and putative mechanisms of resistance for treatment decision-making.

Abstract 2640: DKK1 overexpression might induce crizotinib resistance

Abstract NSCLC patients with pleural effusions tend to show progressive status and malignant features. Newly established lung cancer cell lines from pleural effusions, SNU-2550 and SNU-2563 were harboring ALK rearrangement and they were originally sensitive to crizotinib. After treated with regular crizotinib treatment and recovery at least 1 year, crizotinib-resistant cell lines (SNU-2550CR and SNU-2563CR) that became resistant to crizotinib more than 5 times were established. And then, whole exome sequencing (WES) and RNA-seq were operated in order to understand way to acquire resistance. According to WES result, there were differences in mutations between parental cell lines and resistant cell lines. For example, mutations in MKNK2, IGFN1, PRSS1 and FOXA2 genes were only present in SNU-2550CR not SNU-2550. Variations of ESX1, PRSS1, PCDHA4 and AGAP3 genes were observed in only SNU-2563CR. When the differences were studied and visualized via SPIA two-way evidence plot and heatmap, genes related with cell cycle, p53 and Wnt pathway were commonly changed in RNA expression level. In fact, there were expressional differences in genes related those pathways such as MAPK2, DKK1, APC and GSK3b genes. Among them, Dkk1 expression level was more than doubled in two set. Through those analysis, we examined differences between parental cell lines that have sensitive reactivity and resistant cell lines that acquired resistance. When crizotinib resistance was induced, Dkk1 expression was elevated. Augmentation of Dkk1 expression level induces the level of overall β-catenin expression, and cytoplasmic β-catenin tends to be concentrated adjacent to membrane and into nucleus region. Therefore, Dkk1 can be considered as a factor that is related to crizotinib resistance by up-regulating Wnt/β-catenin pathway in lung cancer. Acquired resistance to crizotinib is major predicament especially when there is ALK rearrangement. Studying the mechanism of crizotinib resistance therefore improves the prognosis of ALK rearrangement lung cancer. We found that Dkk1 overexpression might be correlated to crizotinib resistance. Note: This abstract was not presented at the meeting. Citation Format: Ha Young Seo. DKK1 overexpression might induce crizotinib resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2640.

Amplification of Wild-type KRAS Imparts Resistance to Crizotinib in MET Exon 14 Mutant Non-Small Cell Lung Cancer.

MET inhibitors can be effective therapies in patients with MET exon 14 (METex14) mutant non-small cell lung cancer (NSCLC). However, long-term efficacy is limited by the development of drug resistance. In this study, we characterize acquired amplification of wild-type (WT) KRAS as a molecular mechanism behind crizotinib resistance in three cases of METex14-mutant NSCLC and propose a combination therapy to target it. The patient-derived cell line and xenograft (PDX) DFCI358 were established from a crizotinib-resistant METex14-mutant patient tumor with massive focal amplification of WT KRAS. To characterize the mechanism of KRAS-mediated resistance, molecular signaling was analyzed in the parental cell line and its KRAS siRNA-transfected derivative. Sensitivity of the cell line to ligand stimulation was assessed and KRAS-dependent expression of EGFR ligands was quantified. Drug combinations were screened for efficacy in vivo and in vitro using viability and apoptotic assays. KRAS amplification is a recurrent genetic event in crizotinib-resistant METex14-mutant NSCLC. The key characteristics of this genetic signature include uncoupling MET from downstream effectors, relative insensitivity to dual MET/MEK inhibition due to compensatory induction of PI3K signaling, KRAS-induced expression of EGFR ligands and hypersensitivity to ligand-dependent and independent activation, and reliance on PI3K signaling upon MET inhibition. Using patient-derived cell line and xenografts, we characterize the mechanism of crizotinib resistance mediated by KRAS amplification in METex14-mutant NSCLC and demonstrate the superior efficacy of the dual MET/PI3K inhibition as a therapeutic strategy addressing this resistance mechanism.

