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Dokuz S, Tasdurmazli S, Acar T, Duran GN, Ozdemir C, Ozbey U, Ozbil M, Karadayi S, Bayrak OF, Derman S, Chen JYS, Ozbek T. Evaluation of bacteriophage ϕ11 host recognition protein and its host-binding peptides for diagnosing/targeting Staphylococcus aureus infections. Int J Antimicrob Agents 2024; 64:107230. [PMID: 38824973 DOI: 10.1016/j.ijantimicag.2024.107230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Evaluating the potential of using both synthetic and biological products as targeting agents for the diagnosis, imaging, and treatment of infections due to particularly antibiotic-resistant pathogens is important for controlling infections. This study examined the interaction between Gp45, a receptor-binding protein of the ϕ11 lysogenic phage, and its host Staphylococcus aureus (S. aureus), a common cause of nosocomial infections. METHODS Using molecular dynamics and docking simulations, this study identified the peptides that bind to S. aureus wall teichoic acids via Gp45. It compared the binding affinity of Gp45 and the two highest-scoring peptide sequences (P1 and P3) and their scrambled forms using microscopy, spectroscopy, and ELISA. RESULTS It was found that rGp45 (recombinant Gp45) and chemically synthesised P1 had a higher binding affinity for S. aureus compared with all other peptides, except for Escherichia coli. Furthermore, rGp45 had a capture efficiency of > 86%; P1 had a capture efficiency of > 64%. CONCLUSION These findings suggest that receptor-binding proteins such as rGp45, which provide a critical initiation of the phage life cycle for host adsorption, might play an important role in the diagnosis, imaging, and targeting of bacterial infections. Studying such proteins could accordingly enable the development of effective strategies for controlling infections.
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Affiliation(s)
- Senanur Dokuz
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Semra Tasdurmazli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Tayfun Acar
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Gizem Nur Duran
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Cilem Ozdemir
- Department of Medical Biology, Health Sciences Institution, Mugla Sitki Kocman University, Mugla, Turkey
| | - Utku Ozbey
- Department of Medical Genetics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Mehmet Ozbil
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Sukriye Karadayi
- Department of Medical Laboratory Techniques, Vocational School of Health Services, Altınbas University, Istanbul, Turkey
| | - Omer Faruk Bayrak
- Department of Medical Genetics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Serap Derman
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - John Yu-Shen Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tulin Ozbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey.
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Pashova S, Balabanski L, Elmadjian G, Savov A, Stoyanova E, Shivarov V, Petrov P, Pashov A. Restriction of the Global IgM Repertoire in Antiphospholipid Syndrome. Front Immunol 2022; 13:865232. [PMID: 35493489 PMCID: PMC9043687 DOI: 10.3389/fimmu.2022.865232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
The typical anti-phospholipid antibodies (APLA) in the anti-phospholipid syndrome (APS) are reactive with the phospholipid-binding protein β2GPI as well as a growing list of other protein targets. The relation of APLA to natural antibodies and the fuzzy set of autoantigens involved provoked us to study the changes in the IgM repertoire in APS. To this end, peptides selected by serum IgM from a 7-residue linear peptide phage display library (PDL) were deep sequenced. The analysis was aided by a novel formal representation of the Igome (the mimotope set reflecting the IgM specificities) in the form of a sequence graph. The study involved women with APLA and habitual abortions (n=24) compared to age-matched clinically healthy pregnant women (n=20). Their pooled Igomes (297 028 mimotope sequences) were compared also to the global public repertoire Igome of pooled donor plasma IgM (n=2 796 484) and a set of 7-mer sequences found in the J regions of human immunoglobulins (n=4 433 252). The pooled Igome was represented as a graph connecting the sequences as similar as the mimotopes of the same monoclonal antibody. The criterion was based on previously published data. In the resulting graph, identifiable clusters of vertices were considered related to the footprints of overlapping antibody cross-reactivities. A subgraph based on the clusters with a significant differential expression of APS patients' mimotopes contained predominantly specificities underrepresented in APS. The differentially expressed IgM footprints showed also an increased cross-reactivity with immunoglobulin J regions. The specificities underexpressed in APS had a higher correlation with public specificities than those overexpressed. The APS associated specificities were strongly related also to the human peptidome with 1 072 mimotope sequences found in 7 519 human proteins. These regions were characterized by low complexity. Thus, the IgM repertoire of the APS patients was found to be characterized by a significant reduction of certain public specificities found in the healthy controls with targets representing low complexity linear self-epitopes homologous to human antibody J regions.
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Affiliation(s)
- Shina Pashova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
- Genomics Laboratory, Hospital “Malinov”, Sofia, Bulgaria
| | - Gabriel Elmadjian
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Alexey Savov
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Elena Stoyanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Peter Petrov
- Institute Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anastas Pashov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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3
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Haque S, Swami P, Khan A. S. Typhi derived vaccines and a proposal for outer membrane vesicles (OMVs) as potential vaccine for typhoid fever. Microb Pathog 2021; 158:105082. [PMID: 34265371 DOI: 10.1016/j.micpath.2021.105082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022]
Abstract
Typhoid fever is a serious systemic infection caused by Salmonella Typhi (S. Typhi), spread by the feco-oral route and closely associated with poor food hygiene and inadequate sanitation. Nearly 93% of S. Typhi strains have acquired antibiotic resistance against most antibiotics. Vaccination is the only promising way to prevent typhoid fever. This review covers the nature and composition of S. Typhi, pathogenecity and mode of infection, epidemiology, and nature of drug resistance. Several components (Vi-polysaccharides, O-antigens, flagellar antigens, full length OMPs, and short peptides from OMPs) of S. Typhi have been utilized for vaccine design for protection against typhoid fever. Vaccine delivery systems also contribute to efficacy of the vaccines. In this study, we propose to develop S. Typhi derived OMVs as vaccine for protection against typhoid fevers.
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Affiliation(s)
- Shabirul Haque
- Feinstein Institute for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA.
| | - Pooja Swami
- Feinstein Institute for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA.
| | - Azhar Khan
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal, Pradesh, India.
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4
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Sandomenico A, Caporale A, Doti N, Cross S, Cruciani G, Chambery A, De Falco S, Ruvo M. Synthetic Peptide Libraries: From Random Mixtures to In Vivo Testing. Curr Med Chem 2020; 27:997-1016. [PMID: 30009695 DOI: 10.2174/0929867325666180716110833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 01/13/2023]
Abstract
Combinatorially generated molecular repertoires have been largely used to identify novel bioactive compounds. Ever more sophisticated technological solutions have been proposed to simplify and speed up such process, expanding the chemical diversity space and increasing the prospect to select new molecular entities with specific and potent activities against targets of therapeutic relevance. In this context, random mixtures of oligomeric peptides were originally used and since 25 years they represent a continuous source of bioactive molecules with potencies ranging from the sub-nM to microM concentration. Synthetic peptide libraries are still employed as starting "synthetic broths" of structurally and chemically diversified molecular fragments from which lead compounds can be extracted and further modified. Thousands of studies have been reported describing the application of combinatorial mixtures of synthetic peptides with different complexity and engrafted on diverse structural scaffolds for the identification of new compounds which have been further developed and also tested in in vivo models of relevant diseases. We briefly review some of the most used methodologies for library preparation and screening and the most recent case studies appeared in the literature where compounds have reached at least in vivo testing in animal or similar models. Recent technological advancements in biotechnology, engineering and computer science have suggested new options to facilitate the discovery of new bioactive peptides. In this instance, we anticipate here a new approach for the design of simple but focused tripeptide libraries against druggable cavities of therapeutic targets and its complementation with existing approaches.
