1
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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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2
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Çakır U, Gabed N, Brunet M, Roucou X, Kryvoruchko I. Mosaic translation hypothesis: chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability. FEBS J 2023; 290:370-378. [PMID: 34743413 DOI: 10.1111/febs.16269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/03/2021] [Accepted: 11/05/2021] [Indexed: 02/05/2023]
Abstract
How many different proteins can be produced from a single spliced transcript? Genome annotation projects overlook the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins, have been shown to carry out important functions in various organisms. AltORFs overlapping refORFs or other altORFs in a different reading frame may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. Specialized ribosomes acting as sensors probably played a central role in this process. Importantly, mosaic translation may be the main source of protein diversity in genomes that lack alternative splicing. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is challenging. Should mosaic translation occur, we would currently highly underestimate the complexity of translation mechanisms and thus the proteome.
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Affiliation(s)
- Umut Çakır
- Molecular Biology and Genetics Department, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Noujoud Gabed
- Cellular and Molecular Biology Department, Oran High School of Biological Sciences (ESSBO), Oran, Algeria
| | - Marie Brunet
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, QC, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), QC, Canada
| | - Xavier Roucou
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), QC, Canada.,Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada
| | - Igor Kryvoruchko
- Molecular Biology and Genetics Department, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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3
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Targeting immunoproteasome in neurodegeneration: A glance to the future. Pharmacol Ther 2023; 241:108329. [PMID: 36526014 DOI: 10.1016/j.pharmthera.2022.108329] [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: 10/03/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
The immunoproteasome is a specialized form of proteasome equipped with modified catalytic subunits that was initially discovered to play a pivotal role in MHC class I antigen processing and immune system modulation. However, over the last years, this proteolytic complex has been uncovered to serve additional functions unrelated to antigen presentation. Accordingly, it has been proposed that immunoproteasome synergizes with canonical proteasome in different cell types of the nervous system, regulating neurotransmission, metabolic pathways and adaptation of the cells to redox or inflammatory insults. Hence, studying the alterations of immunoproteasome expression and activity is gaining research interest to define the dynamics of neuroinflammation as well as the early and late molecular events that are likely involved in the pathogenesis of a variety of neurological disorders. Furthermore, these novel functions foster the perspective of immunoproteasome as a potential therapeutic target for neurodegeneration. In this review, we provide a brain and retina-wide overview, trying to correlate present knowledge on structure-function relationships of immunoproteasome with the variety of observed neuro-modulatory functions.
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4
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León-Letelier RA, Katayama H, Hanash S. Mining the Immunopeptidome for Antigenic Peptides in Cancer. Cancers (Basel) 2022; 14:cancers14204968. [PMID: 36291752 PMCID: PMC9599891 DOI: 10.3390/cancers14204968] [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: 08/16/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The immunopeptidome of cancer cells is a treasure trove of neoantigens bound to MHC molecules, thus a great source for mining immunopeptides for immunotherapy applications, including cancer vaccines. Immunopeptides may encompass post-translational modifications that are overlooked by genomic and transcriptomic tools. We review post-translational modifications that have been uncovered, and how this information could be harnessed for cancer vaccines. 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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5
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An unexplored angle: T cell antigen discoveries reveal a marginal contribution of proteasome splicing to the immunogenic MHC class I antigen pool. Proc Natl Acad Sci U S A 2022; 119:e2119736119. [PMID: 35858315 PMCID: PMC9303865 DOI: 10.1073/pnas.2119736119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the current era of T cell–based immunotherapies, it is crucial to understand which types of MHC-presented T cell antigens are produced by tumor cells. In addition to linear peptide antigens, chimeric peptides are generated through proteasome-catalyzed peptide splicing (PCPS). Whether such spliced peptides are abundantly presented by MHC is highly disputed because of disagreement in computational analyses of mass spectrometry data of MHC-eluted peptides. Moreover, such mass spectrometric analyses cannot elucidate how much spliced peptides contribute to the pool of immunogenic antigens. In this Perspective, we explain the significance of knowing the contribution of spliced peptides for accurate analyses of peptidomes on one hand, and to serve as a potential source of targetable tumor antigens on the other hand. Toward a strategy for mass spectrometry independent estimation of the contribution of PCPS to the immunopeptidome, we first reviewed methodologies to identify MHC-presented spliced peptide antigens expressed by tumors. Data from these identifications allowed us to compile three independent datasets containing 103, 74, and 83 confirmed T cell antigens from cancer patients. Only 3.9%, 1.4%, and between 0% and 7.2% of these truly immunogenic antigens are produced by PCPS, therefore providing a marginal contribution to the pool of immunogenic tumor antigens. We conclude that spliced peptides will not serve as a comprehensive source to expand the number of targetable antigens for immunotherapies.
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6
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Neoantigens – the next frontier in precision immunotherapy for B-cell lymphoproliferative disorders. Blood Rev 2022; 56:100969. [DOI: 10.1016/j.blre.2022.100969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/20/2022]
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7
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Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 204] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
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Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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8
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Pritam M, Singh G, Kumar R, Singh SP. Screening of potential antigens from whole proteome and development of multi-epitope vaccine against Rhizopus delemar using immunoinformatics approaches. J Biomol Struct Dyn 2022; 41:2118-2145. [PMID: 35067195 DOI: 10.1080/07391102.2022.2028676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mucormycosis is a deadly fungal disease mainly caused by Rhizopus oryzae (strain 99-880), also known as Rhizopus delemar. Previously, mucormycosis occurs in immunocompromised patients of diabetes mellitus, cancer, organ transplant, etc. But there was a drastic increase in mucormycosis cases in the ongoing COVID-19 pandemic. Despite several available therapies and antifungal treatments, the mortality rate of mucormycosis is about more than 50%. Currently, there is no vaccine available in the market for mucormycosis that urgently needs to develop a potential vaccine against mucormycosis with high efficacy. In the present study, we have screened 4 genome-derived predicted antigens (GDPA) through sequential filtration of the whole proteome of R. delemar using different benchmarked bioinformatics tools. These 4 GDPA along with 4 randomly selected experimentally reported antigens (ERA) were sourced for prediction of B- and T- cell epitopes and utilized in designing of two potential multi-epitope vaccine candidates which can induce both innate and adaptive immunity against R. delemar. Besides these, comparative immune simulation studies and in silico cloning were performed using L. lactis as an expression system for their possible uses as oral vaccines. This is the first multi-epitope vaccine designed against R. delemar through systematic pipelined reverse vaccinology and immunoinformatic approaches. Although the wet-lab based experimental validation of designed vaccines is required before testing in the preclinical model, the current study will significantly help in reducing the cost of experimentation as well as improving the efficacy of vaccine therapy against mucormycosis and other pathogenic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manisha Pritam
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Garima Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
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9
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Rickenbach C, Gericke C. Specificity of Adaptive Immune Responses in Central Nervous System Health, Aging and Diseases. Front Neurosci 2022; 15:806260. [PMID: 35126045 PMCID: PMC8812614 DOI: 10.3389/fnins.2021.806260] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/29/2021] [Indexed: 12/25/2022] Open
Abstract
The field of neuroimmunology endorses the involvement of the adaptive immune system in central nervous system (CNS) health, disease, and aging. While immune cell trafficking into the CNS is highly regulated, small numbers of antigen-experienced lymphocytes can still enter the cerebrospinal fluid (CSF)-filled compartments for regular immune surveillance under homeostatic conditions. Meningeal lymphatics facilitate drainage of brain-derived antigens from the CSF to deep cervical lymph nodes to prime potential adaptive immune responses. During aging and CNS disorders, brain barriers and meningeal lymphatic functions are impaired, and immune cell trafficking and antigen efflux are altered. In this context, alterations in the immune cell repertoire of blood and CSF and T and B cells primed against CNS-derived autoantigens have been observed in various CNS disorders. However, for many diseases, a causal relationship between observed immune responses and neuropathological findings is lacking. Here, we review recent discoveries about the association between the adaptive immune system and CNS disorders such as autoimmune neuroinflammatory and neurodegenerative diseases. We focus on the current challenges in identifying specific T cell epitopes in CNS diseases and discuss the potential implications for future diagnostic and treatment options.
