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van Midden KP, Mantz M, Fonovič M, Gazvoda M, Svete J, Huesgen PF, van der Hoorn RAL, Klemenčič M. Mechanistic insights into CrCEP1: A dual-function cysteine protease with endo- and transpeptidase activity. Int J Biol Macromol 2024; 271:132505. [PMID: 38768911 DOI: 10.1016/j.ijbiomac.2024.132505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/05/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Proteases, essential regulators of plant stress responses, remain enigmatic in their precise functional roles. By employing activity-based probes for real-time monitoring, this study aimed to delve into protease activities in Chlamydomonas reinhardtii exposed to oxidative stress induced by hydrogen peroxide. However, our work revealed that the activity-based probes strongly labelled three non-proteolytic proteins-PsbO, PsbP, and PsbQ-integral components of photosystem II's oxygen-evolving complex. Subsequent biochemical assays and mass spectrometry experiments revealed the involvement of CrCEP1, a previously uncharacterized papain-like cysteine protease, as the catalyst of this labelling reaction. Further experiments with recombinant CrCEP1 and PsbO proteins replicated the reaction in vitro. Our data unveiled that endopeptidase CrCEP1 also has transpeptidase activity, ligating probes and peptides to the N-termini of Psb proteins, thereby expanding the repertoire of its enzymatic activities. The hitherto unknown transpeptidase activity of CrCEP1, working in conjunction with its proteolytic activity, unveils putative complex and versatile roles for proteases in cellular processes during stress responses.
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Affiliation(s)
- Katarina P van Midden
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
| | - Marko Fonovič
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Martin Gazvoda
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Svete
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; CIBSS- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | | | - Marina Klemenčič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
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2
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Pepelnjak M, Rogawski R, Arkind G, Leushkin Y, Fainer I, Ben-Nissan G, Picotti P, Sharon M. Systematic identification of 20S proteasome substrates. Mol Syst Biol 2024; 20:403-427. [PMID: 38287148 PMCID: PMC10987551 DOI: 10.1038/s44320-024-00015-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.
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Affiliation(s)
- Monika Pepelnjak
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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3
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Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
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Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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4
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Zhu Y, Li X, Chen T, Wang J, Zhou Y, Mu X, Du Y, Wang J, Tang J, Liu J. Personalised neoantigen-based therapy in colorectal cancer. Clin Transl Med 2023; 13:e1461. [PMID: 37921274 PMCID: PMC10623652 DOI: 10.1002/ctm2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Colorectal cancer (CRC) has become one of the most common tumours with high morbidity, mortality and distinctive evolution mechanism. The neoantigens arising from the somatic mutations have become considerable treatment targets in the management of CRC. As cancer-specific aberrant peptides, neoantigens can trigger the robust host immune response and exert anti-tumour effects while minimising the emergence of adverse events commonly associated with alternative therapeutic regimens. In this review, we summarised the mechanism, generation, identification and prognostic significance of neoantigens, as well as therapeutic strategies challenges of neoantigen-based therapy in CRC. The evidence suggests that the establishment of personalised neoantigen-based therapy holds great promise as an effective treatment approach for patients with CRC.
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Affiliation(s)
- Ya‐Juan Zhu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiong Li
- Department of GastroenterologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Ting‐Ting Chen
- The Second Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Jia‐Xiang Wang
- Department of Renal Cancer and MelanomaPeking University Cancer Hospital & InstituteBeijingChina
| | - Yi‐Xin Zhou
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiao‐Li Mu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Du
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jia‐Ling Wang
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jie Tang
- Clinical Trial CenterWest China HospitalSichuan UniversityChengduChina
| | - Ji‐Yan Liu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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5
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Li B, Jing P, Zheng G, Pi C, Zhang L, Yin Z, Xu L, Qiu J, Gu H, Qiu T, Fang J. Neo-intline: integrated pipeline enables neoantigen design through the in-silico presentation of T-cell epitope. Signal Transduct Target Ther 2023; 8:397. [PMID: 37848417 PMCID: PMC10582007 DOI: 10.1038/s41392-023-01644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/19/2023] Open
Abstract
Neoantigen vaccines are one of the most effective immunotherapies for personalized tumour treatment. The current immunogen design of neoantigen vaccines is usually based on whole-genome sequencing (WGS) and bioinformatics prediction that focuses on the prediction of binding affinity between peptide and MHC molecules, ignoring other peptide-presenting related steps. This may result in a gap between high prediction accuracy and relatively low clinical effectiveness. In this study, we designed an integrated in-silico pipeline, Neo-intline, which started from the SNPs and indels of the tumour samples to simulate the presentation process of peptides in-vivo through an integrated calculation model. Validation on the benchmark dataset of TESLA and clinically validated neoantigens illustrated that neo-intline could outperform current state-of-the-art tools on both sample level and melanoma level. Furthermore, by taking the mouse melanoma model as an example, we verified the effectiveness of 20 neoantigens, including 10 MHC-I and 10 MHC-II peptides. The in-vitro and in-vivo experiments showed that both peptides predicted by Neo-intline could recruit corresponding CD4+ T cells and CD8+ T cells to induce a T-cell-mediated cellular immune response. Moreover, although the therapeutic effect of neoantigen vaccines alone is not sufficient, combinations with other specific therapies, such as broad-spectrum immune-enhanced adjuvants of granulocyte-macrophage colony-stimulating factor (GM-CSF) and polyinosinic-polycytidylic acid (poly(I:C)), or immune checkpoint inhibitors, such as PD-1/PD-L1 antibodies, can illustrate significant anticancer effects on melanoma. Neo-intline can be used as a benchmark process for the design and screening of immunogenic targets for neoantigen vaccines.
