Figure 1A. MS-proteomic analysis of RCS chondrocytes treated with vehicle (5% ABS) and FGF18 (50 ng/mL) for 16 hours. Biological processes and cellular components regulated by FGF signaling are shown. FDR <0.05. N=4 biological replicates/treatment were analyzed. p-value was calculated using 1D annotation enrichment test based on Wilcoxon-Mann-Whitney test. FACS analysis of Lysotracker (B) dye fluorescence in RCS treated with the indicated FGF ligands (50 ng/mL) for 16h. Fluorescence intensities were expressed as % relative to vehicle (5% ABS). Mean +/- standard error of the mean (sem) of N=3 biological replicates/treatment. Analysis of variance one way (ANOVA) p<0.002 (B) Tukey's post hoc test ***p<0.0005. FACS analysis of DQ-BSA (C) dye fluorescence in RCS treated with the indicated FGF ligands (50 ng/mL) for 16h. Concanamycin A was used at 100 nM for 1h to inhibit lysosomal function. Fluorescence intensities were expressed as % relative to vehicle (5% ABS). Mean +/- standard error of the mean (sem) of N=3 biological replicates/treatment. Analysis of variance one way (ANOVA) =0.005 (C); Tukey's post hoc test ***p<0.0005. D. Lamp1 immunofluorescence (red) in RCS chondrocytes treated with vehicle (5% ABS) and FGF18 (50 ng/mL) for 16 hours. Insets show magnification of the boxed area. Nuclei were stained with DAPI (blue). Scale bar 15 μm and 2 μm (higher magnification boxes) . Bar graph shows quantification of Lamp1-positive vesicles/cell. Mean +/- standard error of the mean (sem) of N=3 biological replicates/treatment. n=45 cells were analyzed. Student paired T-Test *p<0.05. E. Representative TEM images of RCS chondrocytes treated with 5% ABS (vehicle) and FGF18 (50 ng/mL) for 16 hours. BafA1 (100 nM; 4 hours) was used to inhibit lysosome activity. Arrows indicate lysosomes. Higher magnification insets showed presence of ER membranes decorated with ribosomes (arrowheads). Scale bar 500nm. Quantification shows average number of ER membranes and mitochondria number/ lysosome vesicle (Lys). Mean +/- standard error of the mean (sem) of N=3 biological replicates/treatment. ER fragment/vesicle n=60 (vehicle) and n=72 (FGF18) cells were analyzed; Mitochondria number/vesicle: n=40 (vehicle) and n=72 (FGF18) cells were analyzed. Student paired T-Test ***p<0.0005; NS not significant. F. Representative co-immunofluorescence staining of ER (ER tracker BODIPY green) and lysosomes (Lamp1, red) in RCS chondrocytes treated with vehicle (5% ABS) and FGF18 (50 ng/mL) for 16 hours. Insets show higher magnification of boxed area. Scale bar 15 μm and 2 μm (higher magnification boxes). N=3 biological replicates/treatment. G. Schematic representation of EATR assay: eGFP fluorescence, but not mCherry, is lost at acidic pH. Chondrocytes with indicated genotypes (ctrl=wild type) were treated with FGF18 (50 ng/mL; 12 hours) and BafA1 (200 nM; 3 hours) where indicated. ER acidification was measured by FACS. Mean +/- standard error of the mean (sem) of N=3 biological replicates. Analysis of variance one way (ANOVA) p<0.0001; Tukey's post hoc test ***p<0.0005; **p<0.005; NS not significant. H. FACS analysis of DQ-BSA dye fluorescence in chondrocytes with indicated genotypes (ctrl=wild type) treated with FGF18 (50 ng/mL) for 16 hours. Concanamycin A was used at 100 nM for 1h to inhibit lysosomal degradation. Fluorescence intensities were expressed as % relative to vehicle (5% ABS). Mean +/- standard error of the mean (sem) of N=3 biological replicates/treatment/genotype. Analysis of variance (ANOVA) p=0.00279; Tukey's post hoc test **p<0.005; *p<0.05; NS not significant. I. EATR assay. Chondrocytes with indicated genotypes (ctrl=wild type) treated with FGF18 (50 ng/mL; 16 hours) where indicated. ER acidification was measured by FACS. Mean +/- standard error of the mean (sem) of N= 17 (veh), N=17 (FGF18), N=4 (FGFR3;4KO); N=4 (FGFR3;4KO FGF18) biological replicates. Analysis of variance one way (ANOVA) p<0.0001; Tukey's post hoc test ***p<0.0005; NS not significant. J. Representative immunofluorescence staining of ER (CLIMP63, green) and lysosomes (TMEM192-HA, red) in chondrocytes with indicated genotypes (ctrl=wild type) treated with FGF18 (50 ng/mL for 16h). BafA1 was used at 100 nM for 4 hours to inhibit lysosomal degradation. Quantification of relative CLIMP63 fluorescence into TMEM192-HA positive vesicles. N=3 biological replicates; n=21 cells were analyzed. Mean +/- standard error of the mean (sem). Paired Student's T-test NS= not significant. Scale bar 10 μm and 1.3 μm (higher magnification boxes).