1
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Leong SL, Murdolo L, Maddumage JC, Koutsakos M, Kedzierska K, Purcell AW, Gras S, Grant EJ. Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes. Clin Transl Immunology 2024; 13:e1509. [PMID: 38737448 PMCID: PMC11087170 DOI: 10.1002/cti2.1509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Objectives Seasonal influenza viruses cause roughly 650 000 deaths annually despite available vaccines. CD8+ T cells typically recognise influenza-derived peptides from internal structural and non-structural influenza proteins and are an attractive avenue for future vaccine design as they could reduce the severity of disease following infection with diverse influenza strains. CD8+ T cells recognise peptides presented by the highly polymorphic Human Leukocyte Antigens class I molecules (HLA-I). Each HLA-I variant has distinct peptide binding preferences, representing a significant obstacle for designing vaccines that elicit CD8+ T cell responses across broad populations. Consequently, the rational design of a CD8+ T cell-mediated vaccine would require the identification of highly immunogenic peptides restricted to a range of different HLA molecules. Methods Here, we assessed the immunogenicity of six recently published novel influenza-derived peptides identified by mass-spectrometry and predicted to bind to the prevalent HLA-B*18:01 molecule. Results Using CD8+ T cell activation assays and protein biochemistry, we showed that 3/6 of the novel peptides were immunogenic in several HLA-B*18:01+ individuals and confirmed their HLA-B*18:01 restriction. We subsequently compared CD8+ T cell responses towards the previously identified highly immunogenic HLA-B*18:01-restricted NP219 peptide. Using X-ray crystallography, we solved the first crystal structures of HLA-B*18:01 presenting immunogenic influenza-derived peptides. Finally, we dissected the first TCR repertoires specific for HLA-B*18:01 restricted pathogen-derived peptides, identifying private and restricted repertoires against each of the four peptides. Conclusion Overall the characterisation of these novel immunogenic peptides provides additional HLA-B*18:01-restricted vaccine targets derived from the Matrix protein 1 and potentially the non-structural protein and the RNA polymerase catalytic subunit of influenza viruses.
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Affiliation(s)
- Samuel Liwei Leong
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Lawton Murdolo
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Janesha C Maddumage
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Stephanie Gras
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Emma J Grant
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
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2
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Wang M, Lei C, Wang J, Li Y, Li M. TripHLApan: predicting HLA molecules binding peptides based on triple coding matrix and transfer learning. Brief Bioinform 2024; 25:bbae154. [PMID: 38600667 PMCID: PMC11006794 DOI: 10.1093/bib/bbae154] [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: 12/26/2023] [Revised: 02/16/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding motifs. Based on the discovery, we make the preprocessing and coding closer to the natural biological process. Besides, due to the input being based on multiple types of features and the attention module focused on the BiGRU hidden layer, TripHLApan has learned more sequence level binding information. The application of transfer learning strategies ensures the accuracy of prediction results under special lengths (peptides in length 8) and model scalability with the data explosion. Compared with the current optimal models, TripHLApan exhibits strong predictive performance in various prediction environments with different positive and negative sample ratios. In addition, we validate the superiority and scalability of TripHLApan's predictive performance using additional latest data sets, ablation experiments and binding reconstitution ability in the samples of a melanoma patient. The results show that TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines. TripHLApan is publicly available at https://github.com/CSUBioGroup/TripHLApan.git.
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Affiliation(s)
- Meng Wang
- School of Computer Science and engineering, Central South University, Changsha 410083, China
| | - Chuqi Lei
- School of Computer Science and engineering, Central South University, Changsha 410083, China
| | - Jianxin Wang
- School of Computer Science and engineering, Central South University, Changsha 410083, China
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
| | - Min Li
- School of Computer Science and engineering, Central South University, Changsha 410083, China
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3
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Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569310. [PMID: 38077000 PMCID: PMC10705405 DOI: 10.1101/2023.11.29.569310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The precise prediction of Major Histocompatibility Complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning it with a specialized dataset comprised by exclusively high-resolution MHC-peptide crystal structures. This tailored approach aimed to address the generalist nature of AlphaFold's original training, which, while broad-ranging, lacked the granularity necessary for the high-precision demands of MHC-peptide interaction prediction. A comparative analysis was conducted against the homology-modeling-based method Pandora [13], as well as the AlphaFold multimer model [8]. Our results demonstrate that our fine-tuned model outperforms both in terms of RMSD (median value is 0.65 Å) but also provides enhanced predicted lDDT scores, offering a more reliable assessment of the predicted structures. These advances have substantial implications for computational immunology, potentially accelerating the development of novel therapeutics and vaccines by providing a more precise computational lens through which to view MHC-peptide interactions.
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Affiliation(s)
- Ernest Glukhov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Dmytro Kalitin
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Darya Stepanenko
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Yimin Zhu
- Department of Computer Science, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Thu Nguyen
- Department of Computer Science, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, 02215, MA, USA
| | - Ken A. Dill
- Department of Chemistry, Stony Brook University, Stony Brook, 11794, NY, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Dzmitry Padhorny
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
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Erez N, Achdout H, Yahalom-Ronen Y, Adutler-Lieber S, Bar-On L, Bar-Haim E, Politi B, Vitner EB, Tamir H, Melamed S, Paran N, Israely T. Identification of T-Cell Epitopes Using a Combined In-Silico and Experimental Approach in a Mouse Model for SARS-CoV-2. Curr Issues Mol Biol 2023; 45:7944-7955. [PMID: 37886945 PMCID: PMC10605721 DOI: 10.3390/cimb45100502] [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: 08/21/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Following viral infection, T-cells are crucial for an effective immune response to intracellular pathogens, including respiratory viruses. During the COVID-19 pandemic, diverse assays were required in pre-clinical trials to evaluate the immune response following vaccination against SARS-CoV-2 and assess the response following exposure to the virus. To assess the nature and potency of the cellular response to infection or vaccination, a reliable and specific activity assay was needed. A cellular activity assay based on the presentation of short peptides (epitopes) allows the identification of T cell epitopes displayed on different alleles of the MHC, shedding light on the strength of the immune response towards antigens and aiding in antigen design for vaccination. In this report, we describe two approaches for scanning T cell epitopes on the surface glycoprotein of the SARS-CoV-2 (spike), which is utilized for attachment and entry and serves as an antigen in many vaccine candidates. We demonstrate that epitope scanning is feasible using peptide libraries or computational scanning combined with a cellular activity assay. Our scans identified four CD8 T cell epitopes, including one novel undescribed epitope. These epitopes enabled us to establish a reliable T-cell response assay, which was examined and used in various experimental mouse models for SARS-CoV-2 infection and vaccination. These approaches could potentially aid in future antigen design for vaccination and establish cellular activity assays against uncharacterized antigens of emerging pathogens.
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Affiliation(s)
- Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Shimrit Adutler-Lieber
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Liat Bar-On
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (L.B.-O.); (E.B.-H.)
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (L.B.-O.); (E.B.-H.)
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Einat B. Vitner
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
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5
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Chow DT, Rardin MJ. Identification and Mitigation of Defensins in the Immunopurification of Peptide MHC-I Antigens from Lung Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1590-1597. [PMID: 34645265 DOI: 10.1021/jasms.1c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The class I major histocompatibility (MHC-I) complex is a set of diverse cell surface receptors encoded by the human leukocyte antigen gene complex. These receptors present intracellular antigens to cytotoxic T cells providing information on the state and health of cells. Changes in the immunopeptidome during cancer may provide novel targets for therapeutic intervention. To understand how the tumor immunopeptidome is altered, we developed a mass spectrometry (MS) based platform for isolating and identifying MHC-I peptide antigens in lung tumors. In the course of our work, we encountered several large unknown peptide contaminants which had not been previously reported. To understand the source of these major contaminants, we isolated them using offline fractionation and identified them by liquid chromatography-tandem mass spectrometry (LC-MS/MS) as members of the host defense protein family known as the defensins. To mitigate their detrimental effects, we modified our "Original" data-dependent acquisition (DDA) MS method to narrowly target the MHC-I peptides based on their physical properties including charge state and molecular weight ("z state" DDA), evaluated field asymmetric ion mobility spectrometry to attempt gas-phase separation prior to MS analysis, and developed an immunodepletion approach using defensin specific antibodies. This modified approach improves peptide identification and reduces the impact of defensin contamination in lung tissue samples.