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Affiliation(s)
- Bingyu Li
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, Henan, China
| | - Ping Jing
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Genhui Zheng
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
- Oden Institute for Computational Engineering and Sciences (ICES), University of Texas at Austin, Austin, TX, USA
| | - Chenyu Pi
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Lu Zhang
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Zuojing Yin
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lijun Xu
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, Henan, China
| | - Jingxuan Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Hua Gu
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
| | - Jianmin Fang
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China.
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6
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Deshmukh FK, Ben-Nissan G, Olshina MA, Füzesi-Levi MG, Polkinghorn C, Arkind G, Leushkin Y, Fainer I, Fleishman SJ, Tawfik D, Sharon M. Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family. Nat Commun 2023; 14:3126. [PMID: 37253751 DOI: 10.1038/s41467-023-38404-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the degradation routes involves the uncapped 20S proteasome, which cleaves proteins with a partially unfolded region, including those that are damaged or contain intrinsically disordered regions. This degradation route is tightly controlled by a recently discovered family of proteins named Catalytic Core Regulators (CCRs). Here, we show that CCRs function through an allosteric mechanism, coupling the physical binding of the PSMB4 β-subunit with attenuation of the complex's three proteolytic activities. In addition, by dissecting the structural properties that are required for CCR-like function, we could recapitulate this activity using a designed protein that is half the size of natural CCRs. These data uncover an allosteric path that does not involve the proteasome's enzymatic subunits but rather propagates through the non-catalytic subunit PSMB4. This way of 20S proteasome-specific attenuation opens avenues for decoupling the 20S and 26S proteasome degradation pathways as well as for developing selective 20S proteasome inhibitors.
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Affiliation(s)
- Fanindra Kumar Deshmukh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya A Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maria G Füzesi-Levi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Caley Polkinghorn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dan Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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7
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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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8
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Brochier W, Bricard O, Coulie PG. Facts and Hopes in Cancer Antigens Recognized by T Cells. Clin Cancer Res 2023; 29:309-315. [PMID: 36044396 DOI: 10.1158/1078-0432.ccr-21-3798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/13/2022] [Accepted: 08/15/2022] [Indexed: 01/19/2023]
Abstract
T cells are key effectors of our immune response against tumors and exert their antitumor effects upon recognizing a variety of tumor-specific peptides presented by HLA molecules on the surface of tumor cells. The identification of the tumor-specific antigens of a given tumor is not required for immune checkpoint therapy (ICT), which mainly reactivates existing tumor-specific T cells together with T cells of unknown specificities. To decrease the activation of non-tumor-specific T cells, active or passive immunizations against tumor-specific antigens are considered. These immunizations require the identification of at least some of the tumor-specific antigens displayed on the tumor cells of a patient. While this has become an easy task for tumors with a large number of mutations generating neoantigens, it remains difficult for the remainder. Here, we review some facts about human tumor-specific or tumor-associated antigens, as well as some hopes for their future use in cancer immunotherapy.
