title: High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients' sera.
abstract: The characterization of peptides bound to human leukocyte antigen (HLA) class I is of fundamental importance for understanding CD8+ T cell-driven immunological processes and for the development of immunomodulatory therapeutic strategies. However, until now, the mass spectrometric analysis of HLA-bound peptides has typically required billions of cells, still resulting in relatively few high-confidence peptide identifications. Capitalizing on the recent developments in mass spectrometry and bioinformatics, we have implemented a methodology for the efficient recovery of acid-eluted HLA peptides after purification with the pan-reactive antibody W6/32 and have identified a total of 27 862 unique peptides with high confidence (1% false discovery rate) from five human cancer cell lines. More than 93% of the identified peptides were eight to 11 amino acids in length and contained signatures that were in excellent agreement with published HLA binding motifs. Furthermore, by purifying soluble HLA class I complexes (sHLA) from sera of melanoma patients, up to 972 high-confidence peptides could be identified, including melanoma-associated antigens already described in the literature. Knowledge of the HLA class I peptidome should facilitate multiplex tetramer technology-based characterization of T cells, and allow the development of patient selection, stratification and immunomodulatory therapeutic strategies.
authors.affiliation: Philochem AG, Otelfingen, Switzerland.
authors.forename: Danilo
authors.initials: D
authors.lastname: Ritz
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gloger
authors.affiliation: Department of Dermatology, Division of Dermatologic Oncology, Eberhard-Karls-University, Tuebingen, Germany.|Department of Immunology, Eberhard-Karls-University, Tuebingen, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Weide
authors.affiliation: Department of Dermatology, Division of Dermatologic Oncology, Eberhard-Karls-University, Tuebingen, Germany.
authors.forename: Claus
authors.initials: C
authors.lastname: Garbe
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Dario
authors.initials: D
authors.lastname: Neri
authors.affiliation: Philochem AG, Otelfingen, Switzerland.
authors.forename: Tim
authors.initials: T
authors.lastname: Fugmann
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000951:Antigens, Neoplasm / Q000097:blood; D014408:Biomarkers, Tumor / Q000097:blood* / Q000302:isolation & purification; D016022:Case-Control Studies; D016384:Consensus Sequence; D057809:HEK293 Cells; D018922:HL-60 Cells; D015395:Histocompatibility Antigens Class I / Q000502:physiology*; D006801:Humans; D008545:Melanoma / Q000097:blood*; D010455:Peptides / Q000097:blood* / Q000302:isolation & purification; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D013167:Spondylitis, Ankylosing / Q000097:blood
chemical_list: D000951:Antigens, Neoplasm; D014408:Biomarkers, Tumor; D015395:Histocompatibility Antigens Class I; D010455:Peptides
keywords: Biomedicine; HLA class I; Immunopeptidomics; Melanoma; sHLA tumor-associated epitopes