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Affiliation(s)
- David T Chow
- Amgen Research, Discovery Attribute Sciences Amgen, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Amgen Research, Discovery Attribute Sciences Amgen, South San Francisco, California 94080, United States
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6
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Wei X, Li S, Wang S, Feng G, Xie X, Li Z, Zhang N. Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length. Front Immunol 2022; 13:820881. [PMID: 35296092 PMCID: PMC8918614 DOI: 10.3389/fimmu.2022.820881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/10/2022] [Indexed: 12/03/2022] Open
Abstract
Polymorphisms can affect MHC-I binding peptide length preferences, but the mechanism remains unclear. Using a random peptide library combined with LC-MS/MS and de novo sequencing (RPLD-MS) technique, we found that two swine MHC-I molecules with high sequence homology, SLA-1*04:01 and SLA-1*13:01, had significant differences in length preference of the binding peptides. Compared with SLA-1*04:01, SLA-1*13:01 binds fewer short peptides with 8-10 amino acids, but more long peptides. A dodecapeptide peptide (RW12) can bind to both SLA-1*04:01 and SLA-1*13:01, but their crystal structures indicate that the binding modes are significantly different: the entirety of RW12 is embedded in the peptide binding groove of SLA-1*04:01, but it obviously protrudes from the peptide binding groove of SLA-1*13:01. The structural comparative analysis showed that only five differential amino acids of SLA-1*13:01 and SLA-1*04:01 were involved in the binding of RW12, and they determine the different ways of long peptides binding, which makes SLA-1*04:01 more restrictive on long peptides than SLA-1*13:01, and thus binds fewer long peptides. In addition, we found that the N terminus of RW12 extends from the groove of SLA-1*13:01, which is similar to the case previously found in SLA-1*04:01. However, this unusual peptide binding does not affect their preferences of binding peptide length. Our study will be helpful to understand the effect of polymorphisms on the length distribution of MHC-I binding peptides, and to screen SLA-I-restricted epitopes of different lengths and to design effective epitope vaccines.
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Affiliation(s)
- Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Health Commission (NHC) Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shen Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Suqiu Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guojiao Feng
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaoli Xie
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhuolin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
- *Correspondence: Nianzhi Zhang,
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7
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Barbosa CRR, Barton J, Shepherd AJ, Mishto M. Mechanistic diversity in MHC class I antigen recognition. Biochem J 2021; 478:4187-4202. [PMID: 34940832 PMCID: PMC8786304 DOI: 10.1042/bcj20200910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.
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Affiliation(s)
- Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| | - Justin Barton
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Adrian J. Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
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8
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Broad-Based Influenza-Specific CD8 + T Cell Response without the Typical Immunodominance Hierarchy and Its Potential Implication. Viruses 2021; 13:v13061080. [PMID: 34198851 PMCID: PMC8229067 DOI: 10.3390/v13061080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Syngeneic murine systems have pre-fixed MHC, making them an imperfect model for investigating the impact of MHC polymorphism on immunodominance in influenza A virus (IAV) infections. To date, there are few studies focusing on MHC allelic differences and its impact on immunodominance even though it is well documented that an individual’s HLA plays a significant role in determining immunodominance hierarchy. Here, we describe a broad-based CD8+ T cell response in a healthy individual to IAV infection rather than a typical immunodominance hierarchy. We used a systematic antigen screen approach combined with epitope prediction to study such a broad CD8+ T cell response to IAV infection. We show CD8+ T cell responses to nine IAV proteins and identify their minimal epitope sequences. These epitopes are restricted to HLA-B*44:03, HLA-A*24:02 and HLA-A*33:03 and seven out of the nine epitopes are novel (NP319–330# (known and demonstrated minimal epitope positions are subscripted; otherwise, amino acid positions are shown as normal text (for example NP 319–330 or NP 313–330)), M1124–134, M27–15, NA337–346, PB239–49, HA445–453 and NS1195–203). Additionally, most of these novel epitopes are highly conserved among H1N1 and H3N2 strains that circulated in Australia and other parts of the world.
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9
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Alam A, Khan A, Imam N, Siddiqui MF, Waseem M, Malik MZ, Ishrat R. Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach. Brief Bioinform 2021; 22:1309-1323. [PMID: 33285567 PMCID: PMC7799329 DOI: 10.1093/bib/bbaa340] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.
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Affiliation(s)
- Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia University, New Delhi 110025, India
| | - Arbaaz Khan
- Department of computer science, Jamia Millia Islamia University, New Delhi, India
| | - Nikhat Imam
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia University, New Delhi, India
| | | | - Mohd Waseem
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md Zubbair Malik
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia University, New Delhi, India
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10
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Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires. Int J Mol Sci 2021; 22:ijms22041625. [PMID: 33562731 PMCID: PMC7915266 DOI: 10.3390/ijms22041625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022] Open
Abstract
The distinct properties of allo-reactive T-cell repertoires are not well understood. To investigate whether auto-reactive and allo-reactive T-cell repertoires encoded distinct properties, we used dextramer enumeration, enrichment, single-cell T-cell receptor (TCR) sequencing and multiparameter analysis. We found auto-reactive and allo-reactive T-cells differed in mean ex vivo frequency which was antigen dependent. Allo-reactive T-cells showed clear differences in TCR architecture, with enriched usage of specific T-cell receptor variable (TRBJ) genes and broader use of T-cell receptor variable joining (TRBJ) genes. Auto-reactive T-cell repertoires exhibited complementary determining regions three (CDR3) lengths using a Gaussian distribution whereas allo-reactive T-cell repertoires exhibited distorted patterns in CDR3 length. CDR3 loops from allo-reactive T-cells showed distinct physical-chemical properties, tending to encode loops that were more acidic in charge. Allo-reactive T-cell repertoires differed in diversity metrics, tending to show increased overall diversity and increased homogeneity between repertoires. Motif analysis of CDR3 loops showed allo-reactive T-cell repertoires differed in motif preference which included broader motif use. Collectively, these data conclude that allo-reactive T-cell repertoires are indeed different to auto-reactive repertoires and provide tangible metrics for further investigations and validation. Given that the antigens studied here are overexpressed on multiple cancers and that allo-reactive TCRs often show increased ligand affinity, this new TCR bank also has translational potential for adoptive cell therapy, soluble TCR-based therapy and rational TCR design.
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11
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Lee CH, Pinho MP, Buckley PR, Woodhouse IB, Ogg G, Simmons A, Napolitani G, Koohy H. Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains. Front Immunol 2020; 11:579480. [PMID: 33250893 PMCID: PMC7676914 DOI: 10.3389/fimmu.2020.579480] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariana Pereira Pinho
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul R. Buckley
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Isaac B. Woodhouse
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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12
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HIV-1 induced changes in HLA-C*03 : 04-presented peptide repertoires lead to reduced engagement of inhibitory natural killer cell receptors. AIDS 2020; 34:1713-1723. [PMID: 32501836 PMCID: PMC8635260 DOI: 10.1097/qad.0000000000002596] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Viral infections influence intracellular peptide repertoires available for presentation by HLA-I. Alterations in HLA-I/peptide complexes can modulate binding of killer immunoglobuline-like receptors (KIRs) and thereby the function of natural killer (NK) cells. Although multiple studies have provided evidence that HLA-I/KIR interactions play a role in HIV-1 disease progression, the consequence of HIV-1 infection for HLA-I/KIR interactions remain largely unknown. DESIGN We determined changes in HLA-I presented peptides resulting from HIV-1-infection of primary human CD4 T cells and assessed the impact of changes in peptide repertoires on HLA-I/KIR interactions. METHODS Liquid chromatography-coupled tandem mass spectrometry to identify HLA-I presented peptides, cell-based in-vitro assays to evaluate functional consequences of alterations in immunopeptidome and atomistic molecular dynamics simulations to confirm experimental data. RESULTS A total of 583 peptides exclusively presented on HIV-1-infected cells were identified, of which only 0.2% represented HIV-1 derived peptides. Focusing on HLA-C*03 : 04/KIR2DL3 interactions, we observed that HLA-C*03 : 04-presented peptides derived from noninfected CD4 T cells mediated stronger binding of inhibitory KIR2DL3 than peptides derived from HIV-1-infected cells. Furthermore, the most abundant peptide presented by HLA-C*03 : 04 on noninfected CD4 T cells (VIYPARISL) mediated the strongest KIR2DL3-binding, while the most abundant peptide presented on HIV-1-infected cells (YAIQATETL) did not mediate KIR2DL3-binding. Molecular dynamics simulations of HLA-C*03 : 04/KIR2DL3 interactions in the context of these two peptides revealed that VIYPARISL significantly enhanced the HLA-C*03 : 04/peptide contact area to KIR2DL3 compared with YAIQATETL. CONCLUSION These data demonstrate that HIV-1 infection-induced changes in HLA-I-presented peptides can reduce engagement of inhibitory KIRs, providing a mechanism for enhanced activation of NK cells by virus-infected cells.
