Fig. 2. Lysosomal leakage remodels the mitochondrial proteome in macrophages.

a Schematic showing the MITO-tag workflow in iPSDM. b Proteomic analysis of isolated mitochondria from MITO-tag iPSDM untreated (red) or treated with LLOMe (blue). Volcano plot shows proteins with fold change > 1.5 and an adjusted p-value ≤ 0.05. The two most upregulated proteins in the OMM, IMM and matrix (Supplementary Data 1) are shown as illustrative example. Heat maps show the mitochondrial localization of the proteins that were significantly increased in the indicated comparison and ETC proteins significantly decreased after LLOMe treatment are shown (dashed box). Annotations were obtained from MitoCarta3.0. c Significantly regulated proteins from the indicated conditions (Supplementary Table 1) were used for Gene Ontology (GO) cellular component enrichment analysis using the Gene Functional Annotation Tool available at the DAVID v6.7 website (https://david.ncifcrf.gov/). A maximum p-value of 0.05 (Benjamini) was chosen to select only significantly enriched GO cellular components. d Volcano plot and mitochondrial protein localization as in (a) in the presence or absence of protease inhibitors (PI). The ETC proteins from (a) significantly decreased in the presence of the PI are shown (dashed box). See also Supplementary Table 2. e Bar graph showing GO cellular component enrichment analysis from the indicated conditions as in (c). f Volcano plot and mitochondrial protein localization as in (a) in the presence or absence of the proteasome inhibitor Bortezomib (BTZ). g Volcano plot and mitochondrial protein localization as in (a) comparing LLOMe-treated iPSDM in the presence or absence of PI. n = 3 independent experiments. Source data are provided in Supplementary Data 1.