title: Analysis of the HLA-DR peptidome from human dendritic cells reveals high affinity repertoires and nonconventional pathways of peptide generation.
abstract: Dendritic cells (DCs) are the major professional APCs of the immune system; however, their MHC-II-associated peptide repertoires have been hard to analyze, mostly because of their scarce presence in blood and tissues. In vitro matured human monocyte-derived DCs (MoDCs) are widely used as professional APCs in experimental systems. In this work, we have applied mass spectrometry to identify the HLA-DR-associated self-peptide repertoires from small numbers of mature MoDCs (∼5 × 106cells), derived from 7 different donors. Repertoires of 9 different HLA-DR alleles were defined from analysis of 1319 peptides, showing the expected characteristics of MHC-II-associated peptides. Most peptides identified were predicted high binders for their respective allele, formed nested sets, and belonged to endo-lysosomal pathway-degraded proteins. Approximately 20% of the peptides were derived from cytosolic and nuclear proteins, a recurrent finding in HLA-DR peptide repertoires. Of interest, most of these peptides corresponded to single sequences, did not form nested sets, and were located at the C terminus of the parental protein, which suggested alternative processing. Analysis of cleavage patterns for terminal peptides predominantly showed aspartic acid before the cleavage site of both C- and N-terminal peptides and proline immediately after the cleavage site in C-terminal peptides. Proline was also frequent next to the cut sites of internal peptides. These data provide new insights into the Ag processing capabilities of DCs. The relevance of these processing pathways and their contribution to response to infection, tolerance induction, or autoimmunity deserve further analysis.
authors.affiliation: Department of Cell Biology, Physiology and Immunology, Laboratori d'Immunologia Cellular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.
authors.forename: M Teresa
authors.initials: MT
authors.lastname: Ciudad
authors.affiliation: Department of Plasma Proteins, Sanquin-AMC Landsteiner Laboratory, Amsterdam, The Netherlands.|Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Sorvillo
authors.affiliation: Department of Plasma Proteins, Sanquin-AMC Landsteiner Laboratory, Amsterdam, The Netherlands.
authors.forename: Floris P
authors.initials: FP
authors.lastname: van Alphen
authors.affiliation: Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile; and.
authors.forename: Diego
authors.initials: D
authors.lastname: Catalán
authors.affiliation: Department of Plasma Proteins, Sanquin-AMC Landsteiner Laboratory, Amsterdam, The Netherlands.|The Netherlands and Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.
authors.forename: Alexander B
authors.initials: AB
authors.lastname: Meijer
authors.affiliation: Department of Plasma Proteins, Sanquin-AMC Landsteiner Laboratory, Amsterdam, The Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Voorberg
authors.affiliation: Department of Cell Biology, Physiology and Immunology, Laboratori d'Immunologia Cellular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain; dolores.jaraquemada@uab.cat.
authors.forename: Dolores
authors.initials: D
authors.lastname: Jaraquemada
mesh_terms: D000483:Alleles; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002454:Cell Differentiation; D003600:Cytosol / Q000378:metabolism; D030562:Databases, Protein; D003713:Dendritic Cells / Q000378:metabolism*; D011992:Endosomes / Q000378:metabolism; D006684:HLA-DR Antigens / Q000378:metabolism*; D006801:Humans; D008247:Lysosomes / Q000378:metabolism; D009000:Monocytes / Q000166:cytology; D009687:Nuclear Proteins / Q000378:metabolism; D010447:Peptide Hydrolases / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D010641:Phenotype; D020543:Proteome / Q000378:metabolism*
chemical_list: D006684:HLA-DR Antigens; D009687:Nuclear Proteins; D010455:Peptides; D020543:Proteome; D010447:Peptide Hydrolases
keywords: Ag presentation; Ag processing; MHC class II; autologous peptides; mass spectrometry