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Affiliation(s)
- Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Andrea Caporale
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Simon Cross
- Molecular Discovery Ltd, Unit 501 Centennial Park, Centennial Avenue Elstree, Borehamwood, Hertfordshire WD6 3FG, United Kingdom
| | - Gabriele Cruciani
- Molecular Discovery Ltd, Unit 501 Centennial Park, Centennial Avenue Elstree, Borehamwood, Hertfordshire WD6 3FG, United Kingdom.,Dipartimento di Chimica, Biologia e Biotecnologia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Angela Chambery
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Sandro De Falco
- Istituto di Genetica e Biofisica del CNR, via Pietro Castellino, 111, 80131, Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
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5
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Miles JJ, Tan MP, Dolton G, Edwards ES, Galloway SA, Laugel B, Clement M, Makinde J, Ladell K, Matthews KK, Watkins TS, Tungatt K, Wong Y, Lee HS, Clark RJ, Pentier JM, Attaf M, Lissina A, Ager A, Gallimore A, Rizkallah PJ, Gras S, Rossjohn J, Burrows SR, Cole DK, Price DA, Sewell AK. Peptide mimic for influenza vaccination using nonnatural combinatorial chemistry. J Clin Invest 2018; 128:1569-1580. [PMID: 29528337 PMCID: PMC5873848 DOI: 10.1172/jci91512] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/18/2018] [Indexed: 01/11/2023] Open
Abstract
Polypeptide vaccines effectively activate human T cells but suffer from poor biological stability, which confines both transport logistics and in vivo therapeutic activity. Synthetic biology has the potential to address these limitations through the generation of highly stable antigenic "mimics" using subunits that do not exist in the natural world. We developed a platform based on D-amino acid combinatorial chemistry and used this platform to reverse engineer a fully artificial CD8+ T cell agonist that mirrored the immunogenicity profile of a native epitope blueprint from influenza virus. This nonnatural peptide was highly stable in human serum and gastric acid, reflecting an intrinsic resistance to physical and enzymatic degradation. In vitro, the synthetic agonist stimulated and expanded an archetypal repertoire of polyfunctional human influenza virus-specific CD8+ T cells. In vivo, specific responses were elicited in naive humanized mice by subcutaneous vaccination, conferring protection from subsequent lethal influenza challenge. Moreover, the synthetic agonist was immunogenic after oral administration. This proof-of-concept study highlights the power of synthetic biology to expand the horizons of vaccine design and therapeutic delivery.
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Affiliation(s)
- John J. Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Griffith University, Brisbane, Queensland, Australia
| | - Mai Ping Tan
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Emily S.J. Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sarah A.E. Galloway
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Bruno Laugel
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Mathew Clement
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Julia Makinde
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | | | - Thomas S. Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katie Tungatt
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Han Siean Lee
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard J. Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Johanne M. Pentier
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anya Lissina
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ann Ager
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Awen Gallimore
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Pierre J. Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Scott R. Burrows
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David K. Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A. Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Andrew K. Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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6
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Identification of human viral protein-derived ligands recognized by individual MHCI-restricted T-cell receptors. Immunol Cell Biol 2016; 94:573-82. [PMID: 26846725 PMCID: PMC4943067 DOI: 10.1038/icb.2016.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 12/23/2015] [Accepted: 01/18/2016] [Indexed: 12/12/2022]
Abstract
Evidence indicates that autoimmunity can be triggered by virus-specific CD8+ T cells that crossreact with self-derived peptide epitopes presented on the cell surface by major histocompatibility complex class I (MHCI) molecules. Identification of the associated viral pathogens is challenging because individual T-cell receptors can potentially recognize up to a million different peptides. Here, we generate peptide length-matched combinatorial peptide library (CPL) scan data for a panel of virus-specific CD8+ T-cell clones spanning different restriction elements and a range of epitope lengths. CPL scan data drove a protein database search limited to viruses that infect humans. Peptide sequences were ranked in order of likelihood of recognition. For all anti-viral CD8+ T-cell clones examined in this study, the index peptide was either the top-ranked sequence or ranked as one of the most likely sequences to be recognized. Thus, we demonstrate that anti-viral CD8+ T-cell clones are highly focused on their index peptide sequence and that ‘CPL-driven database searching' can be used to identify the inciting virus-derived epitope for a given CD8+ T-cell clone. Moreover, to augment access to CPL-driven database searching, we have created a publicly accessible webtool. Application of these methodologies in the clinical setting may clarify the role of viral pathogens in the etiology of autoimmune diseases.
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Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat Immunol 2016; 17:87-94. [PMID: 26523866 PMCID: PMC4684756 DOI: 10.1038/ni.3310] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/29/2015] [Indexed: 01/07/2023]
Abstract
The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.
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8
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Review on the identification and role of Toxoplasma gondii antigenic epitopes. Parasitol Res 2015; 115:459-68. [PMID: 26581372 DOI: 10.1007/s00436-015-4824-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/10/2015] [Indexed: 12/12/2022]
Abstract
Toxoplasma gondii is an obligate intracellular protozoan parasite with a broad range of hosts, and it causes severe toxoplasmasis in both humans and animals. It is well known that the progression and severity of a disease depend on the immunological status of the host. Immunological studies on antigens indicate that antigens do not exert their functions through the entire protein molecule, but instead, specific epitopes are responsible for the immune response. Protein antigens not only contain epitope structures used by B, T, cytotoxic T lymphocyte (CTL), and NK cells to mediate immunological responses but can also contain structures that are unfavorable for protective immunity. Therefore, the study of antigenic epitopes from T. gondii has not only enhanced our understanding of the structure and function of antigens, the reactions between antigens and antibodies, and many other aspects of immunology but it also plays a significant role in the development of new diagnostic reagents and vaccines. In this review, we summarized the immune mechanisms induced by antigen epitopes and the latest advances in identifying T. gondii antigen epitopes. Particular attention was paid to the potential clinical usefulness of epitopes in this context. Through a critical analysis of the current state of knowledge, we elucidated the latest data concerning the biological effects of epitopes and the immune results aimed at the development of future epitope-based applications, such as vaccines and diagnostic reagents.
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9
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Falconer J, Lowes K, Furmanski AL, Dyson J, Ng WF, Robinson JH. Intramolecular polyspecificity in CD4 T-cell recognition of Ad-restricted epitopes of proteoglycan aggrecan. Immunology 2014; 142:101-110. [PMID: 24843873 DOI: 10.1111/imm.12238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
T-cell recognition of MHC–peptide complexes shows a high degree of polyspecificity extending to recognition of a large number of structurally unrelated peptides. Examples of polyspecificity reported to date are confined to recognition of epitopes from distinct proteins or synthetic peptide libraries. Here we describe intramolecular polyspecificity of CD4 T cells specific for several epitopes within proteoglycan aggrecan, a structural glycoprotein of cartilage and candidate autoantigen in rheumatoid arthritis. T-cell hybridomas from aggrecan-immunized mice recognized four structurally unrelated epitopes from the G1 domain of aggrecan, but not other aggrecan epitopes or a variety of other peptide epitopes restricted by the same MHC class II allele. We also showed that the hierarchy of cross-reactivity broadly correlated with the strength of peptide binding to MHC class II. Similar polyspecificity was observed in responses of lymph node cells from peptide-immunized mice, suggesting polyspecificity of a significant proportion of the in vivo aggrecan specific T-cell repertoire. Polyspecific recognition of several epitopes within the same autoantigen may provide a novel mechanism to reach the activation threshold of low-affinity autoreactive T cells in the initiation of autoimmune diseases.
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Wu B, Zhang Z, Noberini R, Barile E, Giulianotti M, Pinilla C, Houghten RA, Pasquale EB, Pellecchia M. HTS by NMR of combinatorial libraries: a fragment-based approach to ligand discovery. ACTA ACUST UNITED AC 2013; 20:19-33. [PMID: 23352136 DOI: 10.1016/j.chembiol.2012.10.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 10/17/2012] [Accepted: 10/19/2012] [Indexed: 11/29/2022]
Abstract
Fragment-based ligand design (FBLD) approaches have become more widely used in drug discovery projects from both academia and industry, and are even often preferred to traditional high-throughput screening (HTS) of large collection of compounds (>10(5)). A key advantage of FBLD approaches is that these often rely on robust biophysical methods such as NMR spectroscopy for detection of ligand binding, hence are less prone to artifacts that too often plague the results from HTS campaigns. In this article, we introduce a screening strategy that takes advantage of both the robustness of protein NMR spectroscopy as the detection method, and the basic principles of combinatorial chemistry to enable the screening of large libraries of fragments (>10(5) compounds) preassembled on a common backbone. We used the method to identify compounds that target protein-protein interactions.
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Affiliation(s)
- Bainan Wu
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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11
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Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A. Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles. Immunogenetics 2013; 65:371-86. [PMID: 23417323 PMCID: PMC3633659 DOI: 10.1007/s00251-013-0686-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 01/23/2013] [Indexed: 02/07/2023]
Abstract
Chinese rhesus macaques are of particular interest in simian immunodeficiency virus/human immunodeficiency virus (SIV/HIV) research as these animals have prolonged kinetics of disease progression to acquired immunodeficiency syndrome (AIDS), compared to their Indian counterparts, suggesting that they may be a better model for HIV. Nevertheless, the specific mechanism(s) accounting for these kinetics remains unclear. The study of major histocompatibility complex (MHC) molecules, including their MHC/peptide-binding motifs, provides valuable information for measuring cellular immune responses and deciphering outcomes of infection and vaccine efficacy. In this study, we have provided detailed characterization of six prevalent Chinese rhesus macaque MHC class I alleles, yielding a combined phenotypic frequency of 29 %. The peptide-binding specificity of two of these alleles, Mamu-A2*01:02 and Mamu-B*010:01, as well as the previously characterized allele Mamu-B*003:01 (and Indian rhesus Mamu-B*003:01), was found to be analogous to that of alleles in the HLA-B27 supertype family. Specific alleles in the HLA-B27 supertype family, including HLA-B*27:05, have been associated with long-term nonprogression to AIDS in humans. All six alleles characterized in the present study were found to have specificities analogous to HLA supertype alleles. These data contribute to the concept that Chinese rhesus macaque MHC immunogenetics is more similar to HLA than their Indian rhesus macaque counterparts and thereby warrants further studies to decipher the role of these alleles in the context of SIV infection.
