Abstract 2206: Proteome phenotype of stage III metastatic melanoma and response to MEK inhibition

Abstract Introduction: Melanoma accounts for 5% of all skin cancers, yet is the most common cause of skin cancer-related deaths, and is the commonest lethal malignancy in young people (<40yrs). Patients with BRAF mutant melanoma show survival benefit from MAPK pathway inhibition, although response rates vary. We conducted proteomic screening using mass spectrometry to detect cellular processes that might predict response to MEK inhibition more effectively than genotyping alone. Methods: Protein extracts from early passages of ten AJCC Stage III local lymph node metastatic melanoma cell lines with known MAPK mutational status (BRAFmut, NRASmut, MAPKwt,) were used. Further, 32 fresh frozen NRASmut or BRAFmut AJCC Stage IIIC metastatic melanoma (lymph node metastases) specimens were obtained from patients with varying survival. Lysed cells and tissue were digested with trypsin and analysed by LC-MS/MS using a TripleTOF 5600/6600 mass spectrometer. Data-independent acquisition (or SWATH-MS) was used to match multiplexed MS/MS spectra against a spectral ion library enabling relative protein quantification. Cell line viability in the presence of 2µM AZD6244 (MEKi) was determined using a PrestoBlue assay. Results: The SWATH-MS approach enabled quantification of ~2500 proteins across all 10 cell lines. Principal component analysis clearly segregated melanomas based on in vitro sensitivity to MEK inhibition, whereas genotype alone did not. In total, we show 57 proteins whose abundances correlate (r²>0.75) with response to MEKi, revealing roles in cell pigmentation biosynthesis, lipid metabolism, adherence and inter-cell communication. Survival analysis demonstrated that patients whose cell lines were responsive to MEKi had lower mortality than patients whose cells were resistant to MEKi (survival >7.5 years MEKi sensitive versus <1.7 years MEKi resistant, p=0.01). Across the 32 tumour samples, ~2000 proteins were quantifiable. The proteome phenotype associated with MEK inhibition observed in patient cell lines was a dominant signal in fresh frozen stage III metastatic melanoma specimens, suggesting these patients may have profited from MAPK pathway inhibition had these drugs been available. In this patient cohort neither the genotype nor proteome phenotype correlated with survival. Conclusion: Proteomic profiling by mass spectrometry demonstrated a MEK inhibition phenotype in early passage cell lines and fresh frozen melanoma metastases which may provide utility for selecting patients to treat with MEK drugs. Citation Format: Christoph Krisp, Robert Parker, Dana Pascovici, James Wilmott, John F. Thompson, Graham J. Mann, Richard A. Scolyer, Nicholas K. Hayward, Mark P. Molloy. Proteome phenotype of stage III metastatic melanoma and response to MEK inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2206. doi:10.1158/1538-7445.AM2017-2206