TKI-addicted ROS1-rearranged cells are destined to survival or death by the intensity of ROS1 kinase activity

CRISPR/Cas9-edited ROS1 + non-small cell lung cancer cell lines highlight differential drug sensitivity in 2D vs 3D cultures while reflecting established resistance profiles

INTRODUCTION

The study of resistance-causing mutations in oncogene-driven tumors is fundamental to guide clinical decisions. Several point mutations affecting the ROS1 kinase domain have been identified in the clinical setting, but their impact requires further exploration, particularly in improved pre-clinical models. Given the scarcity of solid pre-clinical models to approach rare cancer subtypes like ROS1 + NSCLC, CRISPR/Cas9 technology allows the introduction of mutations in patient-derived cell lines for which resistant variants are difficult to obtain due to the low prevalence of cases within the clinical setting.

METHODS

In the SLC34A2-ROS1 rearranged NSCLC cell line HCC78, we knocked-in through CRISPR/Cas9 technology three ROS1 drug resistance-causing mutations: G2032R, L2026M and S1986Y. Such variants are located in different functional regions of the ROS1 kinase domain, thus conferring TKI resistance through distinct mechanisms. We then performed pharmacological assays in 2D and 3D to assess the cellular response of the mutant lines to crizotinib, entrectinib, lorlatinib, repotrectinib and ceritinib. In addition, immunoblotting assays were performed in 2D-treated cell lines to determine ROS1 phosphorylation and MAP kinase pathway activity. The area over the curve (AOC) defined by the normalized growth rate (NGR_fit) dose-response curves was the variable used to quantify the cellular response towards TKIs.

RESULTS

Spheroids derived from ROS1G2032R cells were significantly more resistant to repotrectinib (AOC fold change = - 7.33), lorlatinib (AOC fold change = - 6.17), ceritinib (AOC fold change = - 2.8) and entrectinib (AOC fold change = - 2.02) than wild type cells. The same cells cultured as a monolayer reflected the inefficacy of crizotinib (AOC fold change = - 2.35), entrectinib (AOC fold change = - 2.44) and ceritinib (AOC fold change = - 2.12) in targeting the ROS1 G2032R mutation. ROS1L2026M cells showed also remarkable resistance both in monolayer and spheroid culture compared to wild type cells, particularly against repotrectinib (spheroid AOC fold change = - 2.19) and entrectinib (spheroid AOC fold change = - 1.98). ROS1S1986Y cells were resistant only towards crizotinib in 2D (AOC fold change = - 1.86). Overall, spheroids showed an increased TKI sensitivity compared to 2D cultures, where the impact of each mutation that confers TKI resistance could be clearly distinguished. Western blotting assays qualitatively reflected the patterns of response towards TKI observed in 2D culture through the levels of phosphorylated-ROS1. However, we observed a dose-response increase of phosphorylated-Erk1/2, suggesting the involvement of the MAPK pathway in the mediation of apoptosis in HCC78 cells.

CONCLUSION

In this study we knock-in for the first time in a ROS1 + patient-derived cell line, three different known resistance-causing mutations using CRISPR/Cas9 in the endogenous translocated ROS1 alleles. Pharmacological assays performed in 2D and 3D cell culture revealed that spheroids are more sensitive to TKIs than cells cultured as a monolayer. This direct comparison between two culture systems could be done thanks to the implementation of normalized growth rates (NGR) to uniformly quantify drug response between 2D and 3D cell culture. Overall, this study presents the added value of using spheroids and positions lorlatinib and repotrectinib as the most effective TKIs against the studied ROS1 resistance point mutations.

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

Non-small cell lung cancer (NSCLC) is a heterogeneous group of diseases which accounts for 80% of newly diagnosed lung cancers. In the previous decade, a new molecular subset of NSCLC patients (around 2%) harboring rearrangements of the c-ros oncogene 1 was defined. ROS1+ NSCLC is typically diagnosed in young, nonsmoker individuals presenting an adenocarcinoma histology. Patients can benefit from tyrosine kinase inhibitors (TKIs) such as crizotinib and entrectinib, compounds initially approved to treat ALK-, MET- or NTRK- rearranged malignancies respectively. Given the low prevalence of ROS1-rearranged tumors, the use of TKIs was authorized based on pre-clinical evidence using limited experimental models, followed by basket clinical trials. After initiating targeted therapy, disease relapse is reported in approximately 50% of cases as a result of the appearance of resistance mechanisms. The restricted availability of TKIs active against resistance events critically reduces the overall survival. In this review we discuss the pre-clinical ROS1+ NSCLC models developed up to date, highlighting their strengths and limitations with respect to the unmet clinical needs. By combining gene-editing tools and novel cell culture approaches, newly developed pre-clinical models will enhance the development of next-generation tyrosine kinase inhibitors that overcome resistant tumor cell subpopulations.

Utility of the Ba/F3 cell system for exploring on-target mechanisms of resistance to targeted therapies for lung cancer

Molecular targeted therapies are the standard of care for front‐line treatment of metastatic non‐small‐cell lung cancers (NSCLCs) harboring driver gene mutations. However, despite the initial dramatic responses, the emergence of acquired resistance is inevitable. Acquisition of secondary mutations in the target gene (on‐target resistance) is one of the major mechanisms of resistance. The mouse pro‐B cell line Ba/F3 is dependent on interleukin‐3 for survival and proliferation. Upon transduction of a driver gene, Ba/F3 cells become independent of interleukin‐3 but dependent on the transduced driver gene. Therefore, the Ba/F3 cell line has been a popular system to generate models with oncogene dependence and vulnerability to specific targeted therapies. These models have been used to estimate oncogenicity of driver mutations or efficacies of molecularly targeted drugs. In addition, Ba/F3 models, together with N‐ethyl‐N‐nitrosourea mutagenesis, have been used to derive acquired resistant cells to investigate on‐target resistance mechanisms. Here, we reviewed studies that used Ba/F3 models with EGFR mutations, ALK/ROS1/NTRK/RET fusions, MET exon 14 skipping mutations, or KRAS G12C mutations to investigate secondary/tertiary drug resistant mutations. We determined that 68% of resistance mutations reproducibly detected in clinical cases were also found in Ba/F3 models. In addition, sensitivity data generated with Ba/F3 models correlated well with clinical responses to each drug. Ba/F3 models are useful to comprehensively identify potential mutations that induce resistance to molecularly targeted drugs and to explore drugs to overcome the resistance.

Hypoxia increases the apoptotic response to betulinic acid and betulin in human non-small cell lung cancer cells

Betulinic acid and betulin show promising activity against cancers cells, but the mechanism of their action is still unclear. In this study, non-small cell lung cancer (NSCLC) cell lines: A549, H358 and NCI-H1703 were treated with betulinic acid and betulin under normoxic and hypoxic conditions as hypoxia is critically involved in the response of solid tumors to chemotherapy. The treatment inhibits viability and proliferation of NSCLC cells. The anti-proliferative effect was induced by G1 cell cycle arrest with increased p21 expression and decreased cyclin D1 and cyclin B1 expression. Additionally, downregulation of p-GSK3β activity and the Wnt/β-catenin pathway were also observed under hypoxia. We found that hypoxia increased apoptosis in NSCLC cells. Cell death was associated with changes in the expression of proteins involved in the mitochondrial apoptosis pathway and induction of apoptotic death by caspase activation. Additionally, hypoxia exposure deregulated HIF-1α and p53 expression levels. Importantly, treatment with betulinic acid and betulin reduced colony-forming ability under normoxia, however, only betulinic acid reduced clonogenic activity under hypoxia. Our findings that betulinic acid increases apoptotic cell death and clonogenic activity under hypoxic conditions reveal new attractive strategies for treating hypoxic cancer tumors, such as NSCLC.