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Affiliation(s)
- Chiara Rickenbach
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland
| | - Christoph Gericke
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland
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10
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Identification of tumor antigens with immunopeptidomics. Nat Biotechnol 2021; 40:175-188. [PMID: 34635837 DOI: 10.1038/s41587-021-01038-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/29/2021] [Indexed: 12/18/2022]
Abstract
The identification of actionable tumor antigens is indispensable for the development of several cancer immunotherapies, including T cell receptor-transduced T cells and patient-specific mRNA or peptide vaccines. Most known tumor antigens have been identified through extensive molecular characterization and are considered canonical if they derive from protein-coding regions of the genome. By eluting human leukocyte antigen-bound peptides from tumors and subjecting these to mass spectrometry analysis, the peptides can be identified by matching the resulting spectra against reference databases. Recently, mass-spectrometry-based immunopeptidomics has enabled the discovery of noncanonical antigens-antigens derived from sequences outside protein-coding regions or generated by noncanonical antigen-processing mechanisms. Coupled with transcriptomics and ribosome profiling, this method enables the identification of thousands of noncanonical peptides, of which a substantial fraction may be detected exclusively in tumors. Spectral matching against the immense noncanonical reference may generate false positives. However, sensitive mass spectrometry, analytical validation and advanced bioinformatics solutions are expected to uncover the full landscape of presented antigens and clinically relevant targets.
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11
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Dall E, Stanojlovic V, Demir F, Briza P, Dahms SO, Huesgen PF, Cabrele C, Brandstetter H. The Peptide Ligase Activity of Human Legumain Depends on Fold Stabilization and Balanced Substrate Affinities. ACS Catal 2021; 11:11885-11896. [PMID: 34621593 PMCID: PMC8491156 DOI: 10.1021/acscatal.1c02057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Indexed: 12/11/2022]
Abstract
Protein modification by enzymatic breaking and forming of peptide bonds significantly expands the repertoire of genetically encoded protein sequences. The dual protease-ligase legumain exerts the two opposing activities within a single protein scaffold. Primarily localized to the endolysosomal system, legumain represents a key enzyme in the generation of antigenic peptides for subsequent presentation on the MHCII complex. Here we show that human legumain catalyzes the ligation and cyclization of linear peptides at near-neutral pH conditions, where legumain is intrinsically unstable. Conformational stabilization significantly enhanced legumain's ligase activity, which further benefited from engineering the prime substrate recognition sites for improved affinity. Additionally, we provide evidence that specific legumain activation states allow for differential regulation of its activities. Together these results set the basis for engineering legumain proteases and ligases with applications in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Peter Briza
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Sven O. Dahms
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
- Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, 50674 Cologne, Germany
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
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12
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Tundo GR, Sbardella D, Oddone F, Kudriaeva AA, Lacal PM, Belogurov AA, Graziani G, Marini S. At the Cutting Edge against Cancer: A Perspective on Immunoproteasome and Immune Checkpoints Modulation as a Potential Therapeutic Intervention. Cancers (Basel) 2021; 13:4852. [PMID: 34638337 PMCID: PMC8507813 DOI: 10.3390/cancers13194852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 01/22/2023] Open
Abstract
Immunoproteasome is a noncanonical form of proteasome with enzymological properties optimized for the generation of antigenic peptides presented in complex with class I MHC molecules. This enzymatic property makes the modulation of its activity a promising area of research. Nevertheless, immunotherapy has emerged as a front-line treatment of advanced/metastatic tumors providing outstanding improvement of life expectancy, even though not all patients achieve a long-lasting clinical benefit. To enhance the efficacy of the currently available immunotherapies and enable the development of new strategies, a broader knowledge of the dynamics of antigen repertoire processing by cancer cells is needed. Therefore, a better understanding of the role of immunoproteasome in antigen processing and of the therapeutic implication of its modulation is mandatory. Studies on the potential crosstalk between proteasome modulators and immune checkpoint inhibitors could provide novel perspectives and an unexplored treatment option for a variety of cancers.
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Affiliation(s)
| | | | | | - Anna A. Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.K.)
| | - Pedro M. Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, 00167 Rome, Italy;
| | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.K.)
- Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Grazia Graziani
- Laboratory of Molecular Oncology, IDI-IRCCS, 00167 Rome, Italy;
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Stefano Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
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13
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Kubo T, Hirohashi Y, Tsukahara T, Kanaseki T, Murata K, Morita R, Torigoe T. Immunopathological basis of immune-related adverse events induced by immune checkpoint blockade therapy. Immunol Med 2021; 45:108-118. [PMID: 34542015 DOI: 10.1080/25785826.2021.1976942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Despite the considerable success of cancer immunotherapy with immune checkpoint inhibitors, their nonspecific release of the immunosuppressive mechanism is often associated with immune-related adverse events (irAEs). irAEs significantly disturb patients' quality of life and can even be life-threatening. Therefore, the appropriate management of irAEs is crucial for the development of further reliable cancer immunotherapies. irAEs have the appearance of ordinary autoimmune diseases in one aspect but often have distinct features. Although the detailed pathogenesis of irAEs remains unclear, increasing numbers of studies have provided numerous clues. Here, we review the current knowledge on irAEs, particularly from an immunopathological basis.
