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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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2
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Mishto M, Horokhovskyi Y, Cormican JA, Yang X, Lynham S, Urlaub H, Liepe J. Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes. Proteomics 2022; 22:e2100226. [PMID: 35184383 PMCID: PMC9286349 DOI: 10.1002/pmic.202100226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/19/2022] [Accepted: 02/10/2022] [Indexed: 11/08/2022]
Abstract
Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry (MS) required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines - that is, Mascot, Mascot+Percolator, and PEAKS DB - as final identification step, as well as the features of target database on the ability to correctly identify non-spliced and cis-spliced peptides. We used ground truth datasets measured by MS to benchmark methods' performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis-spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated.
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Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- Francis Crick InstituteLondonUK
| | | | - John A. Cormican
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
| | - Xiaoping Yang
- Proteomics Core Facility, James Black CentreKing's CollegeLondonUK
| | - Steven Lynham
- Proteomics Core Facility, James Black CentreKing's CollegeLondonUK
| | - Henning Urlaub
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
- Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Juliane Liepe
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
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3
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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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4
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Mishto M. Commentary: Are There Indeed Spliced Peptides in the Immunopeptidome? Mol Cell Proteomics 2021; 20:100158. [PMID: 34607014 PMCID: PMC8724881 DOI: 10.1016/j.mcpro.2021.100158] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022] Open
Abstract
Proteasome-generated spliced epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry triggered heated debates, which find a representative opinion in one of the two fronts in the recent perspective article by Arie Admon. Briefly, he suggests that proteasomes cannot efficiently catalyze such a reaction, and, thus, that all spliced peptides identified in HLA class I immunopeptidomes and other specimens are artifacts. This hypothesis is in contrast with in vitro, in cellula, and in vivo results published since the discovery of proteasome-catalyzed peptide splicing in 2004.
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Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Francis Crick Institute, London, United Kingdom.
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5
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Purcell AW. Is the Immunopeptidome Getting Darker?: A Commentary on the Discussion around Mishto et al., 2019. Front Immunol 2021; 12:720811. [PMID: 34326850 PMCID: PMC8315041 DOI: 10.3389/fimmu.2021.720811] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Anthony W Purcell
- Department of Biochemistry and Molecular Biology, and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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6
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Mishto M, Rodriguez-Hernandez G, Neefjes J, Urlaub H, Liepe J. Response: Commentary: An In Silico-In Vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients. Front Immunol 2021; 12:679836. [PMID: 34326838 PMCID: PMC8315000 DOI: 10.3389/fimmu.2021.679836] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Guillermo Rodriguez-Hernandez
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Henning Urlaub
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Juliane Liepe
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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7
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Admon A. Are There Indeed Spliced Peptides in the Immunopeptidome? Mol Cell Proteomics 2021; 20:100099. [PMID: 34022431 PMCID: PMC8724635 DOI: 10.1016/j.mcpro.2021.100099] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
The claims that a large fraction of the immunopeptidome is composed of spliced major histocompatibility complex (MHC) peptides have stirred significant excitement and raised controversy. Here, I suggest that there are likely no spliced peptides in the immunopeptidome, and if they exist at all, they are extremely rare. I base this claim on both biochemical and bioinformatics considerations. First, as a reactant in normal proteolytic reactions, water will compete with transpeptidation, which has been suggested as the mechanism of peptide splicing. The high mobility and abundance of water in aqueous solutions renders transpeptidation very inefficient and therefore unlikely to occur. Second, new studies have refuted the bioinformatics assignments to spliced peptides of most of the immunopeptidome MS data, suggesting that the correct assignments are likely other canonical, noncanonical, and post-translationally modified peptides. Therefore, I call for rigorous experimental methodology using heavy stable isotope peptides spiking into the immunoaffinity-purified mixtures of natural MHC peptides and analysis by the highly reliable targeted MS, to claim that MHC peptides are indeed spliced. Peptide splicing was suggested to contribute to the immunopeptidome. I suggest that this idea should be reconsidered based on new evidences. Both biochemical and bioinformatics considerations argue against peptide splicing.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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Reed BK, Kappler JW. Hidden in Plain View: Discovery of Chimeric Diabetogenic CD4 T Cell Neo-Epitopes. Front Immunol 2021; 12:669986. [PMID: 33986758 PMCID: PMC8111216 DOI: 10.3389/fimmu.2021.669986] [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: 02/19/2021] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
The T cell antigens driving autoimmune Type 1 Diabetes (T1D) have been pursued for more than three decades. When diabetogenic CD4 T cell clones and their relevant MHCII antigen presenting alleles were first identified in rodents and humans, the path to discovering the peptide epitopes within pancreatic beta cell proteins seemed straightforward. However, as experimental results accumulated, definitive data were often absent or controversial. Work within the last decade has helped to clear up some of the controversy by demonstrating that a number of the important MHCII presented epitopes are not encoded in the natural beta cell proteins, but in fact are fusions between peptide fragments derived from the same or different proteins. Recently, the mechanism for generating these MHCII diabetogenic chimeric epitopes has been attributed to a form of reverse proteolysis, called transpeptidation, a process that has been well-documented in the production of MHCI presented epitopes. In this mini-review we summarize these data and their implications for T1D and other autoimmune responses.