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Affiliation(s)
- Bianca R Mothé
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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12
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Birnbaum ME, Dong S, Garcia KC. Diversity-oriented approaches for interrogating T-cell receptor repertoire, ligand recognition, and function. Immunol Rev 2013; 250:82-101. [PMID: 23046124 DOI: 10.1111/imr.12006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular diversity lies at the heart of adaptive immunity. T-cell receptors and peptide-major histocompatibility complex molecules utilize and rely upon an enormous degree of diversity at the levels of genetics, chemistry, and structure to engage one another and carry out their functions. This high level of diversity complicates the systematic study of important aspects of T-cell biology, but recent technical advances have allowed for the ability to study diversity in a comprehensive manner. In this review, we assess insights gained into T-cell receptor function and biology from our increasingly precise ability to assess the T-cell repertoire as a whole or to perturb individual receptors with engineered reagents. We conclude with a perspective on a new class of high-affinity, non-stimulatory peptide ligands we have recently discovered using diversity-oriented techniques that challenges notions for how we think about T-cell receptor signaling.
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Affiliation(s)
- Michael E Birnbaum
- Department of Molecular and Cellular Physiology, Program in Immunology, Stanford University School of Medicine, CA, USA
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13
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Pinilla C, Appel JR, Judkowski V, Houghten RA. Identification of B cell and T cell epitopes using synthetic peptide combinatorial libraries. CURRENT PROTOCOLS IN IMMUNOLOGY 2012; Chapter 9:9.5.1-9.5.16. [PMID: 23129156 PMCID: PMC3511046 DOI: 10.1002/0471142735.im0905s99] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This unit presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries of peptide molecules. The protocols employ peptide libraries to identify peptides recognized by MAbs and T cells. The first protocol uses a positional scanning peptide library made up of hexapeptides to identify antigenic determinants recognized by MAbs. The 120 mixtures in the hexapeptide library are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide library to identify T cell peptide ligands. The 200 mixtures of the decapeptide library are tested for their ability to induce T cell activation. Support protocols cover optimization of the assay conditions for each MAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide library, along with deconvolution approaches.
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Affiliation(s)
| | - Jon R Appel
- Torrey Pines Institute for Molecular Studies, San Diego, California
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14
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Abstract
Clonal selection theory proposed that individual T cells are specific for a single peptide-MHC antigen. However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide-MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. This compromise on specificity has profound implications because the chance of any natural peptide-MHC ligand being an optimal fit for its cognate TCR is small, as there will almost always be more-potent agonists. Furthermore, any TCR raised against a specific peptide-MHC complex in vivo can only be the best available solution from the naive T cell pool and is unlikely to be the best possible solution from the substantially greater number of TCRs that could theoretically be produced. This 'systems view' of TCR recognition provides a plausible cause for autoimmune disease and substantial scope for multiple therapeutic interventions.
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Affiliation(s)
- Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.
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15
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Sette A, Sidney J, Southwood S, Moore C, Berry J, Dow C, Bradley K, Hoof I, Lewis MG, Hildebrand WH, McMurtrey CP, Wilson NA, Watkins DI, Mothé BR. A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules. Immunogenetics 2012; 64:421-34. [PMID: 22322672 PMCID: PMC3349854 DOI: 10.1007/s00251-011-0598-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/25/2011] [Indexed: 02/07/2023]
Abstract
The SIV-infected rhesus macaque (Macaca mulatta) is the most established model of AIDS disease systems, providing insight into pathogenesis and a model system for testing novel vaccines. The understanding of cellular immune responses based on the identification and study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide-binding motif, provides valuable information to decipher outcomes of infection and vaccine efficacy. Detailed characterization of Mamu-B*039:01, a common allele expressed in Chinese rhesus macaques, revealed a unique MHC:peptide-binding preference consisting of glycine at the second position. Peptides containing a glycine at the second position were shown to be antigenic from animals positive for Mamu-B*039:01. A similar motif was previously described for the Dd mouse MHC allele, but for none of the human HLA molecules for which a motif is known. Further investigation showed that one additional macaque allele, present in Indian rhesus macaques, Mamu-B*052:01, shares this same motif. These “G2” alleles were associated with the presence of specific residues in their B pocket. This pocket structure was found in 6% of macaque sequences but none of 950 human HLA class I alleles. Evolutionary studies using the “G2” alleles points to common ancestry for the macaque sequences, while convergent evolution is suggested when murine and macaque sequences are considered. This is the first detailed characterization of the pocket residues yielding this specific motif in nonhuman primates and mice, revealing a new supertype motif not present in humans.
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Affiliation(s)
- Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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16
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Rosenfeld L, Shreffler W, Bardina L, Niggemann B, Wahn U, Sampson HA, Beyer K. Walnut allergy in peanut-allergic patients: significance of sequential epitopes of walnut homologous to linear epitopes of Ara h 1, 2 and 3 in relation to clinical reactivity. Int Arch Allergy Immunol 2011; 157:238-45. [PMID: 22042002 DOI: 10.1159/000327841] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 03/25/2011] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Peanut allergy is a frequent and potentially life-threatening food allergy. Despite the large taxonomic distance between the plants, peanut-allergic patients often react to tree nuts such as walnuts. While the allergens of peanut and walnut have a high degree of homology in their amino-acid sequences, it is unknown whether this similarity is responsible for the observed co-reactivity. Therefore, we analyzed the binding of specific IgE antibodies to sequential epitopes of peanut and walnut in peanut-allergic patients with and without walnut allergy. METHODS The IgE binding to previously described sequential epitopes of peanut and the homologous regions of walnut was assessed in 32 peanut-allergic patients using a peptide microarray technology. Twelve patients had a clinically relevant walnut allergy and 20 were tolerant to walnut. Inhibition assays with peanut peptides and corresponding walnut sequences were performed to show specific binding to sequential epitopes. RESULTS No differences in the recognition of sequential epitopes could be found between peanut-allergic patients with or without walnut allergy. Only a few patients showed IgE binding to walnut sequences that corresponded to sequential epitopes of peanut. In the inhibition assays, no relevant cross-reacting IgE antibodies could be detected for the peptides analyzed. CONCLUSION Our results indicate that although they share a rather high degree of homology with the corresponding regions of walnut allergens, the sequence stretches previously identified as sequential IgE binding epitopes of Ara h 1, Ara h 2 and Ara h 3 have no IgE binding equivalents in walnut allergens.
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Affiliation(s)
- Leonard Rosenfeld
- Department of Pediatric Pneumology and Immunology, University Children's Hospital Charité, Berlin, Germany
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17
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Wucherpfennig KW, Sethi D. T cell receptor recognition of self and foreign antigens in the induction of autoimmunity. Semin Immunol 2011; 23:84-91. [PMID: 21306912 DOI: 10.1016/j.smim.2011.01.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 01/10/2011] [Indexed: 10/18/2022]
Abstract
The major histocompatibility complex (MHC) on human chromosome 6 represents the most important genetic locus for a number of common human autoimmune diseases. Specific alleles that differ from closely related alleles by only one or a few amino acids in the peptide binding groove are frequently strongly associated with disease susceptibility, raising the important question of which peptide presentation events are critical in disease initiation and progression. This review will cover a number of topics pertinent to this fundamental question, including MHC linked disease susceptibility to autoimmune diseases, molecular mechanisms for the role of MHC molecules in autoimmune diseases as well as the recognition of self and microbial peptides by self-reactive T cell receptors (TCRs).
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Affiliation(s)
- Kai W Wucherpfennig
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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18
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Evans DW, Muller-Loennies S, Brooks CL, Brade L, Kosma P, Brade H, Evans SV. Structural insights into parallel strategies for germline antibody recognition of lipopolysaccharide from Chlamydia. Glycobiology 2011; 21:1049-59. [DOI: 10.1093/glycob/cwr041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Blackler RJ, Müller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV. A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity. Biochemistry 2011; 50:3357-68. [DOI: 10.1021/bi101886v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan J. Blackler
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Sven Müller-Loennies
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Cory L. Brooks
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Dylan W. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Lore Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Helmut Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Stephen V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
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20
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Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities. Immunogenetics 2011; 63:275-90. [PMID: 21274527 PMCID: PMC3068250 DOI: 10.1007/s00251-010-0502-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/07/2010] [Indexed: 01/15/2023]
Abstract
The Simian immunodeficiency virus (SIV)-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection and AIDS-related research, despite the potential that macaques of Chinese origin is a more relevant model. Ongoing efforts to further characterize the Chinese rhesus macaques' major histocompatibility complex (MHC) for composition and function should facilitate greater utilization of the species. Previous studies have demonstrated that Chinese-origin M. mulatta (Mamu) class I alleles are more polymorphic than their Indian counterparts, perhaps inferring a model more representative of human MHC, human leukocyte antigen (HLA). Furthermore, the Chinese rhesus macaque class I allele Mamu-A1*02201, the most frequent allele thus far identified, has recently been characterized and shown to be an HLA-B7 supertype analog, the most frequent supertype in human populations. In this study, we have characterized two additional alleles expressed with high frequency in Chinese rhesus macaques, Mamu-A1*02601 and Mamu-B*08301. Upon the development of MHC-peptide-binding assays and definition of their associated motifs, we reveal that these Mamu alleles share peptide-binding characteristics with the HLA-A2 and HLA-A3 supertypes, respectively, the next most frequent human supertypes after HLA-B7. These data suggest that Chinese rhesus macaques may indeed be a more representative model of HLA gene diversity and function as compared to the species of Indian origin and therefore a better model for investigating human immune responses.
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21
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Solomon C, Southwood S, Hoof I, Rudersdorf R, Peters B, Sidney J, Pinilla C, Marcondes MCG, Ling B, Marx P, Sette A, Mothé BR. The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype. Immunogenetics 2010; 62:451-64. [PMID: 20480161 PMCID: PMC2890073 DOI: 10.1007/s00251-010-0450-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Accepted: 04/19/2010] [Indexed: 01/30/2023]
Abstract
Of the two rhesus macaque subspecies used for AIDS studies, the Simian immunodeficiency virus-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection, providing both insight into pathogenesis and a system for testing novel vaccines. Despite the Chinese rhesus macaque potentially being a more relevant model for AIDS outcomes than the Indian rhesus macaque, the Chinese-origin rhesus macaques have not been well-characterized for their major histocompatibility complex (MHC) composition and function, reducing their greater utilization. In this study, we characterized a total of 50 unique Chinese rhesus macaques from several varying origins for their entire MHC class I allele composition and identified a total of 58 unique complete MHC class I sequences. Only nine of the sequences had been associated with Indian rhesus macaques, and 28/58 (48.3%) of the sequences identified were novel. From all MHC alleles detected, we prioritized Mamu-A1*02201 for functional characterization based on its higher frequency of expression. Upon the development of MHC/peptide binding assays and definition of its associated motif, we revealed that this allele shares peptide binding characteristics with the HLA-B7 supertype, the most frequent supertype in human populations. These studies provide the first functional characterization of an MHC class I molecule in the context of Chinese rhesus macaques and the first instance of HLA-B7 analogy for rhesus macaques.
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Affiliation(s)
- Christopher Solomon
- Department of Biological Sciences, California State University - San Marcos, San Marcos, CA 92096 USA
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
| | - Scott Southwood
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
| | - Ilka Hoof
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Richard Rudersdorf
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Bjoern Peters
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
| | - John Sidney
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, La Jolla, CA 92037 USA
| | | | - Binhua Ling
- Department of Tropical Medicine, School of Public Health, Tulane University, New Orleans, LA 70112 USA
| | - Preston Marx
- Department of Tropical Medicine, School of Public Health, Tulane University, New Orleans, LA 70112 USA
| | - Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
| | - Bianca R. Mothé
- Department of Biological Sciences, California State University - San Marcos, San Marcos, CA 92096 USA
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
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22
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Lucas JM. Microarrays: Molecular allergology and nanotechnology for personalised medicine (II). Allergol Immunopathol (Madr) 2010; 38:217-23. [PMID: 20537785 DOI: 10.1016/j.aller.2010.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 04/20/2010] [Indexed: 02/07/2023]
Abstract
Progress in nanotechnology and DNA recombination techniques have produced tools for the diagnosis and investigation of allergy at molecular level. The most advanced examples of such progress are the microarray techniques, which have been expanded not only in research in the field of proteomics but also in application to the clinical setting. Microarrays of allergic components offer results relating to hundreds of allergenic components in a single test, and using a small amount of serum which can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. Their application opens the door to component-based diagnosis, to the holistic perception of sensitisation as represented by molecular allergy, and to patient-centred medical practice by allowing great diagnostic accuracy and the definition of individualised immunotherapy for each patient. The present article reviews the application of allergenic component microarrays to allergology for diagnosis, management in the form of specific immunotherapy, and epidemiological studies. A review is also made of the use of protein and gene microarray techniques in basic research and in allergological diseases. Lastly, an evaluation is made of the challenges we face in introducing such techniques to clinical practice, and of the future perspectives of this new technology.
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Affiliation(s)
- J M Lucas
- Section of Pediatric Allergy, Virgen de la Arrixaca University Hospital, Murcia, Spain.
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23
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Combining positional scanning peptide libraries, HLA-DR transfectants and bioinformatics to dissect the epitope spectrum of HLA class II cross-restricted CD4+ T cell clones. J Immunol Methods 2010; 353:93-101. [DOI: 10.1016/j.jim.2009.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/06/2009] [Accepted: 12/07/2009] [Indexed: 11/18/2022]
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24
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Cysteine-free proteins in the immunobiology of arthropod-borne diseases. J Biomed Biotechnol 2010; 2010:171537. [PMID: 20069123 PMCID: PMC2804111 DOI: 10.1155/2010/171537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 10/13/2009] [Indexed: 11/21/2022] Open
Abstract
One approach to identify epitopes that could be used in the design of vaccines to control several arthropod-borne diseases simultaneously is to look for common structural features in the secretome of the pathogens that cause them. Using a novel bioinformatics technique, cysteine-abundance and distribution analysis, we found that many different proteins secreted by several arthropod-borne pathogens, including Plasmodium falciparum, Borrelia burgdorferi, and eight species of Proteobacteria, are devoid of cysteine residues. The identification of three cysteine-abundance and distribution patterns in several families of proteins secreted by pathogenic and nonpathogenic Proteobacteria, and not found when the amino acid analyzed was tryptophan, provides evidence of forces restricting the content of cysteine residues in microbial proteins during evolution. We discuss these findings in the context of protein structure and function, antigenicity and immunogenicity, and host-parasite relationships.
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25
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Brooks CL, Blackler RJ, Sixta G, Kosma P, Müller-Loennies S, Brade L, Hirama T, MacKenzie CR, Brade H, Evans SV. The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen. Glycobiology 2009; 20:138-47. [PMID: 19767317 DOI: 10.1093/glycob/cwp150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In order to explore the structural basis for adaptability in near germline monoclonal antibodies (mAb), we have examined the specificity of the promiscuous mAb S67-27 to both naturally derived carbohydrate antigens and a variety of synthetic nonnatural antigens based on the bacterial lipopolysaccharide component 3-deoxy-alpha-D-manno-oct-2-ulosonic acid (Kdo). One such analog, a 7-O-methyl (7-O-Me) Kdo disaccharide, was found to bind to the antibody with at least 30-fold higher affinity than any other antigen tested. The structure of S67-27 in complex with this analog and three other naturally occurring Kdo antigens revealed that the enhanced affinity of the mAb for the synthetic analog was accomplished by the strategic positioning of CDR H3 away from a conserved Kdo binding pocket that allowed the formation of new antibody-antigen contacts. Furthermore, the comparison of this structure with the structures of related mAbs revealed how the position and structure of CDR H3 influence the specificity or promiscuity of near-germline carbohydrate-recognizing antibodies by altering the architecture of the combining site.
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Affiliation(s)
- Cory L Brooks
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
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26
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Voelter V, Rufer N, Reynard S, Greub G, Brookes R, Guillaume P, Grosjean F, Fagerberg T, Michelin O, Rowland-Jones S, Pinilla C, Leyvraz S, Romero P, Appay V. Characterization of Melan-A reactive memory CD8+ T cells in a healthy donor. Int Immunol 2008; 20:1087-96. [DOI: 10.1093/intimm/dxn066] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Pinilla C, Appel JR, Houghten RA. Identification of B cell and T cell epitopes using synthetic peptide combinatorial libraries. CURRENT PROTOCOLS IN IMMUNOLOGY 2008; Chapter 9:9.5.1-9.5.13. [PMID: 18432860 DOI: 10.1002/0471142735.im0905s45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries (SCL) of peptide molecules. The protocols employ peptide SCL to identify peptides recognized by mAbs and T cells. The first protocol uses a positional scanning SCL (PS-SCL) made up of hexapeptides to identify antigenic determinants recognized by mAbs. The 120 mixtures in the hexapeptide PS-SCL are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide PS-SCL to identify T cell peptide ligands. The 200 mixtures of the decapeptide PS-SCL are tested for their ability to induce proliferation. Support protocols cover optimization of the assay conditions for each mAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide PS-SCL, along with deconvolution approaches.
