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Mahadik R, Kiptoo P, Tolbert T, Siahaan TJ. Immune Modulation by Antigenic Peptides and Antigenic Peptide Conjugates for Treatment of Multiple Sclerosis. MEDICAL RESEARCH ARCHIVES 2022; 10:10.18103/mra.v10i5.2804. [PMID: 36381196 PMCID: PMC9648198 DOI: 10.18103/mra.v10i5.2804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The immune system defends our body by fighting infection from pathogens utilizing both the innate and adaptive immune responses. The innate immune response is generated rapidly as the first line of defense. It is followed by the adaptive immune response that selectively targets infected cells. The adaptive immune response is generated more slowly, but selectively, by targeting a wide range of foreign particles (i.e., viruses or bacteria) or molecules that enter the body, known as antigens. Autoimmune diseases are the results of immune system glitches, where the body's adaptive system recognizes self-antigens as foreign. Thus, the host immune system attacks the self-tissues or organs with a high level of inflammation and causes debilitation in patients. Many current treatments for autoimmune diseases (i.e., multiple sclerosis (MS), rheumatoid arthritis (RA)) have been effective but lead to adverse side effects due to general immune system suppression, which makes patients vulnerable to opportunistic infections. To counter these negative effects, many different avenues of antigen specific treatments are being developed to selectively target the autoreactive immune cells for a specific self-antigen or set of self-antigens while not compromising the general immune system. These approaches include soluble antigenic peptides, bifunctional peptide inhibitors (BPI) including IDAC and Fc-BPI, polymer conjugates, and peptide-drug conjugates. Here, various antigen-specific methods of potential treatments, their efficacy, and limitations will be discussed along with the potential mechanisms of action.
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Affiliation(s)
- Rucha Mahadik
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047
| | | | - Tom Tolbert
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047
| | - Teruna J Siahaan
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047
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2
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Differential T cell immune responses to deamidated adeno-associated virus vector. Mol Ther Methods Clin Dev 2022; 24:255-267. [PMID: 35211638 PMCID: PMC8829777 DOI: 10.1016/j.omtm.2022.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/16/2022] [Indexed: 01/09/2023]
Abstract
Despite the high safety profile demonstrated in clinical trials, the immunogenicity of adeno-associated virus (AAV)-mediated gene therapy remains a major hurdle. Specifically, T-cell-mediated immune responses to AAV vectors are related to loss of efficacy and potential liver toxicities. As post-translational modifications in T cell epitopes have the potential to affect immune reactions, the cellular immune responses to peptides derived from spontaneously deamidated AAV were investigated. Here, we report that highly deamidated sites in AAV9 contain CD4 T cell epitopes with a Th1 cytokine pattern in multiple human donors with diverse human leukocyte antigen (HLA) backgrounds. Furthermore, some peripheral blood mononuclear cell (PBMC) samples demonstrated differential T cell activation to deamidated or non-deamidated epitopes. Also, in vitro and in silico HLA binding assays showed differential binding to the deamidated or non-deamidated peptides in some HLA alleles. This study provides critical attributes to vector-immune-mediated responses, as AAV deamidation can impact the immunogenicity, safety, and efficacy of AAV-mediated gene therapy in some patients.
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3
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Candia M, Kratzer B, Pickl WF. On Peptides and Altered Peptide Ligands: From Origin, Mode of Action and Design to Clinical Application (Immunotherapy). Int Arch Allergy Immunol 2016; 170:211-233. [PMID: 27642756 PMCID: PMC7058415 DOI: 10.1159/000448756] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
T lymphocytes equipped with clonotypic T cell antigen receptors (TCR) recognize immunogenic peptides only when presented in the context of their own major histocompatibility complex (MHC) molecules. Peptide loading to MHC molecules occurs in intracellular compartments (ER for class I and MIIC for class II molecules) and relies on the interaction of the respective peptides and peptide binding pockets on MHC molecules. Those peptide residues not engaged in MHC binding point towards the TCR screening for possible peptide MHC complex binding partners. Natural or intentional modification of both MHC binding registers and TCR interacting residues of peptides – leading to the formation of altered peptide ligands (APLs) – might alter the way peptides interact with TCRs and hence influence subsequent T cell activation events, and consequently T cell effector functions. This review article summarizes how APLs were detected and first described, current concepts of how APLs modify T cellular signaling, which biological mechanisms might force the generation of APLs in vivo, and how peptides and APLs might be used for the benefit of patients suffering from allergic or autoimmune diseases.
