Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes
Menée à l'aide d'une lignée isogénique de cellules épithéliales du sein, cette étude compare les effets de 6 oncogènes (KRAS G12V, surexpression de HER2, EGFR L858R, BRAFV600E, MEK S218D/S222D phosphomimétiques et AKT myristoylé) sur l'expression de 700 protéines de surface
The cell surface proteome (surfaceome) mediates interactions between the cell and the extracellular environment and is a major target for immunotherapy in cancer. Here, we compared how six neighboring proliferative oncogenes cause large and bidirectional change in expression of some 700 surface proteins. These large changes converge to common functional consequences that are reversed by small-molecule inhibition of the MAPK pathway. We further complemented the surfaceome analysis with bottom-up glycoproteomics enabled by activated ion electron transfer dissociation and found a dynamic regulation of the glycoproteome. This large-scale comparative study provides important insights for how oncogenes remodel isogenic cells in a cell autologous fashion and suggests opportunities for antibody drug discovery in cancer.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 the strong dependence of the oncogene on the MAPK pathway to propagate signaling. Cell surface protein capture is mediated by covalent tagging of surface glycans, yet current methods do not afford sequencing of intact glycopeptides. Thus, we complement the surfaceome data with whole cell glycoproteomics enabled by a recently developed technique called activated ion electron transfer dissociation (AI-ETD). We found massive oncogene-induced changes to the glycoproteome 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 surfaceome and the glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery.