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Gul A, Pewe LL, Willems P, Mayer R, Thery F, Asselman C, Aernout I, Verbeke R, Eggermont D, Van Moortel L, Upton E, Zhang Y, Boucher K, Miret-Casals L, Demol H, De Smedt SC, Lentacker I, Radoshevich L, Harty JT, Impens F. Immunopeptidomics mapping of Listeria monocytogenes T cell epitopes in mice. Mol Cell Proteomics 2024:100829. [PMID: 39147027 DOI: 10.1016/j.mcpro.2024.100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/21/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
Listeria monocytogenes is a foodborne intracellular bacterial model pathogen. Protective immunity against Listeria depends on an effective CD8+ T cell response, but very few T cell epitopes are known in mice as a common animal infection model for listeriosis. To identify epitopes we screened for Listeria immunopeptides presented in the spleen of infected mice by mass spectrometry-based immunopeptidomics. We mapped more than 6,000 mouse self-peptides presented on MHC Class I molecules, including 12 high confident Listeria peptides from 12 different bacterial proteins. Bacterial immunopeptides with confirmed fragmentation spectra were further tested for their potential to activate CD8+ T cells, revealing VTYNYINI from the putative cell wall surface anchor family protein LMON_0576 as a novel bona fide peptide epitope. The epitope showed high biological potency in a prime boost model and can be used as a research tool to probe CD8+ T cell responses in mouse models of Listeria infection. Together, our results demonstrate the power of immunopeptidomics for bacterial antigen identification.
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Affiliation(s)
- Adillah Gul
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lecia L Pewe
- Department of Pathology, University of Iowa-Carver College of Medicine, Iowa City, IA, USA
| | - Patrick Willems
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Rupert Mayer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium
| | - Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Caroline Asselman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ilke Aernout
- Ghent Research Group on Nanomedicines, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Rein Verbeke
- Ghent Research Group on Nanomedicines, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Denzel Eggermont
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Laura Van Moortel
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ellen Upton
- Department of Microbiology and Immunology, University of Iowa-Carver College of Medicine, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa
| | - Yifeng Zhang
- Department of Microbiology and Immunology, University of Iowa-Carver College of Medicine, Iowa City, IA, USA
| | - Katie Boucher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium
| | - Laia Miret-Casals
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Hans Demol
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ine Lentacker
- Ghent Research Group on Nanomedicines, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Lilliana Radoshevich
- Department of Microbiology and Immunology, University of Iowa-Carver College of Medicine, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa; Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.
| | - John T Harty
- Department of Pathology, University of Iowa-Carver College of Medicine, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa.
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium.
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Wang M, Rousseau B, Qiu K, Huang G, Zhang Y, Su H, Le Bihan-Benjamin C, Khati I, Artz O, Foote MB, Cheng YY, Lee KH, Miao MZ, Sun Y, Bousquet PJ, Hilmi M, Dumas E, Hamy AS, Reyal F, Lin L, Armistead PM, Song W, Vargason A, Arthur JC, Liu Y, Guo J, Zhou X, Nguyen J, He Y, Ting JPY, Anselmo AC, Huang L. Killing tumor-associated bacteria with a liposomal antibiotic generates neoantigens that induce anti-tumor immune responses. Nat Biotechnol 2024; 42:1263-1274. [PMID: 37749267 DOI: 10.1038/s41587-023-01957-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/18/2023] [Indexed: 09/27/2023]
Abstract
Increasing evidence implicates the tumor microbiota as a factor that can influence cancer progression. In patients with colorectal cancer (CRC), we found that pre-resection antibiotics targeting anaerobic bacteria substantially improved disease-free survival by 25.5%. For mouse studies, we designed an antibiotic silver-tinidazole complex encapsulated in liposomes (LipoAgTNZ) to eliminate tumor-associated bacteria in the primary tumor and liver metastases without causing gut microbiome dysbiosis. Mouse CRC models colonized by tumor-promoting bacteria (Fusobacterium nucleatum spp.) or probiotics (Escherichia coli Nissle spp.) responded to LipoAgTNZ therapy, which enabled more than 70% long-term survival in two F. nucleatum-infected CRC models. The antibiotic treatment generated microbial neoantigens that elicited anti-tumor CD8+ T cells. Heterologous and homologous bacterial epitopes contributed to the immunogenicity, priming T cells to recognize both infected and uninfected tumors. Our strategy targets tumor-associated bacteria to elicit anti-tumoral immunity, paving the way for microbiome-immunotherapy interventions.
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Affiliation(s)
- Menglin Wang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Benoit Rousseau
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kunyu Qiu
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Guannan Huang
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Yu Zhang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Hang Su
- Department of Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Christine Le Bihan-Benjamin
- Health Data and Assessment Department, Data Science and Assessment Division, French National Cancer Institute, Boulogne-Billancourt, France
| | - Ines Khati
- Health Data and Assessment Department, Data Science and Assessment Division, French National Cancer Institute, Boulogne-Billancourt, France
| | - Oliver Artz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael B Foote
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yung-Yi Cheng
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- Chinese Medicine Research and Development Center, China Medical University and Hospital, Taichung, Taiwan
| | - Michael Z Miao
- Curriculum in Oral and Craniofacial Biomedicine, Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
- Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Yue Sun
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA
| | - Philippe-Jean Bousquet
- Health Survey, Data Science and Assessment Division, French National Cancer Institute, Boulogne Billancourt, France
| | - Marc Hilmi
- GERCOR Group, Paris, France
- Medical Oncology Department, Curie Institute, Saint Cloud, France
| | - Elise Dumas
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Paris, France
- INSERM, U900, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Anne-Sophie Hamy
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Paris, France
- Department of Medical Oncology, Centre René Hughenin, Saint Cloud, France
| | - Fabien Reyal
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Paris, France
- Department of Surgery, Institut Jean Godinot, Reims, France
- Department of Surgical Oncology, Institut Curie, University of Paris, Paris, France
| | - Lin Lin
- BMTCT Program, Division of Hematology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Paul M Armistead
- BMTCT Program, Division of Hematology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Internal Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Wantong Song
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- Jilin Biomedical Polymers Engineering Laboratory, Changchun, China
| | - Ava Vargason
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Janelle C Arthur
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Yun Liu
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Jianfeng Guo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Xuefei Zhou
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Juliane Nguyen
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jenny P-Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aaron C Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Leaf Huang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
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Khilji MS, Faridi P, Pinheiro-Machado E, Hoefner C, Dahlby T, Aranha R, Buus S, Nielsen M, Klusek J, Mandrup-Poulsen T, Pandey K, Purcell AW, Marzec MT. Defective Proinsulin Handling Modulates the MHC I Bound Peptidome and Activates the Inflammasome in β-Cells. Biomedicines 2022; 10:biomedicines10040814. [PMID: 35453564 PMCID: PMC9024965 DOI: 10.3390/biomedicines10040814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
How immune tolerance is lost to pancreatic β-cell peptides triggering autoimmune type 1 diabetes is enigmatic. We have shown that loss of the proinsulin chaperone glucose-regulated protein (GRP) 94 from the endoplasmic reticulum (ER) leads to mishandling of proinsulin, ER stress, and activation of the immunoproteasome. We hypothesize that inadequate ER proinsulin folding capacity relative to biosynthetic need may lead to an altered β-cell major histocompatibility complex (MHC) class-I bound peptidome and inflammasome activation, sensitizing β-cells to immune attack. We used INS-1E cells with or without GRP94 knockout (KO), or in the presence or absence of GRP94 inhibitor PU-WS13 (GRP94i, 20 µM), or exposed to proinflammatory cytokines interleukin (IL)-1β or interferon gamma (IFNγ) (15 pg/mL and 10 ng/mL, respectively) for 24 h. RT1.A (rat MHC I) expression was evaluated using flow cytometry. The total RT1.A-bound peptidome analysis was performed on cell lysates fractionated by reverse-phase high-performance liquid chromatography (RP-HPLC), followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing protein (NLRP1), nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha (IκBα), and (pro) IL-1β expression and secretion were investigated by Western blotting. GRP94 KO increased RT1.A expression in β-cells, as did cytokine exposure compared to relevant controls. Immunopeptidome analysis showed increased RT1.A-bound peptide repertoire in GRP94 KO/i cells as well as in the cells exposed to cytokines. The GRP94 KO/cytokine exposure groups showed partial overlap in their peptide repertoire. Notably, proinsulin-derived peptide diversity increased among the total RT1.A peptidome in GRP94 KO/i along with cytokines exposure. NLRP1 expression was upregulated in GRP94 deficient cells along with decreased IκBα content while proIL-1β cellular levels declined, coupled with increased secretion of mature IL-1β. Our results suggest that limiting β-cell proinsulin chaperoning enhances RT1.A expression alters the MHC-I peptidome including proinsulin peptides and activates inflammatory pathways, suggesting that stress associated with impeding proinsulin handling may sensitize β-cells to immune-attack.
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Affiliation(s)
- Muhammad Saad Khilji
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (M.S.K.); (C.H.); (T.M.-P.)
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia; (R.A.); (K.P.)
- Department of Physiology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Pouya Faridi
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC 3168, Australia;
| | - Erika Pinheiro-Machado
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 Groningen, The Netherlands;
| | - Carolin Hoefner
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (M.S.K.); (C.H.); (T.M.-P.)
| | - Tina Dahlby
- Laboratory of Translational Nutrition Biology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, 8603 Zürich, Switzerland;
| | - Ritchlynn Aranha
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia; (R.A.); (K.P.)
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, 2800 Lyngby, Denmark;
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín CP1650, Argentina
| | - Justyna Klusek
- Laboratory of Medical Genetics, Department of Surgical Medicine, Collegium Medicum, Jan Kochanowski University, 25-369 Kielce, Poland;
| | - Thomas Mandrup-Poulsen
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (M.S.K.); (C.H.); (T.M.-P.)
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia; (R.A.); (K.P.)
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia; (R.A.); (K.P.)
- Correspondence: (A.W.P.); (M.T.M.); Tel.: +61-39-902-9265 (A.W.P.); +45-25-520-256 (M.T.M.)
| | - Michal T. Marzec
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (M.S.K.); (C.H.); (T.M.-P.)
- Institute of Health Sciences, Collegium Medicum, Jan Kochanowski University, 25-002 Kielce, Poland
- Correspondence: (A.W.P.); (M.T.M.); Tel.: +61-39-902-9265 (A.W.P.); +45-25-520-256 (M.T.M.)
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Determination of T Cell Responses in Thai Systemic Sclerosis Patients. J Immunol Res 2022; 2022:5072154. [PMID: 35310606 PMCID: PMC8924789 DOI: 10.1155/2022/5072154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/12/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022] Open
Abstract
Objectives This study is aimed at determining the role of T cells by assessing the numbers of IFN-γ- and IL-2-secreting T cells following stimulation with peptides derived from DNA topoisomerase-I protein in Thai SSc patients. Methods Fifty Thai SSc patients and 50 healthy controls (HC) joined this study. IFN-γ and IL-2 levels upon stimulation of T cells with 6 peptides derived from DNA topoisomerase-I protein were determined. Anti-nuclear antibodies (ANA) and anti-Scl-70 antibodies were determined by using the ELISA method. Results In SSc patients, we detected a significantly higher number of IFN-γ- and IL-2-secreting CD8+ T cells than IFN-γ- and IL-2-secreting CD4+ T cells after stimulation with pooled peptides derived from DNA topoisomerase-I protein. A similar percentage of CD4+IL-2+, CD4+IFN-γ+, and CD8+IL-2+ were detected following stimulation with DNA topoisomerase-I protein -in SSc patients with anti-Scl-70 antibody (SSc/anti-Scl-70+) and those without. In contrast, the amount of CD8+IFN-γ+ cells was significantly higher in SSc/anti-Scl-70+ than those without. Stimulation with individual peptides showed that CSLRVEHINLHPELD (sPep3; 15 amino acids; position 505-519 of DNA topoisomerase-I protein) was the optimal epitope that induced T cells secreting the highest levels of IFN-γ and IL-2. A higher percentage of IFN-γ+CD4+ T cells was detected in SSc/anti-Scl-70+ than those without the following stimulation with peptides 2 (amino acid position 475-486 [RAVALYFIDKLA] of protein DNA topoisomerase). Conclusion The results from this study emphasize the critical role of DNA topoisomerase-I peptides on the activation of T cells in SSc patients. The findings provide a better understanding of SSc's immunopathogenesis and may lead to the development of diagnostic tools and specific treatments for SSc in the future.
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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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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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7
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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: 64] [Impact Index Per Article: 12.8] [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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8
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Pandya M, Rasmussen M, Hansen A, Nielsen M, Buus S, Golde W, Barlow J. A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules. Immunogenetics 2016; 67:691-703. [PMID: 26496773 DOI: 10.1007/s00251-015-0877-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/07/2015] [Indexed: 01/20/2023]
Abstract
Major histocompatibility complex (MHC) class Imolecules regulate adaptive immune responses through the presentation of antigenic peptides to CD8+ T cells. Polymorphisms in the peptide binding region of class I molecules determine peptide binding affinity and stability during antigen presentation, and different antigen peptide motifs are associated with specific genetic sequences of class I molecules. Understanding bovine leukocyte antigen (BoLA), peptide-MHC class I binding specificities may facilitate development of vaccines or reagents for quantifying the adaptive immune response to intracellular pathogens, such as foot-and-mouth disease virus (FMDV). Six synthetic BoLA class I (BoLA-I) molecules were produced, and the peptide binding motif was generated for five of the six molecules using a combined approach of positional scanning combinatorial peptide libraries (PSCPLs) and neural network-based predictions (NetMHCpan). The updated NetMHCpan server was used to predict BoLA-I binding peptides within the P1 structural polyprotein sequence of FMDV (strain A24 Cruzeiro) for Bo-LA-1*01901, BoLA-2*00801, BoLA-2*01201, and BoLA-4*02401. Peptide binding affinity and stability were determined for these BoLA-I molecules using the luminescent oxygen channeling immunoassay (LOCI) and scintillation proximity assay (SPA). The functional diversity of known BoLA alleles was predicted using theMHCcluster tool, and functional predictions for peptide motifs were compared to observed data from this and prior studies. The results of these analyses showed that BoLA alleles cluster into three distinct groups with the potential to define BBoLA supertypes.^ This streamlined approach identifies potential T cell epitopes from pathogens, such as FMDV, and provides insight into T cell immunity following infection or vaccination.
