Extended Data Fig. 3: LNPK loss reduces membrane protein synthesis and translation near lysosomes.
From: Secretome translation shaped by lysosomes and lunapark-marked ER junctions
a, Schematic of L-homopropargylglycine (HPG) incorporation assay to label newly synthesized proteins in whole-cell and membrane fractions. b, Click-labeled Alexa-488-HPG signal in whole-cell and digitonin-extracted membrane fractions of control (green) and LNPK KO U-2 OS cells (magenta). Whole-cell: no significant difference (unpaired two-tailed t-test, P = 0.8492). Membrane fraction: significant reduction in LNPK KO (****P < 0.0001). c, Tables of proteins and mRNAs differentially regulated in LNPK KO cells ( ≥ 2-fold change in protein or RNA, adjusted P < 0.05). d, Scatter plot of protein fold-change (Protein 2FC, LNPK KO/WT) vs RNA fold-change (RNA 2FC, LNPK KO/WT). Pink, proteins with adjusted P < 0.05; blue, mRNAs with adjusted P < 0.05. Dotted line, 2-fold threshold. e, Log2 protein/mRNA ratios in KO vs WT. Central dotted line, 1:1 ratio; flanking dotted lines, 2-fold boundaries. Pink dots, higher in control; blue, higher in LNPK KO. f, Histogram of log2 difference in protein/mRNA ratio between KO and control. Pink bars, genes with higher ratios in control; blue bars, higher ratios in LNPK KO. g, The average distance between SiT-EGFP mRNA and the nearest lysosome (µm) of translating (T, green) and non-translating (NT, red) mRNA. Each line represents the same cell. N = 15 cells.
