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Kelly JJ, Bloodworth N, Shao Q, Shabanowitz J, Hunt D, Meiler J, Pires MM. A Chemical Approach to Assess the Impact of Post-translational Modification on MHC Peptide Binding and Effector Cell Engagement. ACS Chem Biol 2024; 19:1991-2001. [PMID: 39150956 PMCID: PMC11420952 DOI: 10.1021/acschembio.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
The human major histocompatibility complex (MHC) plays a pivotal role in the presentation of peptidic fragments from proteins, which can originate from self-proteins or from nonhuman antigens, such as those produced by viruses or bacteria. To prevent cytotoxicity against healthy cells, thymocytes expressing T cell receptors (TCRs) that recognize self-peptides are removed from circulation (negative selection), thus leaving T cells that recognize nonself-peptides. Current understanding suggests that post-translationally modified (PTM) proteins and the resulting peptide fragments they generate following proteolysis are largely excluded from negative selection; this feature means that PTMs can generate nonself-peptides that potentially contribute to the development of autoreactive T cells and subsequent autoimmune diseases. Although it is well-established that PTMs are prevalent in peptides present on MHCs, the precise mechanisms by which PTMs influence the antigen presentation machinery remain poorly understood. In the present work, we introduce chemical modifications mimicking PTMs on synthetic peptides. This is the first systematic study isolating the impact of PTMs on MHC binding and also their impact on TCR recognition. Our findings reveal various ways PTMs alter antigen presentation, which could have implications for tumor neoantigen presentation.
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Affiliation(s)
- Joey J Kelly
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Nathaniel Bloodworth
- Division of Clinical Pharmacology, Department of MedicineVanderbilt University Medical Center, Nashville, Tennessee 37240, United States
| | - Qianqian Shao
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Donald Hunt
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Jens Meiler
- Division of Clinical Pharmacology, Department of MedicineVanderbilt University Medical Center, Nashville, Tennessee 37240, United States
- Institute of Drug Discovery, Faculty of MedicineUniversity of Leipzig, Leipzig, SAC 04103, Germany
- Center for Structural Biology Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Marcos M Pires
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
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2
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Juanes-Velasco P, Arias-Hidalgo C, García-Vaquero ML, Sotolongo-Ravelo J, Paíno T, Lécrevisse Q, Landeira-Viñuela A, Góngora R, Hernández ÁP, Fuentes M. Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation. Int J Mol Sci 2024; 25:9564. [PMID: 39273511 PMCID: PMC11395153 DOI: 10.3390/ijms25179564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Immunopeptidomics is the area of knowledge focused on the study of peptides assembled in the major histocompatibility complex (MHC), or human leukocyte antigen (HLA) in humans, which could activate the immune response via specific and selective T cell recognition. Advances in high-sensitivity mass spectrometry have enabled the detailed identification and quantification of the immunopeptidome, significantly impacting fields like oncology, infections, and autoimmune diseases. Current immunopeptidomics approaches primarily focus on workflows to identify immunopeptides from HLA molecules, requiring the isolation of the HLA from relevant cells or tissues. Common critical steps in these workflows, such as cell lysis, HLA immunoenrichment, and peptide isolation, significantly influence outcomes. A systematic evaluation of these steps led to the creation of an 'Immunopeptidome Score' to enhance the reproducibility and robustness of these workflows. This score, derived from LC-MS/MS datasets (ProteomeXchange identifier PXD038165), in combination with available information from public databases, aids in optimizing the immunopeptidome characterization process. The 'Immunopeptidome Score' has been applied in a systematic analysis of protein extraction, HLA immunoprecipitation, and peptide recovery yields across several tumor cell lines enabling the selection of peptides with optimal features and, therefore, the identification of potential biomarker and therapeutic targets.
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Affiliation(s)
- Pablo Juanes-Velasco
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlota Arias-Hidalgo
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Marina L García-Vaquero
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Janet Sotolongo-Ravelo
- Oncohematology Group, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Teresa Paíno
- Oncohematology Group, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Department of Physiology and Pharmacology, University of Salamanca, 37007 Salamanca, Spain
| | - Quentin Lécrevisse
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Alicia Landeira-Viñuela
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Góngora
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ángela-Patricia Hernández
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Pharmaceutical Sciences, Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, 37007 Salamanca, Spain
| | - Manuel Fuentes
- Translational and Clinical Research Program, Cancer Research Center (IBMCC, CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (Universidad de Salamanca), 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Proteomics Unit-IBSAL, Instituto de Investigación Biomédica de Salamanca, Universidad de Salamanca, (IBSAL/USAL), 37007 Salamanca, Spain
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3
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Sankova MV, Nikolenko VN, Oganesyan MV, Sankov SV, Sinelnikov MY, Suslov AV, Trishina AS, Zharikova TS, Pontes-Silva A, Zharikov YO. Magnesium deficiency and its interaction with the musculoskeletal system, exercise, and connective tissue: an evidence synthesis. SPORT SCIENCES FOR HEALTH 2024; 20:715-726. [DOI: 10.1007/s11332-024-01179-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/06/2024] [Indexed: 09/13/2024]
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Pongcharoen S, Kaewsringam N, Somaparn P, Roytrakul S, Maneerat Y, Pintha K, Topanurak S. Immunopeptidomics in the cancer immunotherapy era. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:801-817. [PMID: 39280250 PMCID: PMC11390293 DOI: 10.37349/etat.2024.00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/06/2024] [Indexed: 09/18/2024] Open
Abstract
Cancer is the primary cause of death worldwide, and conventional treatments are painful, complicated, and have negative effects on healthy cells. However, cancer immunotherapy has emerged as a promising alternative. Principle of cancer immunotherapy is the re-activation of T-cell to combat the tumor that presents the peptide antigen on major histocompatibility complex (MHC). Those peptide antigens are identified with the set of omics technology, proteomics, genomics, and bioinformatics, which referred to immunopeptidomics. Indeed, immunopeptidomics can identify the neoantigens that are very useful for cancer immunotherapies. This review explored the use of immunopeptidomics for various immunotherapies, i.e., peptide-based vaccines, immune checkpoint inhibitors, oncolytic viruses, and chimeric antigen receptor T-cell. We also discussed how the diversity of neoantigens allows for the discovery of novel antigenic peptides while post-translationally modified peptides diversify the overall peptides binding to MHC or so-called MHC ligandome. The development of immunopeptidomics is keeping up-to-date and very active, particularly for clinical application. Immunopeptidomics is expected to be fast, accurate and reliable for the application for cancer immunotherapies.
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Affiliation(s)
- Sutatip Pongcharoen
- Division of Immunology, Department of Medicine, Faculty of Medicine, Naresuan University, Phitsanulok 65000, Thailand
| | - Nongphanga Kaewsringam
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Poorichaya Somaparn
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang 12120, Pathum Thani, Thailand
| | - Yaowapa Maneerat
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Komsak Pintha
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand
| | - Supachai Topanurak
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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Fasoulis R, Rigo MM, Lizée G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model 2024; 64:1730-1750. [PMID: 38415656 PMCID: PMC10936522 DOI: 10.1021/acs.jcim.3c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
The recognition of peptides bound to class I major histocompatibility complex (MHC-I) receptors by T-cell receptors (TCRs) is a determinant of triggering the adaptive immune response. While the exact molecular features that drive the TCR recognition are still unknown, studies have suggested that the geometry of the joint peptide-MHC (pMHC) structure plays an important role. As such, there is a definite need for methods and tools that accurately predict the structure of the peptide bound to the MHC-I receptor. In the past few years, many pMHC structural modeling tools have emerged that provide high-quality modeled structures in the general case. However, there are numerous instances of non-canonical cases in the immunopeptidome that the majority of pMHC modeling tools do not attend to, most notably, peptides that exhibit non-standard amino acids and post-translational modifications (PTMs) or peptides that assume non-canonical geometries in the MHC binding cleft. Such chemical and structural properties have been shown to be present in neoantigens; therefore, accurate structural modeling of these instances can be vital for cancer immunotherapy. To this end, we have developed APE-Gen2.0, a tool that improves upon its predecessor and other pMHC modeling tools, both in terms of modeling accuracy and the available modeling range of non-canonical peptide cases. Some of the improvements include (i) the ability to model peptides that have different types of PTMs such as phosphorylation, nitration, and citrullination; (ii) a new and improved anchor identification routine in order to identify and model peptides that exhibit a non-canonical anchor conformation; and (iii) a web server that provides a platform for easy and accessible pMHC modeling. We further show that structures predicted by APE-Gen2.0 can be used to assess the effects that PTMs have in binding affinity in a more accurate manner than just using solely the sequence of the peptide. APE-Gen2.0 is freely available at https://apegen.kavrakilab.org.
