Proteomics identifies markers of MAPKi resistance offering new therapeutic strategies in melanoma- Cytoplasmic (cyt), nuclear (ne) and secreted (sn) proteins of MAPKi sensitive melanoma cells

MAPK inhibitors (MAPKi) show outstanding clinical response rates in melanoma patients harbouring BRAF mutations, but resistance is common. High-throughput, subcellular proteome analyses at two different MS laboratories and RNA-seq on two panels of primary melanoma cells that were either sensitive or MAPKi resistant, revealed that only fifteen proteins were sufficient to discriminate between resistant and sensitive cells. The two proteins with the highest discriminatory power were PTRF and IGFBP7, both highly upregulated in the resistant cells. They were associated with epithelial-mesenchymal transition (EMT) and are mechanistically linked. Knock-out of PTRF revealed targets involved in lysosomal activation, endocytosis, pH regulation, EMT, TGFbeta signalling and cell migration and adhesion. In addition, immunohistochemistry on patient samples showed that PTRF and IGFBP7 expression levels were significant biomarkers of poor progression free survival under MAPKi treatment. A drug screen of MAPKi resistant cells using a 960-compound kinase modulator library identified two lead compounds that were effective in targeting MAPKi resistant cells.