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Affiliation(s)
- Martín Candia
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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4
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Mechanistic Analysis of the Effect of Deamidation on the Immunogenicity of Anthrax Protective Antigen. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2016; 23:396-402. [PMID: 26912784 DOI: 10.1128/cvi.00701-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/18/2016] [Indexed: 11/20/2022]
Abstract
The spontaneous modification of proteins, such as deamidation of asparagine residues, can significantly affect the immunogenicity of protein-based vaccines. Using a "genetically deamidated" form of recombinant protective antigen (rPA), we have previously shown that deamidation can decrease the immunogenicity of rPA, the primary component of new-generation anthrax vaccines. In this study, we investigated the biochemical and immunological mechanisms by which deamidation of rPA might decrease the immunogenicity of the protein. We found that loss of the immunogenicity of rPA vaccine was independent of the presence of adjuvant. We assessed the effect of deamidation on the immunodominant neutralizing B-cell epitopes of rPA and found that these epitopes were not significantly affected by deamidation. In order to assess the effect of deamidation on T-cell help for antibody production elicited by rPA vaccine, we examined the ability of the wild-type and genetically deamidated forms of rPA to serve as hapten carriers. We found that when wild-type and genetically deamidated rPA were modified to similar extents with 2,4-dinitrophenyl hapten (DNP) and then used to immunize mice, higher levels of anti-DNP antibodies were elicited by wild-type DNP-rPA than those elicited by the genetically deamidated DNP-rPA, indicating that wild-type rPA elicits more T-cell help than the genetically deamidated form of the protein. These results suggest that a decrease in the ability of deamidated rPA to elicit T-cell help for antibody production is a possible contributor to its lower immunogenicity.
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5
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Li W, Kerwin JL, Schiel J, Formolo T, Davis D, Mahan A, Benchaar SA. Structural Elucidation of Post-Translational Modifications in Monoclonal Antibodies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Wenzhou Li
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - James L. Kerwin
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - John Schiel
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Trina Formolo
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Darryl Davis
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Andrew Mahan
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Sabrina A. Benchaar
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
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6
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Verma A, McNichol B, Domínguez-Castillo RI, Amador-Molina JC, Arciniega JL, Reiter K, Meade BD, Ngundi MM, Stibitz S, Burns DL. Use of site-directed mutagenesis to model the effects of spontaneous deamidation on the immunogenicity of Bacillus anthracis protective antigen. Infect Immun 2013; 81:278-84. [PMID: 23115046 PMCID: PMC3536148 DOI: 10.1128/iai.00863-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/25/2012] [Indexed: 12/25/2022] Open
Abstract
Long-term stability is a desired characteristic of vaccines, especially anthrax vaccines, which must be stockpiled for large-scale use in an emergency situation; however, spontaneous deamidation of purified vaccine antigens has the potential to adversely affect vaccine immunogenicity over time. In order to explore whether spontaneous deamidation of recombinant protective antigen (rPA)--the major component of new-generation anthrax vaccines--affects vaccine immunogenicity, we created a "genetically deamidated" form of rPA using site-directed mutagenesis to replace six deamidation-prone asparagine residues, at positions 408, 466, 537, 601, 713, and 719, with either aspartate, glutamine, or alanine residues. We found that the structure of the six-Asp mutant rPA was not significantly altered relative to that of the wild-type protein as assessed by circular dichroism (CD) spectroscopy and biological activity. In contrast, immunogenicity of aluminum-adjuvanted six-Asp mutant rPA, as measured by induction of toxin-neutralizing antibodies, was significantly lower than that of the corresponding wild-type rPA vaccine formulation. The six-Gln and six-Ala mutants also exhibited lower immunogenicity than the wild type. While the wild-type rPA vaccine formulation exhibited a high level of immunogenicity initially, its immunogenicity declined significantly upon storage at 25°C for 4 weeks. In contrast, the immunogenicity of the six-Asp mutant rPA vaccine formulation was low initially but did not change significantly upon storage. Taken together, results from this study suggest that spontaneous deamidation of asparagine residues predicted to occur during storage of rPA vaccines would adversely affect vaccine immunogenicity and therefore the storage life of vaccines.