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Affiliation(s)
- Romanos Fasoulis
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Mauricio M. Rigo
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Gregory Lizée
- Department
of Melanoma Medical Oncology—Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Dinler A. Antunes
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77004, United States
| | - Lydia E. Kavraki
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
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6
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O'Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. J Immunother Cancer 2023; 11:e006889. [PMID: 37775115 PMCID: PMC10546156 DOI: 10.1136/jitc-2023-006889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Certain phosphorylated peptides are differentially presented by major histocompatibility complex (MHC) molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their non-phosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, HLA-A*11:01, HLA-C*07:01, and HLA-C*07:02. METHODS We isolated peptide-MHC complexes by immunoprecipitation from 11 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics data sets to assemble a curated set of phosphopeptides presented by 96 samples spanning 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. RESULTS We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their non-phosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B-pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and HLA-A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the non-phosphorylated peptide was co-presented, HLA-A*03:01 or HLA-C*07:01 phosphopeptides were repeatedly non-immunogenic, requiring use of allogeneic T cells to induce phosphopeptide-specific T cells. CONCLUSIONS Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin G Klatt
- Department of Hematology, Oncology and Tumor Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
- Berlin Institute of Health at Charité -Universitätsmedizin Berlin, BIH Biomedical 13 Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jessica Urraca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Scheinberg
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Richard J O'Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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7
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Patskovsky Y, Natarajan A, Patskovska L, Nyovanie S, Joshi B, Morin B, Brittsan C, Huber O, Gordon S, Michelet X, Schmitzberger F, Stein RB, Findeis MA, Hurwitz A, Van Dijk M, Chantzoura E, Yague AS, Pollack Smith D, Buell JS, Underwood D, Krogsgaard M. Molecular mechanism of phosphopeptide neoantigen immunogenicity. Nat Commun 2023; 14:3763. [PMID: 37353482 PMCID: PMC10290117 DOI: 10.1038/s41467-023-39425-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
Altered protein phosphorylation in cancer cells often leads to surface presentation of phosphopeptide neoantigens. However, their role in cancer immunogenicity remains unclear. Here we describe a mechanism by which an HLA-B*0702-specific acute myeloid leukemia phosphoneoantigen, pMLL747-755 (EPR(pS)PSHSM), is recognized by a cognate T cell receptor named TCR27, a candidate for cancer immunotherapy. We show that the replacement of phosphoserine P4 with serine or phosphomimetics does not affect pMHC conformation or peptide-MHC affinity but abrogates TCR27-dependent T cell activation and weakens binding between TCR27 and pMHC. Here we describe the crystal structures for TCR27 and cognate pMHC, map of the interface produced by nuclear magnetic resonance, and a ternary complex generated using information-driven protein docking. Our data show that non-covalent interactions between the epitope phosphate group and TCR27 are crucial for TCR specificity. This study supports development of new treatment options for cancer patients through target expansion and TCR optimization.
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Grants
- P30 GM133893 NIGMS NIH HHS
- P30 CA016087 NCI NIH HHS
- U01 CA214354 NCI NIH HHS
- P50 CA225450 NCI NIH HHS
- R01 GM085586 NIGMS NIH HHS
- R01 GM124489 NIGMS NIH HHS
- R01 CA243486 NCI NIH HHS
- S10 OD016343 NIH HHS
- P41 GM118302 NIGMS NIH HHS
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- This work was supported by the NIH grant NIGMS R01 GM124489 (to M.K.), NCI R01 CA243486 (to M.K) and a Sponsored Research Agreement from Agenus to M.K. Results shown in this report are partially derived from work performed at Argonne National Laboratory, Structural Biology Center at the Advanced Photon Source. SBC is operated by UChicago Argonne, LLC, for the U.S. Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. Results in this report are partially derived from work performed at The Center for BioMolecular Structure (CBMS) primarily supported by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1607011). As part of NSLS-II, a national user facility at Brookhaven National Laboratory, work performed at the CBMS is supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Program under contract number and DE-SC0012704. The NMR spectrometers at the NYU Chemistry Shared Instrumentation Facility were supported by NYU and the NIH Grant 1S10-OD016343. The facilities at the NYSBC were supported by the NIH Grant P41GM118302.
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Affiliation(s)
- Yury Patskovsky
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Aswin Natarajan
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Larysa Patskovska
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Samantha Nyovanie
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michelle Krogsgaard
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA.
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8
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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9
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Pyke RM, Mellacheruvu D, Dea S, Abbott C, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. Precision Neoantigen Discovery Using Large-Scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation. Mol Cell Proteomics 2023; 22:100506. [PMID: 36796642 PMCID: PMC10114598 DOI: 10.1016/j.mcpro.2023.100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anticancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past 2 decades. However, improvement in the accuracy of prediction algorithms is needed for clinical applications like the development of personalized cancer vaccines, the discovery of biomarkers for response to immunotherapies, and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 monoallelic cell lines and created Systematic Human Leukocyte Antigen (HLA) Epitope Ranking Pan Algorithm (SHERPA), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale monoallelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA allele to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC diversity in the training data and extend allelic coverage in underprofiled populations. To improve generalizability, SHERPA systematically integrates 128 monoallelic and 384 multiallelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution, and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44-fold improvement of positive predictive value compared with existing tools when evaluated on independent monoallelic datasets and a 1.17-fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.
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Affiliation(s)
| | | | - Steven Dea
- Personalis, Inc, Menlo Park, California, USA
| | | | | | | | | | | | - Sejal Desai
- Personalis, Inc, Menlo Park, California, USA
| | | | - John West
- Personalis, Inc, Menlo Park, California, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Palo Alto, California, USA
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10
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O’Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527552. [PMID: 36798179 PMCID: PMC9934604 DOI: 10.1101/2023.02.08.527552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Background Certain phosphorylated peptides are differentially presented by MHC molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their nonphosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, -A*11:01, -C*07:01, and - C*07:02. Methods We isolated peptide-MHC complexes by immunoprecipitation from 10 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics datasets to assemble a curated set of phosphopeptides presented by 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. Results We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their nonphosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B- pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and -A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the nonphosphorylated peptide was co-presented, HLA-A*03:01 or -C*07:01 phosphopeptides were repeatedly nonimmunogenic, requiring use of allogeneic T cells to induce phosphopeptide- specific T cells. Conclusions Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences. What is already known on this topic - Phosphorylated peptides presented by the common HLA alleles A*02:01 and B*07:02 are differentially expressed by multiple tumor types, exhibit structural fitness due to phosphorylation, and are targets of healthy donor T cell surveillance, but it is not clear, however, whether such features apply to phosphopeptides presented by other common HLA alleles. What this study adds - We investigated the tumor presentation, binding, structural features, and immunogenicity of phosphopeptides to the prevalent alleles A*03:01, A*11:01, C*07:01, and C*07:02, selected on the basis of their presentation by malignant cells but not normal cells. We found tumor antigens derived from genetic dependencies in lymphomas and leukemias that bind HLA-A3, -A11, -C7 molecules. While we could detect circulating T cell responses in healthy individuals to A*02:01 and A*11:01 phosphopeptides, we did not find such responses to A*03:01 or C*07:01 phosphopeptides, except when utilizing allogeneic donor T cells, indicating that these phosphopeptides may not be immunogenic in an autologous setting but can still be targeted by other means. How this study might affect research, practice or policy - An expanded patient population expressing alleles other than A*02:01 can be addressed through the development of immunotherapies specific for phosphopeptides profiled in the present work, provided the nuances we describe between alleles are taken into consideration.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Martin G. Klatt
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité- University Medicine Berlin, Berlin, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Berlin Institute of Health at Charité –Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jessica Urraca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, NY, NY, USA
| | - Richard J. O’Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, NY, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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11
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Kacen A, Javitt A, Kramer MP, Morgenstern D, Tsaban T, Shmueli MD, Teo GC, da Veiga Leprevost F, Barnea E, Yu F, Admon A, Eisenbach L, Samuels Y, Schueler-Furman O, Levin Y, Nesvizhskii AI, Merbl Y. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nat Biotechnol 2023; 41:239-251. [PMID: 36203013 PMCID: PMC11197725 DOI: 10.1038/s41587-022-01464-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/09/2022] [Indexed: 11/08/2022]
Abstract
Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying antigen PTMs and assessing their role in shaping the immunopeptidome is challenging. Here we describe the Protein Modification Integrated Search Engine (PROMISE), an antigen discovery pipeline that enables the analysis of 29 different PTM combinations from multiple clinical cohorts and cell lines. We expanded the antigen landscape, uncovering human leukocyte antigen class I binding motifs defined by specific PTMs with haplotype-specific binding preferences and revealing disease-specific modified targets, including thousands of new cancer-specific antigens that can be shared between patients and across cancer types. Furthermore, we uncovered a subset of modified peptides that are specific to cancer tissue and driven by post-translational changes that occurred in the tumor proteome. Our findings highlight principles of PTM-driven antigenicity, which may have broad implications for T cell-mediated therapies in cancer and beyond.
