Proteomic phenotyping of metastatic melanoma reveals putative signatures of MEK inhibitor response and prognosis

Christoph Krisp,Georgina V Long,Mark P Molloy,Nicholas K Hayward,Richard A Scolyer,Dana Pascovici,James S Wilmott,Graham J Mann,John F Thompson,Robert Parker

doi:10.1038/s41416-018-0227-2

Abstract

BackgroundGenotyping of melanomas is used to identify patients for treatment with BRAF and MEK inhibitors, but clinical responses are highly variable. This study investigated the utility of protein expression phenotyping to provide an integrated assessment of gene expression programs in BRAF/NRAS melanoma which would be useful for prognosis and may predict response to MEK inhibition.MethodsMass spectrometry profiling of early passage cell lines established from Stage III cutaneous melanomas was conducted. Basal protein expression was correlated with in vitro response to the MEK inhibitor, selumetinib. Protein expression in a cohort of 32 drug naïve BRAF/NRAS metastatic melanoma specimens was examined. The prognostic utility of a subset of these proteins and mRNA transcripts from a separate cohort was determined.ResultsUnsupervised analysis of basal cell line protein abundances delineated response to selumetinib, but BRAF/NRAS genotype did not. Resistance was associated with functions including cell motility, cell adhesion and cytoskeletal organization. Several of these response biomarkers were observed in lymph node biospecimens and correlated with melanoma-specific survival. Loss of ICAM-1 protein and mRNA expression was a strong prognosticator of diminished survival in BRAF/NRAS mutant melanoma.ConclusionsThese results demonstrate the utility of proteomic phenotyping to identify both putative biomarkers of response to MEK inhibition and prognostication associated with metastatic melanoma.

Highlights

In cutaneous melanoma, mutations of either the Ser/Thr protein kinase BRAF, or the small GTPase NRAS are most common.[1,2] Mutations in either of these proteins are usually mutually exclusive and result in unrestrained activation of the MAPK cell proliferative pathway.In clinical practice, it is routine to screen for BRAF V600 mutations in metastatic melanoma patients[3,4] since there are approved targeted therapies to treat advanced melanoma patients
In this study, we demonstrated that mass spectrometry-based protein profiling of early passage cell lines derived from Stage III cutaneous melanoma patients growing under basal conditions displayed a protein expression pattern that correlated with in vitro response to selumitinib, but was not correlated with NRAS/BRAF genotype
This observation is consistent with the clinical experience that not all BRAF-mutant melanomas are sensitive to BRAF inhibition or MEKi11 and suggests that response to MAPK pathway blockade is reflected in the expression of particular proteins

Summary

Introduction

Mutations of either the Ser/Thr protein kinase BRAF (approximately 40%), or the small GTPase NRAS (approximately 25%) are most common.[1,2] Mutations in either of these proteins are usually mutually exclusive and result in unrestrained activation of the MAPK cell proliferative pathway.In clinical practice, it is routine to screen for BRAF V600 mutations in metastatic melanoma patients[3,4] since there are approved targeted therapies to treat advanced melanoma patients. Genotyping of melanomas is used to identify patients for treatment with BRAF and MEK inhibitors, but clinical responses are highly variable. This study investigated the utility of protein expression phenotyping to provide an integrated assessment of gene expression programs in BRAF/NRAS melanoma which would be useful for prognosis and may predict response to MEK inhibition. RESULTS: Unsupervised analysis of basal cell line protein abundances delineated response to selumetinib, but BRAF/NRAS genotype did not. Resistance was associated with functions including cell motility, cell adhesion and cytoskeletal organization Several of these response biomarkers were observed in lymph node biospecimens and correlated with melanoma-specific survival. Loss of ICAM-1 protein and mRNA expression was a strong prognosticator of diminished survival in BRAF/NRAS mutant melanoma. CONCLUSIONS: These results demonstrate the utility of proteomic phenotyping to identify both putative biomarkers of response to MEK inhibition and prognostication associated with metastatic melanoma

Methods

Results

Conclusion