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Picarda E, Bézie S, Usero L, Ossart J, Besnard M, Halim H, Echasserieau K, Usal C, Rossjohn J, Bernardeau K, Gras S, Guillonneau C. Cross-Reactive Donor-Specific CD8 + Tregs Efficiently Prevent Transplant Rejection. Cell Rep 2020; 29:4245-4255.e6. [PMID: 31875536 DOI: 10.1016/j.celrep.2019.11.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 10/14/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
To reduce the use of non-specific immunosuppressive drugs detrimental to transplant patient health, therapies in development aim to achieve antigen-specific tolerance by promoting antigen-specific regulatory T cells (Tregs). However, identification of the natural antigens recognized by Tregs and the contribution of their dominance in transplantation has been challenging. We identify epitopes derived from distinct major histocompatibility complex (MHC) class II molecules, sharing a 7-amino acid consensus sequence positioned in a central mobile section in complex with MHC class I, recognized by cross-reactive CD8+ Tregs, enriched in the graft. Antigen-specific CD8+ Tregs can be induced in vivo with a 16-amino acid-long peptide to trigger transplant tolerance. Peptides derived from human HLA class II molecules, harboring the rat consensus sequence, also activate and expand human CD8+ Tregs, suggesting its potential in human transplantation. Altogether, this work should facilitate the development of therapies with peptide epitopes for transplantation and improve our understanding of CD8+ Treg recognition.
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Affiliation(s)
- Elodie Picarda
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Séverine Bézie
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Lorena Usero
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Jason Ossart
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Marine Besnard
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Hanim Halim
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Klara Echasserieau
- Plateforme de protéines recombinantes P2R IFR26, CRCNA-UMR892 INSERM, Nantes, France
| | - Claire Usal
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Karine Bernardeau
- Plateforme de protéines recombinantes P2R IFR26, CRCNA-UMR892 INSERM, Nantes, France
| | - Stéphanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Carole Guillonneau
- Nantes Université, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.
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14
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Assmus LM, Guan J, Wu T, Farenc C, Sng XYX, Zareie P, Nguyen A, Nguyen AT, Tscharke DC, Thomas PG, Rossjohn J, Gras S, Croft NP, Purcell AW, La Gruta NL. Overlapping Peptides Elicit Distinct CD8 + T Cell Responses following Influenza A Virus Infection. THE JOURNAL OF IMMUNOLOGY 2020; 205:1731-1742. [PMID: 32868409 DOI: 10.4049/jimmunol.2000689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022]
Abstract
The presentation of pathogen-derived peptides on MHC class I molecules is essential for the initiation of adaptive CD8+ T cell immunity, which in turn is critical for effective control of many significant human infections. The identification of immunogenic pathogen-derived epitopes and a detailed understanding of how they are recognized by TCRs is essential for the design of effective T cell-based vaccines. In this study, we have characterized the T cell recognition and immune responses in mice to two naturally presented influenza A virus-derived peptides previously identified from virally infected cells via mass spectrometry. These neuraminidase-derived peptides, NA181-190 (SGPDNGAVAV) and NA181-191 (SGPDNGAVAVL), are completely overlapping with the exception of a 1 aa extension at the C terminus of the longer peptide. This minor peptidic difference results in the induction of two completely independent and non-cross-reactive T cell populations that show distinct functional characteristics after influenza A virus infection of B6 mice. We show that the unique TCR reactivity to the overlapping peptides is present in the naive repertoire prior to immune expansion in B6 mice. Moreover, we provide a structural explanation underlying the distinct CD8+ T cell reactivities, which reinforces the concept that peptide length is a key determinant of Ag specificity in CD8+ T cell responses.
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Affiliation(s)
- Lisa M Assmus
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.,Institute of Experimental Immunology, University Hospital Bonn, 53105 Bonn, Germany
| | - Jing Guan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ting Wu
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Carine Farenc
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Pirooz Zareie
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Angela Nguyen
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Andrea T Nguyen
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash 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; and.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
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15
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Liu G, Carter B, Bricken T, Jain S, Viard M, Carrington M, Gifford DK. Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions. Cell Syst 2020; 11:131-144.e6. [PMID: 32721383 PMCID: PMC7384425 DOI: 10.1016/j.cels.2020.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/31/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022]
Abstract
We present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations for SARS-CoV-2. Our approach optimizes the presentation likelihood of a diverse set of vaccine peptides conditioned on a target human-population HLA haplotype distribution and expected epitope drift. Our proposed SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA average hits per person (≥ 1 peptide: 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our proposed MHC class II vaccine formulations provide 97.21% predicted coverage with at least five vaccine peptide-HLA average hits per person with all peptides having an observed mutation probability of ≤ 0.001. We provide an open-source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts here: https://github.com/gifford-lab/optivax.
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Affiliation(s)
- Ge Liu
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; MIT Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Brandon Carter
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; MIT Electrical Engineering and Computer Science, Cambridge, MA, USA
| | | | - Siddhartha Jain
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - David K Gifford
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; MIT Electrical Engineering and Computer Science, Cambridge, MA, USA; MIT Biological Engineering, Cambridge, MA, USA.
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16
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Liu G, Carter B, Bricken T, Jain S, Viard M, Carrington M, Gifford DK. Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511351 DOI: 10.1101/2020.05.16.088989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations, and we find for SARS-CoV-2 that it provides superior predicted display of viral epitopes by MHC class I and MHC class II molecules over populations when compared to other candidate vaccines. Our method is robust to idiosyncratic errors in the prediction of MHC peptide display and considers target population HLA haplotype frequencies during optimization. To minimize clinical development time our methods validate vaccines with multiple peptide presentation algorithms to increase the probability that a vaccine will be effective. We optimize an objective function that is based on the presentation likelihood of a diverse set of vaccine peptides conditioned on a target population HLA haplotype distribution and expected epitope drift. We produce separate peptide formulations for MHC class I loci (HLA-A, HLA-B, and HLA-C) and class II loci (HLA-DP, HLA-DQ, and HLA-DR) to permit signal sequence based cell compartment targeting using nucleic acid based vaccine platforms. Our SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA hits on average in an individual (≥ 1 peptide 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our MHC class II vaccine formulations provide 90.17% predicted coverage with at least five vaccine peptide-HLA hits on average in an individual with all peptides having observed mutation probability ≤ 0.001. We evaluate 29 previously published peptide vaccine designs with our evaluation tool with the requirement of having at least five vaccine peptide-HLA hits per individual, and they have a predicted maximum of 58.51% MHC class I coverage and 71.65% MHC class II coverage given haplotype based analysis. We provide an open source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts.
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17
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Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H, Hartigan CR, Zhang W, Braun DA, Ligon KL, Bachireddy P, Zervantonakis IK, Rosenbluth JM, Ouspenskaia T, Law T, Justesen S, Stevens J, Lane WJ, Eisenhaure T, Lan Zhang G, Clauser KR, Hacohen N, Carr SA, Wu CJ, Keskin DB. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol 2020; 38:199-209. [PMID: 31844290 PMCID: PMC7008090 DOI: 10.1038/s41587-019-0322-9] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022]
Abstract
Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.
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Affiliation(s)
- Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Phuong M Le
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Letitia W Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A Braun
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Neuropathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Pavan Bachireddy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Travis Law
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - William J Lane
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Guang Lan Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, MA, USA.
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA.