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Affiliation(s)
- Terufumi Kubo
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Yoshihiko Hirohashi
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Tomohide Tsukahara
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Kenji Murata
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Rena Morita
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan.,Division of Fundamental Health Sciences, School of Nursing and Social Services, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Toshihiko Torigoe
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
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14
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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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15
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van Endert P. Beware the algorithm. eLife 2021; 10:69657. [PMID: 34037522 PMCID: PMC8154017 DOI: 10.7554/elife.69657] [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: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Spliced peptides present on tumor cells can help to mount an immune response, but algorithms offer limited help in predicting which ones actually exist and perform this role in vivo.
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Affiliation(s)
- Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université de Paris, Centre National de la Recherche Scientifique, UMR 8253, Paris, France
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16
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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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17
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Fuchs ACD, Ammelburg M, Martin J, Schmitz RA, Hartmann MD, Lupas AN. Archaeal Connectase is a specific and efficient protein ligase related to proteasome β subunits. Proc Natl Acad Sci U S A 2021; 118:e2017871118. [PMID: 33688044 PMCID: PMC7980362 DOI: 10.1073/pnas.2017871118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Sequence-specific protein ligations are widely used to produce customized proteins "on demand." Such chimeric, immobilized, fluorophore-conjugated or segmentally labeled proteins are generated using a range of chemical, (split) intein, split domain, or enzymatic methods. Where short ligation motifs and good chemoselectivity are required, ligase enzymes are often chosen, although they have a number of disadvantages, for example poor catalytic efficiency, low substrate specificity, and side reactions. Here, we describe a sequence-specific protein ligase with more favorable characteristics. This ligase, Connectase, is a monomeric homolog of 20S proteasome subunits in methanogenic archaea. In pulldown experiments with Methanosarcina mazei cell extract, we identify a physiological substrate in methyltransferase A (MtrA), a key enzyme of archaeal methanogenesis. Using microscale thermophoresis and X-ray crystallography, we show that only a short sequence of about 20 residues derived from MtrA and containing a highly conserved KDPGA motif is required for this high-affinity interaction. Finally, in quantitative activity assays, we demonstrate that this recognition tag can be repurposed to allow the ligation of two unrelated proteins. Connectase catalyzes such ligations at substantially higher rates, with higher yields, but without detectable side reactions when compared with a reference enzyme. It thus presents an attractive tool for the development of new methods, for example in the preparation of selectively labeled proteins for NMR, the covalent and geometrically defined attachment of proteins on surfaces for cryo-electron microscopy, or the generation of multispecific antibodies.
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Affiliation(s)
- Adrian C D Fuchs
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Moritz Ammelburg
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrecht University of Kiel, 24118 Kiel, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
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18
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Thomas C, Tampé R. MHC I assembly and peptide editing - chaperones, clients, and molecular plasticity in immunity. Curr Opin Immunol 2021; 70:48-56. [PMID: 33689959 DOI: 10.1016/j.coi.2021.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/07/2021] [Indexed: 11/24/2022]
Abstract
Peptides presented on MHC I molecules allow the immune system to detect diseased cells. The displayed peptides typically stem from proteasomal degradation of cytoplasmic proteins and are translocated into the ER lumen where they are trimmed and loaded onto MHC I. Peptide translocation is carried out by the transporter associated with antigen processing, which forms the central building block of a dynamic assembly called the peptide-loading complex (PLC). By coordinating peptide transfer with MHC I loading and peptide optimization, the PLC is a linchpin in the adaptive immune system. Peptide loading and optimization is catalyzed by the PLC component tapasin and the PLC-independent TAPBPR, two MHC I-dedicated enzymes chaperoning empty or suboptimally loaded MHC I and selecting stable peptide-MHC I complexes in a process called peptide editing or proofreading. Recent structural and functional studies of peptide editing have dramatically improved our understanding of this pivotal event in antigen processing/presentation. This review is dedicated to Vincenzo Cerundolo (1959-2020) for his pioneering work in the field of antigen processing/presentation.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
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19
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Kasahara M. Role of immunoproteasomes and thymoproteasomes in health and disease. Pathol Int 2021; 71:371-382. [PMID: 33657242 DOI: 10.1111/pin.13088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022]
Abstract
The proteasome is a multisubunit protease that degrades intracellular proteins into small peptides. Besides playing a pivotal role in many cellular processes indispensable for survival, it is involved in the production of peptides presented by major histocompatibility complex class I molecules. In addition to the standard proteasome shared in all eukaryotes, jawed vertebrates have two specialized forms of proteasome known as immunoproteasomes and thymoproteasomes. The immunoproteasome, which contains cytokine-inducible catalytic subunits with distinct cleavage specificities, produces peptides presented by class I molecules more efficiently than the standard proteasome. The thymoproteasome, which contains a unique catalytic subunit β5t, is a tissue-specific proteasome expressed exclusively in cortical thymic epithelial cells. It plays a critical role in CD8+ cytotoxic T cell development via positive selection. This review provides a brief overview on the structure and function of these specialized forms of proteasome and their involvement in human disease.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
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20
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Digging deeper into the immunopeptidome: characterization of post-translationally modified peptides presented by MHC I. JOURNAL OF PROTEINS AND PROTEOMICS 2021; 12:151-160. [PMID: 36619276 PMCID: PMC9807509 DOI: 10.1007/s42485-021-00066-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 01/11/2023]
Abstract
Peptides presented by MHC molecules on the cell surface, or the immunopeptidome, play an important role in the adaptive arm of the immune response. Antigen processing for MHC class I molecules is a ubiquitous pathway present in all nucleated cells which generates and presents peptides of both self and non-self-origin. Peptides with post-translational modifications represent one category of peptides presented by MHC class I molecules. However, owing to the complexity of self-peptides presented by cells, the diversity of peptides with post-translational modifications is not well-studied. In this study, we carried out MHC Class I immunopeptidomics analysis of Loucy T-cell leukemia and A375 malignant melanoma cell line to characterize the diversity of post-translational modifications of MHC class I-bound peptides. Using high resolution mass spectrometry, we identified 25,761 MHC-bound peptides across both cell lines using Bolt and Sequest search engines. The enrichment method was highly specific as ~ 90% of the peptides were of typical length (8-12 amino acids long) and the motifs were expected based on previously reported motifs for MHC I alleles. Among the MHC-bound peptides, we identified phosphorylation as a major post-translational modification followed by deamidation. We observed site-specific localization of these post-translational modifications, at position P4 for phosphorylated peptides and position P3 for deamidated peptides. We identified a smaller number of peptides with acetylated and methylated lysine, possibly due to very low stoichiometric levels of these PTMs compared to phosphorylation and deamidation. Using PEAKS de novo sequencing algorithm, we identified spliced peptides that accounted for ~ 5-7% of MHC-bound peptides that were otherwise similar in their features as normal MHC-bound peptides. We validated the identity of several post-translationally modified peptides and spliced peptides through mass spectrometric analysis of synthetic peptides. Our study confirms post-translationally modified peptides to be present at low stoichiometric levels along with unusual spliced peptides through unbiased identification using high resolution mass spectrometry. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-021-00066-x.