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MESH Headings
- Animals
- Anthrax/immunology
- Anthrax/prevention & control
- Anthrax Vaccines/genetics
- Anthrax Vaccines/immunology
- Anthrax Vaccines/metabolism
- Antibodies, Bacterial/biosynthesis
- Antibodies, Bacterial/immunology
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Neutralizing/immunology
- Antibody Formation/genetics
- Antibody Formation/immunology
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Antigens, Bacterial/metabolism
- Asparagine/immunology
- Asparagine/metabolism
- Bacillus anthracis/genetics
- Bacillus anthracis/immunology
- Bacillus anthracis/metabolism
- Cells, Cultured
- Female
- Macrophages/immunology
- Macrophages/metabolism
- Mice
- Mutagenesis, Site-Directed/methods
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/metabolism
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Affiliation(s)
- Anita Verma
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Beth McNichol
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | | | - Juan C. Amador-Molina
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Juan L. Arciniega
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Karine Reiter
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | | | - Miriam M. Ngundi
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Scott Stibitz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Drusilla L. Burns
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
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7
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Abstract
Advances in the engineering of peptides, adjuvants and delivery systems have renewed the enthusiasm for peptide-based vaccination regimens in the setting of cancer, and there are a variety of clinical trials being conducted by pharmaceutical companies based on the use of peptides. The challenges to successful cancer immunotherapy are common to all immunotherapeutic strategies and not unique to peptide-based vaccination regimens. This review will describe the advances in the identification, design and delivery of peptides, the challenges to successful immunotherapy and will discuss potential options for the future.
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Affiliation(s)
- Shreya Kanodia
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, NRT 7517, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, USA.
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8
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Tunheim G, Schjetne KW, Rasmussen IB, Sollid LM, Sandlie I, Bogen B. Recombinant antibodies for delivery of antigen: a single loop between -strands in the constant region can accommodate long, complex and tandem T cell epitopes. Int Immunol 2008; 20:295-306. [DOI: 10.1093/intimm/dxm141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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9
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Chapter 16 Analysis of Deamidation in Proteins. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0166-526x(08)00216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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10
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Analysis of antigen reactive T-cells. METHODS IN MOLECULAR MEDICINE 2007. [PMID: 17983140 DOI: 10.1007/978-1-59745-402-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Because antigen-specific cells are the central coordinators of the immune response to infectious organisms, and the principal effector cells in autoimmune disease, there are many circumstances in which investigators may wish to examine the T-cell responses to particular antigens. This chapter outlines techniques for assessing the responses of polyclonal populations of T-lymphocytes by measuring a variety of outputs each of which gives different kinds of information about the response. The outputs discussed are proliferation and cytokine production, with methods for measuring cytokine secretion by the whole population together with techniques for making an estimate of the numbers of cells producing a cytokine in response to antigen, and examining the phenotype of the responsive cells. In many cases detailed information about responses to particular antigens requires the isolation and characterization of antigen-responsive T-cell clones, and this is also described together with methods of identifying unknown antigens by screening recombinant expression libraries. Lastly, because the techniques differ in many respects, methods for isolating antigen-specific CD8+ T-cells, particularly those which recognize bacteria, are also included.
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11
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Purcell AW, McCluskey J, Rossjohn J. More than one reason to rethink the use of peptides in vaccine design. Nat Rev Drug Discov 2007; 6:404-14. [PMID: 17473845 DOI: 10.1038/nrd2224] [Citation(s) in RCA: 571] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The use of peptides as therapeutics is experiencing renewed enthusiasm owing to advances in delivery, stability and design. Moreover, there is a growing emphasis on the use of peptides in vaccine design as insights into tissue-specific processing of the immunogenic epitopes of proteins and the discovery of unusually long cytotoxic T-lymphocyte epitopes broaden the range of targets and give clues to enhancing peptide immunogenicity. Peptides can also be synthesized with known post-translational modifications and/or deliberately introduced protease-resistant peptide bonds to regulate their processing independent of tissue-specific proteolysis and to stabilize these compounds in vivo. We discuss the potential of peptide-based vaccines for the treatment of chronic viral diseases and cancer, and review recent developments in the field of peptide-based vaccines.
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Affiliation(s)
- Anthony W Purcell
- The Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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12
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Sweenie CH, Mackenzie KJ, Rone-Orugboh A, Liu M, Anderton SM. Distinct T cell recognition of naturally processed and cryptic epitopes within the immunodominant 35-55 region of myelin oligodendrocyte glycoprotein. J Neuroimmunol 2006; 183:7-16. [PMID: 17157925 DOI: 10.1016/j.jneuroim.2006.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 10/23/2006] [Accepted: 10/23/2006] [Indexed: 11/29/2022]
Abstract
We have assessed the complexity in T cell recognition of the immunodominant 35-55 region of myelin oligodendrocyte glycoprotein (MOG) in C57BL/6 mice. Immunization with the p35-55 peptide generated two types of T cell, recognizing either a cryptic, or a naturally-processed epitope. Clear differences in the recognition of residues within a core sequence of 40-48 were observed. The majority of the p35-55-reactive repertoire in vivo appeared responsive to the intact autoantigen, supporting the notion of a failure of central tolerance to this region of MOG. Our data also provide a basis for exploring the requirements for antigen processing of MOG.
