1
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Mishto M, Takala I, Bonfanti P, Liepe J. Proteasome isoforms in human thymi and mouse models. Immunol Lett 2024; 269:106899. [PMID: 39019403 DOI: 10.1016/j.imlet.2024.106899] [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: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
The thymus is the organ where functional and self-tolerant T cells are selected through processes of positive and negative selection before migrating to the periphery. The antigenic peptides presented on MHC class I molecules of thymic epithelial cells (TECs) in the cortex and medulla of the thymus are key players in these processes. It has been theorized that these cells express different proteasome isoforms, which generate MHC class I immunopeptidomes with features that differentiate cortex and medulla, and hence positive and negative CD8+ T cell selection. This theory is largely based on mouse models and does not consider the large variety of noncanonical antigenic peptides that could be produced by proteasomes and presented on MHC class I molecules. Here, we review the multi-omics, biochemical and cellular studies carried out on mouse models and human thymi to investigate their content of proteasome isoforms, briefly summarize the implication that noncanonical antigenic peptide presentation in the thymus could have on CD8+ T cell repertoire and put these aspects in the larger framework of anatomical and immunological differences between these two species.
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Affiliation(s)
- Michele Mishto
- Molecular Immunology laboratory, the Francis Crick Institute, NW1 1AT London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, United Kingdom.
| | - Iina Takala
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, London NW3 2PP, United Kingdom
| | - Juliane Liepe
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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2
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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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3
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Verma C, Dubey S, Bose R, Alfantazi A, Ebenso EE, Rhee KY. Zwitterions and betaines as highly soluble materials for sustainable corrosion protection: Interfacial chemistry and bonding with metal surfaces. Adv Colloid Interface Sci 2024; 324:103091. [PMID: 38281394 DOI: 10.1016/j.cis.2024.103091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/04/2024] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
The primary requirements for interfacial adsorption and corrosion inhibition are solubility and the existence of polar functional groups, particularly charges. Traditional organic inhibitors have a solubility issue due to the hydrophobic moieties they incorporate. Most documented organic inhibitors have aromatic rings, hydrocarbon chains, and a few functional groups. The excellent solubility and high efficacy of zwitterions and betaines make them the perfect replacements for insoluble corrosion inhibitors. Zwitterions and betaines are more easily soluble because of interactions between their positive and negative charges (-COO-, -PO3-, -NH3, -NHR2, -NH2R, -SO3- etc.) and the polar solvents. The positive and negative charges also aid these molecules' physical and chemical adsorption at the metal-electrolyte interfaces. They develop a corrosion-inhibiting layer through their adsorption. After becoming adsorbed at the metal-electrolyte interface, they act as mixed-type inhibitors, slowing both cathodic and anodic processes. They usually adsorb according to the Langmuir adsorption isotherm. In this article, the corrosion inhibition potential of zwitterions and betaines in the aqueous phase, as well as their mode of action, are reviewed. This article details the advantages and disadvantages of utilizing zwitterions and betaines for sustainable corrosion protection.
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Affiliation(s)
- Chandrabhan Verma
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
| | - Shikha Dubey
- Department of Chemistry, School of Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar 246174, Garhwal, India
| | - Ranjith Bose
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Akram Alfantazi
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Eno E Ebenso
- Institute for Nanotechnology and Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1710, South Africa
| | - Kyong Yop Rhee
- Department of Mechanical Engineering, College of Engineering, Kyung Hee University, Yongin 445-701, South Korea.
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Brito-Sierra CA, Lannan MB, Malherbe LP, Siegel RW. The HLA class I immunopeptidomes of AAV capsid proteins. Front Immunol 2023; 14:1212136. [PMID: 37662941 PMCID: PMC10469481 DOI: 10.3389/fimmu.2023.1212136] [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: 04/25/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Cellular immune responses against AAV vector capsid represent an obstacle for successful gene therapy. Previous studies have used overlapping peptides spanning the entire capsid sequence to identify T cell epitopes recognized by AAV-specific CD8+ T cells. However, the repertoire of peptides naturally displayed by HLA class I molecules for CD8 T cell recognition is unknown. Methods Using mRNA transfected monocyte-derived dendritic cells (MDDCs) and MHC-associated peptide proteomics (MAPPs), we identified the HLA class I immunopeptidomes of AAV2, AAV6 and AAV9 capsids. MDDCs were isolated from a panel of healthy donors that have diverse alleles across the US population. mRNA-transfected MDDCs were lysed, the peptide:HLA complexes immunoprecipitated, and peptides eluted and analyzed by mass spectrometry. Results We identified 65 AAV capsid-derived peptides loaded on HLA class I molecules of mRNA transfected monocyte derived dendritic cells. The HLA class I peptides are distributed along the entire capsid and more than 60% are contained within HLA class II clusters. Most of the peptides are organized as single species, however we identified twelve clusters containing at least 2 peptides of different lengths. Only 9% of the identified peptides have been previously identified as T cell epitopes, demonstrating that the immunogenicity potential for the vast majority of the AAV HLA class I immunopeptidome remains uncharacterized. In contrast, 12 immunogenic epitopes identified before were not found to be naturally processed in our study. Remarkably, 11 naturally presented AAV peptides were highly conserved among the three serotypes analyzed suggesting the possibility of cross-reactive AAV-specific CD8 T cells. Discussion This work is the first comprehensive study identifying the naturally displayed HLA class I peptides derived from the capsid of AAVs. The results from this study can be used to generate strategies to assess immunogenicity risk and cross-reactivity among serotypes during gene therapies.
