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Alpízar A, Marino F, Ramos-Fernández A, Lombardía M, Jeko A, Pazos F, Paradela A, Santiago C, Heck AJR, Marcilla M. A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens. Mol Cell Proteomics 2016; 16:181-193. [PMID: 27920218 DOI: 10.1074/mcp.m116.063800] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/16/2016] [Indexed: 01/04/2023] Open
Abstract
As aberrant protein phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify 256 unique phosphorylated ligands associated with HLA-B*40, -B*27, -B*39, or -B*07. Remarkably, these phosphopeptides showed similar molecular features. Besides the specific anchor motifs imposed by the binding groove of each allotype, the predominance of phosphorylation at peptide position 4 (P4) became strikingly evident, as was the enrichment of basic residues at P1. To determine the structural basis of this observation, we carried out a series of peptide binding assays and solved the crystal structures of HLA-B*40 in complex with a phosphorylated ligand or its nonphosphorylated counterpart. Overall, our data provide a clear explanation to the common motif found in the phosphopeptidomes associated to different HLA-B molecules. The high prevalence of phosphorylation at P4 is dictated by the presence of the conserved residue Arg62 in the heavy chain, a structural feature shared by most HLA-B alleles. In contrast, the preference for basic residues at P1 is allotype-dependent and might be linked to the structure of the A pocket. This molecular understanding of the presentation of phosphopeptides by HLA-B molecules provides a base for the improved prediction and identification of phosphorylated neo-antigens, as potentially used for cancer immunotherapy.
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Affiliation(s)
- Adán Alpízar
- From the ‡Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain
| | - Fabio Marino
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,¶Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Antonio Ramos-Fernández
- ‖Proteobotics SL, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain
| | - Manuel Lombardía
- From the ‡Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain
| | - Anita Jeko
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,¶Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Florencio Pazos
- **Computational Systems Biology Group, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain
| | - Alberto Paradela
- From the ‡Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain
| | - César Santiago
- ‡‡Macromolecular X-ray Crystallography Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain
| | - Albert J R Heck
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; .,¶Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Miguel Marcilla
- From the ‡Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049, Madrid, Spain;
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Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MPH, Heck AJR, Mishto M. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science 2016; 354:354-358. [PMID: 27846572 DOI: 10.1126/science.aaf4384] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 09/19/2016] [Indexed: 12/23/2022]
Abstract
The proteasome generates the epitopes presented on human leukocyte antigen (HLA) class I molecules that elicit CD8+ T cell responses. Reports of proteasome-generated spliced epitopes exist, but they have been regarded as rare events. Here, however, we show that the proteasome-generated spliced peptide pool accounts for one-third of the entire HLA class I immunopeptidome in terms of diversity and one-fourth in terms of abundance. This pool also represents a unique set of antigens, possessing particular and distinguishing features. We validated this observation using a range of complementary experimental and bioinformatics approaches, as well as multiple cell types. The widespread appearance and abundance of proteasome-catalyzed peptide splicing events has implications for immunobiology and autoimmunity theories and may provide a previously untapped source of epitopes for use in vaccines and cancer immunotherapy.
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Affiliation(s)
- Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, Netherlands.,Netherlands Proteomics Centre, CH Utrecht, Netherlands
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Anita Jeko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, Netherlands.,Netherlands Proteomics Centre, CH Utrecht, Netherlands
| | - Daniel E Bunting
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Peter M Kloetzel
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.,Berlin Institute of Health, 10117 Berlin, Germany
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, Netherlands.,Netherlands Proteomics Centre, CH Utrecht, Netherlands
| | - Michele Mishto
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany. .,Berlin Institute of Health, 10117 Berlin, Germany
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Marino F, Mommen GPM, Jeko A, Meiring HD, van Gaans-van den Brink JAM, Scheltema RA, van Els CACM, Heck AJR. Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07. J Proteome Res 2016; 16:34-44. [PMID: 27503676 DOI: 10.1021/acs.jproteome.6b00528] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Alterations in protein post-translational modification (PTM) are recognized hallmarks of diseases. These modifications potentially provide a unique source of disease-related human leukocyte antigen (HLA) class I-presented peptides that can elicit specific immune responses. While phosphorylated HLA peptides have already received attention, arginine methylated HLA class I peptide presentation has not been characterized in detail. In a human B-cell line we detected 149 HLA class I peptides harboring mono- and/or dimethylated arginine residues by mass spectrometry. A striking preference was observed in the presentation of arginine (di)methylated peptides for HLA-B*07 molecules, likely because the binding motifs of this allele resemble consensus sequences recognized by arginine methyl-transferases. Moreover, HLA-B*07-bound peptides preferentially harbored dimethylated groups at the P3 position, thus consecutively to the proline anchor residue. Such a proline-arginine sequence has been associated with the arginine methyl-transferases CARM1 and PRMT5. Making use of the specific neutral losses in fragmentation spectra, we found most of the peptides to be asymmetrically dimethylated, most likely by CARM1. These data expand our knowledge of the processing and presentation of arginine (di)methylated HLA class I peptides and demonstrate that these types of modified peptides can be presented for recognition by T-cells. HLA class I peptides with mono- and dimethylated arginine residues may therefore offer a novel target for immunotherapy.
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Affiliation(s)
- Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Geert P M Mommen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Institute for Translational Vaccinology , P.O. Box 450, 3720 AL Bilthoven, The Netherlands
| | - Anita Jeko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hugo D Meiring
- Institute for Translational Vaccinology , P.O. Box 450, 3720 AL Bilthoven, The Netherlands
| | | | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cécile A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment , P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre , Padualaan 8, 3584 CH Utrecht, The Netherlands
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