Abstract 4761: Transcriptomic overview of EML4-ALK lung cancer cells resistant to ALK inhibitors highlights a vulnerability to CDK inhibitors
Authors: Paliouras Athanasios R. , Magee Peter , Sahoo Sudhakar , Leong Hui Sun , Krebs Matthew , Blackhall Fiona , Lovly Christine M. , Garofalo Michela 
Published: August 2019

Introduction: EML4-ALK-driven lung cancer represents about 5% of lung adenocarcinomas. Despite the constant expansion of the armamentarium to inhibit ALK, patients typically develop acquired resistance to ALK inhibitors. In the case of resistance mediated by ALK mutations, sequencing of ALK inhibitors is recommended, but in ALK wild-type patients, a better understanding of acquired resistance, as well as new therapeutic strategies are needed. Here, we aimed to characterize the transcriptional network of EML4-ALK lung cancer and used these data to address acquired resistance to ALK inhibitors.

Methods: We utilized EML4-ALK cell lines treated long-term with ALK inhibitors as a model of acquired resistance. Transcriptomic changes were quantified through means of RNA-seq or RT-qPCR.

Results: We have found a dysregulation of several microRNAs in crizotinib-resistant cells. Specifically, the oncogenic miR-25 and miR-30c were upregulated and their inhibition resulted in cell cycle arrest. We analyzed plasma samples from patients with EML4-ALK lung cancer and found increased circulating levels of these miRNAs in 2 patients upon progression with crizotinib. In addition, the known tumour-suppressing miRNAs miR-103a and miR-149 were downregulated in crizotinib-resistant cells and restoration of miR-149 resulted in apoptotic induction. We show that CDK6 is a direct target of miR-103 and an indirect target of miR-149. Moreover, by comparing the transcriptome of parental and crizotinib-resistant cells we uncovered an upregulation of genes implicated in cell cycle. Treatment with Cyclin-Dependent Kinase (CDK) inhibitors led to suppression of cell proliferation and potent induction of apoptosis. Moreover, these inhibitors spared normal epithelial cells while they induced higher levels of apoptosis in EML4-ALK cells compared with other NSCLC cell lines, suggesting a preferential targeting of EML4-ALK cells .Lastly, a pilot xenograft experiment with a crizotinib-resistant cell line showed in vivo anti-tumor activity of CDK inhibition and we are currently expanding this in a larger mouse cohort.

Conclusions: Crizotinib-resistant cells may exhibit several concurrent oncogenic alterations including miRNA- or coding gene-dysregulation, in the absence of ALK mutations. Moreover, the contribution of these alterations to acquired resistance cannot be easily and quickly assessed. A therapeutic intervention which does not rely on identifying the driver of resistance would be of high practical value. We suggest that CDK inhibition may be a new avenue to target relapsed EML4-ALK lung cancer refractory to ALK inhibitors.

Citation Format: Athanasios R. Paliouras, Peter Magee, Sudhakar Sahoo, Hui Sun Leong, Matthew Krebs, Fiona Blackhall, Christine M. Lovly, Michela Garofalo. Transcriptomic overview of EML4-ALK lung cancer cells resistant to ALK inhibitors highlights a vulnerability to CDK inhibitors [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 4761.