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21
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Abstract
Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.
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22
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Critical Review of Existing MHC I Immunopeptidome Isolation Methods. Molecules 2020; 25:molecules25225409. [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] [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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23
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Buonaguro L, Tagliamonte M. Selecting Target Antigens for Cancer Vaccine Development. Vaccines (Basel) 2020; 8:vaccines8040615. [PMID: 33080888 PMCID: PMC7711972 DOI: 10.3390/vaccines8040615] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Abstract
One of the principal goals of cancer immunotherapy is the development of efficient therapeutic cancer vaccines that are able to elicit an effector as well as memory T cell response specific to tumor antigens. In recent years, the attention has been focused on the personalization of cancer vaccines. However, the efficacy of therapeutic cancer vaccines is still disappointing despite the large number of vaccine strategies targeting different tumors that have been evaluated in recent years. While the preclinical data have frequently shown encouraging results, clinical trials have not provided satisfactory data to date. The main reason for such failures is the complexity of identifying specific target tumor antigens that should be unique or overexpressed only by the tumor cells compared to normal cells. Most of the tumor antigens included in cancer vaccines are non-mutated overexpressed self-antigens, eliciting mainly T cells with low-affinity T cell receptors (TCR) unable to mediate an effective anti-tumor response. In this review, the target tumor antigens employed in recent years in the development of therapeutic cancer vaccine strategies are described, along with potential new classes of tumor antigens such as the human endogenous retroviral elements (HERVs), unconventional antigens, and/or heteroclitic peptides.
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24
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Wiles TA, Saba LM, Delong T. Peptide-Spectrum Match Validation with Internal Standards (P-VIS): Internally-Controlled Validation of Mass Spectrometry-Based Peptide Identifications. J Proteome Res 2020; 20:236-249. [PMID: 32924495 DOI: 10.1021/acs.jproteome.0c00355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Liquid chromatography-tandem mass spectrometry is an increasingly powerful tool for studying proteins in the context of disease. As technological advances in instrumentation and data analysis have enabled deeper profiling of proteomes and peptidomes, the need for a rigorous, standardized approach to validate individual peptide-spectrum matches (PSMs) has emerged. To address this need, we developed a novel and broadly applicable workflow: PSM validation with internal standards (P-VIS). In this approach, the fragmentation spectrum and chromatographic retention time of a peptide within a biological sample are compared with those of a synthetic version of the putative peptide sequence match. Similarity measurements obtained for a panel of internal standard peptides are then used to calculate a prediction interval for valid matches. If the observed degree of similarity between the biological and the synthetic peptide falls within this prediction interval, then the match is considered valid. P-VIS enables systematic and objective assessment of the validity of individual PSMs, providing a measurable degree of confidence when identifying peptides by mass spectrometry.
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Affiliation(s)
- Timothy Aaron Wiles
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045-0508, United States States
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045-0508, United States States
| | - Thomas Delong
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045-0508, United States States
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25
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Zaitoua AJ, Kaur A, Raghavan M. Variations in MHC class I antigen presentation and immunopeptidome selection pathways. F1000Res 2020; 9. [PMID: 33014341 PMCID: PMC7525337 DOI: 10.12688/f1000research.26935.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Major histocompatibility class I (MHC-I) proteins mediate immunosurveillance against pathogens and cancers by presenting antigenic or mutated peptides to antigen receptors of CD8+ T cells and by engaging receptors of natural killer (NK) cells. In humans, MHC-I molecules are highly polymorphic. MHC-I variations permit the display of thousands of distinct peptides at the cell surface. Recent mass spectrometric studies have revealed unique and shared characteristics of the peptidomes of individual MHC-I variants. The cell surface expression of MHC-I–peptide complexes requires the functions of many intracellular assembly factors, including the transporter associated with antigen presentation (TAP), tapasin, calreticulin, ERp57, TAP-binding protein related (TAPBPR), endoplasmic reticulum aminopeptidases (ERAPs), and the proteasomes. Recent studies provide important insights into the structural features of these factors that govern MHC-I assembly as well as the mechanisms underlying peptide exchange. Conformational sensing of MHC-I molecules mediates the quality control of intracellular MHC-I assembly and contributes to immune recognition by CD8 at the cell surface. Recent studies also show that several MHC-I variants can follow unconventional assembly routes to the cell surface, conferring selective immune advantages that can be exploited for immunotherapy.