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Affiliation(s)
- C Pinilla
- Torrey Pines Institute for Molecular Studies, San Diego, California, USA
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28
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Exploration of Specificity in Germline Monoclonal Antibody Recognition of a Range of Natural and Synthetic Epitopes. J Mol Biol 2008; 377:450-68. [DOI: 10.1016/j.jmb.2008.01.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/30/2007] [Accepted: 01/02/2008] [Indexed: 11/21/2022]
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29
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McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. A new twist in TCR diversity revealed by a forbidden alphabeta TCR. J Mol Biol 2008; 375:1306-19. [PMID: 18155234 PMCID: PMC2330282 DOI: 10.1016/j.jmb.2007.11.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Revised: 10/27/2007] [Accepted: 11/08/2007] [Indexed: 11/26/2022]
Abstract
We report crystal structures of a negatively selected T cell receptor (TCR) that recognizes two I-A(u)-restricted myelin basic protein peptides and one of its peptide/major histocompatibility complex (pMHC) ligands. Unusual complementarity-determining region (CDR) structural features revealed by our analyses identify a previously unrecognized mechanism by which the highly variable CDR3 regions define ligand specificity. In addition to the pMHC contact residues contributed by CDR3, the CDR3 residues buried deep within the V alpha/V beta interface exert indirect effects on recognition by influencing the V alpha/V beta interdomain angle. This phenomenon represents an additional mechanism for increasing the potential diversity of the TCR repertoire. Both the direct and indirect effects exerted by CDR residues can impact global TCR/MHC docking. Analysis of the available TCR structures in light of these results highlights the significance of the V alpha/V beta interdomain angle in determining specificity and indicates that TCR/pMHC interface features do not distinguish autoimmune from non-autoimmune class II-restricted TCRs.
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MESH Headings
- Alanine/metabolism
- Amino Acid Substitution
- Animals
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Complementarity Determining Regions/metabolism
- Computer Simulation
- Crystallography, X-Ray
- DNA, Complementary
- Epitopes
- Escherichia coli/genetics
- Genetic Variation
- Glycine/metabolism
- Hydrogen Bonding
- Immunization
- Ligands
- Major Histocompatibility Complex/genetics
- Major Histocompatibility Complex/immunology
- Mice
- Mice, Knockout
- Models, Chemical
- Models, Molecular
- Mutagenesis, Site-Directed
- Myelin Basic Protein/immunology
- Peptides/chemistry
- Peptides/immunology
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/isolation & purification
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Retroviridae/genetics
- Selection, Genetic
- Sensitivity and Specificity
- Spodoptera/cytology
- Surface Plasmon Resonance
- Thymus Gland/immunology
- Transfection
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Affiliation(s)
- Christine McBeth
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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30
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Sidney J, Assarsson E, Moore C, Ngo S, Pinilla C, Sette A, Peters B. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res 2008; 4:2. [PMID: 18221540 PMCID: PMC2248166 DOI: 10.1186/1745-7580-4-2] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2007] [Accepted: 01/25/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been previously shown that combinatorial peptide libraries are a useful tool to characterize the binding specificity of class I MHC molecules. Compared to other methodologies, such as pool sequencing or measuring the affinities of individual peptides, utilizing positional scanning combinatorial libraries provides a baseline characterization of MHC molecular specificity that is cost effective, quantitative and unbiased. RESULTS Here, we present a large-scale application of this technology to 19 different human and mouse class I alleles. These include very well characterized alleles (e.g. HLA A*0201), alleles with little previous data available (e.g. HLA A*3201), and alleles with conflicting previous reports on specificity (e.g. HLA A*3001). For all alleles, the positional scanning combinatorial libraries were able to elucidate distinct binding patterns defined with a uniform approach, which we make available here. We introduce a heuristic method to translate this data into classical definitions of main and secondary anchor positions and their preferred residues. Finally, we validate that these matrices can be used to identify candidate MHC binding peptides and T cell epitopes in the vaccinia virus and influenza virus systems, respectively. CONCLUSION These data confirm, on a large scale, including 15 human and 4 mouse class I alleles, the efficacy of the positional scanning combinatorial library approach for describing MHC class I binding specificity and identifying high affinity binding peptides. These libraries were shown to be useful for identifying specific primary and secondary anchor positions, and thereby simpler motifs, analogous to those described by other approaches. The present study also provides matrices useful for predicting high affinity binders for several alleles for which detailed quantitative descriptions of binding specificity were previously unavailable, including A*3001, A*3201, B*0801, B*1501 and B*1503.
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Affiliation(s)
- John Sidney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Erika Assarsson
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Carrie Moore
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Sandy Ngo
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, 2-129, San Diego, CA 92121, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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Sidney J, Peters B, Moore C, Pencille TJ, Ngo S, Masterman KA, Asabe S, Pinilla C, Chisari FV, Sette A. Characterization of the peptide-binding specificity of the chimpanzee class I alleles A 0301 and A 0401 using a combinatorial peptide library. Immunogenetics 2007; 59:745-51. [PMID: 17701407 DOI: 10.1007/s00251-007-0243-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Accepted: 07/13/2007] [Indexed: 10/23/2022]
Abstract
Chimpanzees represent important models for studying several human pathogens. In the present study, we utilized a combinatorial peptide library to characterize the binding specificities of the chimpanzee class I molecules Patr A 0301 and A 0401, both of which are present in about 17% of chimpanzees. Patr A 0301 was found to recognize peptides using the canonical position 2/C-terminus spacing, with the small residues S, T, and A being the most preferred in position 2, and the positively charged residues R and K preferred at the C terminus. Patr A 0401 was found to recognize a more complex motif where the C terminus and then the residue in positions 1 and/or 5 are the primary anchors. Like A 0301, the C-terminal preference of A 0401 is for positively charged residues. At positions 1 and 5, positively charged and large residues are the most preferred, respectively. Coefficient values derived from the combinatorial library proved to be an efficient means for predicting A 0301 and A 0401 binders. The present data provide detailed information to facilitate the identification of potential T cell epitopes recognized in the context of two common chimpanzee class I alleles, and further validate the combinatorial library approach as an efficient method to characterize class I binding specificities.
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Affiliation(s)
- John Sidney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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Wucherpfennig KW, Allen PM, Celada F, Cohen IR, De Boer R, Garcia KC, Goldstein B, Greenspan R, Hafler D, Hodgkin P, Huseby ES, Krakauer DC, Nemazee D, Perelson AS, Pinilla C, Strong RK, Sercarz EE. Polyspecificity of T cell and B cell receptor recognition. Semin Immunol 2007; 19:216-24. [PMID: 17398114 PMCID: PMC2034306 DOI: 10.1016/j.smim.2007.02.012] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 02/26/2007] [Indexed: 02/06/2023]
Abstract
A recent workshop discussed the recognition of multiple distinct ligands by individual T cell and B cell receptors and the implications of this discovery for lymphocyte biology. The workshop recommends general use of the term polyspecificity because it emphasizes two fundamental aspects, the inherent specificity of receptor recognition and the ability to recognize multiple ligands. Many different examples of polyspecificity and the structural mechanisms were discussed, and the group concluded that polyspecificity is a general, inherent feature of TCR and antibody recognition. This review summarizes the relevance of polyspecificity for lymphocyte development, activation and disease processes.
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Affiliation(s)
- Kai W Wucherpfennig
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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Douat-Casassus C, Marchand-Geneste N, Diez E, Gervois N, Jotereau F, Quideau S. Synthetic anticancer vaccine candidates: rational design of antigenic peptide mimetics that activate tumor-specific T-cells. J Med Chem 2007; 50:1598-609. [PMID: 17328535 DOI: 10.1021/jm0613368] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rational design approach was followed to develop peptidomimetic analogues of a cytotoxic T-cell epitope capable of stimulating T-cell responses as strong as or stronger (heteroclytic) than those of parental antigenic peptides. The work described herein focused on structural alterations of the central amino acids of the melanoma tumor-associated antigenic peptide Melan-A/MART-1(26-35) using nonpeptidic units. A screening was first realized in silico to select altered peptides potentially capable of fitting at the interface between the major histocompatibilty complex (MHC) class-I HLA-A2 molecule and T-cell receptors (TCRs). Two compounds appeared to be high-affinity ligands to the HLA-A2 molecule and stimulated several Melan-A/MART-1 specific T-cell clones. Most remarkably, one of them even managed to amplify the response of one clone. Together, these results indicate that central TCR-contact residues of antigenic peptides can be replaced by nonpeptidic motifs without loss of binding affinity to MHC class-I molecules and T-cell triggering capacity.