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Affiliation(s)
- Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Aaron Javitt
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias P Kramer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Tsaban
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lea Eisenbach
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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12
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Post-Translational Modifications in Tumor-Associated Antigens as a Platform for Novel Immuno-Oncology Therapies. Cancers (Basel) 2022; 15:cancers15010138. [PMID: 36612133 PMCID: PMC9817968 DOI: 10.3390/cancers15010138] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Post-translational modifications (PTMs) are generated by adding small chemical groups to amino acid residues after the translation of proteins. Many PTMs have been reported to correlate with tumor progression, growth, and survival by modifying the normal functions of the protein in tumor cells. PTMs can also elicit humoral and cellular immune responses, making them attractive targets for cancer immunotherapy. This review will discuss how the acetylation, citrullination, and phosphorylation of proteins expressed by tumor cells render the corresponding tumor-associated antigen more antigenic and affect the immune response in multiple cancers. In addition, the role of glycosylated protein mucins in anti-cancer immunotherapy will be considered. Mucin peptides in combination with stimulating adjuvants have, in fact, been utilized to produce anti-tumor antibodies and vaccines. Finally, we will also outline the results of the clinical trial exploiting glycosylated-MUC1 as a vaccine in different cancers. Overall, PTMs in TAAs could be considered in future therapies to result in lasting anti-tumor responses.
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13
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Zeng WF, Zhou XX, Willems S, Ammar C, Wahle M, Bludau I, Voytik E, Strauss MT, Mann M. AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics. Nat Commun 2022; 13:7238. [PMID: 36433986 PMCID: PMC9700817 DOI: 10.1038/s41467-022-34904-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Machine learning and in particular deep learning (DL) are increasingly important in mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention time, ion mobility and fragment intensities of a peptide just from the amino acid sequence with good accuracy. However, DL is a very rapidly developing field with new neural network architectures frequently appearing, which are challenging to incorporate for proteomics researchers. Here we introduce AlphaPeptDeep, a modular Python framework built on the PyTorch DL library that learns and predicts the properties of peptides ( https://github.com/MannLabs/alphapeptdeep ). It features a model shop that enables non-specialists to create models in just a few lines of code. AlphaPeptDeep represents post-translational modifications in a generic manner, even if only the chemical composition is known. Extensive use of transfer learning obviates the need for large data sets to refine models for particular experimental conditions. The AlphaPeptDeep models for predicting retention time, collisional cross sections and fragment intensities are at least on par with existing tools. Additional sequence-based properties can also be predicted by AlphaPeptDeep, as demonstrated with a HLA peptide prediction model to improve HLA peptide identification for data-independent acquisition ( https://github.com/MannLabs/PeptDeep-HLA ).
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Affiliation(s)
- Wen-Feng Zeng
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Xie-Xuan Zhou
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sander Willems
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Constantin Ammar
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria Wahle
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Eugenia Voytik
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximillian T Strauss
- Proteomics Program, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Proteomics Program, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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14
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León-Letelier RA, Katayama H, Hanash S. Mining the Immunopeptidome for Antigenic Peptides in Cancer. Cancers (Basel) 2022; 14:4968. [PMID: 36291752 PMCID: PMC9599891 DOI: 10.3390/cancers14204968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Although harnessing the immune system for cancer therapy has shown success, response to immunotherapy has been limited. The immunopeptidome of cancer cells presents an opportunity to discover novel antigens for immunotherapy applications. These neoantigens bind to MHC class I and class II molecules. Remarkably, the immunopeptidome encompasses protein post-translation modifications (PTMs) that may not be evident from genome or transcriptome profiling. A case in point is citrullination, which has been demonstrated to induce a strong immune response. In this review, we cover how the immunopeptidome, with a special focus on PTMs, can be utilized to identify cancer-specific antigens for immunotherapeutic applications.
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Affiliation(s)
| | | | - Sam Hanash
- Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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15
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Sandalova T, Sala BM, Achour A. Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition. Front Chem 2022; 10:861609. [PMID: 36017166 PMCID: PMC9395651 DOI: 10.3389/fchem.2022.861609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Significant advances in mass-spectroscopy (MS) have made it possible to investigate the cellular immunopeptidome, a large collection of MHC-associated epitopes presented on the surface of healthy, stressed and infected cells. These approaches have hitherto allowed the unambiguous identification of large cohorts of epitope sequences that are restricted to specific MHC class I and II molecules, enhancing our understanding of the quantities, qualities and origins of these peptide populations. Most importantly these analyses provide essential information about the immunopeptidome in responses to pathogens, autoimmunity and cancer, and will hopefully allow for future tailored individual therapies. Protein post-translational modifications (PTM) play a key role in cellular functions, and are essential for both maintaining cellular homeostasis and increasing the diversity of the proteome. A significant proportion of proteins is post-translationally modified, and thus a deeper understanding of the importance of PTM epitopes in immunopeptidomes is essential for a thorough and stringent understanding of these peptide populations. The aim of the present review is to provide a structural insight into the impact of PTM peptides on stability of MHC/peptide complexes, and how these may alter/modulate immune responses.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Benedetta Maria Sala
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- *Correspondence: Adnane Achour,
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16
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Min F, Fan C, Zeng Y, He N, Zeng T, Qin B, Shi Y. Carbamazepine-modified HLA-A*24:02-bound peptidome: Implication of CORO1A in skin rash. Int Immunopharmacol 2022; 109:108804. [DOI: 10.1016/j.intimp.2022.108804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 11/05/2022]
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17
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Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Lizée G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS NEXUS 2022; 1:pgac124. [PMID: 36003074 PMCID: PMC9391200 DOI: 10.1093/pnasnexus/pgac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Human leukocyte antigen class I (HLA-I) molecules bind and present peptides at the cell surface to facilitate the induction of appropriate CD8+ T cell-mediated immune responses to pathogen- and self-derived proteins. The HLA-I peptide-binding cleft contains dominant anchor sites in the B and F pockets that interact primarily with amino acids at peptide position 2 and the C-terminus, respectively. Nonpocket peptide-HLA interactions also contribute to peptide binding and stability, but these secondary interactions are thought to be unique to individual HLA allotypes or to specific peptide antigens. Here, we show that two positively charged residues located near the top of peptide-binding cleft facilitate interactions with negatively charged residues at position 4 of presented peptides, which occur at elevated frequencies across most HLA-I allotypes. Loss of these interactions was shown to impair HLA-I/peptide binding and complex stability, as demonstrated by both in vitro and in silico experiments. Furthermore, mutation of these Arginine-65 (R65) and/or Lysine-66 (K66) residues in HLA-A*02:01 and A*24:02 significantly reduced HLA-I cell surface expression while also reducing the diversity of the presented peptide repertoire by up to 5-fold. The impact of the R65 mutation demonstrates that nonpocket HLA-I/peptide interactions can constitute anchor motifs that exert an unexpectedly broad influence on HLA-I-mediated antigen presentation. These findings provide fundamental insights into peptide antigen binding that could broadly inform epitope discovery in the context of viral vaccine development and cancer immunotherapy.
