Fig. 7: Characterization of macromolecular complexes copurifying with sEVs.
From: Defining the reference proteomes for small extracellular vesicles and non-vesicular components
a, Percentage of proteins belonging to macromolecular complexes (as annotated in CORUM) among sEV, NV-dual and NV categories. Each colour line represents a different cell line (n = 15 independent cell lines). Box plot elements: centre lines indicate medians; the box limits represent the 25th and 75th percentiles; the whiskers extend to 1.5× the interquartile range. b, DG profiles of all eight ARP2/3 complex subunits in UACC62 as a representative example. The scatterplot compares their abundances in our dataset (EXO) versus intracellular levels (PRO). The heat map shows Spearman correlation values between EXO, PRO and RNA levels across all cell lines. c, Same as in b, but for CCT chaperonin complex subunits. d, DG profiles of 40S (purple) and 60S (green) ribosomal subunits in UACC62. Examples of top-correlating proteins with ribosomal subunits are highlighted in pink. e, Relative abundance of 40S and 60S ribosomal subunits in our data (EXO), intracellular protein (PRO) and mRNA (RNA) levels across all cell lines. f, Correlation between ribosomal protein abundance in EXO versus PRO in UACC62. The heat map shows Spearman correlation values between EXO, PRO and RNA levels across all cell lines. g, DG profiles of collagen VI subunits in UACC62. Examples of top-correlating proteins with collagen VI are highlighted in pink. h, DG profiles of core histones in UACC62. Epigenetically modified peptides are highlighted in pink and compared with their corresponding unmodified histones. i, DG profiles of 19S and 20S proteasome subunits in UACC62. The scatterplot compares their abundance in EXO versus PRO. The heat map shows Spearman correlation values between EXO, PRO and RNA levels across all cell lines. j, Relative abundance of 19S (lid and base) and 20S (beta and alpha) proteasome subunits in EXO, PRO and RNA levels across all cell lines. k, DG profiles of the 19S subunit PSMD4 (top) and the 20S subunit PSMB8 (bottom), highlighted in pink, compared with all other detected 19S and 20S subunits, respectively. l, DG profiles of the indicated complexes and proteins in our data. The bar chart represents their abundances across sEV, NV, exomere (EXOm) and supermere (SUPERm) fractions, from the re-analysis of ref. 61 data. The scatterplot compares protein abundance between NV and exomere fractions, with the respective complex or protein highlighted.