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Affiliation(s)
- Céline Douat-Casassus
- Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
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Kangueane P, Sakharkar MK. HLA-peptide binding prediction using structural and modeling principles. Methods Mol Biol 2007; 409:293-299. [PMID: 18450009 DOI: 10.1007/978-1-60327-118-9_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Short peptides binding to specific human leukocyte antigen (HLA) alleles elicit immune response. These candidate peptides have potential utility in peptide vaccine design and development. The binding of peptides to allele-specific HLA molecule is estimated using competitive binding assay and biochemical binding constants. Application of this method for proteome-wide screening in parasites, viruses, and virulent bacterial strains is laborious and expensive. However, short listing of candidate peptides using prediction approaches have been realized lately. Prediction of peptide binding to HLA alleles using structural and modeling principles has gained momentum in recent years. Here, we discuss the current status of such prediction.
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Abstract
The smallpox vaccine consists of live vaccinia virus and is generally considered the gold standard of vaccines, since it is the only one that has led to the complete eradication of an infectious disease from the human population. Renewed fears that smallpox might be deliberately released in an act of bioterrorism have led to resurgence in the study of immunity and immunological memory to vaccinia virus and other poxviruses. Here we review our current understanding of memory T-cell, memory B-cell, and antibody responses to vaccinia and related poxviruses, both in animal models and human subjects. Of particular interest are recent advances in understanding protective immunity to poxviruses, quantifying immunological memory to the smallpox vaccine in humans, and identifying major vaccinia-specific T-cell and B-cell epitopes. In addition, potential mechanisms for maintenance of immunological memory are discussed.
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Affiliation(s)
- Ian J Amanna
- OHSU Vaccine and Gene Therapy Institute, Beaverton, OR, USA
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36
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Appay V, Speiser DE, Rufer N, Reynard S, Barbey C, Cerottini JC, Leyvraz S, Pinilla C, Romero P. Decreased specific CD8+ T cell cross-reactivity of antigen recognition following vaccination with Melan-A peptide. Eur J Immunol 2006; 36:1805-14. [PMID: 16761313 DOI: 10.1002/eji.200535805] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of T cell vaccines is the expansion of antigen-specific T cells able to confer immune protection against pathogens or tumors. Although increase in absolute cell numbers, effector functions and TCR repertoire of vaccine-induced T cells are often evaluated, their reactivity for the cognate antigen versus their cross-reactive potential is rarely considered. In fact, little information is available regarding the influence of vaccines on T cell fine specificity of antigen recognition despite the impact that this feature may have in protective immunity. To shed light on the cross-reactive potential of vaccine-induced cells, we analyzed the reactivity of CD8(+) T cells following vaccination of HLA-A2(+) melanoma patients with Melan-A peptide, incomplete Freund's adjuvant and CpG-oligodeoxynucleotide adjuvant, which was shown to induce strong expansion of Melan-A-reactive CD8(+) T cells in vivo. A collection of predicted Melan-A cross-reactive peptides, identified from a combinatorial peptide library, was used to probe functional antigen recognition of PBMC ex vivo and Melan-A-reactive CD8(+) T cell clones. While Melan-A-reactive CD8(+) T cells prior to vaccination are usually constituted of widely cross-reactive naive cells, we show that peptide vaccination resulted in expansion of memory T cells displaying a reactivity predominantly restricted to the antigen of interest. Importantly, these cells are tumor-reactive.
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Affiliation(s)
- Victor Appay
- Multidisciplinary Oncology Center, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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Demengeot J, Zelenay S, Moraes-Fontes MF, Caramalho I, Coutinho A. Regulatory T cells in microbial infection. ACTA ACUST UNITED AC 2006; 28:41-50. [PMID: 16874537 DOI: 10.1007/s00281-006-0024-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 06/19/2006] [Indexed: 11/25/2022]
Abstract
Natural T regulatory cells (NatTReg) limit immunopathology and protective immune responses induced upon microbial infection. In addition, infection increases the number and activity of NatTReg. These findings need to be conciliated with the process of 'self-nonself' discrimination based on the function of NatTReg committed intrathymically and positively selected (and activated) on thymic epithelial cells. A review of the available evidence comforts the assumptions that, in physiological conditions, NatTReg engaged in the immune responses to microbial infections are drawn from the autoreactive repertoire even if some may appear to be microbe specific. This contention also provides a suitable explanation for the 'hygiene hypothesis': infections re-enforce the physiological mechanisms of natural dominant tolerance, through the expansion of naturally occurring regulatory T cells. Accumulating evidence demonstrates that pro-inflammatory ligands of Toll-like receptors expressed by NatTReg, both of microbial (e.g., lipopolysaccharide, flagellin, peptidoglycans) and endogenous (e.g., stress proteins and degradation products of the extracellular matrix) origin, may play a critical role in their activation and expansion. As NatTReg vigorously respond to IL-2/IL-15 locally produced by ongoing effector responses, this whole set of mechanisms provides for a robust feedback process that limits tissue damage and accounts for an 'organism-centered' quality control of immune responses. Detailed knowledge on these molecular and cellular bases should open novel opportunities for intervention in a variety of critical conditions, such as autoimmunity, allergy, chronic infections, and cancer, for which we currently lack effective therapies.
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Affiliation(s)
- Jocelyne Demengeot
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande #6, Apartado 14, 2781-901, Oeiras, Portugal.
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38
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Otte L, Knaute T, Schneider-Mergener J, Kramer A. Molecular basis for the binding polyspecificity of an anti-cholera toxin peptide 3 monoclonal antibody. J Mol Recognit 2006; 19:49-59. [PMID: 16273596 DOI: 10.1002/jmr.757] [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] [Indexed: 11/07/2022]
Abstract
The onset of autoimmune diseases is proposed to involve binding promiscuity of antibodies (Abs) and T-cells, an often reported yet poorly understood phenomenon. Here, we attempt to approach two questions: first, is binding promiscuity a general feature of monoclonal antibodies (mAbs) and second, what is the molecular basis for polyspecificity? To this end, the anti-cholera toxin peptide 3 (CTP3) mAb TE33 was investigated for polyspecific binding properties. Screening of phage display libraries identified two epitope-unrelated peptides that specifically bound TE33 with affinities similar to or 100-fold higher than the wild-type epitope. Substitutional analyses revealed distinct key residue patterns recognized by the antibody suggesting a unique binding mode for each peptide. A database query with one of the consensus motifs and a subsequent binding study uncovered 45 peptides (derived from heterologous proteins) that bound TE33. To better understand the structural basis of the observed polyspecificity we modeled the new cyclic epitope in complex with TE33. The interactions between this peptide and TE33 suggested by our model are substantially different from the interactions observed in the X-ray structure of the wild-type epitope complex. However, the overall binding conformation of the peptides is similar. Together, our results support the theory of a general polyspecific potential of mAbs.
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Affiliation(s)
- Livia Otte
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Lustgarten J, Dominguez AL, Pinilla C. Identification of Cross-Reactive Peptides Using Combinatorial Libraries Circumvents Tolerance against Her-2/neu-Immunodominant Epitope. THE JOURNAL OF IMMUNOLOGY 2006; 176:1796-805. [PMID: 16424210 DOI: 10.4049/jimmunol.176.3.1796] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The majority of the currently defined tumor-associated Ags are often overexpressed products of normal cellular genes. Therefore, tolerance deletes high-affinity T cells directed against the TAAs, leaving only a low-affinity repertoire. We have demonstrated previously that the T cell repertoire against the immunodominant p773-782 A2.1-Her-2/neu-restricted peptide has low affinity in A2xneu mice (Her-2/neu mice crossed with A2.1/Kb mice), compared with A2xFVB mice (A2.1/Kb crossed with FVB-wild-type mice). Immunizations with this peptide have a minor impact in preventing tumor growth in A2xneu mice. Therefore, attempts to expand these responses may be of little clinical value. We hypothesized that if not all possible cross-reactive peptides (CPs) are naturally processed and presented, the possibility exists that T cells against these CPs persist in the repertoire and can be used to induce antitumor responses with higher avidity against native epitopes present on the tumor cells. We have used the positional scanning synthetic peptide combinatorial library methodology to screen the p773-782 T cell clone. The screening data identified potential amino acids that can be substituted in the primary sequences of the p773-782 peptide. The designed CPs induce CTL responses of higher affinity in A2xneu mice compared with the native p773-783 peptide. These CTLs recognize A2+-Her-2/neu(+) tumors with high efficiency. Moreover, multiple immunizations with CPs significantly prolonged the survival of tumor-bearing A2xneu mice. These results have demonstrated that it was possible to circumvent tolerance with the identification of CPs and that these peptides could be of significant clinical value.
