title: Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry.
abstract: Although mutations may represent attractive targets for immunotherapy, direct identification of mutated peptide ligands isolated from human leucocyte antigens (HLA) on the surface of native tumour tissue has so far not been successful. Using advanced mass spectrometry (MS) analysis, we survey the melanoma-associated immunopeptidome to a depth of 95,500 patient-presented peptides. We thereby discover a large spectrum of attractive target antigen candidates including cancer testis antigens and phosphopeptides. Most importantly, we identify peptide ligands presented on native tumour tissue samples harbouring somatic mutations. Four of eleven mutated ligands prove to be immunogenic by neoantigen-specific T-cell responses. Moreover, tumour-reactive T cells with specificity for selected neoantigens identified by MS are detected in the patient's tumour and peripheral blood. We conclude that direct identification of mutated peptide ligands from primary tumour material by MS is possible and yields true neoepitopes with high relevance for immunotherapeutic strategies in cancer.
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
authors.forename: Michal
authors.initials: M
authors.lastname: Bassani-Sternberg
authors.affiliation: IIIrd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Bräunlein
authors.affiliation: IIIrd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Klar
authors.affiliation: IInd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.|German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Engleitner
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
authors.forename: Pavel
authors.initials: P
authors.lastname: Sinitcyn
authors.affiliation: IIIrd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Audehm
authors.affiliation: Institute of Pathology, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.
authors.forename: Melanie
authors.initials: M
authors.lastname: Straub
authors.affiliation: IInd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.|German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Weber
authors.affiliation: Institute of Pathology, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.|MRI-TUM-Biobank at the Institute of Pathology, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Slotta-Huspenina
authors.affiliation: Institute of Pathology, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.
authors.forename: Katja
authors.initials: K
authors.lastname: Specht
authors.affiliation: Surgery Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich, 81675, Germany.
authors.forename: Marc E
authors.initials: ME
authors.lastname: Martignoni
authors.affiliation: Surgery Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich, 81675, Germany.
authors.forename: Angelika
authors.initials: A
authors.lastname: Werner
authors.affiliation: Dermatology Department, Klinikum rechts der Isar, Technische Universität München, Biedersteiner Str 29, Munich 80802, Germany.
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Hein
authors.affiliation: Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstr. 30, Munich 81675, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: H Busch
authors.affiliation: IIIrd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.|German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Peschel
authors.affiliation: IInd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.|German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Rad
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Cox
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.affiliation: IIIrd Medical Department, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, Munich 81675, Germany.|German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Angela M
authors.initials: AM
authors.lastname: Krackhardt
mesh_terms: D017951:Antigen Presentation; D000951:Antigens, Neoplasm; D001483:Base Sequence; D003001:Cloning, Molecular; D000939:Epitopes / Q000235:genetics / Q000378:metabolism*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008024:Ligands; D013058:Mass Spectrometry; D008545:Melanoma / Q000276:immunology / Q000378:metabolism*; D009154:Mutation; D010455:Peptides / Q000378:metabolism
chemical_list: D000951:Antigens, Neoplasm; D000939:Epitopes; D008024:Ligands; D010455:Peptides