title: Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking.
abstract: Dendritic cells (DC) take up pathogens through phagocytosis and process them into protein and lipid fragments for presentation to T cells. So far, the proteome of the human DC phagosome, a detrimental compartment for antigen processing and presentation as well as for DC activation, remains largely uncharacterized. Here we have analyzed the protein composition of phagosomes from human monocyte-derived DC. For LC-MS/MS analysis we purified phagosomes from DC using latex beads targeted to DC-SIGN, and quantified proteins using a label-free method. We used organellar enrichment ranking (OER) to select proteins with a high potential to be relevant for phagosome function. The method compares phagosome protein abundance with protein abundance in whole DC. Phagosome enrichment indicates specific recruitment to the phagosome rather than co-purification or passive incorporation. Using OER we extracted the most enriched proteins that we further complemented with functionally associated proteins to define a set of 90 phagosomal proteins that included many proteins with established relevance on DC phagosomes as well as high potential novel candidates. We already experimentally confirmed phagosomal recruitment of Galectin-9, which has not been previously associated with phagocytosis, to both bead and pathogen containing phagosomes, suggesting a role for Galectin-9 in DC phagocytosis.
authors.affiliation: Department of Tumor Immunology at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Postbox 9101, 6500 HB Nijmegen, The Netherlands.
authors.forename: Sonja I
authors.initials: SI
authors.lastname: Buschow
authors.forename: Edwin
authors.initials: E
authors.lastname: Lasonder
authors.forename: Radek
authors.initials: R
authors.lastname: Szklarczyk
authors.forename: Machteld M
authors.initials: MM
authors.lastname: Oud
authors.forename: I Jolanda M
authors.initials: IJ
authors.lastname: de Vries
authors.forename: Carl G
authors.initials: CG
authors.lastname: Figdor
mesh_terms: D017951:Antigen Presentation / Q000502:physiology; D002478:Cells, Cultured; D003713:Dendritic Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry; D009000:Monocytes / Q000166:cytology / Q000378:metabolism*; D010587:Phagocytosis / Q000502:physiology; D010588:Phagosomes / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*
chemical_list: D020543:Proteome