Spatially Resolved Phosphoproteomics Reveals Fibroblast Growth Factor Receptor Recycling-driven Regulation of Autophagy and Survival

Abstract

SummaryReceptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we revealed FGFR signalling partners proximal to recycling endosomes (REs) by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphopeptide enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncovered that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the REs, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve celllar signalling.

SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment

“…The endosomal system is notoriously hard to characterise ( 16 ), therefore our tool will be a valuable resource for distinguishing gene lists based on enrichment for different endosomal compartments. The endosomal view of SubcellulaRVis has recently been effectively utilised for visualisation of spatially resolved phosphoproteomics data describing intracellular signalling modules following dynamic cell surface receptor internalisation ( 28 ). In the future, SubcellulaRVis can be further expanded to provide more detailed views of sub-compartments of, for example, the nucleus or endomembrane systems.…”