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Affiliation(s)
| | - Orian Bricard
- de Duve Institute, UCLouvain, Brussels, Belgium.,Immunology Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Pierre G Coulie
- de Duve Institute, UCLouvain, Brussels, Belgium.,Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavre, Belgium
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9
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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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10
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Yewdell JW. MHC Class I Immunopeptidome: Past, Present, and Future. Mol Cell Proteomics 2022; 21:100230. [PMID: 35395404 PMCID: PMC9243166 DOI: 10.1016/j.mcpro.2022.100230] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
In the 35 years since the revelation that short peptides bound to major histocompatibility complex class I and II molecules are the secret of the major histocompatibility complex–restricted nature of T-cell recognition, there has been enormous progress in characterizing the immunopeptidome, the repertoire of peptide presented for immunosurveillance. Here, the major milestones in the journey are marked, the contribution of proteasome-mediated splicing to the immunopeptidome is discussed, and exciting recent findings relating the immunopeptidome to the translatome revealed by ribosome profiling (RiboSeq) is detailed. Finally, what is needed for continued progress is opined about, which includes the infusion of talented young scientists into the antigen-processing field, currently undergoing a renaissance; thanks in part to the astounding success of T-cell–based cancer immunotherapy. Concise history of the discoveries leading to the molecular explanation for the phenomenon of the MHC class I–restricted nature of T-cell recognition. Historical review of how MS became a critical technique for defining MHC class I–associated peptides and understanding how peptides are generated from proteins biosynthesized by the antigen-presenting cell. Critical review of recent findings linking the translatome to the MHC class I immunopeptidome and the controversy regarding contribution of proteasome-mediated peptide splicing to the immunopeptidome. Speculative discussion of the future contributions of MS to understanding the generation of the MHC class I immunopeptidome.
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Affiliation(s)
- Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.
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11
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Redwood AJ, Dick IM, Creaney J, Robinson BWS. What’s next in cancer immunotherapy? - The promise and challenges of neoantigen vaccination. Oncoimmunology 2022; 11:2038403. [PMID: 35186441 PMCID: PMC8855878 DOI: 10.1080/2162402x.2022.2038403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The process of tumorigenesis leaves a series of indelible genetic changes in tumor cells, that when expressed, have the potential to be tumor-specific immune targets. Neoantigen vaccines that capitalize on this potential immunogenicity have shown efficacy in preclinical models and have now entered clinical trials. Here we discuss the status of personalized neoantigen vaccines and the current major challenges to this nascent field. In particular, we focus on the types of antigens that can be targeted by vaccination and on the role that preexisting immunosuppression, and in particular T-cell exhaustion, will play in the development of effective cancer vaccines.
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Affiliation(s)
- Alec J. Redwood
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
| | - Ian M. Dick
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Jenette Creaney
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia
| | - Bruce W. S. Robinson
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia
- Medical School, University of Western Australia, Perth, Australia
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12
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Tripathi SC, Vedpathak D, Ostrin EJ. The Functional and Mechanistic Roles of Immunoproteasome Subunits in Cancer. Cells 2021; 10:cells10123587. [PMID: 34944095 PMCID: PMC8700164 DOI: 10.3390/cells10123587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
Cell-mediated immunity is driven by antigenic peptide presentation on major histocompatibility complex (MHC) molecules. Specialized proteasome complexes called immunoproteasomes process viral, bacterial, and tumor antigens for presentation on MHC class I molecules, which can induce CD8 T cells to mount effective immune responses. Immunoproteasomes are distinguished by three subunits that alter the catalytic activity of the proteasome and are inducible by inflammatory stimuli such as interferon-γ (IFN-γ). This inducible activity places them in central roles in cancer, autoimmunity, and inflammation. While accelerated proteasomal degradation is an important tumorigenic mechanism deployed by several cancers, there is some ambiguity regarding the role of immunoproteasome induction in neoplastic transformation. Understanding the mechanistic and functional relevance of the immunoproteasome provides essential insights into developing targeted therapies, including overcoming resistance to standard proteasome inhibition and immunomodulation of the tumor microenvironment. In this review, we discuss the roles of the immunoproteasome in different cancers.
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Affiliation(s)
- Satyendra Chandra Tripathi
- Department of Biochemistry, All India Institute of Medical Sciences Nagpur, Nagpur 441108, MH, India;
- Correspondence: (S.C.T.); (E.J.O.)
| | - Disha Vedpathak
- Department of Biochemistry, All India Institute of Medical Sciences Nagpur, Nagpur 441108, MH, India;
| | - Edwin Justin Ostrin
- Department of General Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (S.C.T.); (E.J.O.)