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Affiliation(s)
- Kyle R Jackson
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ariana R Maleki
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kano Amagai
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Avery Salmon
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun S Katailiha
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Romanos Fasoulis
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Brenda D Melendez
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yimo Sun
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | - Yang Liu
- ThermoFisher Scientific, San Jose, CA, USA
| | - David Horn
- ThermoFisher Scientific, San Jose, CA, USA
| | | | | | - Patrick Hwu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Gregory Lizée
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
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18
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Conev A, Devaurs D, Rigo MM, Antunes DA, Kavraki LE. 3pHLA-score improves structure-based peptide-HLA binding affinity prediction. Sci Rep 2022; 12:10749. [PMID: 35750701 PMCID: PMC9232595 DOI: 10.1038/s41598-022-14526-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/08/2022] [Indexed: 12/30/2022] Open
Abstract
Binding of peptides to Human Leukocyte Antigen (HLA) receptors is a prerequisite for triggering immune response. Estimating peptide-HLA (pHLA) binding is crucial for peptide vaccine target identification and epitope discovery pipelines. Computational methods for binding affinity prediction can accelerate these pipelines. Currently, most of those computational methods rely exclusively on sequence-based data, which leads to inherent limitations. Recent studies have shown that structure-based data can address some of these limitations. In this work we propose a novel machine learning (ML) structure-based protocol to predict binding affinity of peptides to HLA receptors. For that, we engineer the input features for ML models by decoupling energy contributions at different residue positions in peptides, which leads to our novel per-peptide-position protocol. Using Rosetta's ref2015 scoring function as a baseline we use this protocol to develop 3pHLA-score. Our per-peptide-position protocol outperforms the standard training protocol and leads to an increase from 0.82 to 0.99 of the area under the precision-recall curve. 3pHLA-score outperforms widely used scoring functions (AutoDock4, Vina, Dope, Vinardo, FoldX, GradDock) in a structural virtual screening task. Overall, this work brings structure-based methods one step closer to epitope discovery pipelines and could help advance the development of cancer and viral vaccines.
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Affiliation(s)
- Anja Conev
- grid.21940.3e0000 0004 1936 8278Department of Computer Science, Rice University, Houston, 77005 USA
| | - Didier Devaurs
- grid.4305.20000 0004 1936 7988MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Mauricio Menegatti Rigo
- grid.21940.3e0000 0004 1936 8278Department of Computer Science, Rice University, Houston, 77005 USA
| | | | - Lydia E. Kavraki
- grid.21940.3e0000 0004 1936 8278Department of Computer Science, Rice University, Houston, 77005 USA
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19
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Solleder M, Racle J, Guillaume P, Coukos G, Bassani-Sternberg M, Gfeller D. Deciphering the landscape of phosphorylated HLA-II ligands. iScience 2022; 25:104215. [PMID: 35494241 PMCID: PMC9051626 DOI: 10.1016/j.isci.2022.104215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
CD4+ T cell activation in infectious diseases and cancer is governed by the recognition of peptides presented on class II human leukocyte antigen (HLA-II) molecules. Therefore, HLA-II ligands represent promising targets for vaccine design and personalized cancer immunotherapy. Much work has been done to identify and predict unmodified peptides presented on HLA-II molecules. However, little is known about the presentation of phosphorylated HLA-II ligands. Here, we analyzed Mass Spectrometry HLA-II peptidomics data and identified 1,943 unique phosphorylated HLA-II ligands. This enabled us to precisely define phosphorylated binding motifs for more than 30 common HLA-II alleles and to explore various molecular properties of phosphorylated peptides. Our data were further used to develop the first predictor of phosphorylated peptide presentation on HLA-II molecules. 1,943 unique phosphorylated HLA-II ligands from MS HLA-II peptidomics data Binding motifs of phosphorylated HLA-II ligands identified for more than 30 alleles Predictor trained on phosphorylated peptides achieves higher accuracy
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Affiliation(s)
- Marthe Solleder
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
- Corresponding author
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
- Corresponding author
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20
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Barbosa CRR, Barton J, Shepherd AJ, Mishto M. Mechanistic diversity in MHC class I antigen recognition. Biochem J 2021; 478:4187-4202. [PMID: 34940832 PMCID: PMC8786304 DOI: 10.1042/bcj20200910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.
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Affiliation(s)
- Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| | - Justin Barton
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Adrian J. Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
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21
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Mukherjee S, Sanchez-Bernabeu A, Demmers LC, Wu W, Heck AJR. The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02. Front Immunol 2021; 12:796584. [PMID: 34925382 PMCID: PMC8671986 DOI: 10.3389/fimmu.2021.796584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Mass-spectrometry based immunopeptidomics has provided unprecedented insights into antigen presentation, not only charting an enormous ligandome of self-antigens, but also cancer neoantigens and peptide antigens harbouring post-translational modifications. Here we concentrate on the latter, focusing on the small subset of HLA Class I peptides (less than 1%) that has been observed to be post-translationally modified (PTM) by a O-linked N-acetylglucosamine (GlcNAc). Just like neoantigens these modified antigens may have specific immunomodulatory functions. Here we compiled from literature, and a new dataset originating from the JY B cell lymphoblastoid cell line, a concise albeit comprehensive list of O-GlcNAcylated HLA class I peptides. This cumulative list of O-GlcNAcylated HLA peptides were derived from normal and cancerous origin, as well as tissue specimen. Remarkably, the overlap in detected O-GlcNAcylated HLA peptides as well as their source proteins is strikingly high. Most of the O-GlcNAcylated HLA peptides originate from nuclear proteins, notably transcription factors. From this list, we extract that O-GlcNAcylated HLA Class I peptides are preferentially presented by the HLA-B*07:02 allele. This allele loads peptides with a Proline residue anchor at position 2, and features a binding groove that can accommodate well the recently proposed consensus sequence for O-GlcNAcylation, P(V/A/T/S)g(S/T), essentially explaining why HLA-B*07:02 is a favoured binding allele. The observations drawn from the compiled list, may assist in the prediction of novel O-GlcNAcylated HLA antigens, which will be best presented by patients harbouring HLA-B*07:02 or related alleles that use Proline as anchoring residue.
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Affiliation(s)
- Soumya Mukherjee
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Alvaro Sanchez-Bernabeu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
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22
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Boyne C, Lennox D, Beech O, Powis SJ, Kumar P. What Is the Role of HLA-I on Cancer Derived Extracellular Vesicles? Defining the Challenges in Characterisation and Potential Uses of This Ligandome. Int J Mol Sci 2021; 22:ijms222413554. [PMID: 34948350 PMCID: PMC8703738 DOI: 10.3390/ijms222413554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
The Human Leukocyte Antigen class I (HLA-I) system is an essential part of the immune system that is fundamental to the successful activation of cytotoxic lymphocytes, and an effective subsequent immune attack against both pathogen-infected and cancer cells. The importance of cytotoxic T cell activity and ability to detect foreign cancer-related antigenic peptides has recently been highlighted by the successful application of monoclonal antibody-based checkpoint inhibitors as novel immune therapies. Thus, there is an increased interest in fully characterising the repertoire of peptides that are being presented to cytotoxic CD8+ T cells by cancer cells. However, HLA-I is also known to be present on the surface of extracellular vesicles, which are released by most if not all cancer cells. Whilst the peptide ligandome presented by cell surface HLA class I molecules on cancer cells has been studied extensively, the ligandome of extracellular vesicles remains relatively poorly defined. Here, we will describe the current understanding of the HLA-I peptide ligandome and its role on cancer-derived extracellular vesicles, and evaluate the aspects of the system that have the potential to advance immune-based therapeutic approaches for the effective treatment of cancer.
