Fig. 4: Spatially resolved proteomics and phosphoproteomics reveal FGFR2b-dependent regulation of mTOR signalling and autophagy.
a Workflow of the spatially resolved proteomics and phosphoproteomics experiments in HeLa cells expressing the indicated constructs. b Summarised data analysis pipeline of proximal phosphoproteome data. c Cluster analysis of the proximal phosphoproteome from the indicated conditions normalised to the proximal phosphoproteome of HeLa_FGFR2bST GFP-APEX2 for each time point. Phosphorylated sites upregulated at 40 min stimulation with FGF10 in both HeLa_FGFR2bST RAB11-APEX2 and HeLa_FGFR2b-APEX2ST RAB11 are marked as the FGFR2b Recycling Proximal Signalling Cluster. d Overlap of proteins and phosphorylated proteins detected in the proximal proteome and phosphoproteome samples, respectively. e Distribution of the phosphorylated sites, 77,4% of which were found in the FGFR2b Recycling Proximal Signalling Cluster. f Overlap between the phosphorylated sites upregulated in the global phosphoproteome upon FGF10 stimulation and the phosphorylated sites upregulated in the FGFR2b Recycling Proximal Signalling cluster from the proximal phosphoproteome (Fig. 4c). g Phosphorylated sites identified on FGFR2 and EGFR in the global (blue light) or in the proximal phosphoproteome (red) or in both (blue), and in the phosphoproteome from HeLa_FGFR2bST cells expressing GFP, GFP-DnRAB11 or GFP-DnDNM2 (Fig. 2a). Light blue with green border indicates phosphorylated sites found in internalisation response clusters and dark blue with green border indicates sites found in recycling response clusters (Fig. 2d). h KEGG pathway enrichment (calculated with Fishers Exact Test and FDR adjustment with FDR <0.005) of the phosphorylated sites found in the FGF10 global phosphoproteome (blue light), FGFR2b Recycling Proximal Signalling Cluster (red) and among the phosphorylated sites on proteins quantified at the proteome level from 4e (orange). Source data are provided as a Source Data file.