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13
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Amdare N, Purcell AW, DiLorenzo TP. Noncontiguous T cell epitopes in autoimmune diabetes: From mice to men and back again. J Biol Chem 2021; 297:100827. [PMID: 34044020 PMCID: PMC8233151 DOI: 10.1016/j.jbc.2021.100827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
Type 1 diabetes (T1D) is a T cell-mediated autoimmune disease that affects the insulin-producing beta cells of the pancreatic islets. The nonobese diabetic mouse is a widely studied spontaneous model of the disease that has contributed greatly to our understanding of T1D pathogenesis. This is especially true in the case of antigen discovery. Upon review of existing knowledge concerning the antigens and peptide epitopes that are recognized by T cells in this model, good concordance is observed between mouse and human antigens. A fascinating recent illustration of the contribution of the nonobese diabetic mouse in the area of epitope identification is the discovery of noncontiguous CD4+ T cell epitopes. This novel epitope class is characterized by the linkage of an insulin-derived peptide to, most commonly, a fragment of a natural cleavage product of another beta cell secretory granule constituent. These so-called hybrid insulin peptides are also recognized by T cells in patients with T1D, although the precise mechanism for their generation has yet to be defined and is the subject of active investigation. Although evidence from the tumor immunology arena documented the existence of noncontiguous CD8+ T cell epitopes, generated by proteasome-mediated peptide splicing involving transpeptidation, such CD8+ T cell epitopes were thought to be a rare immunological curiosity. However, recent advances in bioinformatics and mass spectrometry have challenged this view. These developments, coupled with the discovery of hybrid insulin peptides, have spurred a search for noncontiguous CD8+ T cell epitopes in T1D, an exciting frontier area still in its infancy.
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Affiliation(s)
- Nitin Amdare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA; Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA; Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA; The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York, USA.
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15
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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: 11] [Impact Index Per Article: 3.7] [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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16
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Willimsky G, Beier C, Immisch L, Papafotiou G, Scheuplein V, Goede A, Holzhütter HG, Blankenstein T, Kloetzel PM. In vitro proteasome processing of neo-splicetopes does not predict their presentation in vivo. eLife 2021; 10:e62019. [PMID: 33875134 PMCID: PMC8154032 DOI: 10.7554/elife.62019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/15/2021] [Indexed: 12/25/2022] Open
Abstract
Proteasome-catalyzed peptide splicing (PCPS) of cancer-driving antigens could generate attractive neoepitopes to be targeted by T cell receptor (TCR)-based adoptive T cell therapy. Based on a spliced peptide prediction algorithm, TCRs were generated against putative KRASG12V- and RAC2P29L-derived neo-splicetopes with high HLA-A*02:01 binding affinity. TCRs generated in mice with a diverse human TCR repertoire specifically recognized the respective target peptides with high efficacy. However, we failed to detect any neo-splicetope-specific T cell response when testing the in vivo neo-splicetope generation and obtained no experimental evidence that the putative KRASG12V- and RAC2P29L-derived neo-splicetopes were naturally processed and presented. Furthermore, only the putative RAC2P29L-derived neo-splicetopes was generated by in vitro PCPS. The experiments pose severe questions on the notion that available algorithms or the in vitro PCPS reaction reliably simulate in vivo splicing and argue against the general applicability of an algorithm-driven 'reverse immunology' pipeline for the identification of cancer-specific neo-splicetopes.
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MESH Headings
- Animals
- Antigen Presentation
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Epitopes
- HEK293 Cells
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- Humans
- K562 Cells
- Mice
- Mice, Transgenic
- Mutation
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/metabolism
- Proof of Concept Study
- Proteasome Endopeptidase Complex/metabolism
- Protein Processing, Post-Translational
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/immunology
- Proto-Oncogene Proteins p21(ras)/metabolism
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- rac GTP-Binding Proteins/genetics
- rac GTP-Binding Proteins/immunology
- rac GTP-Binding Proteins/metabolism
- RAC2 GTP-Binding Protein
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Affiliation(s)
- Gerald Willimsky
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, partner site Berlin, Berlin, Germany
| | - Christin Beier
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lena Immisch
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, partner site Berlin, Berlin, Germany
- Humboldt-Universität zu Berlin, Berlin, Germany
| | - George Papafotiou
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, partner site Berlin, Berlin, Germany
| | - Vivian Scheuplein
- Max Delbrück Center for Molecular Medicine in Helmholtz Association, Berlin, Germany
| | - Andrean Goede
- Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hermann-Georg Holzhütter
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Blankenstein
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in Helmholtz Association, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Peter M Kloetzel
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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17
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20S proteasomes secreted by the malaria parasite promote its growth. Nat Commun 2021; 12:1172. [PMID: 33608523 PMCID: PMC7895969 DOI: 10.1038/s41467-021-21344-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Mature red blood cells (RBCs) lack internal organelles and canonical defense mechanisms, making them both a fascinating host cell, in general, and an intriguing choice for the deadly malaria parasite Plasmodium falciparum (Pf), in particular. Pf, while growing inside its natural host, the human RBC, secretes multipurpose extracellular vesicles (EVs), yet their influence on this essential host cell remains unknown. Here we demonstrate that Pf parasites, cultured in fresh human donor blood, secrete within such EVs assembled and functional 20S proteasome complexes (EV-20S). The EV-20S proteasomes modulate the mechanical properties of naïve human RBCs by remodeling their cytoskeletal network. Furthermore, we identify four degradation targets of the secreted 20S proteasome, the phosphorylated cytoskeletal proteins β-adducin, ankyrin-1, dematin and Epb4.1. Overall, our findings reveal a previously unknown 20S proteasome secretion mechanism employed by the human malaria parasite, which primes RBCs for parasite invasion by altering membrane stiffness, to facilitate malaria parasite growth. Plasmodium falciparum secretes extracellular vesicles (EVs) while growing inside red blood cells (RBCs). Here the authors show that these EVs contain assembled and functional 20S proteasome complexes that remodel the cytoskeleton of naïve human RBCs, priming the RBCs for parasite invasion.