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23
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Bauzá-Martinez J, Heck AJR, Wu W. HLA-B and cysteinylated ligands distinguish the antigen presentation landscape of extracellular vesicles. Commun Biol 2021; 4:825. [PMID: 34211107 PMCID: PMC8249458 DOI: 10.1038/s42003-021-02364-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles can modulate diverse processes ranging from proliferation and tissue repair, to chemo-resistance and cellular differentiation. With the advent of tissue and immunological targeting, extracellular vesicles are also increasingly viewed as promising vectors to deliver peptide-based cancer antigens to the human immune system. Despite the clinical relevance and therapeutic potential of such 'cell-free' approaches, the natural antigen presentation landscape exported in extracellular vesicles is still largely uncharted, due to the challenging nature of such preparations and analyses. In the context of therapeutic vesicle production, a critical evaluation of the similarity in vesicular antigen presentation is also urgently needed. In this work, we compared the HLA-I peptide ligandomes of extracellular vesicles against that of whole-cells of the same cell line. We found that extracellular vesicles not only over-represent HLA-B complexes and peptide ligands, but also cysteinylated peptides that may modulate immune responses. Collectively, these findings describe the pre-existing provision of vesicular HLA complexes that may be utilized to carry peptide vaccines, as well as the propensity for different peptide and post-translationally modified ligands to be presented, and will outline critical considerations in devising novel EV vaccination strategies.
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Affiliation(s)
- Julia Bauzá-Martinez
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Albert J. R. Heck
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Wei Wu
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Netherlands Proteomics Centre, Utrecht, The Netherlands
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24
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Pyke RM, Mellacheruvu D, Dea S, Abbott CW, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. Withdrawn: Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation. Mol Cell Proteomics 2021; 20:100111. [PMID: 34126241 PMCID: PMC8318994 DOI: 10.1016/j.mcpro.2021.100111] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/07/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
This article has been withdrawn by the authors. A publication of the manuscript with the correct figures and tables has been approved and the authors state the conclusions of the manuscript remain unaffected. Specifically, errors are in Figure 6A, Supplementary Figure 10B, Supplementary Figure 10C, and Supplementary Table 5. The details of the errors are as follows: the HLA types for one sample were incorrectly assigned because of a tumor/normal mislabeling from the biobank vendor. Due to the differing HLA types between the tumor and normal sample, the sequence analysis established that the HLA alleles for this patient had been deleted (HLA LOH). The authors conclude that this was an artifact caused by the normal sample mislabeling. The corrected version can be accessed (Pyke, R.M., Mellacheruvu, D., Dea, S., Abbott, C.W., Zhang, S.V., Philips, N.A., Harris, J., Bartha, G., Desai, S., McClory, R., West, J., Snyder, M,P., Chen, R., Boyle, S.M. (2022) Precision Neoantigen Discovery Using Large-Scale Immunopeptidomics and Composite Modeling of MHC Peptide Presentation. Mol. Cell. Proteomics 22, 100506
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Affiliation(s)
| | | | - Steven Dea
- Personalis, Inc, Menlo Park, California, USA
| | | | | | | | | | | | - Sejal Desai
- Personalis, Inc, Menlo Park, California, USA
| | | | - John West
- Personalis, Inc, Menlo Park, California, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Palo Alto, California, USA
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25
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Mayer RL, Impens F. Immunopeptidomics for next-generation bacterial vaccine development. Trends Microbiol 2021; 29:1034-1045. [PMID: 34030969 DOI: 10.1016/j.tim.2021.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is an increasing global threat and alternative treatments substituting failing antibiotics are urgently needed. Vaccines are recognized as highly effective tools to mitigate antimicrobial resistance; however, the selection of bacterial antigens as vaccine candidates remains challenging. In recent years, advances in mass spectrometry-based proteomics have led to the development of so-called immunopeptidomics approaches that allow the untargeted discovery of bacterial epitopes that are presented on the surface of infected cells. Especially for intracellular bacterial pathogens, immunopeptidomics holds great promise to uncover antigens that can be encoded in viral vector- or nucleic acid-based vaccines. This review provides an overview of immunopeptidomics studies on intracellular bacterial pathogens and considers future directions and challenges in advancing towards next-generation vaccines.
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Affiliation(s)
- Rupert L Mayer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium.
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26
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Kuznetsov A, Voronina A, Govorun V, Arapidi G. Critical Review of Existing MHC I Immunopeptidome Isolation Methods. Molecules 2020; 25:E5409. [PMID: 33228004 PMCID: PMC7699222 DOI: 10.3390/molecules25225409] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
Major histocompatibility complex class I (MHC I) plays a crucial role in the development of adaptive immune response in vertebrates. MHC molecules are cell surface protein complexes loaded with short peptides and recognized by the T-cell receptors (TCR). Peptides associated with MHC are named immunopeptidome. The MHC I immunopeptidome is produced by the proteasome degradation of intracellular proteins. The knowledge of the immunopeptidome repertoire facilitates the creation of personalized antitumor or antiviral vaccines. A huge number of publications on the immunopeptidome diversity of different human and mouse biological samples-plasma, peripheral blood mononuclear cells (PBMCs), and solid tissues, including tumors-appeared in the scientific journals in the last decade. Significant immunopeptidome identification efficiency was achieved by advances in technology: the immunoprecipitation of MHC and mass spectrometry-based approaches. Researchers optimized common strategies to isolate MHC-associated peptides for individual tasks. They published many protocols with differences in the amount and type of biological sample, amount of antibodies, type and amount of insoluble support, methods of post-fractionation and purification, and approaches to LC-MS/MS identification of immunopeptidome. These parameters have a large impact on the final repertoire of isolated immunopeptidome. In this review, we summarize and compare immunopeptidome isolation techniques with an emphasis on the results obtained.
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Affiliation(s)
- Alexandr Kuznetsov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
| | - Alice Voronina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Georgij Arapidi
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
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27
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Abstract
Worldwide, approximately half a million people are diagnosed with pancreatic cancer every year, with mortality rates of more than 90%. T cells within pancreatic tumors are generally infrequent and incapable of eliciting antitumor immunity. Thus, pancreatic cancer is considered an "immunologically cold" tumor. However, recent studies clearly show that when T-cell immunity in pancreatic cancer is sufficiently induced, T cells become effective weapons. This fact suggests that to improve pancreatic cancer patients' clinical outcomes, we need to unveil the complex immune biology of this disease. In this review, we discuss the elements of tumor immunogenicity in the specific context of pancreatic malignancy.
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28
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Mei S, Ayala R, Ramarathinam SH, Illing PT, Faridi P, Song J, Purcell AW, Croft NP. Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors. Mol Cell Proteomics 2020; 19:1236-1247. [PMID: 32357974 PMCID: PMC7338083 DOI: 10.1074/mcp.ra119.001846] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
The presentation of post-translationally modified (PTM) peptides by cell surface HLA molecules has the potential to increase the diversity of targets for surveilling T cells. Although immunopeptidomics studies routinely identify thousands of HLA-bound peptides from cell lines and tissue samples, in-depth analyses of the proportion and nature of peptides bearing one or more PTMs remains challenging. Here we have analyzed HLA-bound peptides from a variety of allotypes and assessed the distribution of mass spectrometry-detected PTMs, finding deamidation of asparagine or glutamine to be highly prevalent. Given that asparagine deamidation may arise either spontaneously or through enzymatic reaction, we assessed allele-specific and global motifs flanking the modified residues. Notably, we found that the N-linked glycosylation motif NX(S/T) was highly abundant across asparagine-deamidated HLA-bound peptides. This finding, demonstrated previously for a handful of deamidated T cell epitopes, implicates a more global role for the retrograde transport of nascently N-glycosylated polypeptides from the ER and their subsequent degradation within the cytosol to form HLA-ligand precursors. Chemical inhibition of Peptide:N-Glycanase (PNGase), the endoglycosidase responsible for the removal of glycans from misfolded and retrotranslocated glycoproteins, greatly reduced presentation of this subset of deamidated HLA-bound peptides. Importantly, there was no impact of PNGase inhibition on peptides not containing a consensus NX(S/T) motif. This indicates that a large proportion of HLA-I bound asparagine deamidated peptides are generated from formerly glycosylated proteins that have undergone deglycosylation via the ER-associated protein degradation (ERAD) pathway. The information herein will help train deamidation prediction models for HLA-peptide repertoires and aid in the design of novel T cell therapeutic targets derived from glycoprotein antigens.