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Affiliation(s)
- Anita J Zaitoua
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amanpreet Kaur
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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26
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Paes W, Leonov G, Partridge T, Nicastri A, Ternette N, Borrow P. Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing. Front Immunol 2020; 11:563800. [PMID: 33072102 PMCID: PMC7541919 DOI: 10.3389/fimmu.2020.563800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
Proteasomes catalyze the degradation of endogenous proteins into oligopeptides, but can concurrently create spliced oligopeptides through ligation of previously non-contiguous peptide fragments. Recent studies have uncovered a formerly unappreciated role for proteasome-catalyzed peptide splicing (PCPS) in the generation of non-genomically templated human leukocyte antigen class I (HLA-I)-bound cis-spliced peptides that can be targeted by CD8+ T cells in cancer and infection. However, the mechanisms defining PCPS reactions are poorly understood. Here, we experimentally define the biochemical constraints of proteasome-catalyzed cis-splicing reactions by examination of in vitro proteasomal digests of a panel of viral- and self-derived polypeptide substrates using a tailored mass-spectrometry-based de novo sequencing workflow. We show that forward and reverse PCPS reactions display unique splicing signatures, defined by preferential fusion of distinct amino acid residues with stringent peptide length distributions, suggesting sequence- and size-dependent accessibility of splice reactants for proteasomal substrate binding pockets. Our data provide the basis for a more informed mechanistic understanding of PCPS that will facilitate future prediction of spliced peptides from protein sequences.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - German Leonov
- York Cross-Disciplinary Center for Systems Analysis, University of York, York, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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27
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Faridi P, Woods K, Ostrouska S, Deceneux C, Aranha R, Duscharla D, Wong SQ, Chen W, Ramarathinam SH, Lim Kam Sian TCC, Croft NP, Li C, Ayala R, Cebon JS, Purcell AW, Schittenhelm RB, Behren A. Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma. Cancer Immunol Res 2020; 8:1322-1334. [PMID: 32938616 DOI: 10.1158/2326-6066.cir-19-0894] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/20/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022]
Abstract
Antigen recognition by CD8+ T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of noncontiguous regions of proteins to form novel peptide antigens. Here, we used high-resolution mass spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of IFNγ. In total, we identified more than 60,000 peptides from a single patient-derived cell line (LM-MEL-44) and demonstrated that IFNγ induced changes in the peptidome, with an overlap of only approximately 50% between basal and treated cells. Around 6% to 8% of the peptides were identified as cis-spliced peptides, and 2,213 peptides (1,827 linear and 386 cis-spliced peptides) were derived from known melanoma-associated antigens. These peptide antigens were equally distributed between the constitutive- and IFNγ-induced peptidome. We next examined additional HLA-matched patient-derived cell lines to investigate how frequently these peptides were identified and found that a high proportion of both linear and spliced peptides was conserved between individual patient tumors, drawing on data amassing to more than 100,000 peptide sequences. Several of these peptides showed in vitro immunogenicity across multiple patients with melanoma. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that can be exploited therapeutically and suggest that spliced peptides are a major class of tumor antigens.
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Affiliation(s)
- Pouya Faridi
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katherine Woods
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Simone Ostrouska
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Cyril Deceneux
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Ritchlynn Aranha
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Divya Duscharla
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Stephen Q Wong
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Terry C C Lim Kam Sian
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Chen Li
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jonathan S Cebon
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Andreas Behren
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
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28
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Taylor SK, Houshdaran S, Robinson JF, Gormley MJ, Kwan EY, Kapidzic M, Schilling B, Giudice LC, Fisher SJ. Cytotrophoblast extracellular vesicles enhance decidual cell secretion of immune modulators via TNFα. Development 2020; 147:dev.187013. [PMID: 32747437 DOI: 10.1242/dev.187013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022]
Abstract
The placenta releases large quantities of extracellular vesicles (EVs) that likely facilitate communication between the embryo/fetus and the mother. We isolated EVs from second trimester human cytotrophoblasts (CTBs) by differential ultracentrifugation and characterized them using transmission electron microscopy, immunoblotting and mass spectrometry. The 100,000 g pellet was enriched for vesicles with a cup-like morphology typical of exosomes. They expressed markers specific to this vesicle type, CD9 and HRS, and the trophoblast proteins placental alkaline phosphatase and HLA-G. Global profiling by mass spectrometry showed that placental EVs were enriched for proteins that function in transport and viral processes. A cytokine array revealed that the CTB 100,000 g pellet contained a significant amount of tumor necrosis factor α (TNFα). CTB EVs increased decidual stromal cell (dESF) transcription and secretion of NF-κB targets, including IL8, as measured by qRT-PCR and cytokine array. A soluble form of the TNFα receptor inhibited the ability of CTB 100,000 g EVs to increase dESF secretion of IL8. Overall, the data suggest that CTB EVs enhance decidual cell release of inflammatory cytokines, which we theorize is an important component of successful pregnancy.
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Affiliation(s)
- Sara K Taylor
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Sahar Houshdaran
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Joshua F Robinson
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Matthew J Gormley
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Elaine Y Kwan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Mirhan Kapidzic
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Birgit Schilling
- Chemistry & Mass Spectrometry, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Linda C Giudice
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Susan J Fisher
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA .,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,Division of Maternal Fetal Medicine, University of California, San Francisco, CA 94143, USA.,Department of Anatomy, University of California, San Francisco, CA 94143, USA.,Human Embryonic Stem Cell Program, University of California, San Francisco, CA 94143, USA
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29
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Imai J, Koganezawa Y, Tuzuki H, Ishikawa I, Sakai T. An optical and non-invasive method to detect the accumulation of ubiquitin chains. Cell Biol Int 2019; 43:1393-1406. [PMID: 31136031 DOI: 10.1002/cbin.11186] [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] [Received: 03/15/2019] [Accepted: 05/25/2019] [Indexed: 01/24/2023]
Abstract
The accumulations of excess amounts of polyubiquitinated proteins are cytotoxic and frequently observed in pathologic tissue from patients of neurodegenerative diseases. Therefore, optical and non-invasive methods to detect the increase of the amounts of polyubiquitinated proteins in living cells is a promising strategy to find out symptoms and environmental cause of neurodegenerative diseases, also for identifying compounds that could inhibit gathering of polyubiquitinated proteins. Therefore, we generated a pair of fluorescent protein [Azamigreen (Azg) and Kusabiraorange (Kuo)] tagged ubiquitin on its N-terminus (Azg-Ub and Kuo-Ub) and developed an Azg/Kuo-based Fluorescence Resonance Energy Transfer (FRET) assay to estimate the amount of polyubiquitin chains in vitro and in vivo. The FRET intensity was attenuated in the presence of ubiquitin-activating enzyme inhibitor, PYR-41, indicating that both fluorescent ubiquitin is incorporated into ubiquitin chains likewise normal ubiquitin. The FRET intensity was enhanced by the addition of the proteasome inhibitor, MG-132, and was reduced in the presence of the autophagy activator Rapamycin, designating that ubiquitin chains with fluorescent ubiquitin act as the degradation signal equally with normal ubiquitin chains. In summary, the above optical methods provide powerful research tools to estimate the amounts of polyubiquitin chains in vitro and in vivo, especially non-invasively in living cells.