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9
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Massilamany C, Gangaplara A, Basavalingappa RH, Rajasekaran RA, Khalilzad-Sharghi V, Han Z, Othman S, Steffen D, Reddy J. Localization of CD8 T cell epitope within cardiac myosin heavy chain-α334-352 that induces autoimmune myocarditis in A/J mice. Int J Cardiol 2015; 202:311-21. [PMID: 26422020 DOI: 10.1016/j.ijcard.2015.09.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/02/2015] [Accepted: 09/15/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND Cardiac myosin heavy chain-α (Myhc), an intracellular protein expressed in the cardiomyocytes, has been identified as a major autoantigen in cardiac autoimmunity. In our studies with Myhc334-352-induced experimental autoimmune myocarditis in A/J mice (H-2a), we discovered that Myhc334-352, supposedly a CD4 T cell epitope, also induced antigen-specific CD8 T cells that transfer disease to naive animals. METHODS AND RESULTS In our efforts to identify the CD8 T cell determinants, we localized Myhc338-348 within the full length-Myhc334-352, leading to four key findings. (1) By acting as a dual epitope, Myhc338-348 induces both CD4 and CD8 T cell responses. (2) In a major histocompatibility complex (MHC) class I-stabilization assay, Myhc338-348 was found to bind H-2Dd-but not H-2Kk or H-2Ld-alleles. (3) The CD8 T cell response induced by Myhc338-348 was antigen-specific, as evaluated by MHC class I/H-2Dd dextramer staining. The antigen-sensitized T cells predominantly produced interferon-γ, the critical cytokine of effector cytotoxic T lymphocytes. (4) Myhc338-348 was found to induce myocarditis in immunized animals as determined by histology and magnetic resonance microscopy imaging. CONCLUSIONS Our data provide new insights as to how different immune cells can recognize the same antigen and inflict damage through different mechanisms.
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Affiliation(s)
- Chandirasegaran Massilamany
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Arunakumar Gangaplara
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Rakesh H Basavalingappa
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Rajkumar A Rajasekaran
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Vahid Khalilzad-Sharghi
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Zhongji Han
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Shadi Othman
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - David Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
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10
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Picarda E, Bézie S, Venturi V, Echasserieau K, Mérieau E, Delhumeau A, Renaudin K, Brouard S, Bernardeau K, Anegon I, Guillonneau C. MHC-derived allopeptide activates TCR-biased CD8+ Tregs and suppresses organ rejection. J Clin Invest 2014; 124:2497-512. [PMID: 24789907 DOI: 10.1172/jci71533] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In a rat heart allograft model, preventing T cell costimulation with CD40Ig leads to indefinite allograft survival, which is mediated by the induction of CD8+CD45RClo regulatory T cells (CD8+CD40Ig Tregs) interacting with plasmacytoid dendritic cells (pDCs). The role of TCR-MHC-peptide interaction in regulating Treg activity remains a topic of debate. Here, we identified a donor MHC class II-derived peptide (Du51) that is recognized by TCR-biased CD8+CD40Ig Tregs and activating CD8+CD40Ig Tregs in both its phenotype and suppression of antidonor alloreactive T cell responses. We generated a labeled tetramer (MHC-I RT1.Aa/Du51) to localize and quantify Du51-specific T cells within rat cardiac allografts and spleen. RT1.Aa/Du51-specific CD8+CD40Ig Tregs were the most suppressive subset of the total Treg population, were essential for in vivo tolerance induction, and expressed a biased, restricted Vβ11-TCR repertoire in the spleen and the graft. Finally, we demonstrated that treatment of transplant recipients with the Du51 peptide resulted in indefinite prolongation of allograft survival. These results show that CD8+CD40Ig Tregs recognize a dominant donor antigen, resulting in TCR repertoire alterations in the graft and periphery. Furthermore, this allopeptide has strong therapeutic activity and highlights the importance of TCR-peptide-MHC interaction for Treg generation and function.
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11
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Cárdenas C, Bidon-Chanal A, Conejeros P, Arenas G, Marshall S, Luque FJ. Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar. J Comput Aided Mol Des 2010; 24:1035-51. [DOI: 10.1007/s10822-010-9387-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
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12
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Ola TO, Biro PA, Hawa MI, Ludvigsson J, Locatelli M, Puglisi MA, Bottazzo GF, Fierabracci A. Importin beta: a novel autoantigen in human autoimmunity identified by screening random peptide libraries on phage. J Autoimmun 2006; 26:197-207. [PMID: 16549322 DOI: 10.1016/j.jaut.2006.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Revised: 01/24/2006] [Accepted: 01/25/2006] [Indexed: 10/24/2022]
Abstract
By screening random peptide libraries (RPLs) with sera of Type 1 diabetes (T1D) patients, we previously identified 5 disease-specific 'mimotopes' displayed on phages (phagotopes). We already characterised 1 phagotope (CH1p), as an epitope of human osteopontin, an autoantigen expressed within the somatostatin cells of human islets. In this paper, we report the characterization of the second phagotope, 195Dyn, by immunohistochemistry, Western Blotting and screening of a human islet cDNA library using rabbit anti-195Dyn antibodies. The 195Dyn mimotope was detected in human islets. The screening of a lambdagt11 cDNA library from human islets has identified a clone, which corresponded to human importin beta. ELISA detected autoantibodies against this protein in sera of around 60% of TD1 patients and in 30% of patients affected by other autoimmune diseases. In summary, RPLs technology proved again successful in identifying another novel autoantigen (importin beta), whose significance in the autoimmune process remains to be fully elucidated.