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Affiliation(s)
- Shutao Mei
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Rochelle Ayala
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Sri H Ramarathinam
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Patricia T Illing
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Pouya Faridi
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.
| | - Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.
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29
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Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D. Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. Mol Cell Proteomics 2020; 19:390-404. [PMID: 31848261 PMCID: PMC7000122 DOI: 10.1074/mcp.tir119.001641] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/06/2019] [Indexed: 12/19/2022] Open
Abstract
The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.
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Affiliation(s)
- Marthe Solleder
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Hui-Song Pak
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Markus Müller
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland.
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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30
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Vizcaíno JA, Kubiniok P, Kovalchik KA, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E. The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases. Mol Cell Proteomics 2020; 19:31-49. [PMID: 31744855 PMCID: PMC6944237 DOI: 10.1074/mcp.r119.001743] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
The science that investigates the ensembles of all peptides associated to human leukocyte antigen (HLA) molecules is termed "immunopeptidomics" and is typically driven by mass spectrometry (MS) technologies. Recent advances in MS technologies, neoantigen discovery and cancer immunotherapy have catalyzed the launch of the Human Immunopeptidome Project (HIPP) with the goal of providing a complete map of the human immunopeptidome and making the technology so robust that it will be available in every clinic. Here, we provide a long-term perspective of the field and we use this framework to explore how we think the completion of the HIPP will truly impact the society in the future. In this context, we introduce the concept of immunopeptidome-wide association studies (IWAS). We highlight the importance of large cohort studies for the future and how applying quantitative immunopeptidomics at population scale may provide a new look at individual predisposition to common immune diseases as well as responsiveness to vaccines and immunotherapies. Through this vision, we aim to provide a fresh view of the field to stimulate new discussions within the community, and present what we see as the key challenges for the future for unlocking the full potential of immunopeptidomics in this era of precision medicine.
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Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | - Qing Ma
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | - Ian Mongrain
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada; Montreal Heart Institute, Montreal, QC, Canada
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington, 98109
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, California, 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, 92037
| | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada.
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31
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Heather JM, Myers PT, Shi F, Aziz-Zanjani MO, Mahoney KE, Perez M, Morin B, Brittsan C, Shabanowitz J, Hunt DF, Cobbold M. Murine xenograft bioreactors for human immunopeptidome discovery. Sci Rep 2019; 9:18558. [PMID: 31811195 PMCID: PMC6898210 DOI: 10.1038/s41598-019-54700-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/05/2019] [Indexed: 11/17/2022] Open
Abstract
The study of peptides presented by MHC class I and class II molecules is limited by the need for relatively large cell numbers, especially when studying post-translationally modified or otherwise rare peptide species. To overcome this problem, we pose the hypothesis that human cells grown as xenografts in immunodeficient mice should produce equivalent immunopeptidomes as cultured cells. Comparing human cell lines grown either in vitro or as murine xenografts, we show that the immunopeptidome is substantially preserved. Numerous features are shared across both sample types, including peptides and proteins featured, length distributions, and HLA-binding motifs. Peptides well-represented in both groups were from more abundant proteins, or those with stronger predicted HLA binding affinities. Samples grown in vivo also recapitulated a similar phospho-immunopeptidome, with common sequences being those found at high copy number on the cell surface. These data indicate that xenografts are indeed a viable methodology for the production of cells for immunopeptidomic discovery.
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Affiliation(s)
- James M Heather
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | | | - Feng Shi
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Keira E Mahoney
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Mark Cobbold
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
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32
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Ternette N, Purcell AW. Immunopeptidomics Special Issue. Proteomics 2019; 18:e1800145. [PMID: 29949244 DOI: 10.1002/pmic.201800145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, OX3, 7FZ, UK
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
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33
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Purcell AW, Sechi S, DiLorenzo TP. The Evolving Landscape of Autoantigen Discovery and Characterization in Type 1 Diabetes. Diabetes 2019; 68:879-886. [PMID: 31010879 PMCID: PMC6477901 DOI: 10.2337/dbi18-0066] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/29/2019] [Indexed: 12/20/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that is caused, in part, by T cell-mediated destruction of insulin-producing β-cells. High risk for disease, in those with genetic susceptibility, is predicted by the presence of two or more autoantibodies against insulin, the 65-kDa form of glutamic acid decarboxylase (GAD65), insulinoma-associated protein 2 (IA-2), and zinc transporter 8 (ZnT8). Despite this knowledge, we still do not know what leads to the breakdown of tolerance to these autoantigens, and we have an incomplete understanding of T1D etiology and pathophysiology. Several new autoantibodies have recently been discovered using innovative technologies, but neither their potential utility in monitoring disease development and treatment nor their role in the pathophysiology and etiology of T1D has been explored. Moreover, neoantigen generation (through posttranslational modification, the formation of hybrid peptides containing two distinct regions of an antigen or antigens, alternative open reading frame usage, and translation of RNA splicing variants) has been reported, and autoreactive T cells that target these neoantigens have been identified. Collectively, these new studies provide a conceptual framework to understand the breakdown of self-tolerance, if such modifications occur in a tissue- or disease-specific context. A recent workshop sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases brought together investigators who are using new methods and technologies to identify autoantigens and characterize immune responses toward these proteins. Researchers with diverse expertise shared ideas and identified resources to accelerate antigen discovery and the detection of autoimmune responses in T1D. The application of this knowledge will direct strategies for the identification of improved biomarkers for disease progression and treatment response monitoring and, ultimately, will form the foundation for novel antigen-specific therapeutics. This Perspective highlights the key issues that were addressed at the workshop and identifies areas for future investigation.
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Affiliation(s)
- Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Salvatore Sechi
- Division of Diabetes, Endocrinology, and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY
- Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
- Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY
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Demmers LC, Heck AJR, Wu W. Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandome. J Proteome Res 2019; 18:1634-1643. [PMID: 30784271 PMCID: PMC6456874 DOI: 10.1021/acs.jproteome.8b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
HLA
class Ι molecules can communicate a range of cellular
alterations (mutations, changes in protein copy number, aberrant post-translational
modifications, or pathogen proteins) to CD8+ T lymphocytes in the
form of HLA peptide ligands. At any given moment, tens of thousands
of different self and foreign HLA class Ι peptides may be presented
on the cell surface by HLA class Ι complexes. Due to the enormous
biochemical diversity and low abundance of each of these peptides,
HLA ligandome analysis presents unique challenges. Even with advances
in enrichment strategies and MS instrumentation and fragmentation,
sufficient ligandome depth for identification of viral pathogens and
immuno therapeutically important tumor neo-antigens is still not routinely
achievable. In this study, we evaluated two pre-fractionation techniques,
high-pH reversed-phase and strong cation exchange, for the complementary
analyses of HLA class Ι peptide ligands. We observe that pre-fractionation
substantially extends the detectable HLA class Ι ligandome but
also creates an identification bias. We thus advocate a rational choice
between high-pH reversed-phase or strong cation exchange pre-fractionation
for deeper HLA class Ι ligandome analysis, depending on the
HLA locus, allele, or peptide ligand modification in question.
