1
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Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J, Mishto M. Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nat Commun 2024; 15:1147. [PMID: 38326304 PMCID: PMC10850103 DOI: 10.1038/s41467-024-45339-3] [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] [Received: 01/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
If and how proteasomes catalyze not only peptide hydrolysis but also peptide splicing is an open question that has divided the scientific community. The debate has so far been based on immunopeptidomics, in vitro digestions of synthetic polypeptides as well as ex vivo and in vivo experiments, which could only indirectly describe proteasome-catalyzed peptide splicing of full-length proteins. Here we develop a workflow-and cognate software - to analyze proteasome-generated non-spliced and spliced peptides produced from entire proteins and apply it to in vitro digestions of 15 proteins, including well-known intrinsically disordered proteins such as human tau and α-Synuclein. The results confirm that 20S proteasomes produce a sizeable variety of cis-spliced peptides, whereas trans-spliced peptides are a minority. Both peptide hydrolysis and splicing produce peptides with well-defined characteristics, which hint toward an intricate regulation of both catalytic activities. At protein level, both non-spliced and spliced peptides are not randomly localized within protein sequences, but rather concentrated in hotspots of peptide products, in part driven by protein sequence motifs and proteasomal preferences. At sequence level, the different peptide sequence preference of peptide hydrolysis and peptide splicing suggests a competition between the two catalytic activities of 20S proteasomes during protein degradation.
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Affiliation(s)
- Wai Tuck Soh
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Hanna P Roetschke
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Bei Fang Teo
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Nyet Cheng Chiam
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Monika Raabe
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ralf Pflanz
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ashwin Chari
- Research Group of Structural Biochemistry and Mechanisms, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Juliane Liepe
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK.
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK.
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2
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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3
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Roetschke HP, Rodriguez-Hernandez G, Cormican JA, Yang X, Lynham S, Mishto M, Liepe J. InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides. Sci Data 2023; 10:18. [PMID: 36627305 PMCID: PMC9832164 DOI: 10.1038/s41597-022-01890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/01/2022] [Indexed: 01/12/2023] Open
Abstract
Noncanonical epitopes presented by Human Leucocyte Antigen class I (HLA-I) complexes to CD8+ T cells attracted the spotlight in the research of novel immunotherapies against cancer, infection and autoimmunity. Proteasomes, which are the main producers of HLA-I-bound antigenic peptides, can catalyze both peptide hydrolysis and peptide splicing. The prediction of proteasome-generated spliced peptides is an objective that still requires a reliable (and large) database of non-spliced and spliced peptides produced by these proteases. Here, we present an extended database of proteasome-generated spliced and non-spliced peptides, which was obtained by analyzing in vitro digestions of 80 unique synthetic polypeptide substrates, measured by different mass spectrometers. Peptides were identified through invitroSPI method, which was validated through in silico and in vitro strategies. The peptide product database contains 16,631 unique peptide products (5,493 non-spliced, 6,453 cis-spliced and 4,685 trans-spliced peptide products), and a substrate sequence variety that is a valuable source for predictors of proteasome-catalyzed peptide hydrolysis and splicing. Potential artefacts and skewed results due to different identification and analysis strategies are discussed.
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Affiliation(s)
- Hanna P Roetschke
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK
| | - Guillermo Rodriguez-Hernandez
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK
- Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Göttingen, Germany
| | - Xiaoping Yang
- Proteomics Core Facility, James Black Centre, King's College London (KCL), SE5 9NU, London, UK
| | - Steven Lynham
- Proteomics Core Facility, James Black Centre, King's College London (KCL), SE5 9NU, London, UK
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK.
- Francis Crick Institute, NW1 1AT, London, UK.
| | - Juliane Liepe
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Göttingen, Germany.
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4
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Gutman I, Gutman R, Sidney J, Chihab L, Mishto M, Liepe J, Chiem A, Greenbaum J, Yan Z, Sette A, Koşaloğlu-Yalçın Z, Peters B. Predicting the Success of Fmoc-Based Peptide Synthesis. ACS OMEGA 2022; 7:23771-23781. [PMID: 35847273 PMCID: PMC9280948 DOI: 10.1021/acsomega.2c02425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. While peptide synthesis is generally easy and reliable, the chemical nature of some amino acids as well as the many steps and chemical compounds involved can render the synthesis of some peptide sequences difficult. Identification of these problematic sequences and mitigation of issues they may present can be important for the reliable use of peptide reagents in several contexts. Here, we assembled a large dataset of peptides that were synthesized using standard Fmoc chemistry and whose identity was validated using mass spectrometry. We analyzed the mass spectra to identify errors in peptide syntheses and sought to develop a computational tool to predict the likelihood that any given peptide sequence would be synthesized accurately. Our model, named Peptide Synthesis Score (PepSySco), is able to predict the likelihood that a peptide will be successfully synthesized based on its amino acid sequence.