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18
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Li L, Batliwala M, Bouvier M. ERAP1 enzyme-mediated trimming and structural analyses of MHC I-bound precursor peptides yield novel insights into antigen processing and presentation. J Biol Chem 2019; 294:18534-18544. [PMID: 31601650 PMCID: PMC6901306 DOI: 10.1074/jbc.ra119.010102] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/20/2019] [Indexed: 01/07/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 critically shape the major histocompatibility complex I (MHC I) immunopeptidome. The ERAPs remove N-terminal residues from antigenic precursor peptides and generate optimal-length peptides (i.e. 8-10-mers) to fit into the MHC class I groove. It is therefore intriguing that MHC class I molecules can present N-terminally extended peptides on the cell surface that can elicit CD8+ T-cell responses. This observation likely reflects gaps in our understanding of how antigens are processed by the ERAP enzymes. To better understand ERAPs' function in antigen processing, here we generated a nested set of N-terminally extended 10-20-mer peptides (RA) n AAKKKYCL covalently bound to the human leukocyte antigen (HLA)-B*0801. We used X-ray crystallography, thermostability assessments, and an ERAP1-trimming assay to characterize these complexes. The X-ray structures determined at 1.40-1.65 Å resolutions revealed that the residue extensions (RA) n unexpectedly protrude out of the A pocket of HLA-B*0801, whereas the AAKKKYCL core of all peptides adopts similar, bound conformations. HLA-B*0801 residue 62 was critical to open the A pocket. We also show that HLA-B*0801 and antigenic precursor peptides form stable complexes. Finally, ERAP1-mediated trimming of the MHC I-bound peptides required a minimal length of 14 amino acids. We propose a mechanistic model explaining how ERAP1-mediated trimming of MHC I-bound peptides in cells can generate peptides of canonical as well as noncanonical lengths that still serve as stable MHC I ligands. Our results provide a framework to better understand how the ERAP enzymes influence the MHC I immunopeptidome.
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Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612, To whom correspondence should be addressed:
Dept. of Microbiology and Immunology, University of Illinois at Chicago, 909 S. Wolcott Ave., Chicago, IL 60612. Tel.:
312-355-0664; E-mail:
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19
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Zhao T, Cheng L, Zang T, Hu Y. Peptide-Major Histocompatibility Complex Class I Binding Prediction Based on Deep Learning With Novel Feature. Front Genet 2019; 10:1191. [PMID: 31850062 PMCID: PMC6892951 DOI: 10.3389/fgene.2019.01191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/28/2019] [Indexed: 12/27/2022] Open
Abstract
Peptide-based vaccine development needs accurate prediction of the binding affinity between major histocompatibility complex I (MHC I) proteins and their peptide ligands. Nowadays more and more machine learning methods have been developed to predict binding affinity and some of them have become the popular tools. However most of them are designed by the shallow neural networks. Bengio said that deep neural networks can learn better fits with less data than shallow neural networks. In our case, some of the alleles only have dozens of peptide data. In addition, we transform each peptide into a characteristic matrix and input it into the model. As we know when dealing with the problem that the input is a matrix, convolutional neural network (CNN) can find the most critical features by itself. Obviously, compared with the traditional neural network model, CNN is more suitable for predicting binding affinity. Different from the previous studies which are based on blocks substitution matrix (BLOSUM), we used novel feature to do the prediction. Since we consider that the order of the sequence, hydropathy index, polarity and the length of the peptide could affect the binding affinity and the properties of these amino acids are key factors for their binding to MHC, we extracted these information from each peptide. In order to make full use of the data we have obtained, we have integrated different lengths of peptides into 15mer based on the binding mode of peptide to MHC I. In order to demonstrate that our method is reliable to predict peptide-MHC binding, we compared our method with several popular methods. The experiments show the superiority of our method.
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Affiliation(s)
- Tianyi Zhao
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tianyi Zang
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yang Hu
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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20
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Zhang X, Qi Y, Zhang Q, Liu W. Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy. Biomed Pharmacother 2019; 120:109542. [PMID: 31629254 DOI: 10.1016/j.biopha.2019.109542] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
One of the challenges for cancer vaccine and adoptive T-cell-based immunotherapy is to identify the major histocompatibility complex (MHC)-associated non-self neoantigens recognized by T cells. T cell epitope in silico prediction algorithms have been widely used for neoantigen prediction; nonetheless, this platform lacks the experimental evidence of directly identification of the presented epitopes on cell surface. Currently, mass spectrometry (MS)-based proteomics is an advanced analytical technology for large-scale peptide sequencing, which has become a powerful tool for directly profiling the immunopeptidome presented by MHC molecules. Integrating with next-generation sequencing, proteogenomic analysis provides the "gold standard" for neoantigen identification at protein level. This method discovers the tumor-specific neoantigens derived from somatic mutations, proteasome splicing, noncoding RNA, and post-translational modified antigens. Herein, we review basis of antigen processing and presentation, tumor antigen classification, existing approaches for neoantigen discovery, quantitative proteomics, epitope prediction programs, and advantages and drawbacks of proteomics workflow for MHC immunopeptidome profiling. Furthermore, we summarize 40 recently published reports addressing the fundamental theory, breakthrough and most advanced updates for the mass spectrometry-based neoantigen discovery for cancer immunotherapy.
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Affiliation(s)
- Xiaomei Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Yue Qi
- Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA
| | - Qi Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA.
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21
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Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses. Nat Commun 2019; 10:2846. [PMID: 31253788 PMCID: PMC6599079 DOI: 10.1038/s41467-019-10661-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/24/2019] [Indexed: 11/08/2022] Open
Abstract
The magnitude of T cell responses to infection is a function of the naïve T cell repertoire combined with the context and duration of antigen presentation. Using mass spectrometry, we identify and quantify 21 class 1 MHC-restricted influenza A virus (IAV)-peptides following either direct or cross-presentation. All these peptides, including seven novel epitopes, elicit T cell responses in infected C57BL/6 mice. Directly presented IAV epitopes maintain their relative abundance across distinct cell types and reveal a broad range of epitope abundances. In contrast, cross-presented epitopes are more uniform in abundance. We observe a clear disparity in the abundance of the two key immunodominant IAV antigens, wherein direct infection drives optimal nucleoprotein (NP)366–374 presentation, while cross-presentation is optimal for acid polymerase (PA)224–233 presentation. The study demonstrates how assessment of epitope abundance in both modes of antigen presentation is necessary to fully understand the immunogenicity and response magnitude to T cell epitopes. CTL responses are critical in protection against pathogens. Here, using mass spectrometry and flow cytometry, the authors characterize the kinetics of influenza A virus class I MHC epitopes cross-presented in professional antigen presenting cells and identify new epitopes that elicit T cell responses in infected mice.
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22
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de Araujo CB, Heimann AS, Remer RA, Russo LC, Colquhoun A, Forti FL, Ferro ES. Intracellular Peptides in Cell Biology and Pharmacology. Biomolecules 2019; 9:biom9040150. [PMID: 30995799 PMCID: PMC6523763 DOI: 10.3390/biom9040150] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 12/11/2022] Open
Abstract
Intracellular peptides are produced by proteasomes following degradation of nuclear, cytosolic, and mitochondrial proteins, and can be further processed by additional peptidases generating a larger pool of peptides within cells. Thousands of intracellular peptides have been sequenced in plants, yeast, zebrafish, rodents, and in human cells and tissues. Relative levels of intracellular peptides undergo changes in human diseases and also when cells are stimulated, corroborating their biological function. However, only a few intracellular peptides have been pharmacologically characterized and their biological significance and mechanism of action remains elusive. Here, some historical and general aspects on intracellular peptides' biology and pharmacology are presented. Hemopressin and Pep19 are examples of intracellular peptides pharmacologically characterized as inverse agonists to cannabinoid type 1 G-protein coupled receptors (CB1R), and hemopressin fragment NFKF is shown herein to attenuate the symptoms of pilocarpine-induced epileptic seizures. Intracellular peptides EL28 (derived from proteasome 26S protease regulatory subunit 4; Rpt2), PepH (derived from Histone H2B type 1-H), and Pep5 (derived from G1/S-specific cyclin D2) are examples of peptides that function intracellularly. Intracellular peptides are suggested as biological functional molecules, and are also promising prototypes for new drug development.
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Affiliation(s)
- Christiane B de Araujo
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Butantan Institute, São Paulo SP 05503-900, Brazil.
| | | | | | - Lilian C Russo
- Department of Biochemistry, Chemistry Institute, University of São Paulo 1111, São Paulo 05508-000, Brazil.
| | - Alison Colquhoun
- Department of Cell and Developmental Biology, University of São Paulo (USP), São Paulo 05508-000, Brazil.
| | - Fábio L Forti
- Department of Biochemistry, Chemistry Institute, University of São Paulo 1111, São Paulo 05508-000, Brazil.
| | - Emer S Ferro
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil.