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Affiliation(s)
- Laura C Demmers
- 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
| | - 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
| | - Wei Wu
- 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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35
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Getts D, Hofmeister R, Quintás-Cardama A. Synthetic T cell receptor-based lymphocytes for cancer therapy. Adv Drug Deliv Rev 2019; 141:47-54. [PMID: 30981835 DOI: 10.1016/j.addr.2019.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 02/12/2019] [Accepted: 04/08/2019] [Indexed: 12/27/2022]
Abstract
Chimeric antigen receptor (CAR) T cells have been remarkably successful in patients with hematological malignancies expressing the CD19 surface antigen, but such level of success is far from being replicated in solid tumors. Engineered T cell receptor (TCR) T cells targeting cancer antigens were first developed over two decades ago and represent an alternative adoptive T cell approach that has produced provocative clinical data in solid cancers. However, several factors may hinder this technology from realizing its full potential, including the need for HLA matching, HLA downregulation by cancer cells, the suppressive tumor microenvironment, and tissue liabilities resulting from targeting antigens shared with normal tissues. Efforts therefore continue to engineer enhanced versions of CAR T and TCR T therapies that can overcome current barriers. Furthermore, emergent novel TCR-based, HLA-unrestricted platforms may also provide unique tools that integrate the complexity of the TCR signaling cascade that can be applied to treat solid tumors. This article reviews the current state of development of TCR T cell approaches and discusses next generation improvements to overcome their current limitations.
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Affiliation(s)
- Daniel Getts
- TCR(2) Therapeutics, 100 Binney St., Suite 710, Cambridge, MA 02142, USA
| | - Robert Hofmeister
- TCR(2) Therapeutics, 100 Binney St., Suite 710, Cambridge, MA 02142, USA
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Boehm KM, Bhinder B, Raja VJ, Dephoure N, Elemento O. Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. BMC Bioinformatics 2019; 20:7. [PMID: 30611210 PMCID: PMC6321722 DOI: 10.1186/s12859-018-2561-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/06/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometry, and other tools are limited by incomplete exploration of machine learning approaches. Herein, we assemble publicly available data describing human peptides discovered by sampling the MHC-I immunopeptidome with mass spectrometry and use this database to train random forest classifiers (ForestMHC) to predict presentation by MHC-I. RESULTS As measured by precision in the top 1% of predictions, our method outperforms NetMHC and NetMHCpan on test sets, and it outperforms both these methods and MixMHCpred on new data from an ovarian carcinoma cell line. We also find that random forest scores correlate monotonically, but not linearly, with known chemical binding affinities, and an information-based analysis of classifier features shows the importance of anchor positions for our classification. The random-forest approach also outperforms a deep neural network and a convolutional neural network trained on identical data. Finally, we use our large database to confirm that gene expression partially determines peptide presentation. CONCLUSIONS ForestMHC is a promising method to identify peptides bound by MHC-I. We have demonstrated the utility of random forest-based approaches in predicting peptide presentation by MHC-I, assembled the largest known database of MS binding data, and mined this database to show the effect of gene expression on peptide presentation. ForestMHC has potential applicability to basic immunology, rational vaccine design, and neoantigen binding prediction for cancer immunotherapy. This method is publicly available for applications and further validation.
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Affiliation(s)
- Kevin Michael Boehm
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, 1300 York Avenue, New York, NY USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medical College, 413 East 69th Street, New York, NY USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY USA
| | - Vijay Joseph Raja
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medical College, 413 East 69th Street, New York, NY USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY USA
- Meyer Cancer Center, Weill Cornell Medical College, 1300 York Avenue, New York, NY USA
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37
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Ramarathinam SH, Croft NP, Illing PT, Faridi P, Purcell AW. Employing proteomics in the study of antigen presentation: an update. Expert Rev Proteomics 2018; 15:637-645. [PMID: 30080115 DOI: 10.1080/14789450.2018.1509000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system. Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.
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Affiliation(s)
- Sri H Ramarathinam
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Nathan P Croft
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Patricia T Illing
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Pouya Faridi
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Anthony W Purcell
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
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Gfeller D, Bassani-Sternberg M. Predicting Antigen Presentation-What Could We Learn From a Million Peptides? Front Immunol 2018; 9:1716. [PMID: 30090105 PMCID: PMC6068240 DOI: 10.3389/fimmu.2018.01716] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/12/2018] [Indexed: 12/30/2022] Open
Abstract
Antigen presentation lies at the heart of immune recognition of infected or malignant cells. For this reason, important efforts have been made to predict which peptides are more likely to bind and be presented by the human leukocyte antigen (HLA) complex at the surface of cells. These predictions have become even more important with the advent of next-generation sequencing technologies that enable researchers and clinicians to rapidly determine the sequences of pathogens (and their multiple variants) or identify non-synonymous genetic alterations in cancer cells. Here, we review recent advances in predicting HLA binding and antigen presentation in human cells. We argue that the very large amount of high-quality mass spectrometry data of eluted (mainly self) HLA ligands generated in the last few years provides unprecedented opportunities to improve our ability to predict antigen presentation and learn new properties of HLA molecules, as demonstrated in many recent studies of naturally presented HLA-I ligands. Although major challenges still lie on the road toward the ultimate goal of predicting immunogenicity, these experimental and computational developments will facilitate screening of putative epitopes, which may eventually help decipher the rules governing T cell recognition.
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Affiliation(s)
- David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
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39
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Clemente LF, Hernáez ML, Ramos-Fernández A, Ligero G, Gil C, Corrales FJ, Marcilla M. Identification of the Missing Protein Hyaluronan Synthase 1 in Human Mesenchymal Stem Cells Derived from Adipose Tissue or Umbilical Cord. J Proteome Res 2018; 17:4325-4328. [PMID: 29974749 DOI: 10.1021/acs.jproteome.8b00384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Currently, 14% of the human proteome is made up of proteins whose existence is not confirmed by mass spectrometry. We performed a proteomic profiling of human mesenchymal stem cells derived from adipose tissue or umbilical cord (PRIDE accession number: PXD009893) and identified peptides derived from 13 of such missing proteins. Remarkably, we found compelling evidence of the expression of hyaluronan synthase 1 (NX_Q92839-1) and confirmed its identification by the fragmentation of four heavy-labeled peptides that coeluted with their endogenous light counterparts. Our data also suggest that mesenchymal stem cells constitute a promising source for the detection of missing proteins.
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Affiliation(s)
- Luis Felipe Clemente
- Proteomics Unit, Faculty of Pharmacy , Complutense University of Madrid (UCM) , Plaza Ramón y Cajal s/n , 28040 Madrid , Spain
| | - María Luisa Hernáez
- Proteomics Unit, Faculty of Pharmacy , Complutense University of Madrid (UCM) , Plaza Ramón y Cajal s/n , 28040 Madrid , Spain
| | | | - Gertrudis Ligero
- Andalusian Public Health System Biobank , Avenida Del Conocimiento s/n , 18016 Granada , Spain
| | - Concha Gil
- Proteomics Unit, Faculty of Pharmacy , Complutense University of Madrid (UCM) , Plaza Ramón y Cajal s/n , 28040 Madrid , Spain.,Department of Microbiology & Parasitology, Faculty of Pharmacy , Complutense University of Madrid (UCM) and Ramón y Cajal Institute of Health Research (IRYCIS) , Plaza Ramón y Cajal s/n , 28040 Madrid , Spain
| | - Fernando José Corrales
- Proteomics Unit , Spanish National Biotechnology Centre (CNB-CISC) , Darwin 3 , 28049 Madrid , Spain
| | - Miguel Marcilla
- Proteomics Unit , Spanish National Biotechnology Centre (CNB-CISC) , Darwin 3 , 28049 Madrid , Spain
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40
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Why do proteases mess up with antigen presentation by re-shuffling antigen sequences? Curr Opin Immunol 2018; 52:81-86. [PMID: 29723668 DOI: 10.1016/j.coi.2018.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/17/2018] [Indexed: 12/27/2022]
Abstract
The sequence of a large number of MHC-presented epitopes is not present as such in the original antigen because it has been re-shuffled by the proteasome or other proteases. Why do proteases throw a spanner in the works of our model of antigen tagging and immune recognition? We describe in this review what we know about the immunological relevance of post-translationally spliced epitopes and why proteases seem to have a second (dark) personality, which is keen to create new peptide bonds.
