Fig. 3: Cilia dysfunction alters EV protein composition.

a–c Proteins identified via liquid chromatography-mass spectrometry analysis in four out of six pellets isolated from control and ciliated mutant KM cell supernatant. Source data are provided as a Supplementary data file. a Repeat of scatter plot in Fig. 2c depicted to demonstrate change in the mode of protein release from lgEVs in control to smEVs upon cilia dysfunction for the subset of proteins. b, c Proteins identified in smEV preparations from control vs. cilia mutant cells. Proteins in the right cluster were enriched in smEVs released from mutant cells. Proteins demarked in red and purple were proteins considered enriched in control lgEVs and absent from control smEVs. Their shift to the right cluster suggests an altered method of release from mutant cells. d Simplified schematic representation of possible modes of EV release. lgEVs are released at the ciliary tip and smEVs from the cell membrane. Upon ciliary dysfunction, this is hampered and increased MVB-derived smEVs are released directly from the cell membrane (figure created by V.Kretschmer). e Absolute numbers of different protein populations depicted in (b, c). Bbs4^−/− and Bbs6^−/− smEVs contained twice as many proteins compared to control. f Number of proteins significantly enriched (P value −log ≥2) in Bbs4^−/− and Bbs6^−/− smEVs compared to the control.