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Affiliation(s)
- Thomas O Ola
- St Bartholomew's and the Royal London School of Medicine and Dentistry, Queen Mary College, London, UK
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13
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Margalit A, Sheikhet HM, Carmi Y, Berko D, Tzehoval E, Eisenbach L, Gross G. Induction of antitumor immunity by CTL epitopes genetically linked to membrane-anchored beta2-microglobulin. THE JOURNAL OF IMMUNOLOGY 2006; 176:217-24. [PMID: 16365413 DOI: 10.4049/jimmunol.176.1.217] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Level and persistence of antigenic peptides presented by APCs on MHC class I (MHC-I) molecules influence the magnitude and quality of the ensuing CTL response. We recently demonstrated the unique immunological properties conferred on APCs by expressing beta2-microglobulin (beta2m) as an integral membrane protein. In this study, we explored membrane-anchored beta2m as a platform for cancer vaccines using as a model MO5, an OVA-expressing mouse B16 melanoma. We expressed in mouse RMA-S cells two H-2Kb binding peptides from MO5, OVA257-264, and TRP-2181-188, each genetically fused with the N terminus of membranal beta2m via a short linker. Specific Ab staining and T cell hybridoma activation confirmed that OVA257-264 was properly situated in the MHC-I binding groove. In vivo, transfectants expressing both peptides elicited stronger CTLs and conferred better protection against MO5 than peptide-saturated RMA-S cells. Cells expressing OVA257-264/beta2m were significantly superior to OVA257-264-charged cells in their ability to inhibit the growth of pre-established MO5 tumors. Our results highlight the immunotherapeutic potential of membranal beta2m as a universal scaffold for optimizing Ag presentation by MHC-I molecules.
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Affiliation(s)
- Alon Margalit
- Laboratory of Immunology, MIGAL-Galilee Technology Center, Kiryat Shmona, Israel
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14
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Duyar H, Dengjel J, de Graaf KL, Wiesmüller KH, Stevanović S, Weissert R. Peptide motif for the rat MHC class II molecule RT1.Da: similarities to the multiple sclerosis-associated HLA-DRB1*1501 molecule. Immunogenetics 2005; 57:69-76. [PMID: 15711804 DOI: 10.1007/s00251-004-0761-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Revised: 11/25/2004] [Indexed: 10/25/2022]
Abstract
Experimental autoimmune encephalomyelitis induced with myelin proteins in DA and LEW.1AV1 rats is a model of multiple sclerosis (MS). It reproduces major aspects of this detrimental disease of the central nervous system. MS is associated with the HLA-DRB1*1501, DRB5*0101, and DQB1*0602 haplotype. DA and LEW.1AV1 rats share the RT1av1 haplotype. So far, no MHC class II peptide motif of RT1.Da molecules has been described. Sequence alignment of the beta chain of the rat MHC class II molecule RT1.Da with human HLA class II molecules revealed strong similarity in the peptide-binding groove of RT1.Da and HLA-DRB1*1501. According to the putative peptide-binding pockets of RT1.Da, after comparison with the pockets of HLA-DRB1*1501, we predicted the peptide motif of RT1.Da. To verify the predicted motif, naturally processed peptides were eluted by acidic treatment from immunoaffinity-purified RT1.Da molecules of lymphoid tissue of DA rats and subsequently analyzed by ESI tandem mass spectrometry. In addition, we performed binding studies with combinatorial nonapeptide libraries to purified RT1.Da molecules. Based on these studies we could define a peptide-binding motif for RT1.Da characterized by aliphatic amino acid residues (L, I, V, M) and of F for the peptide pocket P1, aromatic residues (F, Y, W) for P4, basic residues (K, R) for P6, aliphatic residues (I, L, V) for P7, and aromatic residues (F, Y, W) and L for P9. Both methods revealed similar binding characteristics for peptides to RT1.Da. This data will allow epitope predictions for analysis of peptides, relevant for experimental autoimmune diseases.
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Affiliation(s)
- Hüseyin Duyar
- Experimental Neuroimmunology Laboratory, Department of General Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Strasse 3, 72076, Tübingen, Germany
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15
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de Graaf KL, Barth S, Herrmann MM, Storch MK, Otto C, Olsson T, Melms A, Jung G, Wiesmüller KH, Weissert R. MHC Class II Isotype- and Allele-Specific Attenuation of Experimental Autoimmune Encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2004; 173:2792-802. [PMID: 15294998 DOI: 10.4049/jimmunol.173.4.2792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Most autoimmune diseases are associated with certain MHC class II haplotypes. Autoantigen-based specific immune therapy can lead either to beneficial or, in the context of inflammatory conditions, detrimental outcomes. Therefore, we designed a platform of peptides by combinatorial chemistry selected in a nonbiased Ag-independent approach for strong binding to the rat MHC class II isotype RT1.D(n) allelic product of the RT1(n) haplotype that is presenting autoantigen in myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis in LEW.1N rats. Peptide p17 (Ac-FWFLDNAPL-NH(2)) was capable of suppressing the induction of and also ameliorated established experimental autoimmune encephalomyelitis. MHC class II isotype and allele specificity of the therapeutic principle were demonstrated in myelin basic protein-induced experimental autoimmune encephalomyelitis in LEW rats bearing the RT1(l) haplotype. A general immunosuppressive effect of the treatment was excluded by allogeneic heart transplantation studies. In vitro studies demonstrated the blocking effect of p17 on autoantigenic T cell responses. We thus demonstrate a rational design of strong MHC class II-binding peptides with absolute isotype and allele specificity able to compete for autoantigenic sequences presented on disease-associated MHC class II molecules.