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41
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Freudenmann LK, Marcu A, Stevanović S. Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. Immunology 2018; 154:331-345. [PMID: 29658117 DOI: 10.1111/imm.12936] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/13/2022] Open
Abstract
The entirety of human leukocyte antigen (HLA)-presented peptides is referred to as the HLA ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the tumour immunopeptidome by mass spectrometry (MS) comprehensively views the pathophysiologically relevant antigenic signature of human malignancies. MS is an unbiased approach stringently filtering the candidates to be tested as opposed to epitope prediction algorithms. In the setting of peptide-specific immunotherapies, MS-based strategies significantly diminish the risk of lacking clinical benefit, as they yield highly enriched amounts of truly presented peptides. Early immunopeptidomic efforts were severely limited by technical sensitivity and manual spectra interpretation. The technological progress with development of orbitrap mass analysers and enhanced chromatographic performance led to vast improvements in mass accuracy, sensitivity, resolution, and speed. Concomitantly, bioinformatic tools were developed to process MS data, integrate sequencing results, and deconvolute multi-allelic datasets. This enabled the immense advancement of tumour immunopeptidomics. Studying the HLA-presented peptide repertoire bears high potential for both answering basic scientific questions and translational application. Mapping the tumour HLA ligandome has started to significantly contribute to target identification for the design of peptide-specific cancer immunotherapies in clinical trials and compassionate need treatments. In contrast to prediction algorithms, rare HLA allotypes and HLA class II can be adequately addressed when choosing MS-guided target identification platforms. Herein, we review the identification of tumour HLA ligands focusing on sources, methods, bioinformatic data analysis, translational application, and provide an outlook on future developments.
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Affiliation(s)
- Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
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42
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Marino F. Gaining Insight Into Posttranslationally Modified HIV Antigens and Their Underlying Characteristics. Proteomics 2018. [PMID: 29513933 DOI: 10.1002/pmic.201800041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mass spectrometry (MS)-based immunopeptidomics has developed as one of the leading methodologies for comprehensive characterization of in vivo presented human leukocyte antigen (HLA)-bound peptides. Unveiling the identity of HLA-bound peptides derived from diseased cells is crucial to gain knowledge on the constitution of efficient disease-specific T cell responses. The HLA-presented peptidome reflects the status of the cellular proteome, hence disease-related aberrations of posttranslational modifications (PTMs) might lead to presentation of peptides harboring PTMs. Therefore, characterization of HLA-bound PTM peptides could shed light on their relevance in immune and disease processes. In this issue, Ramarathinam et al. investigate the presentation of HIV envelope (HIVenv) peptides bound to the HLA-B*57:01 allele. Among these peptides, the authors specifically focused on a kynurenine-modified peptide. To this end, they characterize the possible origin of the kynurenine modification, its effect on HLA binding affinity, stability, conformation within the complex, and its immunogenicity compared to the native counterpart.
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Affiliation(s)
- Fabio Marino
- Departement de Medecine-Oncology, Centre Hospitalier Universitaire Vaudois, Switzerland
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43
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Chong C, Marino F, Pak H, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M. High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics 2018; 17:533-548. [PMID: 29242379 PMCID: PMC5836376 DOI: 10.1074/mcp.tir117.000383] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues. Our methodology drastically reduces sample-handling and can be completed within five hours. We challenged our methodology by extracting HLA peptides from multiple replicates of tissues (n = 7) and cell lines (n = 21, 108 cells per replicate), which resulted in unprecedented depth, sensitivity and high reproducibility (Pearson correlations up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved sensitivity, even single measurements of peptides purified from 107 B-cells resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma (IFNγ). Our analysis revealed an augmented presentation of chymotryptic-like and longer ligands associated with IFNγ induced changes of the antigen processing and presentation machinery. This straightforward method is applicable for basic and clinical applications.
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Affiliation(s)
- Chloe Chong
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Fabio Marino
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - HuiSong Pak
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Julien Racle
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Roy T Daniel
- ¶Service of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Markus Müller
- ‖Vital IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Gfeller
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - George Coukos
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland;
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
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44
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Toward Engineered Cells as Transformational and Broadly Available Medicines for the Treatment of Cancer. Oncoimmunology 2018. [DOI: 10.1007/978-3-319-62431-0_42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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45
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Nyman TA, Lorey MB, Cypryk W, Matikainen S. Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells. Expert Rev Proteomics 2017; 14:395-407. [PMID: 28406322 DOI: 10.1080/14789450.2017.1319768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The immune system is our defense system against microbial infections and tissue injury, and understanding how it works in detail is essential for developing drugs for different diseases. Mass spectrometry-based proteomics can provide in-depth information on the molecular mechanisms involved in immune responses. Areas covered: Summarized are the key immunology findings obtained with MS-based proteomics in the past five years, with a focus on inflammasome activation, global protein secretion, mucosal immunology, immunopeptidome and T cells. Special focus is on extracellular vesicle-mediated protein secretion and its role in immune responses. Expert commentary: Proteomics is an essential part of modern omics-scale immunology research. To date, MS-based proteomics has been used in immunology to study protein expression levels, their subcellular localization, secretion, post-translational modifications, and interactions in immune cells upon activation by different stimuli. These studies have made major contributions to understanding the molecular mechanisms involved in innate and adaptive immune responses. New developments in proteomics offer constantly novel possibilities for exploring the immune system. Examples of these techniques include mass cytometry and different MS-based imaging approaches which can be widely used in immunology.
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Affiliation(s)
- Tuula A Nyman
- a Department of Immunology , Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo , Oslo , Norway
| | - Martina B Lorey
- b Rheumatology , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
| | - Wojciech Cypryk
- c Department of Bioorganic Chemistry , Center of Molecular and Macromolecular Studies , Lodz , Poland
| | - Sampsa Matikainen
- b Rheumatology , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
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Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A. The Human Leukocyte Antigen (HLA)-B27 Peptidome in Vivo, in Spondyloarthritis-susceptible HLA-B27 Transgenic Rats and the Effect of Erap1 Deletion. Mol Cell Proteomics 2017; 16:642-662. [PMID: 28188227 DOI: 10.1074/mcp.m116.066241] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/05/2017] [Indexed: 01/20/2023] Open
Abstract
HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large scale quantitative mass spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats. Heterozygous deletion of Erap1, which reduced the Erap1 level to less than half, had no qualitative or quantitative effects on the B27 peptidome. Homozygous deletion of Erap1 affected approximately one-third of the B27 peptidome but left most of the B27 peptidome unchanged, suggesting the possibility that some of the HLA-B27 immunopeptidome is not processed in the presence of Erap1. Deletion of Erap1 was permissive for the AS-like phenotype, increased mean peptide length and increased the frequency of C-terminal hydrophobic residues and of N-terminal Ala, Ser, or Lys. The presence of Erap1 increased the frequency of C-terminal Lys and Arg, of Glu and Asp at intermediate residues, and of N-terminal Gly. Several peptides of potential interest in AS pathogenesis, previously identified in human cell lines, were isolated. However, rats susceptible to arthritis had B27 peptidomes similar to those of non-susceptible rats, and no peptides were found to be uniquely associated with arthritis. Whether specific B27-bound peptides are required for AS pathogenesis remains to be determined. Data are available via ProteomeXchange with identifier PXD005502.
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Affiliation(s)
- Eilon Barnea
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dganit Melamed Kadosh
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Haimovich
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimman Satumtira
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Martha L Dorris
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Mylinh T Nguyen
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Robert E Hammer
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Tri M Tran
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Robert A Colbert
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Joel D Taurog
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884;
| | - Arie Admon
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
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