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Affiliation(s)
- Brendan K Reed
- Research Division, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, United States.,Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, United States.,Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | - John W Kappler
- Research Division, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, United States.,Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, United States.,Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States.,Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, United States
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9
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Mishto M, Mansurkhodzhaev A, Rodriguez-Calvo T, Liepe J. Potential Mimicry of Viral and Pancreatic β Cell Antigens Through Non-Spliced and cis-Spliced Zwitter Epitope Candidates in Type 1 Diabetes. Front Immunol 2021; 12:656451. [PMID: 33936085 PMCID: PMC8082463 DOI: 10.3389/fimmu.2021.656451] [Citation(s) in RCA: 9] [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: 01/20/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence suggests that post-translational peptide splicing can play a role in the immune response under pathological conditions. This seems to be particularly relevant in Type 1 Diabetes (T1D) since post-translationally spliced epitopes derived from T1D-associated antigens have been identified among those peptides bound to Human Leucocyte Antigen (HLA) class I and II complexes. Their immunogenicity has been confirmed through CD4+ and CD8+ T cell-mediated responses in T1D patients. Spliced peptides theoretically have a large sequence variability. This might increase the frequency of viral-human zwitter peptides, i.e. peptides that share a complete sequence homology irrespective of whether they originate from human or viral antigens, thereby impinging upon the discrimination between self and non-self antigens by T cells. This might increase the risk of autoimmune responses triggered by viral infections. Since enteroviruses and other viral infections have historically been associated with T1D, we investigated whether cis-spliced peptides derived from selected viruses might be able to trigger CD8+ T cell-mediated autoimmunity. We computed in silico viral-human non-spliced and cis-spliced zwitter epitope candidates, and prioritized peptide candidates based on: (i) their binding affinity to HLA class I complexes, (ii) human pancreatic β cell and medullary thymic epithelial cell (mTEC) antigens' mRNA expression, (iii) antigen association with T1D, and (iv) potential hotspot regions in those antigens. Neglecting potential T cell receptor (TCR) degeneracy, no viral-human zwitter non-spliced peptide was found to be an optimal candidate to trigger a virus-induced CD8+ T cell response against human pancreatic β cells. Conversely, we identified some zwitter peptide candidates, which may be produced by proteasome-catalyzed peptide splicing, and might increase the likelihood of pancreatic β cells recognition by virus-specific CD8+ T cell clones, therefore promoting β cell destruction in the context of viral infections.
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Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | | | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Juliane Liepe
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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10
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Mansurkhodzhaev A, Barbosa CRR, Mishto M, Liepe J. Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8 + T Cell Tolerance. Front Immunol 2021; 12:614276. [PMID: 33717099 PMCID: PMC7943738 DOI: 10.3389/fimmu.2021.614276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/28/2021] [Indexed: 01/09/2023] Open
Abstract
The human immune system relies on the capability of CD8+ T cells to patrol body cells, spot infected cells and eliminate them. This cytotoxic response is supposed to be limited to infected cells to avoid killing of healthy cells. To enable this, CD8+ T cells have T Cell Receptors (TCRs) which should discriminate between self and non-self through the recognition of antigenic peptides bound to Human Leukocyte Antigen class I (HLA-I) complexes-i.e., HLA-I immunopeptidomes-of patrolled cells. The majority of these antigenic peptides are produced by proteasomes through either peptide hydrolysis or peptide splicing. Proteasome-generated cis-spliced peptides derive from a given antigen, are immunogenic and frequently presented by HLA-I complexes. Theoretically, they also have a very large sequence variability, which might impinge upon our model of self/non-self discrimination and central and peripheral CD8+ T cell tolerance. Indeed, a large variety of cis-spliced epitopes might enlarge the pool of viral-human zwitter epitopes, i.e., peptides that may be generated with the exact same sequence from both self (human) and non-self (viral) antigens. Antigenic viral-human zwitter peptides may be recognized by CD8+ thymocytes and T cells, induce clonal deletion or other tolerance processes, thereby restraining CD8+ T cell response against viruses. To test this hypothesis, we computed in silico the theoretical frequency of zwitter non-spliced and cis-spliced epitope candidates derived from human proteome (self) and from the proteomes of a large pool of viruses (non-self). We considered their binding affinity to the representative HLA-A*02:01 complex, self-antigen expression in Medullary Thymic Epithelial cells (mTECs) and the relative frequency of non-spliced and cis-spliced peptides in HLA-I immunopeptidomes. Based on the present knowledge of proteasome-catalyzed peptide splicing and neglecting CD8+ TCR degeneracy, our study suggests that, despite their frequency, the portion of the cis-spliced peptides we investigated could only marginally impinge upon the variety of functional CD8+ cytotoxic T cells (CTLs) involved in anti-viral response.
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Affiliation(s)
- Artem Mansurkhodzhaev
- Quantitative and Systems Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Juliane Liepe
- Quantitative and Systems Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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Çetin G, Klafack S, Studencka-Turski M, Krüger E, Ebstein F. The Ubiquitin-Proteasome System in Immune Cells. Biomolecules 2021; 11:biom11010060. [PMID: 33466553 PMCID: PMC7824874 DOI: 10.3390/biom11010060] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin–proteasome system (UPS) is the major intracellular and non-lysosomal protein degradation system. Thanks to its unique capacity of eliminating old, damaged, misfolded, and/or regulatory proteins in a highly specific manner, the UPS is virtually involved in almost all aspects of eukaryotic life. The critical importance of the UPS is particularly visible in immune cells which undergo a rapid and profound functional remodelling upon pathogen recognition. Innate and/or adaptive immune activation is indeed characterized by a number of substantial changes impacting various cellular processes including protein homeostasis, signal transduction, cell proliferation, and antigen processing which are all tightly regulated by the UPS. In this review, we summarize and discuss recent progress in our understanding of the molecular mechanisms by which the UPS contributes to the generation of an adequate immune response. In this regard, we also discuss the consequences of UPS dysfunction and its role in the pathogenesis of recently described immune disorders including cancer and auto-inflammatory diseases.
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