Oncogene driver mutations and copy number variation as markers for predicting drug resistance and disease outcome in NSCLC

Introduction: Worldwide, lung cancer is the leading cause of death. Non-small cell lung cancer (NSCLC) patients with KRAS mutations have a poor prognosis and show drug resistance, with MCL-1 implicated in this mechanism via evasion of apoptosis. This study is aimed at evaluating the relationship between key oncogene driver mutations, MCL-1 regulation and MCL-1-induced drug resistance. Methods: We analysed 39 adenocarcinomas (ADCs), 38 squamous cell carcinomas (SCCs), two large cell lung carcinomas (LCCs) and cell lines. A PNA-LNA-based TaqMan qPCR approach was performed for eight KRAS, one BRAF, three PIK3CA and one EGFR mutations. MCL-1, PIK3CA and SOX2 were analysed for copy number variation (CNV). Immunohistochemistry (IHC) and in situ hybridization (ISH) was performed for protein and mRNA, respectively. Alamar blue assay was used to evaluate drug responses. Results: KRAS mutations were detected in 36% of ADCs and 0% of SCCs, whereas PIK3CA mutation was most common in SCC (15.7%) and found in 5% of ADCs. MCL-1, PIK3CA and SOX2 amplification were detected in 13%, 74% and 86.6% of SCCs respectively, and were detected in 2.5%, 25.9% and 13.3% of ADCs respectively. MCL-1-amplified tumours demonstrated high expression of MCL-1 mRNA compared to non-amplified (p < 0.05). Cases with high phospho-ERK and phospho-AKT also showed high expression of MCL-1 mRNA. No growth inhibition was detected in cell lines treated with 5 μM of SH-4-54 inhibitor; however, 10 μM caused 99.9% growth inhibition. Ex vivo experiments mimicking the in vivo tumour environment demonstrated that NSCLCs are sensitive to cisplatin, one of which was MCL-1amplified. Conclusion: We have shown that KRAS mutation is common in ADC, whereas PIK3CA is more common in SCC. Importantly, we have highlighted that CNV of MCL-1 may be an important driver in resistance to chemotherapy. The JAK/STAT pathway was the key regulator for MCL-1 transcription. Resistance to cisplatin was observed in the KRAS mutant cell, MCL-1-amplified cell, cells harbouring MCL-1 gain and Chr1 polysomy but not the SOX2-amplified cell