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Affiliation(s)
| | | | - Laurent P. Malherbe
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Robert W. Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
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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: 1] [Impact Index Per Article: 1.0] [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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Cormican JA, Horokhovskyi Y, Soh WT, Mishto M, Liepe J. inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction. Mol Cell Proteomics 2022; 21:100432. [PMID: 36280141 PMCID: PMC9720494 DOI: 10.1016/j.mcpro.2022.100432] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Rescoring of mass spectrometry (MS) search results using spectral predictors can strongly increase peptide spectrum match (PSM) identification rates. This approach is particularly effective when aiming to search MS data against large databases, for example, when dealing with nonspecific cleavage in immunopeptidomics or inflation of the reference database for noncanonical peptide identification. Here, we present inSPIRE (in silico Spectral Predictor Informed REscoring), a flexible and performant open-source rescoring pipeline built on Prosit MS spectral prediction, which is compatible with common database search engines. inSPIRE allows large-scale rescoring with data from multiple MS search files, increases sensitivity to minor differences in amino acid residue position, and can be applied to various MS sample types, including tryptic proteome digestions and immunopeptidomes. inSPIRE boosts PSM identification rates in immunopeptidomics, leading to better performance than the original Prosit rescoring pipeline, as confirmed by benchmarking of inSPIRE performance on ground truth datasets. The integration of various features in the inSPIRE backbone further boosts the PSM identification in immunopeptidomics, with a potential benefit for the identification of noncanonical peptides.
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Affiliation(s)
- John A Cormican
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), Göttingen, Germany
| | - Yehor Horokhovskyi
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), Göttingen, Germany
| | - Wai Tuck Soh
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), Göttingen, Germany
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; The Francis Crick Institute, London, United Kingdom.
| | - Juliane Liepe
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), Göttingen, Germany.
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Xiang H, Zhang L, Bu F, Guan X, Chen L, Zhang H, Zhao Y, Chen H, Zhang W, Li Y, Lee LJ, Mei Z, Rao Y, Gu Y, Hou Y, Mu F, Dong X. A Novel Proteogenomic Integration Strategy Expands the Breadth of Neo-Epitope Sources. Cancers (Basel) 2022; 14:cancers14123016. [PMID: 35740681 PMCID: PMC9220843 DOI: 10.3390/cancers14123016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor-specific antigens can activate T cell-based antitumor immune responses and are ideal targets for cancer immunotherapy. However, their identification is still challenging. Although mass spectrometry can directly identify human leukocyte antigen (HLA) binding peptides in tumor cells, it focuses on tumor-specific antigens derived from annotated protein-coding regions constituting only 1.5% of the genome. We developed a novel proteogenomic integration strategy to expand the breadth of tumor-specific epitopes derived from all genomic regions. Using the colorectal cancer cell line HCT116 as a model, we accurately identified 10,737 HLA-presented peptides, 1293 of which were non-canonical peptides that traditional database searches could not identify. Moreover, we found eight tumor neo-epitopes derived from somatic mutations, four of which were not previously reported. Our findings suggest that this new proteogenomic approach holds great promise for increasing the number of tumor-specific antigen candidates, potentially enlarging the tumor target pool and improving cancer immunotherapy.
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Affiliation(s)
- Haitao Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Le Zhang
- BGI-GenoImmune, BGI-Shenzhen, Shenzhen 518083, China; (L.Z.); (L.J.L.)
| | - Fanyu Bu
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Xiangyu Guan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Lei Chen
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Haibo Zhang
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Yuntong Zhao
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Huanyi Chen
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Weicong Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Yijian Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen 518083, China
| | - Leo Jingyu Lee
- BGI-GenoImmune, BGI-Shenzhen, Shenzhen 518083, China; (L.Z.); (L.J.L.)
| | - Zhanlong Mei
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
| | - Yuan Rao
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Yong Hou
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
| | - Feng Mu
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
- Correspondence: (F.M.); (X.D.)
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen 518083, China
- Correspondence: (F.M.); (X.D.)
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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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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: 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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10
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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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11
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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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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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