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40
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Venturini S, Allicotti G, Zhao Y, Simon R, Burton DR, Pinilla C, Poignard P. Identification of peptides from human pathogens able to cross-activate an HIV-1-gag-specific CD4+ T cell clone. Eur J Immunol 2006; 36:27-36. [PMID: 16323241 DOI: 10.1002/eji.200425767] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antigen recognition by T cells is degenerate both at the MHC and the TCR level. In this study, we analyzed the cross-reactivity of a human HIV-1 gag p24-specific CD4(+) T cell clone obtained from an HIV-1-seronegative donor using a positional scanning synthetic combinatorial peptide library (PS-SCL)-based biometrical analysis. A number of decapeptides able to activate the HIV-1 gag-specific clone were identified and shown to correspond to sequences found in other human pathogens. Two of these peptides activated the T cell clone with the same stimulatory potency as the original HIV-1 gag p24 peptide. These findings show that an HIV-1-specific human T helper clone can react efficiently with peptides from other pathogens and suggest that cellular immune responses identified as being specific for one human pathogen (HIV-1) could arise from exposure to other pathogens.
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Affiliation(s)
- Sara Venturini
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
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41
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Shreffler WG, Lencer DA, Bardina L, Sampson HA. IgE and IgG4 epitope mapping by microarray immunoassay reveals the diversity of immune response to the peanut allergen, Ara h 2. J Allergy Clin Immunol 2005; 116:893-9. [PMID: 16210066 DOI: 10.1016/j.jaci.2005.06.033] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 06/09/2005] [Accepted: 06/10/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Detailed assessment of antibody responses to allergens reveals clinically relevant information about both host response and antigen structure. Microarray technology offers advantages of scale and parallel design over previous methods of epitope mapping. OBJECTIVE We designed a redundant peptide microarray for IgE and IgG4 epitope mapping of the previously characterized peanut allergen, Ara h 2. METHODS Six complete sets of overlapping peptides were commercially synthesized and site-specifically bound to epoxy-derivatized glass slides in triplicate. Peptides were 10, 15, or 20 amino acids in length with an offset of either 2 or 3 amino acids. A total of 10 control and 45 peanut-allergic sera were assayed. Specific IgE and IgG4 were detected by using fluorochrome-labeled monoclonal secondary antibodies. RESULTS By using 15-mer and 20-mer peptides, we could define 11 antigenic regions, whereas only 5 were identifiable using 10-mers. Controls and patients produced IgG4 recognizing a comparable number of Ara h 2 peptides, although the dominant epitopes were distinct. As expected, patient IgE bound a larger number of Ara h 2 peptides (9.4% vs 0.9%). IgE and IgG4 epitopes recognized by patients were largely the same, and there was a positive association between IgE and IgG(4) signal, suggesting coordinate regulation. Cluster analysis of peptide binding patterns confirmed the specificity of antibody-peptide interactions and was used to define 9 core epitopes ranging from 6 to 16 residues in length-7 of which (78%) agreed with previous mapping. CONCLUSION Epitope mapping by microarray peptide immunoassay and cluster analysis reveals interpatient heterogeneity and a more detailed map.
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Affiliation(s)
- Wayne G Shreffler
- Jaffe Food Allergy Institute, Department of Pediatrics, Division of Allergy and Immunology, Mount Sinai School of Medicine, New York, NY 10029, USA.
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42
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Li Y, Huang Y, Lue J, Quandt JA, Martin R, Mariuzza RA. Structure of a human autoimmune TCR bound to a myelin basic protein self-peptide and a multiple sclerosis-associated MHC class II molecule. EMBO J 2005; 24:2968-79. [PMID: 16079912 PMCID: PMC1201352 DOI: 10.1038/sj.emboj.7600771] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Accepted: 07/14/2005] [Indexed: 11/09/2022] Open
Abstract
Multiple sclerosis is mediated by T-cell responses to central nervous system antigens such as myelin basic protein (MBP). To investigate self-peptide/major histocompatibility complex (MHC) recognition and T-cell receptor (TCR) degeneracy, we determined the crystal structure, at 2.8 A resolution, of an autoimmune TCR (3A6) bound to an MBP self-peptide and the multiple sclerosis-associated MHC class II molecule, human leukocyte antigen (HLA)-DR2a. The complex reveals that 3A6 primarily recognizes the N-terminal portion of MBP, in contrast with antimicrobial and alloreactive TCRs, which focus on the peptide center. Moreover, this binding mode, which may be frequent among autoimmune TCRs, is compatible with a wide range of orientation angles of TCR to peptide/MHC. The interface is characterized by a scarcity of hydrogen bonds between TCR and peptide, and TCR-induced conformational changes in MBP/HLA-DR2a, which likely explain the low observed affinity. Degeneracy of 3A6, manifested by recognition of superagonist peptides bearing substitutions at nearly all TCR-contacting positions, results from the few specific interactions between 3A6 and MBP, allowing optimization of interface complementarity through variations in the peptide.
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Affiliation(s)
- Yili Li
- Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, MD, USA
| | - Yuping Huang
- Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, MD, USA
| | - Jessica Lue
- Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, MD, USA
| | - Jacqueline A Quandt
- Cellular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Roland Martin
- Cellular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Roy A Mariuzza
- Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, MD, USA
- Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA. Tel.: +1 301 738 6243; Fax: +1 301 738 6255; E-mail:
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43
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Boggiano C, Moya R, Pinilla C, Bihl F, Brander C, Sidney J, Sette A, Blondelle SE. Discovery and characterization of highly immunogenic and broadly recognized mimics of the HIV-1 CTL epitope Gag77-85. Eur J Immunol 2005; 35:1428-37. [PMID: 15789356 DOI: 10.1002/eji.200425903] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes (CTL) play an important role in HIV infection. Given the viral genetic diversity, the selection of suitable antigens and epitope variants will be important in the design of an effective vaccine. We have previously shown that combinatorial libraries are useful tools to identify epitope mimics as well as potentially cross-reactive natural sequences in protein databases. We have applied this approach to the HIV Gag p17-derived epitope SL9 (SLYNTVATL) to identify broadly recognized SL9 mimics and to assess the cross-recognition of naturally occurring SL9 variants. Nine nonapeptides were identified that were up to one order of magnitude more effective than SL9 in stimulating CTL responses in PBMC from HIV-infected subjects. Using transgenic mice, we demonstrate that a number of these epitope mimics were able to generate de novo T cell responses that cross-reacted with the original SL9 sequence. Particularly, mimics with changes at the relatively conserved F-pocket anchor residue were frequently cross-recognized. This approach may lead to vaccine candidates with higher in vivo immunogenicity and increased potential for cross-recognition of naturally occurring SL9 variants.
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Affiliation(s)
- César Boggiano
- Torrey Pines Institute for Molecular Studies, San Diego, USA
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44
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Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 2005; 6:132. [PMID: 15927070 PMCID: PMC1173087 DOI: 10.1186/1471-2105-6-132] [Citation(s) in RCA: 382] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Accepted: 05/31/2005] [Indexed: 12/12/2022] Open
Abstract
Background Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM). This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP) and proteasomal cleavage of protein sequences. Results Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1) the output generated is easy to interpret, (2) input and output are both quantitative, (3) specific computational strategies to handle experimental noise are built in, (4) the algorithm is designed to effectively handle bounded experimental data, (5) experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6) it is possible to incorporate pair interactions between positions of a sequence. Conclusion Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.
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Affiliation(s)
- Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
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45
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Maynard J, Petersson K, Wilson DH, Adams EJ, Blondelle SE, Boulanger MJ, Wilson DB, Garcia KC. Structure of an autoimmune T cell receptor complexed with class II peptide-MHC: insights into MHC bias and antigen specificity. Immunity 2005; 22:81-92. [PMID: 15664161 DOI: 10.1016/j.immuni.2004.11.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 10/07/2004] [Accepted: 11/17/2004] [Indexed: 11/15/2022]
Abstract
T cell receptor crossreactivity with different peptide ligands and biased recognition of MHC are coupled features of antigen recognition that are necessary for the T cell's diverse functional repertoire. In the crystal structure between an autoreactive, EAE T cell clone 172.10 and myelin basic protein (1-11) presented by class II MHC I-Au, recognition of the MHC is dominated by the Vbeta domain of the TCR, which interacts with the MHC alpha chain in a manner suggestive of a germline-encoded TCR/MHC "anchor point." Strikingly, there are few specific contacts between the TCR CDR3 loops and the MBP peptide. We also find that over 1,000,000 different peptides derived from combinatorial libraries can activate 172.10, yet the TCR strongly prefers the native MBP contact residues. We suggest that while TCR scanning of pMHC may be degenerate due to the TCR germline bias for MHC, recognition of structurally distinct agonist peptides is not indicative of TCR promiscuity, but rather highly specific alternative solutions to TCR engagement.
