Figure 3. Proteomic profiling reveals a... | Rockefeller University Press

Figure 3.

$Figure 3. Proteomic profiling reveals a migration-promoting protein signature in TNFα EEV fractions. (a–d) EEV fractions from basolateral culture supernatants of ss (n = 3) or TNFα-stimulated LECs (n = 3) were proteomically profiled with TMT-based LC-MSMS analysis. (a) Heat map of all significantly (P < 0.05) quantified proteins of EEV fractions. Three left lanes: Replicate EEV fractions from ss LECs; three right lanes: Replicate EEV fractions from TNFα-stimulated LECs. Values in heat maps are log10 of interprotein abundance of a given sample divided by the mean abundance of the three ss samples. (b) Ratio density plot of EEV fractions from ss and TNFα-stimulated LECs. X axis: Log10 ratio of interprotein abundance of TNFα-EEV fractions over ss-EEV fractions. Y axis: Relative number of proteins. (c) The quantitatively identified proteins of EEV fractions were grouped into biologically relevant clusters according to the databases of ExoCarta (exosomes), EVpedia (extracellular vesicles), and the Gene Ontology Consortium (cellular components). Mean interprotein abundances of proteins in the respective clusters were compared with the mean interprotein abundance of all proteins in ss-EEV fractions (red dotted line) and TNFα-EEV fractions (blue dotted line). X axis: Logarithmic scale of interprotein abundances. Y axis: Biologically relevant clusters. For each cluster, the floating bars display the minimum-to-maximum intervals of the interprotein abundance for ss-EEV (red) and TNFα-EEV (blue) fractions. Vertical lines show the mean interprotein abundance for ss-EEV (red) and TNFα-EEV (blue) fractions. **, P < 0.01; *** P ≤ 0.001. (d) Heat maps of significantly (P < 0.05) quantified proteins of EEV fractions that are either endothelial markers or chemokines and growth factors.$

Proteomic profiling reveals a migration-promoting protein signature in TNFα EEV fractions. (a–d) EEV fractions from basolateral culture supernatants of ss (n = 3) or TNFα-stimulated LECs (n = 3) were proteomically profiled with TMT-based LC-MSMS analysis. (a) Heat map of all significantly (P < 0.05) quantified proteins of EEV fractions. Three left lanes: Replicate EEV fractions from ss LECs; three right lanes: Replicate EEV fractions from TNFα-stimulated LECs. Values in heat maps are log₁₀ of interprotein abundance of a given sample divided by the mean abundance of the three ss samples. (b) Ratio density plot of EEV fractions from ss and TNFα-stimulated LECs. X axis: Log₁₀ ratio of interprotein abundance of TNFα-EEV fractions over ss-EEV fractions. Y axis: Relative number of proteins. (c) The quantitatively identified proteins of EEV fractions were grouped into biologically relevant clusters according to the databases of ExoCarta (exosomes), EVpedia (extracellular vesicles), and the Gene Ontology Consortium (cellular components). Mean interprotein abundances of proteins in the respective clusters were compared with the mean interprotein abundance of all proteins in ss-EEV fractions (red dotted line) and TNFα-EEV fractions (blue dotted line). X axis: Logarithmic scale of interprotein abundances. Y axis: Biologically relevant clusters. For each cluster, the floating bars display the minimum-to-maximum intervals of the interprotein abundance for ss-EEV (red) and TNFα-EEV (blue) fractions. Vertical lines show the mean interprotein abundance for ss-EEV (red) and TNFα-EEV (blue) fractions. **, P < 0.01; *** P ≤ 0.001. (d) Heat maps of significantly (P < 0.05) quantified proteins of EEV fractions that are either endothelial markers or chemokines and growth factors.