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HLA-F*01:01 presents peptides with N-terminal flexibility and a preferred length of 16 residues. Immunogenetics 2019; 71:353-360. [PMID: 30941482 PMCID: PMC6525141 DOI: 10.1007/s00251-019-01112-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022]
Abstract
HLA-F belongs to the non-classical HLA-Ib molecules with a marginal polymorphic nature and tissue-restricted distribution. HLA-F is a ligand of the NK cell receptor KIR3DS1, whose activation initiates an antiviral downstream immune response and lead to delayed disease progression of HIV-1. During the time course of HIV infection, the expression of HLA-F is upregulated while its interaction with KIR3DS1 is diminished. Understanding HLA-F peptide selection and presentation is essential to a comprehensive understanding of this dynamic immune response and the molecules function. In this study, we were able to recover stable pHLA-F*01:01 complexes and analyze the characteristics of peptides naturally presented by HLA-F. These HLA-F-restricted peptides exhibit a non-canonical length without a defined N-terminal anchor. The peptide characteristics lead to a unique presentation profile and influence the stability of the protein. Furthermore, we demonstrate that almost all source proteins of HLA-F-restricted peptides are described to interact with HIV proteins. Understanding the balance switch between HLA-Ia and HLA-F expression and peptide selection will support to understand the role of HLA-F in viral pathogenesis.
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24
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Broad CD8 + T cell cross-recognition of distinct influenza A strains in humans. Nat Commun 2018; 9:5427. [PMID: 30575715 PMCID: PMC6303473 DOI: 10.1038/s41467-018-07815-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/23/2018] [Indexed: 11/29/2022] Open
Abstract
Newly-emerged and vaccine-mismatched influenza A viruses (IAVs) result in a rapid global spread of the virus due to minimal antibody-mediated immunity. In that case, established CD8+ T-cells can reduce disease severity. However, as mutations occur sporadically within immunogenic IAV-derived T-cell peptides, understanding of T-cell receptor (TCRαβ) cross-reactivity towards IAV variants is needed for a vaccine design. Here, we investigate TCRαβ cross-strain recognition across IAV variants within two immunodominant human IAV-specific CD8+ T-cell epitopes, HLA-B*37:01-restricted NP338-346 (B37-NP338) and HLA-A*01:01-restricted NP44-52 (A1-NP44). We find high abundance of cross-reactive TCRαβ clonotypes recognizing distinct IAV variants. Structures of the wild-type and variant peptides revealed preserved conformation of the bound peptides. Structures of a cross-reactive TCR-HLA-B37-NP338 complex suggest that the conserved conformation of the variants underpins TCR cross-reactivity. Overall, cross-reactive CD8+ T-cell responses, underpinned by conserved epitope structure, facilitates recognition of distinct IAV variants, thus CD8+ T-cell-targeted vaccines could provide protection across different IAV strains. Mutations within immunological epitope containing regions of influenza A virus can impair the established immune response between influenza strains and could impact rational vaccine design. Here Grant et al. examine the presence, structural impact and cross reactivity of two human immunodominant influenza epitope variants.
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25
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Dhanda SK, Vaughan K, Schulten V, Grifoni A, Weiskopf D, Sidney J, Peters B, Sette A. Development of a novel clustering tool for linear peptide sequences. Immunology 2018; 155:331-345. [PMID: 30014462 PMCID: PMC6187223 DOI: 10.1111/imm.12984] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 02/06/2023] Open
Abstract
Epitopes identified in large-scale screens of overlapping peptides often share significant levels of sequence identity, complicating the analysis of epitope-related data. Clustering algorithms are often used to facilitate these analyses, but available methods are generally insufficient in their capacity to define biologically meaningful epitope clusters in the context of the immune response. To fulfil this need we developed an algorithm that generates epitope clusters based on representative or consensus sequences. This tool allows the user to cluster peptide sequences on the basis of a specified level of identity by selecting among three different method options. These include the 'clique method', in which all members of the cluster must share the same minimal level of identity with each other, and the 'connected graph method', in which all members of a cluster must share a defined level of identity with at least one other member of the cluster. In cases where it is not possible to define a clear consensus sequence with the connected graph method, a third option provides a novel 'cluster-breaking algorithm' for consensus sequence driven sub-clustering. Herein we demonstrate the tool's clustering performance and applicability using (i) a selection of dengue virus epitopes for the 'clique method', (ii) sets of allergen-derived peptides from related species for the 'connected graph method' and (iii) large data sets of eluted ligand, major histocompatibility complex binding and T-cell recognition data captured within the Immune Epitope Database (IEDB) with the newly developed 'cluster-breaking algorithm'. This novel clustering tool is accessible at http://tools.iedb.org/cluster2/.
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Affiliation(s)
- Sandeep K. Dhanda
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Kerrie Vaughan
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Veronique Schulten
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Alba Grifoni
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Daniela Weiskopf
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - John Sidney
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Bjoern Peters
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
- Department of MedicineUniversity of CaliforniaSan DiegoCAUSA
| | - Alessandro Sette
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
- Department of MedicineUniversity of CaliforniaSan DiegoCAUSA
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27
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Abstract
Human leukocyte antigen (HLA)-I molecules generally bind short peptides (8–10 amino acids), although extended HLA-I restricted peptides (>10 amino acids) can be presented to T cells. However, the function of such extended HLA-I epitopes in tumour immunity, and how they would be recognised by T-cell receptors (TCR) remains unclear. Here we show that the structures of two distinct TCRs (TRAV4+TRAJ21+-TRBV28+TRBJ2-3+ and TRAV4+TRAJ8+-TRBV9+TRBJ2-1+), originating from a polyclonal T-cell repertoire, bind to HLA-B*07:02, presenting a 13-amino-acid-long tumour-associated peptide, NY-ESO-160–72. Comparison of the structures reveals that the two TCRs differentially binds NY-ESO-160–72–HLA-B*07:02 complex, and induces differing extent of conformational change of the NY-ESO-160–72 epitope. Accordingly, polyclonal TCR usage towards an extended HLA-I restricted tumour epitope translates to differing TCR recognition modes, whereby extensive flexibility at the TCR–pHLA-I interface engenders recognition. Human leukocyte antigen (HLA) presents peptides to activate T cells, but many aspects in the T cell receptor (TCR)/HLA interaction remain unclear. Here the authors show, via structural data, that two TCRs differentially recognize the same tumour peptide/HLA complex and induce contrasting conformation changes of the peptide.
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28
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Gravett AM, Trautwein N, Stevanović S, Dalgleish AG, Copier J. Gemcitabine alters the proteasome composition and immunopeptidome of tumour cells. Oncoimmunology 2018; 7:e1438107. [PMID: 29930882 PMCID: PMC5990974 DOI: 10.1080/2162402x.2018.1438107] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 01/05/2023] Open
Abstract
The antigenic makeup of tumour cells can have a profound effect on the progression of cancer and success of immunotherapies. Therefore, one strategy to improve the efficacy of cancer treatments is to augment the antigens displayed by tumours. The present study explores how the recognition of tumour cells may be altered by non-cytotoxic concentrations of gemcitabine (GEM). Testing a panel of chemotherapeutics in human cancer cell lines in vitro, it was found that GEM increased surface expression of HLA-A,B,C and that underlying this were specific increases in β-2-microglobulin and immunoproteasome subunit proteins. Furthermore, the peptide antigen repertoire displayed on HLA class I was altered, revealing a number of novel antigens, many of which that were derived from proteins involved in the DNA-damage response. Changes in the nature of the peptide antigens eluted from HLA-A,B,C after GEM treatment consisted of amino acid anchor-residue modifications and changes in peptide length which rendered peptides likely to favour alternative HLA-alleles and increased their predicted immunogenicity. Signalling through the MAPK/ERK and NFκB/RelB pathways was associated with these changes. These data may explain observations made in previous in vivo studies, advise as to which antigens should be used in future vaccination protocols and reinforce the idea that chemotherapy and immunotherapy could be used in combination.