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Affiliation(s)
- Jennifer Maynard
- Departments of Microbiology and Immunology, Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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46
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Zanetti M, Hernandez X, Langlade-Demoyen P. Telomerase reverse transcriptase as target for anti-tumor T cell responses in humans. ACTA ACUST UNITED AC 2005; 27:87-104. [PMID: 15711953 DOI: 10.1007/s00281-004-0197-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Accepted: 12/15/2004] [Indexed: 10/25/2022]
Abstract
Human telomerase reverse transcriptase, a ribonucleoprotein intimately connected with the process of cell immortalization, is overexpressed in the vast majority of cancer cells, irrespective of their histological origin. Telomerase is currently viewed as the first antigen with the characteristics of common tumor antigen in humans, and it constitutes a potentially valuable target for attempts to control tumors through CD8 T cell immunity. Telomerase is a self antigen, making it possible that self tolerance imposes severe restrictions on our ability to generate effective anti-tumor immune responses in humans. In this article we review current studies on the antigenic and immunogenic properties of the human telomerase reverse transcriptase, placing them in the context of self tolerance and the size of the available CD8 T cell repertoire restricted by the HLA A2 molecule.
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Affiliation(s)
- Maurizio Zanetti
- The Laboratory of Immunology, Department of Medicine and Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0837, USA.
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47
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Tomar D, Chattree V, Tripathi V, Khan AA, Bakshi AR, Rao DN. New dimensions in vaccinology: A new insight. Indian J Clin Biochem 2005; 20:213-30. [PMID: 23105525 PMCID: PMC3454171 DOI: 10.1007/bf02893073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The development of vaccines to prevent infectious diseases has been one of the most important contributions of biomedical sciences. Increasing understanding in biochemistry, molecular biology, molecular genetics and related fields have provided an opportunity for the development of new generation vaccines that are based on rational design approaches. This is possible because of proper understanding of the microbial-genetics, biochemistry, host-pathogen interaction and recent developments in molecular immunology. Another important improvement made in the quality of vaccine production is the incorporation of immunomodulators or adjuvants with modified delivery vehicles viz liposomes, Iscoms and microspheres apart from alum being used as a gold standard. This article reviews the art of vaccination from Jenner period to present day context highlighting all the developments made at each stage of the vaccine development. Various criteria have been discussed regarding the selection of epitopes that expand B & T cells, its linkage with other accessory cells of the immune system, means to overcome MHC linked immune unresponsiveness, enhanced antigen processing and presentations that specially induce either helper or cytotoxic or mucosal immune responses were critically discussed.
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Affiliation(s)
- D Tomar
- Department of Biochemistry, All India Institute of Medical Sciences, 110029 New Delhi
| | - V Chattree
- Department of Biochemistry, All India Institute of Medical Sciences, 110029 New Delhi
| | - V Tripathi
- Department of Biochemistry, All India Institute of Medical Sciences, 110029 New Delhi
| | - A A Khan
- Department of Biochemistry, All India Institute of Medical Sciences, 110029 New Delhi
| | - A R Bakshi
- Department of Biochemistry, All India Institute of Medical Sciences, 110029 New Delhi
| | - D N Rao
- Department of Biochemistry, All India Institute of Medical Sciences, 110029 New Delhi
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48
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Kohlmann WM, Urban W, Sterry W, Foerster J. Correlation of psoriasis activity with abundance of CD25+CD8+ T cells: conditions for cloning T cells from psoriatic plaques. Exp Dermatol 2004; 13:607-12. [PMID: 15447720 DOI: 10.1111/j.0906-6705.2004.00195.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of T cells in the pathogenesis of psoriasis is widely acknowledged. However, key aspects of their precise function in the disease as well as the relative pathogenic contribution of T-cell subsets are still unknown. T-cell clones have been isolated from psoriatic plaques but a study of conditions affecting the isolation and expansion of T-cell clones from psoriatic skin has not been reported to date. Here, we observe a correlation of disease activity with the frequency of the CD3(+)CD8(+)CD25(+) subset. We show that prolonged in vitro culture changes the phenotypic subset distribution of T-cell lines derived from psoriatic skin and that T-cell clones can be isolated by sorting of CD25(+) cells emigrated from skin fragments after 7 days. We evaluate various conditions affecting expansion of psoriatic T-cell clones in vitro and show that blocking apoptosis can facilitate proliferation of activated T-cell clones in vitro. Our results indicate a prominent role of the CD8(+)CD25(+) T-cell subset in disease pathogenesis and should be useful in the design of experiments aiming at a systematic analysis of the specificity of clones present in psoriatic plaques.
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Affiliation(s)
- Wayan M Kohlmann
- Klinik für Dermatologie, Venerologie und Allergologie, Charité, Berlin, Germany
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49
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Dummer R, Mittelman A, Fanizzi FP, Lucchese G, Willers J, Kanduc D. Non-self-discrimination as a driving concept in the identification of an immunodominant HMW-MAA epitopic peptide sequence by autoantibodies from melanoma cancer patients. Int J Cancer 2004; 111:720-6. [PMID: 15252841 DOI: 10.1002/ijc.20310] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We analyzed the sera of patients with melanoma to define the human humoral autoantibody profile towards HMW-MAA. Computational proteome scanning using the non-self-discrimination principle as a guide led to the individuation of the low-similarity HMW-MAA781-789RATVWMLRL peptide fragment as an immunodominant B-cell epitope. Linear B-cell determinant individuation was experimentally validated by dot blot immunoassay and NMR spectroscopy analysis. Regulation of physiologic self-reactivity by the non-self-discrimination principle is discussed.
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Affiliation(s)
- Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
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50
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Mycko MP, Waldner H, Anderson DE, Bourcier KD, Wucherpfennig KW, Kuchroo VK, Hafler DA. Cross-Reactive TCR Responses to Self Antigens Presented by Different MHC Class II Molecules. THE JOURNAL OF IMMUNOLOGY 2004; 173:1689-98. [PMID: 15265898 DOI: 10.4049/jimmunol.173.3.1689] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Autoreactive T cells represent a natural repertoire of T cells in both diseased patients and healthy individuals. The mechanisms regulating the function of these autoreactive T cells are still unknown. Ob1A12 is a myelin basic protein (MBP)-reactive Th cell clone derived from a patient with relapsing-remitting multiple sclerosis. Mice transgenic for this human TCR and DRA and DRB1*1501 chains develop spontaneous experimental autoimmune encephalomyelitis. The reactivity of Ob1A12 is reported to be restricted to recognition of MBP peptide 85-99 in the context of DRB1*1501. DRA/DRB1*1501 and the patient's other restriction element, DRA/DRB1*0401, differ significantly in their amino acid sequences. In this study we describe an altered peptide ligand derived from MBP(85-99) with a single amino acid substitution at position 88 (Val to Lys; 88V-->K), that could stimulate the Ob1A12.TCR in the context of both DRA/DRB1*1501 and DRA/DRB1*0401. Analysis of a panel of transfected T cell hybridomas expressing Ob1A12.TCR and CD4 indicated that Ob1A12.TCR cross-reactivity in the context of DRA/DRB1*0401 is critically dependent on the presence of the CD4 coreceptor. Furthermore, we found that activation of Ob1A12.TCR with MBP altered peptide ligand 85-99 88V-->K presented by DRB1*1501 or DRB1*0401 resulted in significant differences in TCR zeta phosphorylation. Our data indicate that injection of altered peptide ligand into patients heterozygous for MHC class II molecules may result in unexpected cross-reactivities, leading to activation of autoreactive T cells.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Antigen Presentation
- Autoantigens/immunology
- CD4 Antigens/immunology
- Cross Reactions
- Encephalomyelitis, Autoimmune, Experimental/immunology
- HLA-DR Antigens/immunology
- HLA-DR alpha-Chains
- HLA-DRB1 Chains
- Humans
- Hybridomas/immunology
- L Cells
- Lymphocyte Activation
- Membrane Proteins/metabolism
- Mice
- Molecular Sequence Data
- Multiple Sclerosis, Relapsing-Remitting/immunology
- Myelin Basic Protein/immunology
- Peptide Fragments/immunology
- Phosphorylation
- Protein Processing, Post-Translational
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- T-Lymphocyte Subsets/immunology
- Transfection
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Affiliation(s)
- Marcin P Mycko
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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