A Chemoproteomic Approach Reveals Massive Reprogramming of the Epithelial Cell Surface during Oncogenic KRAS-mediated Transformation.

Aubert, Léo [UCL] Nandagopal, Neethi Nourreddine, Sami Lavoie, Genevieve Houles, Thibault Roux, Philippe P.

Background KRAS is frequently mutated in human cancers, including ~45% of colorectal adenocarcinoma (CRC). The most promising therapeutic strategy for advanced CRC is the use of monoclonal antibodies (cetuximab, panitumumab) that block activation of the epidermal growth factor receptor (EGFR). However, activating mutations in KRAS were shown to be common drivers of acquired resistance, and recent retrospective studies have shown that they negatively predict responsiveness to anti-EGFR therapy. Despite continuous efforts, oncogenic KRAS is still deemed “undruggable”, warranting the need for alternative therapeutic approaches. While oncogenic KRAS is described to regulate many intracellular signaling events that are currently being evaluated as potential therapeutic targets, much less is known about its potential impact on the cell surface. Elucidating how oncogenic KRAS modifies the cell surface proteome (surfaceome) could help understand its complex mechanism of action, and possibly identify new “druggable” targets and/or tumor-specific biomarkers. Material and methods Herein, we have optimized a cutting-edge chemoproteomic approach based on the labeling of cell surface proteins with biotin reagents, their subsequent purification with avidin chromatography, and quantification using label-free quantitative proteomics with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Results Using an intestinal crypt epithelial cell model that reflects KRAS-induced malignant transformation, our LC-MS/MS analyses allowed the identification of over 350 cell surface molecules from which 13% and 22% were significantly upregulated and downregulated in KRAS-transformed cells, respectively. Thus, we found that oncogenic KRAS modulates the surface expression of a large network of proteins, including cell adhesion molecules, receptor tyrosine kinases, G protein-coupled receptors, ion channels, transporters, and peptidases/proteinases. Interestingly, while many of these changes are associated with a KRAS-dependent gene expression signature, we also identified numerous surface proteins that appear to be regulated in a transcription-independent manner. Conclusion Taken together, these results indicate that oncogenic KRAS leads to a massive reprogramming of the epithelial cell surface, and suggest multiple cell surface proteins as molecular targets or diagnostic markers for KRAS-dependent cancers.