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Affiliation(s)
- Katrien L de Graaf
- Experimental Neuroimmunology Laboratory, Department of General Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
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16
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Doytchinova IA, Taylor P, Flower DR. Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone. J Biomed Biotechnol 2003; 2003:267-290. [PMID: 14688414 PMCID: PMC521502 DOI: 10.1155/s1110724303209232] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 12/18/2002] [Indexed: 01/02/2023] Open
Abstract
The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution. In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria.
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Affiliation(s)
- Irini A Doytchinova
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Paul Taylor
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Darren R Flower
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
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17
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Rudolph MG, Stevens J, Speir JA, Trowsdale J, Butcher GW, Joly E, Wilson IA. Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B. J Mol Biol 2002; 324:975-90. [PMID: 12470953 DOI: 10.1016/s0022-2836(02)01095-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antigenic peptides are loaded onto class I MHC molecules in the endoplasmic reticulum (ER) by a complex consisting of the MHC class I heavy chain, beta(2)-microglobulin, calreticulin, tapasin, Erp57 (ER60) and the transporter associated with antigen processing (TAP). While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, that are present in different inbred strains. Each TAP delivers a different spectrum of peptides and is associated genetically with distinct subsets of MHC class Ia alleles, but the molecular basis for the conservation (or co-evolution) of the two transporter alleles is unknown. We have determined the crystal structures of a representative of each MHC subset, viz RT1-A(a) and RT1-A1(c), in association with high-affinity nonamer peptides. The structures reveal how the chemical properties of the two different rat MHC F-pockets match those of the corresponding C termini of the peptides, corroborating biochemical data on the rates of peptide-MHC complex assembly. An unusual sequence in RT1-A1(c) leads to a major deviation from the highly conserved beta(3)/alpha(1) loop (residues 40-59) conformation in mouse and human MHC class I structures. This loop change contributes to profound changes in the shape of the A-pocket in the peptide-binding groove and may explain the function of RT1-A1(c) as an inhibitory natural killer cell ligand.
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Affiliation(s)
- Markus G Rudolph
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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18
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Planz O, Dumrese T, Hulpusch S, Schirle M, Stevanovic S, Stitz L. A naturally processed rat major histocompatibility complex class I-associated viral peptide as target structure of borna disease virus-specific CD8+ T cells. J Biol Chem 2001; 276:13689-94. [PMID: 11278578 DOI: 10.1074/jbc.m009889200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The first naturally processed peptide synthesized by a virus and recognized by classical CD8(+) T cells in association with the RT1.A(l) major histocompatibility complex class I molecule of the Lewis rat is reported. Borna disease virus-specific CD8(+) T cells recognize syngeneic target cells pulsed with peptides extracted from Borna disease virus-infected cells. The predicted peptide sequence ASYAQMTTY from the viral p40 protein coeluted with the cytotoxic T-lymphocyte-reactive fraction was identified among natural ligands by tandem mass spectrometry. Numerous naturally processed peptides derived from intracellular bacteria, viruses, or tumors and recognized by CD8(+) T cells of man and mice are known, leading to a better understanding of cellular immune mechanisms against pathogens in these two species. In contrast, for the rat little information exists with regard to the function and role of CD8(+) T cells as part of their cellular immune defense system. This first naturally processed viral epitope in the rat contributes to the understanding of the rat cellular immune response and might trigger the identification of more cytotoxic T-lymphocyte epitopes in this animal.
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Affiliation(s)
- O Planz
- Institut für Immunologie, Bundesforschungsanstalt für Viruskrankheiten der Tiere and Interfakultäres Institut für Zellbiologie, Abteilung Immunologie, 72076 Tübingen, Germany.
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19
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Geginat G, Schenk S, Skoberne M, Goebel W, Hof H. A novel approach of direct ex vivo epitope mapping identifies dominant and subdominant CD4 and CD8 T cell epitopes from Listeria monocytogenes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 166:1877-84. [PMID: 11160235 DOI: 10.4049/jimmunol.166.3.1877] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We used a novel approach for the direct ex vivo identification and characterization of T cell epitopes based on the screening of peptide spot libraries with freshly isolated splenocytes in a sensitive enzyme-linked immunospot (ELISPOT) assay. This technique was applied for the analysis of splenocytes from Listeria monocytogenes-infected BALB/c and C57BL/6 mice. The screening of peptide spot libraries covering the whole listeriolysin O and p60 of L. monocytogenes confirmed all known CD4 and CD8 T cell epitopes of these proteins and additionally revealed six new H-2(d) and six new H-2(b)-restricted T cell epitopes. New epitopes were categorized into CD4 and CD8 T cell epitopes by ex vivo ELISPOT analysis with separated T cell populations. The quantitative analysis of cells reactive with these CD4 and CD8 T cell epitopes revealed the existence of dominant and subdominant CD4 and CD8 T cell populations during L. monocytogenes infection. As a consequence of these data we suggest that ELISPOT-based screening of peptide spot libraries could be a general approach for the rapid identification and characterization of pathogen-specific T cell populations during various infectious diseases.