Abstract 1818: Activation of IGF-1R pathway and NPM-ALK G1269A mutation confer resistance to crizotinib in NPM-ALK positive lymphoma

Abstract ALK-positive Anaplastic Large Cell Lymphoma (ALCL), harboring NPM-ALK fusion gene, is sensitive to dual ALK/MET inhibitor crizotinib. However, cancer cells eventually develop resistance to crizotinib after remarkable initial responses, the mechanisms of crizotinib resistance in NPM-ALK positive ALCL remained unclear. To investigate the mechanisms of ALCL cells resistant to crizotinib, we established a model of acquired resistance to crizotinib by gradually exposing sensitive NPM-ALK-positive ALCL cell line to higher concentration of crizotinib. We found that NPM-ALK G1269A mutation were selected in 400nM resistant clones and activation of IGF-1R pathway. Then we generated a G1269A-mutated sub-lines by limiting dilution, which were sensitive to second-generation ALK inhibitor NVP-TAE684. IGF-1R inhibitor picropodophyllotoxin had no effect on these sub-clones and didn't change sensitivity to first and second generation ALK TKIs. But IGF-1R inhibitor increased sensitivity to crizotinib and NVP-TAE684 in 400nM crizotinib-resistant cells. Thus, we have shown that IGF-1R pathway and NPM-ALK G1269A mutation contribute to resistance to ALK TKIs and combined ALK/IGF1R inhibition improves therapeutic efficacy. Citation Format: Yanrong Li, Kai Wang, Jingdong Zhang. Activation of IGF-1R pathway and NPM-ALK G1269A mutation confer resistance to crizotinib in NPM-ALK positive lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1818.

Mutations in EMT-Related Genes in ALK Positive Crizotinib Resistant Non-Small Cell Lung Cancers.

Crizotinib is an effective drug for patients with anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer (NSCLC), but upon treatment, the tumors inevitably become crizotinib resistant in time. The resistance mechanisms are only partly understood. In this study, we aim to identify gene mutations associated with resistance in ALKpositive advanced non-squamous NSCLC treated with crizotinib. Four ALK positive patients with progressive disease following crizotinib treatment were identified with paired pre- and post-crizotinib tumor tissue from our previously published cohort. Somatic variants in these samples were detected by whole exome sequencing. In one of the four patients, an ALK-resistance associated mutation was identified. In the other three patients, no ALK-resistance associated mutations were present. In these patients we identified 89 relevant somatic mutations in 74 genes that were specific to the resistant tumors. These genes were enriched in 15 pathways. Four pathways, were related to epithelial-mesenchymal transition (EMT): proteoglycans in cancer, HIF-1 signaling, FoxO signaling pathway, and ECM-receptor interaction. Analysis of other EMT-related pathways revealed three additional genes with mutations specific to the crizotinib-resistant tumor samples. The enrichment of mutations in genes associated with EMT-related pathways indicates that loss of epithelial differentiation may represent a relevant resistance mechanism for crizotinib.

Exploring the crizotinib resistance mechanism of NSCLC with the L1196M mutation using molecular dynamics simulation.

Crizotinib is an anticancer tyrosine kinase inhibitor that is approved for use as a first-line treatment for some non-small-cell lung cancers. L1196M is the most frequently observed mutation in NSCLC patients. This mutation, known as the gatekeeper mutation in the ALK kinase domain, confers resistance to crizotinib by sterically blocking the binding of the drug. However, the molecular mechanism of crizotinib resistance caused by the L1196M mutation is still unclear. Molecular dynamics simulation was therefore utilized in this study to investigate the mechanism by which the L1196M mutation may affect crizotinib resistance. Our results suggest that larger fluctuations in some important regions of the mutant complex compared to the wild-type complex may contribute to the resistance of the mutant complex to crizotinib. Also, mutation-induced alterations to the secondary structure of the complex as well as unstable hydrogen-bonding patterns in the A-loop and P-loop regions decrease the total binding energy of the complex. This study therefore provides a molecular explanation for the resistance to crizotinib caused by the L1196M mutation, which could aid the design of more efficient and selective drugs.

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

The ROS1 tyrosine kinase is activated through ROS1 gene rearrangements in 1-2% of non-small cell lung cancer (NSCLC), conferring sensitivity to treatment with the ALK/ROS1/MET inhibitor crizotinib. Currently, insights into patterns of metastatic spread and mechanisms of crizotinib resistance among ROS1-positive patients are limited. We reviewed clinical and radiographic imaging data of patients with ROS1- and ALK-positive NSCLC in order to compare patterns of metastatic spread at initial metastatic diagnosis. To determine molecular mechanisms of crizotinib resistance, we also analyzed repeat biopsies from a cohort of ROS1-positive patients progressing on crizotinib. We identified 39 and 196 patients with advanced ROS1- and ALK-positive NSCLC, respectively. ROS1-positive patients had significantly lower rates of extrathoracic metastases (ROS1 59.0%, ALK 83.2%, P=0.002), including lower rates of brain metastases (ROS1 19.4%, ALK 39.1%; P = 0.033), at initial metastatic diagnosis. Despite similar overall survival between ALK- and ROS1-positive patients treated with crizotinib (median 3.0 versus 2.5 years, respectively; P=0.786), ROS1-positive patients also had a significantly lower cumulative incidence of brain metastases (34% vs. 73% at 5 years; P<0.0001). Additionally, we identified 16 patients who underwent a total of 17 repeat biopsies following progression on crizotinib. ROS1 resistance mutations were identified in 53% of specimens, including 9/14 (64%) non-brain metastasis specimens. ROS1 mutations included: G2032R (41%), D2033N (6%), and S1986F (6%). Compared to ALK rearrangements, ROS1 rearrangements are associated with lower rates of extrathoracic metastases, including fewer brain metastases, at initial metastatic diagnosis. ROS1 resistance mutations, particularly G2032R, appear to be the predominant mechanism of resistance to crizotinib, underscoring the need to develop novel ROS1 inhibitors with activity against these resistant mutants.