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Affiliation(s)
- A M Gravett
- Institute for infection and immunity, St George's, University of London, London, UK
| | - N Trautwein
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - S Stevanović
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - A G Dalgleish
- Institute for infection and immunity, St George's, University of London, London, UK
| | - J Copier
- Institute for infection and immunity, St George's, University of London, London, UK
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29
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Yuliwulandari R, Kristin E, Prayuni K, Sachrowardi Q, Suyatna FD, Menaldi SL, Wichukchinda N, Mahasirimongkol S, Cavallari LH. Association of the HLA-B alleles with carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis in the Javanese and Sundanese population of Indonesia: the important role of the HLA-B75 serotype. Pharmacogenomics 2017; 18:1643-1648. [PMID: 29053440 PMCID: PMC5753619 DOI: 10.2217/pgs-2017-0103] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Carbamazepine (CBZ) is a common cause of life-threatening cutaneous adverse drug reactions such as Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Previous studies have reported a strong association between the HLA genotype and CBZ-induced SJS/TEN. We investigated the association between the HLA genotype and CBZ-induced SJS/TEN in Javanese and Sundanese patients in Indonesia. Nine unrelated patients with CBZ-induced SJS/TEN and 236 healthy Javanese and Sundanese controls were genotyped for HLA-B and their allele frequencies were compared. The HLA-B*15:02 allele was found in 66.7% of the patients with CBZ-induced SJS/TEN, but only in 29.4% of tolerant control (p = 0.029; odds ratio [OR]: 6.5; 95% CI: 1.2-33.57) and 22.9% of healthy controls (p = 0.0021; OR: 6.78; 95% CI: 1.96-23.38). These findings support the involvement of HLA-B*15:02 in CBZ-induced SJS/TEN reported in other Asian populations. Interestingly, we also observed the presence of the HLA-B*15:21 allele. HLA-B*15:02 and HLA-B*15:21 are members of the HLA-B75 serotype, for which a greater frequency was observed in CBZ-induced SJS/TEN (vs tolerant control [p = 0.0078; OR: 12; 95% CI: 1.90-75.72] and vs normal control [p = 0.0018; OR: 8.56; 95% CI: 1.83-40]). Our findings suggest that screening for the HLA-B75 serotype can predict the risk of CBZ-induced SJS/TEN more accurately than screening for a specific allele.
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Affiliation(s)
- Rika Yuliwulandari
- Department of Pharmacology, Faculty of Medicine, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia.,Genomic Medicine Research Centre, YARSI Research Institute, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia.,The Indonesian Pharmacogenomics Working Group, DKI Jakarta, Indonesia
| | - Erna Kristin
- The Indonesian Pharmacogenomics Working Group, DKI Jakarta, Indonesia.,Department of Pharmacology & Therapy, Faculty of Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Kinasih Prayuni
- Genomic Medicine Research Centre, YARSI Research Institute, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia
| | - Qomariyah Sachrowardi
- Department of Physiology, Faculty of Medicine, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia
| | - Franciscus D Suyatna
- The Indonesian Pharmacogenomics Working Group, DKI Jakarta, Indonesia.,Department of Pharmacology & Therapeutic, Faculty of Medicine, University of Indonesia, Salemba, Jakarta Pusat, DKI Jakarta, Indonesia
| | - Sri Linuwih Menaldi
- Department of Dermatology Clinic, Faculty of Medicine, University of Indonesia, Salemba, Jakarta Pusat, DKI Jakarta, Indonesia
| | - Nuanjun Wichukchinda
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
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Josephs TM, Grant EJ, Gras S. Molecular challenges imposed by MHC-I restricted long epitopes on T cell immunity. Biol Chem 2017; 398:1027-1036. [PMID: 28141543 DOI: 10.1515/hsz-2016-0305] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 11/15/2022]
Abstract
It has widely been accepted that major histocompatibility complex class I molecules (MHC-I) are limited to binding small peptides of 8-10 residues in length. However, this consensus has recently been challenged with the identification of longer peptides (≥11 residues) that can also elicit cytotoxic CD8+ T cell responses. Indeed, a growing number of studies demonstrate that these non-canonical epitopes are important targets for the immune system. As long epitopes represent up to 10% of the peptide repertoire bound to MHC-I molecules, here we review their impact on antigen presentation by MHC-I, TCR recognition, and T cell immunity.
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31
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Caron E, Kowalewski DJ, Chiek Koh C, Sturm T, Schuster H, Aebersold R. Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Mol Cell Proteomics 2016; 14:3105-17. [PMID: 26628741 DOI: 10.1074/mcp.o115.052431] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field.
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Affiliation(s)
- Etienne Caron
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland;
| | - Daniel J Kowalewski
- §Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ching Chiek Koh
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Theo Sturm
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Heiko Schuster
- §Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; ¶Faculty of Science, University of Zurich, Zurich, Switzerland
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32
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Wang JJ, Macardle C, Weedon H, Beroukas D, Banovic T. Mucosal-associated invariant T cells are reduced and functionally immature in the peripheral blood of primary Sjögren's syndrome patients. Eur J Immunol 2016; 46:2444-2453. [DOI: 10.1002/eji.201646300] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/17/2016] [Accepted: 07/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jing J. Wang
- Department of Immunology; SA Pathology; Flinders Medical Centre; Bedford Park South Australia
- Department of Immunology; Flinders University; Bedford Park South Australia
| | - Cindy Macardle
- Department of Immunology; SA Pathology; Flinders Medical Centre; Bedford Park South Australia
- Department of Immunology; Flinders University; Bedford Park South Australia
| | - Helen Weedon
- Rheumatology Research Unit; Repatriation General Hospital; Daw Park Adelaide South Australia
| | - Dimitra Beroukas
- Department of Immunology; SA Pathology; Flinders Medical Centre; Bedford Park South Australia
- Department of Immunology; Flinders University; Bedford Park South Australia
| | - Tatjana Banovic
- Department of Immunology; SA Pathology; Flinders Medical Centre; Bedford Park South Australia
- Department of Immunology; Flinders University; Bedford Park South Australia
- Department of Immunology; SA Pathology; IMVS; Adelaide South Australia
- Department of Clinical Immunology and Allergy; Royal Adelaide Hospital; Adelaide South Australia
- Discipline of Pediatrics; School of Pediatrics and Reproductive Health; Faculty of Health Sciences; University of Adelaide; Adelaide South Australia
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33
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Dreyfus DH. Gene sharing between Epstein–Barr virus and human immune response genes. Immunol Res 2016; 65:37-45. [DOI: 10.1007/s12026-016-8814-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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34
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Shraibman B, Kadosh DM, Barnea E, Admon A. Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy. Mol Cell Proteomics 2016; 15:3058-70. [PMID: 27412690 DOI: 10.1074/mcp.m116.060350] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 11/06/2022] Open
Abstract
Treatment of cancer cells with anticancer drugs often fails to achieve complete remission. Yet, such drug treatments may induce alteration in the tumor's gene expression patterns, including those of Cancer/Testis Antigens (CTA). The degradation products of such antigens can be presented as HLA peptides on the surface of the tumor cells and be developed into anticancer immunotherapeutics. For example, the DNA methyl transferase inhibitor, 5-aza-2'-deoxycytidine (Decitabine) has limited antitumor efficacy, yet it induces the expression of many genes, including CTAs that are normally silenced in the healthy adult tissues. In this study, the presentation of many new HLA peptides derived from CTAs and induced by Decitabine was demonstrated in three human Glioblastoma cell lines. Such presentation of CTA-derived HLA peptides can be exploited for development of new treatment modalities, combining drug treatment with anti-CTA targeted immunotherapy. The Decitabine-induced HLA peptidomes include many CTAs that are not normally detected in healthy tissues or in cancer cells, unless treated with the drug. In addition, the study included large-scale analyses of the simultaneous effects of Decitabine on the transcriptomes, proteomes and HLA peptidomes of the human Glioblastoma cells. It demonstrates the poor correlations between these three levels of gene expression, both in their total levels and in their response to the drug. The proteomics and HLA peptidomics data are available via ProteomeXchange with identifier PXD003790 and the transcriptomics data are available via GEO with identifier GSE80137.
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Affiliation(s)
- Bracha Shraibman
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa, Israel
| | - Dganit Melamed Kadosh
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa, Israel
| | - Eilon Barnea
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa, Israel
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Deciphering the clinical relevance of allo-human leukocyte antigen cross-reactivity in mediating alloimmunity following transplantation. Curr Opin Organ Transplant 2016; 21:29-39. [PMID: 26575852 DOI: 10.1097/mot.0000000000000264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE OF REVIEW Despite a growing awareness regarding the potential of cross-reactive virus-specific memory T cells to mediate alloimmunity, there has been limited clinical evaluation on allograft immunopathology. This review will explore published models of human T-cell cross-reactivity and discuss criteria required to drive this mechanism as a contributing cause of allograft dysfunction in transplantation. RECENT FINDINGS Published models of human allogeneic (allo)-human leukocyte antigen (HLA) cross-reactivity have enabled dissection of the cross-reactive T cell receptor/peptide/major histocompatibility complex (TCR/peptide/MHC) interaction. In many of the models, the cross-reactive T cells express a unique TCR, although the relevance of a public cross-reactive TCR repertoire has yet to be determined. Equally, allopeptide identity, a vital component driving cross-recognition, remains unknown in the majority of models thereby prompting further characterization utilizing novel technologies. Although clinical studies examining the presence and impact of specific cross-reactive virus-specific T cells have been minimally explored, the existing data suggest that there may be a marginal set of requirements that need to be satisfied before the potentially damaging effects of allo-HLA cross-reactivity can be realized. SUMMARY Our understanding of allo-HLA cross-reactivity continues to evolve as improved technology and novel strategies allow us to better question the contribution of allo-HLA cross-reactivity in clinically relevant allograft dysfunction.