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Affiliation(s)
- G Geginat
- Institut für Medizinische Mikrobiologie und Hygiene, Fakultät für Klinische Medizin Mannheim der Universität Heidelberg, Mannheim, Germany.
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20
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Speir JA, Stevens J, Joly E, Butcher GW, Wilson IA. Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa. Immunity 2001; 14:81-92. [PMID: 11163232 DOI: 10.1016/s1074-7613(01)00091-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. The antigenic structure of MTF-E was unpredictable due to its extraordinary length and two arginines that could serve as potential anchor residues. The crystal structure of RT1-Aa-MTF-E at 2.55 A shows that both peptide termini are anchored, as in other class I molecules, but the central residues in two independent pMHC complexes adopt completely different bulged conformations based on local environment. The MTF-E epitope is fully exposed within the putative T cell receptor (TCR) footprint. The flexibility demonstrated by the MTF-E structures illustrates how different TCRs may be raised against chemically identical, but structurally dissimilar, pMHC complexes.
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Affiliation(s)
- J A Speir
- Department of Molecular Biology and, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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21
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Stevens J, Jones RC, Bordoli RS, Trowsdale J, Gaskell SJ, Butcher GW, Joly E. Peptide specificity of RT1-A1(c), an inhibitory rat major histocompatibility complex class I natural killer cell ligand. J Biol Chem 2000; 275:29217-24. [PMID: 10856297 DOI: 10.1074/jbc.m002565200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rat major histocompatibility complex class Ia allelomorph RT1-A1(c) is a potent ligand for the recently identified inhibitory rLy-49 receptor, STOK-2. With the ultimate objective of studying the interactions of these molecules using structural and functional methods, we undertook a detailed study of its peptide specificity. The study revealed that designing an "ideal peptide" by choosing the most abundant residues in the "binding motif" obtained by pool sequencing does not necessarily yield an optimal binding peptide. For RT1-A1(c), as many as four positions, P2, P4, P5, and P9, were detected as putative anchors. Since this molecule displays a preference for highly hydrophobic peptides, we tested binding of peptides derived from the known leader peptide sequences of other rat histocompatibility complex class I molecules. One such peptide, found to bind well, requiring 1.6 microm peptide to achieve 50% stabilization, was searched for in vivo. Natural RT1-A1(c) binding peptides were purified from rat splenocytes and characterized by mass spectrometry using a combined matrix-assisted laser desorption ionization/time-of-flight and quadrupole time-of-flight approach. Results showed that the signal sequence-derived peptide was not detectable in the purified peptide pool, which was composed of a complex spectrum of peptides. Seven of these self-peptides were successfully sequenced.
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Affiliation(s)
- J Stevens
- Molecular Immunology Programme, Babraham Institute, Cambridge CB2 4AT, UK.
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22
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Zhang QJ, Chen SS, Saari CA, Massuci MG, Tufaro F, Jefferies WA. Evidence of selective processing of immunodominant epitopes in virally infected cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 164:4513-21. [PMID: 10779752 DOI: 10.4049/jimmunol.164.9.4513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent advances in clarifying the molecular mechanisms involved in Ag processing and presentation have relied heavily on the use of somatic cell mutants deficient in proteasome subunits, TAP transporter, and cell surface expression of MHC class I molecules. Of particular interest currently are those mutants that lack specific protease activity involved in the generation of antigenic peptides. It is theoretically possible that deficiencies of this nature could selectively prevent the cleavage of certain peptide bonds and thus generate only a subset of antigenic peptides. Gro29/Kb cell line is derived from the wild-type murine Ltk- cell line. This cell line is one example of a mutant that lacks specific protease activities. This deficiency manifests itself in an inability to generate a subset of immunodominant peptide epitopes derived from vesicular stomatitis virus and herpes simplex virus. This in turn leads to a general inability to present these viral epitopes to cytotoxic T lymphocytes (CTL). These studies describe a unique Ag processing deficiency and provide new insight into the role of proteasome-independent proteases in MHC class I-restricted peptide generation.