F1174V mutation alters the ALK active conformation in response to Crizotinib in NSCLC: Insight from molecular simulations

Crizotinib is an efficient antineoplastic drug for treatment of non-small cell lung carcinoma (NSCLC), which is identified as an anaplastic lymphoma kinase (ALK) inhibitor. F1174V is a recently identified acquired point mutation relating to the Crizotinib resistance in NSCLC patients. The mechanism of Crizotinib resistance relating to F1174V mutation as a non-active site mutation remains unclear. In this study, the molecular dynamic simulation was used to investigate the possible mechanisms by which F1174V mutation may affect the structure and activity of ALK kinase domain. The results suggested that F1174V mutation could cause two important secondary structure alterations, which led to the local conformational change in ALK kinase domain. This causes more positive free energy in the mutant complex in comparison with the wild-type one. In addition, our structural analyses illustrated that F1174V mutation could result in some important interactions, which represent the key characteristics of the ALK active conformation. This study provided a molecular mechanism for ALK Crizotinib resistance caused by F1174V mutation,which could facilitate designing more efficient drugs.

Gaining insight into crizotinib resistance mechanisms caused by L2026M and G2032R mutations in ROS1 via molecular dynamics simulations and free-energy calculations.

ROS1 fusion kinase-highly expressed in a variety of human cancers-has emerged as an important and attractive target for anticancer drug design. Crizotinib, a well-known drug approved by the FDA as an ALK inhibitor to treat advanced NSCLC, also shows potent inhibitoy activity against ROS1. However, the development of serious resistance due to secondary mutations has been observed in clinical studies. To provide insight into the mechanisms of this drug resistance, molecular dynamics simulations and free-energy calculations were carried out for complexes of crizotinib with wild-type (WT) ROS1 as well as the mutated L2026M and G2032R forms. MD simulations indicated that the L2026M and G2032R systems are slightly less flexible than the WT system. Binding free energy calculations showed that the L2026M and G2032R mutations significantly reduce the binding affinity of crizotinib for ROS1, and that the resistance to crizotinib caused by the L2026M and G2032R mutations arises mostly from increases in entropic terms. Furthermore, calculations of per-residue binding free energies highlighted increased and decreased contributions of some residues in the L2026M and G2032R systems relative to those in the WT system. The present study therefore yielded detailed insight into the mechanisms of resistance to crizotinib caused by the L2026M and G2032R mutations, which should provide the basis for rational drug design to combat crizotinib resistance. Graphical Abstract Superposition of the average structures obtained from the last 10ns of the molecular dynamics simulation trajectoriy for WT (green) and mutated ROS1 (cyan).

Circulating tumor DNA profiling by next generation sequencing reveals heterogeneity of crizotinib resistance mechanisms in a gastric cancer patient with MET amplification.

Crizotinib has been used to counter MET gene amplification in a number of different human malignancies. Transient response to crizotinib in MET-amplified gastric cancer has been reported, but the mechanisms of resistance are not well studied. Here, we reported a stage IV gastric cancer patient with high levels of MET amplification. The implementation of crizotinib treatment led to significant symptomatic improvement in the first 2 months, but was followed by rapid disease progression. Periodic mutation profiling of patient's circulating tumor DNA (ctDNA) by next generation sequencing (NGS) revealed a number of genetic alterations including re-occurrence of MET amplification, multiple secondary MET mutations, a dramatic increase of FGFR2 gene relative copy number as well as mutations in other downstream and bypassing elements, which may collectively related to the patient's cancer progression. Our results illustrate the complex and heterogeneous molecular mechanisms for crizotinib resistance in this patient, and demonstrate the great potential of ctDNA profiling for treatment decision-making and prognosis in clinical practice.

Emergence of resistance to tyrosine kinase inhibitors in non-small-cell lung cancer can be delayed by an upfront combination with the HSP90 inhibitor onalespib.