ROS1-dependent cancers - biology, diagnostics and therapeutics

The proto-oncogene ROS1 encodes a receptor tyrosine kinase with an unknown physiological role in humans. Somatic chromosomal fusions involving ROS1 produce chimeric oncoproteins that drive a diverse range of cancers in adult and paediatric patients. ROS1-directed tyrosine kinase inhibitors (TKIs) are therapeutically active against these cancers, although only early-generation multikinase inhibitors have been granted regulatory approval, specifically for the treatment of ROS1 fusion-positive non-small-cell lung cancers; histology-agnostic approvals have yet to be granted. Intrinsic or extrinsic mechanisms of resistance to ROS1 TKIs can emerge in patients. Potential factors that influence resistance acquisition include the subcellular localization of the particular ROS1 oncoprotein and the TKI properties such as the preferential kinase conformation engaged and the spectrum of targets beyond ROS1. Importantly, the polyclonal nature of resistance remains underexplored. Higher-affinity next-generation ROS1 TKIs developed to have improved intracranial activity and to mitigate ROS1-intrinsic resistance mechanisms have demonstrated clinical efficacy in these regards, thus highlighting the utility of sequential ROS1 TKI therapy. Selective ROS1 inhibitors have yet to be developed, and thus the specific adverse effects of ROS1 inhibition cannot be deconvoluted from the toxicity profiles of the available multikinase inhibitors. Herein, we discuss the non-malignant and malignant biology of ROS1, the diagnostic challenges that ROS1 fusions present and the strategies to target ROS1 fusion proteins in both treatment-naive and acquired-resistance settings.

Targeted Therapies in Non-small-Cell Lung Cancer

The treatment landscape for non-small-cell lung cancer (NSCLC) has dramatically shifted over the past two decades. Targeted or precision medicine has primarily been responsible for this shift. Older paradigms of treating metastatic NSCLC with cytotoxic chemotherapy, while still important, have given way to evaluating tumor tissues for specific driver mutations that can be treated with targeted agents. Patients treated with targeted agents frequently have improved progression-free survival and overall survival compared to patients without a targetable driver mutation, highlighting the clinical benefit of precision medicine. In this chapter, we explore the historic landmark trials, the current state of the field, and potential future targets under investigation, in this exciting, rapidly evolving discipline of precision medicine in lung cancer.

Recurrent 8q24 rearrangement in blastic plasmacytoid dendritic cell neoplasm: association with immunoblastoid cytomorphology, MYC expression, and drug response

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare skin-tropic hematological malignancy of uncertain pathogenesis and poor prognosis. We examined 118 BPDCN cases for cytomorphology, MYC locus rearrangement, and MYC expression. Sixty-two (53%) and 41 (35%) cases showed the classic and immunoblastoid cytomorphology, respectively. Forty-one (38%) MYC⁺BPDCN (positive for rearrangement and expression) and 59 (54%) MYC^-BPDCN (both negative) cases were identified. Immunoblastoid cytomorphology was significantly associated with MYC⁺BPDCN. All examined MYC⁺BPDCNs were negative for MYB/MYBL1 rearrangement (0/36). Clinically, MYC⁺BPDCN showed older onset, poorer outcome, and localized skin tumors more commonly than MYC^-BPDCN. MYC was demonstrated by expression profiling as one of the clearest discriminators between CAL-1 (MYC⁺BPDCN) and PMDC05 (MYC^-BPDCN) cell lines, and its shRNA knockdown suppressed CAL-1 viability. Inhibitors for bromodomain and extra-terminal protein (BETis), and aurora kinases (AKis) inhibited CAL-1 growth more effectively than PMDC05. We further showed that a BCL2 inhibitor was effective in both CAL-1 and PMDC05, indicating that this inhibitor can be used to treat MYC^-BPDCN, to which BETis and AKis are probably less effective. Our data will provide a rationale for the development of new treatment strategies for patients with BPDCN, in accordance with precision medicine.