Fig. 3: Mitochondrial proteins are not overrepresented p62 cargo candidates in autophagosome lumen.
a Schematic depiction of experimental procedure for autophagosome content profiling to identify p62 cargo candidates via APEX2-mediated proximity biotinylation. Image partly created in BioRender. b Volcano plots showing log2-transformed fold change in BafA1 versus DMSO (vehicle) treated conditions across the cell lines used. Selected known p62 interactors are annotated. Data is generated from mass spectrometry analysis of n = 3–4 biological replicates (see Supplementary Fig. 1e, f, and Supplementary Data 2). c Gene ontology (GO) over-representation analysis of the p62 cargo candidates common to all karyotypes, shared among all polysomic cell lines, and exclusive to each karyotype (Supplementary Fig. 4c). Blue bars represent negative log-transformed p values (one-sided hypergeometric test) for GO terms with FDR < 0.05. d Boxplots indicating fold changes in abundance of catalogued p62-specific autophagosome lumen cargo (42, black) and mitochondrial proteins as defined by the MitoCarta3.0 inventory (magenta) compared to all other proteins (grey) enriched among the p62 cargo candidates from (b). Boxplots represent median with 25th and 75th percentile. Whiskers extend from upper and lower bound of the box to the largest and smallest values, respectively, no further than 1.5x inter-quartile range from the respective bound (Tukey method). P values are derived from two-sided Wilcoxon’s ranks sum tests.