Background:Tyrosine kinase inhibitors, such as crizotinib and erlotinib, are widely used to treat non-small-cell lung cancer, but after initial response, relapse is common because of the emergence of resistance through multiple mechanisms. Here, we investigated whether a frontline combination with an HSP90 inhibitor could delay the emergence of resistance to these inhibitors in preclinical lung cancer models.Methods:The HSP90 inhibitor, onalespib, was combined with either crizotinib or erlotinib in ALK- or EGFR-activated xenograft models respectively (H2228, HCC827).Results:In both models, after initial response to the monotherapy kinase inhibitors, tumour relapse was observed. In contrast, tumour growth remained inhibited when treated with an onalespib/kinase inhibitor combination. Analysis of H2228 tumours, which had relapsed on crizotinib monotherapy, identified a number of clinically relevant crizotinib resistance mechanisms, suggesting that HSP90 inhibitor treatment was capable of suppressing multiple mechanisms of resistance. Resistant cell lines, derived from these tumours, retained sensitivity to onalespib (proliferation and signalling pathways were inhibited), indicating that, despite their resistance to crizotinib, they were still sensitive to HSP90 inhibition.Conclusions:Together, these preclinical data suggest that frontline combination with an HSP90 inhibitor may be a method for delaying the emergence of resistance to targeted therapies.

Abstract 1889: AXL and EGFR signaling mediate resistance to Crizotinib in non-small cell lung cancer cells harboring the ROS1 fusion gene

Abstract Background: The multi-tyrosine kinase inhibitor (TKI) crizotinib elicits a dramatic response in patients with non-small cell lung cancer (NSCLC) harboring the c-ros oncogene 1 (ROS1) fusion gene (Shaw et al. NEJM 2014); however, these patients inevitably develop resistance to crizotinib within a year, which limits the efficacy of crizotinib. Although reported molecular changes include ROS1 tyrosine kinase mutations, epidermal growth factor receptor (EGFR) activation, and epithelial-to mesenchymal transition, the detailed mechanism of crizotinib resistance has not been elucidated. Methods: To explore the molecular mechanisms of acquired crizotinib resistance in detail, we used a cell line model. HCC78 cells harboring the SLC34A2-ROS1 fusion gene, which are sensitive to crizotinib, were exposed continuously to increasing concentrations of crizotinib in a step-wise manner. A crizotinib-resistant cell line designated HCC78R was established and assessed by MTT assay, Western blotting, a receptor tyrosine kinase (RTK) array, quantitative PCR (RT-PCR), ELISA, and an RNA kinome targeted kinome panel (612 genes) with next-generation sequencing. Results: Crizotinib-resistant HCC78R (50% inhibitory concentration [IC50] 4085.9 nmol/L) was 47-fold more resistant to crizotinib than was parental HCC78 (IC50 85.8 nmol/L) (p = 0.0145) according to MTT assay. The RTK array revealed that EGFR phosphorylation was upregulated in HCC78R cells. Western blotting confirmed the activation of EGFR and its downstream signaling pathways. RT-PCR screening of EGFR ligand family member expression showed increased heparin-binding EGF-like growth factor (HB-EGF) in HCC78R compared with HCC78 cells. Consistently, addition of the HB-EGF or conditioned medium from HCC78R cells rendered the HCC78 parental cells moderately resistant to crizotinib. EGFR overexpression or activating mutations were not detected. Furthermore, RNA kinome sequencing revealed 16-fold higher AXL mRNA expression and 1.68-fold lower ROS1 fusion gene expression in HCC78R compared with HCC78. Overexpression of the AXL protein and downregulation of the ROS1 protein were confirmed by Western blotting. Monotherapy with gefitinib (EGFR-TKI) or R428 (AXL inhibitor) or cabozantinib (AXL inhibitor) moderately inhibited the growth of HCC78R cells, while combined therapy suppressed proliferation more significantly compared with each monotherapy. Conclusions: AXL and EGFR signaling mediate resistance to crizotinib, and combination treatment of an EGFR-TKI and AXL inhibitor may be an alternative strategy in ROS1 fusion gene-driven lung cancer cells. Citation Format: Yuka Kato, Kadoaki Ohashi, Eiki Ichihara, Shuuta Tomida, Hiroe Kayatani, Kenichiro Kudo, Daisuke Minami, Takashi Ninomiya, Toshio Kubo, Toshiyuki Kozuki, Katsuyuki Hotta, Nagio Takigawa, Mitsune Tanimoto, Katsuyuki Kiura. AXL and EGFR signaling mediate resistance to Crizotinib in non-small cell lung cancer cells harboring the ROS1 fusion gene. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1889.