Broad and thematic remodeling of the surface glycoproteome on isogenic cells transformed with driving proliferative oncogenes

Abstract

The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here we apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK and AKT. We find that each oncogene has somewhat different surfaceomes but the functions of these proteins are harmonized by common biological themes including up-regulation of nutrient transporters, down-regulation of adhesion molecules and tumor suppressing phosphatases, and alteration in immune modulators. Addition of a potent MEK inhibitor that blocks MAPK signaling brings each oncogene-induced surfaceome back to a common state reflecting their strong dependence on the MAPK pathway to propagate signaling. Using a recently developed glyco-proteomics method of activated ion electron transfer dissociation (AI-ETD) we found massive oncogene-induced changes in 142 N-linked glycans and differential increases in complex hybrid glycans especially for KRAS and HER2 oncogenes. Overall, these studies provide a broad systems level view of how specific driver oncogenes remodel the surface glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery.\n\nSignificant statementThe cell surface glycoproteome (surfaceome) mediates interactions between the cell and the extracellular environment, and is a major target for immunotherapy in cancer. Using state-of-the-art proteomics methods, we compared how six neighboring proliferative oncogenes cause large and bidirectional expression of some 700 surface proteins and the 142 different glycans that decorate them. While each oncogene induces large and somewhat unique glycoproteomes relative to non-transformed cells, we find common functional consequences that are massively reversed by small molecule inhibition of the MAPK pathway. This large-scale comparative study provides important insights for how oncogenes remodel isogenic cells in a cell autologous fashion, and suggest possible new opportunities for antibody drug discovery in more complex tumor settings.