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Affiliation(s)
- Q J Zhang
- Biotechnology Laboratory and Biomedical Research Centre, Medical Genetics and Zoology, University of British Columbia, Vancouver, Canada
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Stevens J, Wiesmüller KH, Butcher GW, Joly E. Analysis of peptide length preference of the rat MHC class Ia molecule RT1-A(u), by a modified random peptide library approach. Int Immunol 2000; 12:83-9. [PMID: 10607753 DOI: 10.1093/intimm/12.1.83] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using random peptide libraries we have previously shown that both mouse and rat class I molecules can exhibit different peptide length preferences. Such studies required expression of the particular class I molecules in RMA-S, a cell line deficient in the transporter associated with antigen presentation (TAP). For another rat class I molecule called RT1-A(u), however, we found that expression in RMA-S was poor and could not be increased sufficiently by incubation at 26 degrees C. To circumvent this problem we performed our studies on C58, a rat cell line that expresses RT1-A(u) naturally in the presence of a functional TAP transporter. Using C58 cells, cell-surface-expressed class I molecules were 'stripped' of peptides and beta(2)-microglobulin by washing the cells with an acidic citrate buffer (pH 3.3). Peptide stabilization assays, assessed by FACS analysis, were then performed using either specific peptides or synthetic random peptide libraries of different lengths (7-15 amino acids), supplemented with recombinant rat beta(2)-microglobulin. As a positive control an RT1-A(u)-specific nonamer peptide was designed using the previously determined peptide binding motif and this was found to bind to RT1-A(u) at nanomolar concentrations. Both length preference and importance of free N- and C-termini were tested using free base, formylated and acetylated peptide libraries. Results showed that RT1-A(u) was not able to accommodate N- or C-terminally blocked peptides but displayed a preference for peptides of 9-12 amino acids, similar to the preference observed for the RT1-A1(c) allotype, the other rat TAP-B-associated molecule tested thus far. These results suggest that length preference remains a consideration to explain the allelic class I-TAP associations of the RT1-A region.
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Affiliation(s)
- J Stevens
- Laboratory of Functional Immunogenetics, The Babraham Institute, Cambridge CB2 4AT, UK. EMC Microcollections, Sindelfinger Strasse 3, 7020 Tübingen, Germany
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Fierabracci A, Biro PA, Yiangou Y, Mennuni C, Luzzago A, Ludvigsson J, Cortese R, Bottazzo GF. Osteopontin is an autoantigen of the somatostatin cells in human islets: identification by screening random peptide libraries with sera of patients with insulin-dependent diabetes mellitus. Vaccine 1999; 18:342-54. [PMID: 10506661 DOI: 10.1016/s0264-410x(99)00204-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Random peptide libraries (RPLs) screening with IDDM sera has identified 5 disease-specific 'mimotopes' displayed on phage (phagotopes). We characterised one phagotope (CH1p), by raising a rabbit antibody against the peptide insert on phage, which was employed in immunohistochemistry, Western blotting and cDNA libraries screening. The CH1p mimotope was detected in somatostatin cells of human islets and experimentally raised anti-osteopontin antibodies or human sera positive for the phagotope, detected a similar subpopulation of islet cells. The screening of cDNA library identified a clone corresponding to human osteopontin. In summary, RPLs proved to be successful in the identification of a novel islet-related autoantigen (osteopontin), whose significance in disease remains to be established.
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Affiliation(s)
- A Fierabracci
- Department of Immunology, St Bartholomew's and the Royal London School of Medicine and Dentistry, Turner Street, London, UK
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25
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Hansen JD, Strassburger P, Thorgaard GH, Young WP, Du Pasquier L. Expression, Linkage, and Polymorphism of MHC-Related Genes in Rainbow Trout, Oncorhynchus mykiss. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.163.2.774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The architecture of the MHC in teleost fish, which display a lack of linkage between class I and II genes, differs from all other vertebrates. Because rainbow trout have been examined for a variety of immunologically relevant genes, they present a good teleost model for examining both the expression and organization of MHC-related genes. Full-length cDNA and partial gDNA clones for proteasome δ, low molecular mass polypeptide (LMP) 2, TAP1, TAP2A, TAP2B, class Ia, and class IIB were isolated for this study. Aside from the expected polymorphisms associated with class I genes, LMP2 and TAP2 are polygenic. More specifically, we found a unique lineage of LMP2 (LMP2/δ) that shares identity to both LMP2 and δ but is expressed like the standard LMP2. Additionally, two very different TAP2 loci were found, one of which encodes polymorphic alleles. In general, the class I pathway genes are expressed in most tissues, with highest levels in lymphoid tissue. We then analyzed the basic genomic organization of the trout MHC in an isogenic backcross. The main class Ia region does not cosegregate with the class IIB locus, but LMP2, LMP2/δ, TAP1A, and TAP2B are linked to the class Ia locus. Interestingly, TAP2A (second TAP2 locus) is a unique lineage in sequence composition that appears not to be linked to this cluster or to class IIB. These results support and extend the recent findings of nonlinkage between class I and II in a different teleost order (cyprinids), suggesting that this unique arrangement is common to all teleosts.
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Affiliation(s)
- John D. Hansen
- *Basel Institute for Immunology, Basel, Switzerland; and Departments of
| | | | - Gary H. Thorgaard
- †Zoology,
- ‡Genetics, and Cell Biology, Washington State University, Pulman, WA
| | | | - Louis Du Pasquier
- *Basel Institute for Immunology, Basel, Switzerland; and Departments of
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Abstract
Degeneracy rather than unique ligand specificity seems to guide T cell functions. This view has evolved from analyses of T cell development and responses in vivo, as well as studies with synthetic molecular libraries in vitro, and has opened new prospects both for understanding T cell biology and for applied immunology.
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Affiliation(s)
- K Sparbier
- Department of Dermatology, Medical Faculty Charité, Humboldt University, D-10089, Berlin, Germany
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Affiliation(s)
- E Joly
- Dept of Immunology, Babraham Institute, Cambridge, UK.
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