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Affiliation(s)
- Jun Imai
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Yuuta Koganezawa
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Haruka Tuzuki
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Ikumi Ishikawa
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Takahiro Sakai
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
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30
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Berryman K, Buhimschi CS, Zhao G, Axe M, Locke M, Buhimschi IA. Proteasome Levels and Activity in Pregnancies Complicated by Severe Preeclampsia and Hemolysis, Elevated Liver Enzymes, and Thrombocytopenia (HELLP) Syndrome. Hypertension 2019; 73:1308-1318. [PMID: 31067191 DOI: 10.1161/hypertensionaha.118.12437] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Excessive accumulation of misfolded proteins was recently demonstrated in preeclampsia. We examined levels and activity of circulatory proteasome and immunoproteasome (inflammatory subtype) in preeclampsia and hemolysis, elevated liver enzymes, and thrombocytopenia (HELLP) syndrome. We analyzed samples from women with hypertensive pregnancy disorders (n=115), including preeclampsia with severe features (sPE) and HELLP syndrome, and normotensive controls (n=45). Plasma proteasome and immunoproteasome immunoreactivity were determined by quantifying the α-subunit of the 20S core and β5i (proteasome subunit beta 8 [PSMB8]), respectively. Plasma proteasome activity was analyzed with fluorogenic substrates. MG132, lactacystin, and ONX0914 were used to inhibit the circulating proteasome and immunoproteasome, respectively. Plasma cytokine profiles were evaluated by multiplex immunoassay. Placental expression of β5 (constitutive proteasome) and β5i (immunoproteasome) was interrogated by immunohistochemistry. Women with sPE had increased plasma 20S levels ( P<0.001) and elevated lytic activities (chymotrypsin-like 7-fold, caspase-like 4.2-fold, trypsin-like 2.2-fold; P <0.001 for all) compared with pregnant controls. Women with features of HELLP displayed the highest plasma proteasome levels and activity, which correlated with decreased IFN-γ (interferon-γ), and increased IL (interleukin)-8 and IL-10. In sPE and HELLP, chymotrypsin-like activity was suppressed by proteasome inhibitors including ONX0914. Compared with gestational age-matched controls, sPE placentas harbored increased β5 and β5i immunostaining in trophoblasts. β5i signal was elevated in HELLP with predominant staining in villous core, extravillous trophoblasts in placental islands, and extracellular vesicles in intervillous spaces. Pregnancy represents a state of increased proteostatic stress. sPE and HELLP were characterized by significant upregulation in circulating levels and lytic activity of the proteasome that was partially explained by placental immunoproteasome upregulation.
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Affiliation(s)
- Kathryn Berryman
- From the Department of Obstetrics and Gynecology (K.B., C.S.B.), The Ohio State University College of Medicine, Columbus
| | - Catalin S Buhimschi
- From the Department of Obstetrics and Gynecology (K.B., C.S.B.), The Ohio State University College of Medicine, Columbus.,Department of Pediatrics (C.S.B., I.A.B.), The Ohio State University College of Medicine, Columbus
| | - Guomao Zhao
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH (G.Z., M.A., M.L., I.A.B.)
| | - Michelle Axe
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH (G.Z., M.A., M.L., I.A.B.)
| | - Megan Locke
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH (G.Z., M.A., M.L., I.A.B.)
| | - Irina A Buhimschi
- Department of Pediatrics (C.S.B., I.A.B.), The Ohio State University College of Medicine, Columbus.,Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH (G.Z., M.A., M.L., I.A.B.)
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31
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Faridi P, Li C, Ramarathinam SH, Vivian JP, Illing PT, Mifsud NA, Ayala R, Song J, Gearing LJ, Hertzog PJ, Ternette N, Rossjohn J, Croft NP, Purcell AW. A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands. Sci Immunol 2019; 3:3/28/eaar3947. [PMID: 30315122 DOI: 10.1126/sciimmunol.aar3947] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 05/29/2018] [Accepted: 08/31/2018] [Indexed: 12/19/2022]
Abstract
The diversity of peptides displayed by class I human leukocyte antigen (HLA) plays an essential role in T cell immunity. The peptide repertoire is extended by various posttranslational modifications, including proteasomal splicing of peptide fragments from distinct regions of an antigen to form nongenomically templated cis-spliced sequences. Previously, it has been suggested that a fraction of the immunopeptidome constitutes such cis-spliced peptides; however, because of computational limitations, it has not been possible to assess whether trans-spliced peptides (i.e., the fusion of peptide segments from distinct antigens) are also bound and presented by HLA molecules, and if so, in what proportion. Here, we have developed and applied a bioinformatic workflow and demonstrated that trans-spliced peptides are presented by HLA-I, and their abundance challenges current models of proteasomal splicing that predict cis-splicing as the most probable outcome. These trans-spliced peptides display canonical HLA-binding sequence features and are as frequently identified as cis-spliced peptides found bound to a number of different HLA-A and HLA-B allotypes. Structural analysis reveals that the junction between spliced peptides is highly solvent exposed and likely to participate in T cell receptor interactions. These results highlight the unanticipated diversity of the immunopeptidome and have important implications for autoimmunity, vaccine design, and immunotherapy.
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Affiliation(s)
- Pouya Faridi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Chen Li
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Biology, Institute of Molecular Systems Biology,ETH Zurich, Zurich 8093, Switzerland
| | - Sri H Ramarathinam
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rochelle Ayala
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jiangning Song
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, Victoria 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | | | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine,Heath Park, Cardiff CF14 4XN, UK
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - 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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Abstract
T cells recognize antigen peptides displayed by HLA molecules and specifically eliminate their target cells. Identification of responsible antigens as well as understanding the mechanism by which antigens are produced inside cells are equally crucial for cancer immunology. In this review, we introduce proteogenomics and its applications in cancer antigen research, which leverages mass spectrometry and next-generation sequencing. The approach comprehensively captures immunopeptidome displayed by HLA, revealing new classes of antigens, such as mutation-derived neoantigens, spliced peptides, and non-coding region derived peptides. These antigens may serve as therapeutic targets or biomarkers. Thus, proteogenomics is a promising approach for cancer antigen research and contributes to immunotherapy development.
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Affiliation(s)
- Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University , Sapporo , Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University , Sapporo , Japan
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33
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Nakayasu ES, Qian WJ, Evans-Molina C, Mirmira RG, Eizirik DL, Metz TO. The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes. Expert Rev Proteomics 2019; 16:569-582. [PMID: 31232620 PMCID: PMC6628911 DOI: 10.1080/14789450.2019.1634548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/18/2019] [Indexed: 12/17/2022]
Abstract
Introduction: Type 1 diabetes (T1D) is characterized by autoimmune-induced dysfunction and destruction of the pancreatic beta cells. Unfortunately, this process is poorly understood, and the current best treatment for type 1 diabetes is the administration of exogenous insulin. To better understand these mechanisms and to develop new therapies, there is an urgent need for biomarkers that can reliably predict disease stage. Areas covered: Mass spectrometry (MS)-based proteomics and complementary techniques play an important role in understanding the autoimmune response, inflammation and beta-cell death. MS is also a leading technology for the identification of biomarkers. This, and the technical difficulties and new technologies that provide opportunities to characterize small amounts of sample in great depth and to analyze large sample cohorts will be discussed in this review. Expert opinion: Understanding disease mechanisms and the discovery of disease-associated biomarkers are highly interconnected goals. Ideal biomarkers would be molecules specific to the different stages of the disease process that are released from beta cells to the bloodstream. However, such molecules are likely to be present in trace amounts in the blood due to the small number of pancreatic beta cells in the human body and the heterogeneity of the target organ and disease process.