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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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Dwivedi V, Yaniv K, Sharon M. Beyond cells: The extracellular circulating 20S proteasomes. Biochim Biophys Acta Mol Basis Dis 2020; 1867:166041. [PMID: 33338594 DOI: 10.1016/j.bbadis.2020.166041] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 01/08/2023]
Abstract
Accumulating evidence arising from numerous clinical studies indicate that assembled and functional 20S proteasome complexes circulate freely in plasma. Elevated levels of this core proteolytic complex have been found in the plasma of patients suffering from blood, skin and solid cancers, autoimmune disorders, trauma and sepsis. Moreover, in various diseases, there is a positive correlation between circulating 20S proteasome (c20S) levels and treatment efficacy and survival rates, suggesting the involvement of this under-studied c20S complex in pathophysiology. However, many aspects of this system remain enigmatic, as we still do not know the origin, biological role or mechanisms of extracellular transport and regulation of c20S proteasomes. In this review, we provide an overview of the current understanding of the c20S proteasome system and discuss the remaining gaps in knowledge.
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Affiliation(s)
- Vandita Dwivedi
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Karina Yaniv
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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20
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Gopanenko AV, Kosobokova EN, Kosorukov VS. Main Strategies for the Identification of Neoantigens. Cancers (Basel) 2020; 12:E2879. [PMID: 33036391 PMCID: PMC7600129 DOI: 10.3390/cancers12102879] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
Genetic instability of tumors leads to the appearance of numerous tumor-specific somatic mutations that could potentially result in the production of mutated peptides that are presented on the cell surface by the MHC molecules. Peptides of this kind are commonly called neoantigens. Their presence on the cell surface specifically distinguishes tumors from healthy tissues. This feature makes neoantigens a promising target for immunotherapy. The rapid evolution of high-throughput genomics and proteomics makes it possible to implement these techniques in clinical practice. In particular, they provide useful tools for the investigation of neoantigens. The most valuable genomic approach to this problem is whole-exome sequencing coupled with RNA-seq. High-throughput mass-spectrometry is another option for direct identification of MHC-bound peptides, which is capable of revealing the entire MHC-bound peptidome. Finally, structure-based predictions could significantly improve the understanding of physicochemical and structural features that affect the immunogenicity of peptides. The development of pipelines combining such tools could improve the accuracy of the peptide selection process and decrease the required time. Here we present a review of the main existing approaches to investigating the neoantigens and suggest a possible ideal pipeline that takes into account all modern trends in the context of neoantigen discovery.
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Affiliation(s)
| | | | - Vyacheslav S. Kosorukov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (A.V.G.); (E.N.K.)
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21
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Rolfs Z, Müller M, Shortreed MR, Smith LM, Bassani-Sternberg M. Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands". Sci Immunol 2020; 4:4/38/eaaw1622. [PMID: 31420320 DOI: 10.1126/sciimmunol.aaw1622] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
Abstract
There is still no convincing evidence for the frequent occurrence of posttranslationally spliced HLA-I peptides.
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Affiliation(s)
- Zach Rolfs
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Markus Müller
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Michal Bassani-Sternberg
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland. .,Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
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22
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Croft NP. Peptide Presentation to T Cells: Solving the Immunogenic Puzzle: Systems Immunology Profiling of Antigen Presentation for Prediction of CD8 + T Cell Immunogenicity. Bioessays 2020; 42:e1900200. [PMID: 31958157 DOI: 10.1002/bies.201900200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Indexed: 02/02/2023]
Abstract
The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real-time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic-to elicit a T cell response-has remained both enigmatic and a long sought-after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.
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Affiliation(s)
- Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
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