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Nielsen M, Andreatta M. NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med 2016; 8:33. [PMID: 27029192 PMCID: PMC4812631 DOI: 10.1186/s13073-016-0288-x] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/15/2016] [Indexed: 01/07/2023] Open
Abstract
Background Binding of peptides to MHC class I molecules (MHC-I) is essential for antigen presentation to cytotoxic T-cells. Results Here, we demonstrate how a simple alignment step allowing insertions and deletions in a pan-specific MHC-I binding machine-learning model enables combining information across both multiple MHC molecules and peptide lengths. This pan-allele/pan-length algorithm significantly outperforms state-of-the-art methods, and captures differences in the length profile of binders to different MHC molecules leading to increased accuracy for ligand identification. Using this model, we demonstrate that percentile ranks in contrast to affinity-based thresholds are optimal for ligand identification due to uniform sampling of the MHC space. Conclusions We have developed a neural network-based machine-learning algorithm leveraging information across multiple receptor specificities and ligand length scales, and demonstrated how this approach significantly improves the accuracy for prediction of peptide binding and identification of MHC ligands. The method is available at www.cbs.dtu.dk/services/NetMHCpan-3.0. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0288-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina. .,Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
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Battaglia S, Muhitch JB. Unmasking targets of antitumor immunity via high-throughput antigen profiling. Curr Opin Biotechnol 2016; 42:92-97. [PMID: 27010105 DOI: 10.1016/j.copbio.2016.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 10/22/2022]
Abstract
More than three decades of evidence has established that antitumor immune responses, initially shown with IL-2 treatment, can result in complete, durable eradication of malignant disease in metastatic patients. Recent studies have demonstrated that immune checkpoint blockade as well as cellular therapies, including dendritic cell activation of T cells and adoptive T cell transfer, can induce long-lasting responses. To elicit cytolysis of tumor cells, effector T cells rely on tumor expression of target antigens. However, the antigens targeted during antitumor responses are largely unknown. Technological advancements and availability of sequencing data have paved the way for more efficient screening and validation of tumor-associated antigens and neoantigens derived from non-synonymous mutations targeted by T cells under baseline conditions and in the context of immunotherapy.
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Affiliation(s)
- Sebastiano Battaglia
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, United States.
| | - Jason B Muhitch
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, United States.
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38
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Ng JHJ, Tachedjian M, Deakin J, Wynne JW, Cui J, Haring V, Broz I, Chen H, Belov K, Wang LF, Baker ML. Evolution and comparative analysis of the bat MHC-I region. Sci Rep 2016; 6:21256. [PMID: 26876644 PMCID: PMC4753418 DOI: 10.1038/srep21256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/20/2016] [Indexed: 12/22/2022] Open
Abstract
Bats are natural hosts to numerous viruses and have ancient origins, having diverged from other eutherian mammals early in evolution. These characteristics place them in an important position to provide insights into the evolution of the mammalian immune system and antiviral immunity. We describe the first detailed partial map of a bat (Pteropus alecto) MHC-I region with comparative analysis of the MHC-I region and genes. The bat MHC-I region is highly condensed, yet relatively conserved in organisation, and is unusual in that MHC-I genes are present within only one of the three highly conserved class I duplication blocks. We hypothesise that MHC-I genes first originated in the β duplication block, and subsequently duplicated in a step-wise manner across the MHC-I region during mammalian evolution. Furthermore, bat MHC-I genes contain unique insertions within their peptide-binding grooves potentially affecting the peptide repertoire presented to T cells, which may have implications for the ability of bats to control infection without overt disease.
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Affiliation(s)
- Justin H. J. Ng
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857
| | - Mary Tachedjian
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Janine Deakin
- Institute for Applied Ecology, The University of Canberra, ACT 2617, Australia
| | - James W. Wynne
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Jie Cui
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857
| | - Volker Haring
- CSIRO, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Ivano Broz
- CSIRO, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Honglei Chen
- CSIRO, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857
| | - Michelle L. Baker
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
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Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B. The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. THE JOURNAL OF IMMUNOLOGY 2016; 196:1480-7. [PMID: 26783342 DOI: 10.4049/jimmunol.1501721] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/13/2015] [Indexed: 12/11/2022]
Abstract
HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes.
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Affiliation(s)
- Thomas Trolle
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Curtis P McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Wilfried Bardet
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Sean C Osborn
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Thomas Kaever
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Morten Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, B 1650 HMP Buenos Aires, Argentina
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
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40
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Andreatta M, Nielsen M. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. ACTA ACUST UNITED AC 2015; 32:511-7. [PMID: 26515819 DOI: 10.1093/bioinformatics/btv639] [Citation(s) in RCA: 682] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/25/2015] [Indexed: 01/18/2023]
Abstract
MOTIVATION Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to peptides of length 8-11 amino acids. On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment. RESULTS We show that prediction methods based on alignments that include insertions and deletions have significantly higher performance than methods trained on peptides of single lengths. Also, we illustrate how the location of deletions can aid the interpretation of the modes of binding of the peptide-MHC, as in the case of long peptides bulging out of the MHC groove or protruding at either terminus. Finally, we demonstrate that the method can learn the length profile of different MHC molecules, and quantified the reduction of the experimental effort required to identify potential epitopes using our prediction algorithm. AVAILABILITY AND IMPLEMENTATION The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment is publicly available at: http://www.cbs.dtu.dk/services/NetMHC-4.0.
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Affiliation(s)
- Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina and
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina and Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
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41
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Rist MJ, Hibbert KM, Croft NP, Smith C, Neller MA, Burrows JM, Miles JJ, Purcell AW, Rossjohn J, Gras S, Burrows SR. T Cell Cross-Reactivity between a Highly Immunogenic EBV Epitope and a Self-Peptide Naturally Presented by HLA-B*18:01+ Cells. THE JOURNAL OF IMMUNOLOGY 2015; 194:4668-75. [PMID: 25855358 DOI: 10.4049/jimmunol.1500233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/12/2015] [Indexed: 01/06/2023]
Abstract
T cell cross-reactivity underpins the molecular mimicry hypothesis in which microbial peptides sharing structural features with host peptides stimulate T cells that cross-react with self-peptides, thereby initiating and/or perpetuating autoimmune disease. EBV represents a potentially important factor in the pathogenesis of several T cell-mediated autoimmune disorders, with molecular mimicry a likely mechanism. In this study, we describe a human self-peptide (DELEIKAY) that is a homolog of a highly immunogenic EBV T cell epitope (SELEIKRY) presented by HLA-B*18:01. This self-peptide was shown to bind stably to HLA-B*18:01, and peptide elution/mass spectrometric studies showed it is naturally presented by this HLA molecule on the surface of human cells. A significant proportion of CD8(+) T cells raised from some healthy individuals against this EBV epitope cross-reacted with the self-peptide. A diverse array of TCRs was expressed by the cross-reactive T cells, with variable functional avidity for the self-peptide, including some T cells that appeared to avoid autoreactivity by a narrow margin, with only 10-fold more of the self-peptide required for equivalent activation as compared with the EBV peptide. Structural studies revealed that the self-peptide-HLA-B*18:01 complex is a structural mimic of the EBV peptide-HLA-B*18:01 complex, and that the strong antiviral T cell response is primarily dependent on the alanine/arginine mismatch at position 7. To our knowledge, this is the first report confirming the natural presentation of a self-peptide cross-recognized in the context of self-HLA by EBV-reactive CD8(+) T cells. These results illustrate how aberrant immune responses and immunopathological diseases could be generated by EBV infection.