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Affiliation(s)
- Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Raghavendra G. Mirmira
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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Abstract
Mounting evidence implicates hybrid insulin peptides (HIPs) as important autoantigens in the development of type 1 diabetes (T1D). These fusion peptides formed between insulin and other pancreatic beta cell-derived peptides contain non-genomically encoded amino acid sequences, making them plausible targets for autoreactive T cells in T1D. HIPs are detectable by mass spectrometry in human and murine islets and are targeted by diabetes-inducing T cells in non-obese diabetic mice as well as by T cells isolated from the residual pancreatic islets of human organ donors with T1D. The discovery of HIPs comes with numerous new challenges, as well as opportunities to study the pathogenesis of T1D. Here we review the original discovery of HIPs and describe recent studies investigating the role of HIP-reactive T cells in the development of diabetes. We also discuss potential mechanisms that may be responsible for the generation of HIPs in beta cells and describe challenges that need to be addressed in the field of mass spectrometry to enable the discovery of new HIPs. The identification of these potentially disease-driving antigens in T1D is of key interest to the field as it may provide new tools to predict, prevent and potentially reverse the disease.
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Affiliation(s)
- T A Wiles
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz, Aurora, CO, USA
| | - T Delong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz, Aurora, CO, USA
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35
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Collins C, Lorenzen N, Collet B. DNA vaccination for finfish aquaculture. FISH & SHELLFISH IMMUNOLOGY 2019; 85:106-125. [PMID: 30017931 DOI: 10.1016/j.fsi.2018.07.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
In fish, DNA vaccines have been shown to give very high protection in experimental facilities against a number of viral diseases, particularly diseases caused by rhabdoviruses. However, their efficacy in generating protection against other families of fish viral pathogens is less clear. One DNA vaccine is currently in use commercially in fish farms in Canada and the commercialisation of another was authorised in Europe in 2017. The mechanism of action of DNA vaccines, including the role of the innate immune responses induced shortly after DNA vaccination in the activation of the adaptive immunity providing longer term specific protection, is still not fully understood. In Europe the procedure for the commercialisation of a veterinary DNA vaccine requires the resolution of certain concerns particularly about safety for the host vaccinated fish, the consumer and the environment. Relating to consumer acceptance and particularly environmental safety, a key question is whether a DNA vaccinated fish is considered a Genetically Modified Organism (GMO). In the present opinion paper these key aspects relating to the mechanisms of action, and to the development and the use of DNA vaccines in farmed fish are reviewed and discussed.
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Affiliation(s)
| | | | - Bertrand Collet
- Marine Scotland, Aberdeen, United Kingdom; Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France.
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36
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Wiles TA, Powell R, Michel C, Beard KS, Hohenstein A, Bradley B, Reisdorph N, Haskins K, Delong T. Identification of Hybrid Insulin Peptides (HIPs) in Mouse and Human Islets by Mass Spectrometry. J Proteome Res 2019; 18:814-825. [PMID: 30585061 DOI: 10.1021/acs.jproteome.8b00875] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We recently discovered hybrid insulin peptides (HIPs) as a novel class of post-translationally modified peptides in murine-derived beta cell tumors, and we demonstrated that these molecules are autoantigens in type 1 diabetes (T1D). A HIP consists of an insulin fragment linked to another secretory granule peptide via a peptide bond. We verified that autoreactive CD4 T cells in both mouse and human autoimmune diabetes recognize these modified peptides. Here, we use mass spectrometric analyses to confirm the presence of HIPs in both mouse and human pancreatic islets. We also present criteria for the confident identification of these peptides. This work supports the hypothesis that HIPs are autoantigens in human T1D and provides a foundation for future efforts to interrogate this previously unknown component of the beta cell proteome.
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Affiliation(s)
- T. Aaron Wiles
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - Roger Powell
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - Cole Michel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - K. Scott Beard
- Barbara Davis Center for Childhood Diabetes , Aurora , Colorado 80045 , United States
| | - Anita Hohenstein
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States,Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - Brenda Bradley
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - Nichole Reisdorph
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - Kathryn Haskins
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045,
United States
| | - Thomas Delong
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045,
United States
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37
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Gao FS, Feng L, Jiang P, Li ZB, Gao H, Zhai XX, Zhang ZH, Hu X. Expression, purification, crystallization and preliminary X-ray diffraction analysis of swine leukocyte antigen 2 complexed with a CTL epitope AS64 derived from Asia1 serotype of foot-and-mouth disease virus. BMC Vet Res 2018; 14:407. [PMID: 30563524 PMCID: PMC6299498 DOI: 10.1186/s12917-018-1742-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023] Open
Abstract
Background Currently, the structural characteristics of the swine major histocompatibility complex (MHC) class I molecule, also named swine leukocyte antigen class I (SLA-I) molecule need to be further clarified. Results A complex of SLA-I constituted by an SLA-2*HB01 molecule with swine β2-microglobulin and a cytotoxic T lymphocyte (CTL) epitope FMDV-AS64 (ALLRSATYY) derived from VP1 protein (residues 64–72) of Asia 1 serotype of foot-and-mouth disease virus (FMDV) was expressed, refolded, purified and crystallized. By preliminary X-ray diffraction analysis, it was shown that the diffraction resolution of the crystal was 2.4 Å and the space group belonged to P212121 with unit cell parameters a = 48.37, b = 97.75, c = 166.163 Å. Conclusion This research will be in favor of illuminating the structural characteristics of an SLA-2 molecule associated with a CTL epitope derived from Asia1 serotype of FMDV.