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Affiliation(s)
- Ilanit Gutman
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Ron Gutman
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - John Sidney
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Leila Chihab
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Michele Mishto
- Centre
for Inflammation Biology and Cancer Immunology (CIBCI) & Peter
Gorer Department of Immunobiology, King’s
College London, London SE1 1UL, U.K.
- Francis
Crick Institute, London NW1 1AT, U.K.
| | - Juliane Liepe
- Max-Planck-Institute
for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Anthony Chiem
- TC
Peptide Lab, San Diego, California 92121-4708, United States
| | - Jason Greenbaum
- Bioinformatics
Core Facility, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Zhen Yan
- Bioinformatics
Core Facility, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Alessandro Sette
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
- Department
of Medicine, University of California San
Diego, La Jolla, California 92037-1387, United States
| | - Zeynep Koşaloğlu-Yalçın
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Bjoern Peters
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
- Department
of Medicine, University of California San
Diego, La Jolla, California 92037-1387, United States
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5
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Kloetzel PM. Neo-Splicetopes in Tumor Therapy: A Lost Case? Front Immunol 2022; 13:849863. [PMID: 35265089 PMCID: PMC8898901 DOI: 10.3389/fimmu.2022.849863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Proteasome generates spliced peptides by ligating two distant cleavage products in a reverse proteolysis reaction. The observation that CD8+ T cells recognizing a spliced peptide induced T cell rejection in a melanoma patient following adoptive T cell transfer (ATT), raised some hopes with regard to the general therapeutic and immune relevance of spliced peptides. Concomitantly, the identification of spliced peptides was also the start of a controversy with respect to their frequency, abundancy and their therapeutic applicability. Here I review some of the recent evidence favoring or disfavoring an immune relevance of splicetopes and discuss from a theoretical point of view the potential usefulness of tumor specific splicetopes and why against all odds it still may seem worth trying to identify such tumor and patient-specific neosplicetopes for application in ATT.
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Affiliation(s)
- Peter M Kloetzel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
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6
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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: 2] [Impact Index Per Article: 1.0] [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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7
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Lichti CF, Vigneron N, Clauser KR, Van den Eynde BJ, Bassani-Sternberg M. Navigating Critical Challenges Associated with Immunopeptidomics-Based Detection of Proteasomal Spliced Peptide Candidates. Cancer Immunol Res 2022; 10:275-284. [PMID: 35105607 DOI: 10.1158/2326-6066.cir-21-0727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/26/2021] [Accepted: 01/14/2022] [Indexed: 11/16/2022]
Abstract
Within the tumor immunology community, the topic of proteasomal spliced peptides (PSP) has generated a great deal of controversy. In the earliest reports, careful biological validation led to the conclusion that proteasome-catalyzed peptide splicing was a rare event. To date, six PSPs have been validated biologically. However, the advent of algorithms to identify candidate PSPs in mass spectrometry data challenged this notion, with several studies concluding that the frequency of spliced peptides binding to MHC class I was quite high. Since this time, much debate has centered around the methodologies used in these studies. Several reanalyses of data from these studies have led to questions about the validity of the conclusions. Furthermore, the biological and technical validation that should be necessary for verifying PSP assignments was often lacking. It has been suggested therefore that the research community should unite around a common set of standards for validating candidate PSPs. In this review, we propose and highlight the necessary steps for validation of proteasomal splicing at both the mass spectrometry and biological levels. We hope that these guidelines will serve as a foundation for critical assessment of results from proteasomal splicing studies.
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Affiliation(s)
- Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri. .,Bursky Center for Human Immunology and Immunotherapy, Washington University School of Medicine, St. Louis, Missouri
| | - Nathalie Vigneron
- Ludwig Institute for Cancer Research, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne Branch-University of Lausanne (UNIL), Lausanne, Switzerland. .,Department of Oncology-Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
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8
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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: 3] [Impact Index Per Article: 1.0] [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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9
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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: 5] [Impact Index Per Article: 1.7] [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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