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Affiliation(s)
- Melissa J Rist
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kelly M Hibbert
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Corey Smith
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Michelle A Neller
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | | | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and
| | - Scott R Burrows
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia;
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42
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Hassan C, Chabrol E, Jahn L, Kester MGD, de Ru AH, Drijfhout JW, Rossjohn J, Falkenburg JHF, Heemskerk MHM, Gras S, van Veelen PA. Naturally processed non-canonical HLA-A*02:01 presented peptides. J Biol Chem 2014; 290:2593-603. [PMID: 25505266 DOI: 10.1074/jbc.m114.607028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules generally present peptides (p) of 8 to 11 amino acids (aa) in length. Although an increasing number of examples with lengthy (>11 aa) peptides, presented mostly by HLA-B alleles, have been reported. Here we characterize HLA-A*02:01 restricted, in addition to the HLA-B*0702 and HLA-B*4402 restricted, lengthy peptides (>11 aa) arising from the B-cell ligandome. We analyzed a number of 15-mer peptides presented by HLA-A*02:01, and confirmed pHLA-I formation by HLA folding and thermal stability assays. Surprisingly the binding affinity and stability of the 15-mer epitopes in complex with HLA-A*02:01 were comparable with the values observed for canonical length (8 to 11 aa) HLA-A*02:01-restricted peptides. We solved the structures of two 15-mer epitopes in complex with HLA-A*02:01, within which the peptides adopted distinct super-bulged conformations. Moreover, we demonstrate that T-cells can recognize the 15-mer peptides in the context of HLA-A*02:01, indicating that these 15-mer peptides represent immunogenic ligands. Collectively, our data expand our understanding of longer epitopes in the context of HLA-I, highlighting that they are not limited to the HLA-B family, but can bind the ubiquitous HLA-A*02:01 molecule, and play an important role in T-cell immunity.
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Affiliation(s)
- Chopie Hassan
- From the Departments of Immunohematology and Blood Transfusion and
| | - Eric Chabrol
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia
| | - Lorenz Jahn
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Michel G D Kester
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arnoud H de Ru
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jan W Drijfhout
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jamie Rossjohn
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom
| | | | | | - Stephanie Gras
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and
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T cell epitope clustering in the highly immunogenic BZLF1 antigen of Epstein-Barr virus. J Virol 2014; 89:703-12. [PMID: 25355876 DOI: 10.1128/jvi.02642-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED Polymorphism in the human leukocyte antigen (HLA) loci ensures that the CD8(+) T cell response to viruses is directed against a diverse range of antigenic epitopes, thereby minimizing the impact of virus escape mutation across the population. The BZLF1 antigen of Epstein-Barr virus is an immunodominant target for CD8(+) T cells, but the response has been characterized only in the context of a limited number of HLA molecules due to incomplete epitope mapping. We have now greatly expanded the number of defined CD8(+) T cell epitopes from BZLF1, allowing the response to be evaluated in a much larger proportion of the population. Some regions of the antigen fail to be recognized by CD8(+) T cells, while others include clusters of overlapping epitopes presented by different HLA molecules. These highly immunogenic regions of BZLF1 include polymorphic sequences, such that up to four overlapping epitopes are impacted by a single amino acid variation common in different regions of the world. This focusing of the immune response to limited regions of the viral protein could be due to sequence similarity to human proteins creating "immune blind spots" through self-tolerance. This study significantly enhances the understanding of the immune response to BZLF1, and the precisely mapped T cell epitopes may be directly exploited in vaccine development and adoptive immunotherapy. IMPORTANCE Epstein-Barr virus (EBV) is an important human pathogen, associated with several malignancies, including nasopharyngeal carcinoma and Hodgkin lymphoma. T lymphocytes are critical for virus control, and clinical trials aimed at manipulating this arm of the immune system have demonstrated efficacy in treating these EBV-associated diseases. These trials have utilized information on the precise location of viral epitopes for T cell recognition, for either measuring or enhancing responses. In this study, we have characterized the T cell response to the highly immunogenic BZLF1 antigen of EBV by greatly expanding the number of defined T cell epitopes. An unusual clustering of epitopes was identified, highlighting a small region of BZLF1 that is targeted by the immune response of a high proportion of the world's population. This focusing of the immune response could be utilized in developing vaccines/therapies with wide coverage, or it could potentially be exploited by the virus to escape the immune response.
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Soluble HLA technology as a strategy to evaluate the impact of HLA mismatches. J Immunol Res 2014; 2014:246171. [PMID: 25254222 PMCID: PMC4165401 DOI: 10.1155/2014/246171] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/15/2014] [Accepted: 08/05/2014] [Indexed: 11/17/2022] Open
Abstract
HLA class I incompatibilities still remain one of the main barriers for unrelated bone marrow transplantation (BMT); hence the molecular understanding of how to mismatch patients and donors and still have successful clinical outcomes will guide towards the future of unrelated BMT. One way to estimate the magnitude of polymorphisms within the PBR is to determine which peptides can be selected by individual HLA alleles and subsequently presented for recognition by T cells. The features (structure, length, and sequence) of different peptides each confer an individual pHLA landscape and thus directly shape the individual immune response. The elution and sequencing of peptides by mass spectrometric analysis enable determining the bona fide repertoire of presented peptides for a given allele. This is an effective and simple way to compare the functions of allelic variants and make a first assessment of their degree of permissivity. We describe the methodology used for peptide sequencing and the limitations of peptide prediction tools compared to experimental methods. We highlight the altered peptide features that are observed between allelic variants and the need to discover the altered peptide repertoire in situations of "artificial" graft versus host disease (GvHD) that occur in HLA-specific hypersensitive immune responses to drugs.
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Motozono C, Yokoyama M, Sato H, Ueno T. Cross-reactivity analysis of T cell receptors specific for overlapping HIV-1 Nef epitopes of different lengths. Microbes Infect 2013; 16:320-7. [PMID: 24380790 DOI: 10.1016/j.micinf.2013.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/20/2013] [Accepted: 12/22/2013] [Indexed: 11/29/2022]
Abstract
Overlapping peptides of different lengths from a certain immunodominant region can be presented by the same HLA class I molecule and elicit different T cell responses. However, how peptide-length specificity of antigen-specific CD8(+) T lymphocytes influence cross-reactivity profiles of these cells remains elusive. This question is particularly important in the face of highly variable pathogens such as HIV-1. Here, we examined this problem by using HLA-B*35:01-restricted CD8(+) T lymphocytes specific for Nef epitopes, i.e., RY11 (RPQVPLRPMTY), VY8 (VPLRPMTY), and RM9 (RPQVPLRPM), in which VY8 and RM9 were contained entirely within RY11, in combination with a T cell receptor (TCR) reconstruction system as well as HLA-B35 tetramers and a set of a single-variant peptide library. The TCR reactivity toward the peptide-length variants was classified into three types: mutually exclusive specificity toward (1) RY11 or (2) VY8 and (3) cross-recognition toward RM9 and RY11. TCR cross-reactivity toward variant peptides was similar within the same peptide-length reactivity type but was markedly different between the types. Thus, TCRs showing similar peptide-length reactivity have shared peptide recognition footprints and thereby similar weakness to antigenic variations, providing us with further insight into the antiviral vaccine design.
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Affiliation(s)
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.
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Abbott RJM, Quinn LL, Leese AM, Scholes HM, Pachnio A, Rickinson AB. CD8+ T cell responses to lytic EBV infection: late antigen specificities as subdominant components of the total response. THE JOURNAL OF IMMUNOLOGY 2013; 191:5398-409. [PMID: 24146041 DOI: 10.4049/jimmunol.1301629] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
EBV elicits primary CD8(+) T cell responses that, by T cell cloning from infectious mononucleosis (IM) patients, appear skewed toward immediate early (IE) and some early (E) lytic cycle proteins, with late (L) proteins rarely targeted. However, L Ag-specific responses have been detected regularly in polyclonal T cell cultures from long-term virus carriers. To resolve this apparent difference between responses to primary and persistent infection, 13 long-term carriers were screened in ex vivo IFN-γ ELISPOT assays using peptides spanning the two IE, six representative E, and seven representative L proteins. This revealed memory CD8 responses to 44 new lytic cycle epitopes that straddle all three protein classes but, in terms of both frequency and size, maintain the IE > E > L hierarchy of immunodominance. Having identified the HLA restriction of 10 (including 7 L) new epitopes using memory CD8(+) T cell clones, we looked in HLA-matched IM patients and found such reactivities but typically at low levels, explaining why they had gone undetected in the original IM clonal screens. Wherever tested, all CD8(+) T cell clones against these novel lytic cycle epitopes recognized lytically infected cells naturally expressing their target Ag. Surprisingly, however, clones against the most frequently recognized L Ag, the BNRF1 tegument protein, also recognized latently infected, growth-transformed cells. We infer that BNRF1 is also a latent Ag that could be targeted in T cell therapy of EBV-driven B-lymphoproliferative disease.
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Affiliation(s)
- Rachel J M Abbott
- School of Cancer Sciences and Medical Research Council Centre for Immune Regulation, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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