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Affiliation(s)
- Feng-Shan Gao
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China.
| | - Lei Feng
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Ping Jiang
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Zi-Bin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100094, People's Republic of China
| | - Hua Gao
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Xiao-Xin Zhai
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Zong-Hui Zhang
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Xiao Hu
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
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38
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Otsubo R, Mimuro H, Ashida H, Hamazaki J, Murata S, Sasakawa C. Shigella effector IpaH4.5 targets 19S regulatory particle subunit RPN13 in the 26S proteasome to dampen cytotoxic T lymphocyte activation. Cell Microbiol 2018; 21:e12974. [PMID: 30414351 DOI: 10.1111/cmi.12974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/17/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022]
Abstract
Subversion of antigen-specific immune responses by intracellular pathogens is pivotal for successful colonisation. Bacterial pathogens, including Shigella, deliver effectors into host cells via the type III secretion system (T3SS) in order to manipulate host innate and adaptive immune responses, thereby promoting infection. However, the strategy for subverting antigen-specific immunity is not well understood. Here, we show that Shigella flexneri invasion plasmid antigen H (IpaH) 4.5, a member of the E3 ubiquitin ligase effector family, targets the proteasome regulatory particle non-ATPase 13 (RPN13) and induces its degradation via the ubiquitin-proteasome system (UPS). IpaH4.5-mediated RPN13 degradation causes dysfunction of the 19S regulatory particle (RP) in the 26S proteasome, inhibiting guidance of ubiquitinated proteins to the proteolytically active 20S core particle (CP) of 26S proteasome and thereby suppressing proteasome-catalysed peptide splicing. This, in turn, reduces antigen cross-presentation to CD8+ T cells via major histocompatibility complex (MHC) class I in vitro. In RPN13 knockout mouse embryonic fibroblasts (MEFs), loss of RPN13 suppressed CD8+ T cell priming during Shigella infection. Our results uncover the unique tactics employed by Shigella to dampen the antigen-specific cytotoxic T lymphocyte (CTL) response.
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Affiliation(s)
- Ryota Otsubo
- Department of infection Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Hitomi Mimuro
- Department of infection Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan.,Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Ashida
- Department of Bacterial pathogenesis, Infection and Host Response, Graduate of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jun Hamazaki
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Chihiro Sasakawa
- Research Department, Nippon Institute for Biological Science, Tokyo, Japan.,Medical Mycology Research Center, Chiba University, Chiba, Japan
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39
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Thomaidou S, Zaldumbide A, Roep BO. Islet stress, degradation and autoimmunity. Diabetes Obes Metab 2018; 20 Suppl 2:88-94. [PMID: 30230178 PMCID: PMC6174957 DOI: 10.1111/dom.13387] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/18/2018] [Accepted: 05/30/2018] [Indexed: 12/15/2022]
Abstract
β-cell destruction in type 1 diabetes (T1D) results from the effect of inflammation and autoimmunity. In response to inflammatory signals, islet cells engage adaptive mechanisms to restore and maintain cellular homeostasis. Among these mechanisms, the unfolded protein response (UPR) leads to a reduction of the general protein translation rate, increased production of endoplasmic reticulum chaperones and the initiation of degradation by activation of the ER associated degradation pathway (ERAD) in which newly synthetized proteins are ubiquitinylated and processed through the proteasome. This adaptive phase is also believed to play a critical role in the development of autoimmunity by the generation of neoantigens. While we have previously investigated the effect of stress on transcription, translation and post-translational events as possible source for neoantigens, the participation of the degradation machinery, yet crucial in the generation of antigenic peptides, remains to be investigated in the context of T1D pathology. In this review, we will describe the relation between the unfolded protein response and the Ubiquitin Proteasome System (UPS) and address the role of the cellular degradation machinery in the generation of antigens. Learning from tumour immunology, we propose how these processes may unmask β-cells by triggering the generation of aberrant peptides recognized by the immune cells.
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Affiliation(s)
- Sofia Thomaidou
- Department of Cell and Chemical BiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Arnaud Zaldumbide
- Department of Cell and Chemical BiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Bart O. Roep
- Department of Immunohematology and Blood bank Leiden University Medical CenterLeiden University Medical CenterLeidenThe Netherlands
- Department of Diabetes ImmunologyDiabetes & Metabolism Research Institute at the Beckman Research InstituteDuarteCalifornia
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40
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Pishesha N, Ingram JR, Ploegh HL. Sortase A: A Model for Transpeptidation and Its Biological Applications. Annu Rev Cell Dev Biol 2018; 34:163-188. [PMID: 30110557 DOI: 10.1146/annurev-cellbio-100617-062527] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular biologists and chemists alike have long sought to modify proteins with substituents that cannot be installed by standard or even advanced genetic approaches. We here describe the use of transpeptidases to achieve these goals. Living systems encode a variety of transpeptidases and peptide ligases that allow for the enzyme-catalyzed formation of peptide bonds, and protein engineers have used directed evolution to enhance these enzymes for biological applications. We focus primarily on the transpeptidase sortase A, which has become popular over the past few years for its ability to perform a remarkably wide variety of protein modifications, both in vitro and in living cells.
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Affiliation(s)
- Novalia Pishesha
- Program in Molecular and Cellular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jessica R Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Hidde L Ploegh
- Program in Molecular and Cellular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
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41
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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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The immunoproteasome and thymoproteasome: functions, evolution and human disease. Nat Immunol 2018; 19:923-931. [PMID: 30104634 DOI: 10.1038/s41590-018-0186-z] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/12/2018] [Accepted: 07/19/2018] [Indexed: 01/12/2023]
Abstract
The basic principle of adaptive immunity is to strictly discriminate between self and non-self, and a central challenge to overcome is the enormous variety of pathogens that might be encountered. In cell-mediated immunity, immunological discernment takes place at a molecular or cellular level. Central to both mechanisms of discernment is the generation of antigenic peptides associated with MHC class I molecules, which is achieved by a proteolytic complex called the proteasome. To adequately accomplish the discrimination between self and non-self that is essential for adaptive immunity and self-tolerance, two proteasome subtypes have evolved via gene duplication: the immunoproteasome and the thymoproteasome. In this Review, we describe various aspects of these immunity-dedicated proteasomes, from their discovery to recent findings.
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Cosma G, Eisenlohr L. CD8 + T-cell responses in vaccination: reconsidering targets and function in the context of chronic antigen stimulation. F1000Res 2018; 7. [PMID: 29770202 PMCID: PMC5931265 DOI: 10.12688/f1000research.14115.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/20/2018] [Indexed: 12/23/2022] Open
Abstract
Cytotoxic CD8 T cells play important roles in eliminating infected and transformed cells. Owing to their potential for therapeutic applications, significant efforts are dedicated toward developing CD8 T cell–based vaccines. Thus far, CD8 T-cell vaccination strategies have had limited success therapeutically in contrast to those targeting antibody-based immunity. However, if the current challenges and gaps in the understanding of T-cell biology are overcome, the full potential of rational CD8 T-cell vaccine design might be realized. Here, we review recent progress in this direction, focusing on target selection and maintenance of function in the settings of chronic infections and cancers.
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Affiliation(s)
- Gabriela Cosma
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
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