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Affiliation(s)
- Claire H Sweenie
- University of Edinburgh, Institute of Immunology and Infection Research, School of Biological Sciences, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
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13
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Li B, Schowen RL, Topp EM, Borchardt RT. Effect of N-1 and N-2 residues on peptide deamidation rate in solution and solid state. AAPS J 2006; 8:E166-73. [PMID: 16584125 PMCID: PMC2751436 DOI: 10.1208/aapsj080120] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 01/18/2006] [Indexed: 11/30/2022] Open
Abstract
The deamidation kinetics of 7 model peptides (VYPNGA, VYGNGA, VFGNGA, VIGNGA, VGGNGA, VGPNGA, and VGYNGA) were studied at 70 degrees C in pH 10 buffer solutions and at 70 degrees C and 50% relative humidity in lyophilized solid formulations containing polyvinyl pyrrolidone (PVP). The disappearance of the model peptides from solution and solid-state formulations followed apparent first-order kinetics, proceeding to completion in solution. In the solid state, the reactions showed plateaus with approximately 10% to 30% of the model peptides remaining; this was thought to be due to reversible complexation of the peptides and the PVP followed by slow dissociation of the complexes. The residues immediately N-terminal to asparagine (N-1, N-2) influenced the rate of deamidation significantly in the solid state but had minimal effect in solution. Increases in the volume and hydrophobicity of the N-1 and N-2 residues decreased the rate of deamidation in the solid state, but neither parameter alone adequately accounted for the observed effects. An empirical model using a linear combination of volume and hydrophobicity was developed; it showed that the influences of the volume and the hydrophobicity of the residues in the N-1 and N-2 positions are approximately equally important for the N-1 and N-2 residues.
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Affiliation(s)
- Bei Li
- />Department of Pharmaceutical Chemistry, University of Kansas, 66047 Lawrence, KS
| | - Richard L. Schowen
- />Department of Pharmaceutical Chemistry, University of Kansas, 66047 Lawrence, KS
| | - Elizabeth M. Topp
- />Department of Pharmaceutical Chemistry, University of Kansas, 66047 Lawrence, KS
| | - Ronald T. Borchardt
- />Department of Pharmaceutical Chemistry, University of Kansas, 66047 Lawrence, KS
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14
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Abstract
T-cell-epitope mapping has emerged as one of the most powerful new drug discovery tools for a range of biomedical applications. Initially, T-cell-epitope discovery was applied to the development of vaccines for infectious diseases and cancer. T-cell-epitope-mapping applications have now expanded to include reengineering of protein therapeutics (a process now called deimmunization), as well as the fields of autoimmunity, endocrinology, allergy, transplantation and diagnostics. Research employing T-cell-epitope mapping falls within the realm of immunomics, a new field that addresses the interface between host and (pathogen) proteome, bridging informatics, genomics, proteomics, immunology and clinical medicine. This review highlights aspects of recent immunomics research that are related to the discovery of the T-cell immunome.
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15
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Guan P, Doytchinova IA, Walshe VA, Borrow P, Flower DR. Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201. J Med Chem 2006; 48:7418-25. [PMID: 16279801 DOI: 10.1021/jm0505258] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amino acid descriptors are often used in quantitative structure-activity relationship (QSAR) analysis of proteins and peptides. In the present study, descriptors were used to characterize peptides binding to the human MHC allele HLA-A0201. Two sets of amino acid descriptors were chosen: 93 descriptors taken from the amino acid descriptor database AAindex and the z descriptors defined by Wold and Sandberg. Variable selection techniques (SIMCA, genetic algorithm, and GOLPE) were applied to remove redundant descriptors. Our results indicate that QSAR models generated using five z descriptors had the highest predictivity and explained variance (q2 between 0.6 and 0.7 and r2 between 0.6 and 0.9). Further to the QSAR analysis, 15 peptides were synthesized and tested using a T2 stabilization assay. All peptides bound to HLA-A0201 well, and four peptides were identified as high-affinity binders.
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Affiliation(s)
- Pingping Guan
- Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK.
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16
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Engelhard VH, Altrich-Vanlith M, Ostankovitch M, Zarling AL. Post-translational modifications of naturally processed MHC-binding epitopes. Curr Opin Immunol 2005; 18:92-7. [PMID: 16343885 DOI: 10.1016/j.coi.2005.11.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Accepted: 11/25/2005] [Indexed: 01/21/2023]
Abstract
A variety of different post-translational modifications of peptides displayed by class I and II MHC molecules have now been described. Some modifications promote the binding of peptides to MHC molecules, and might also influence the ability of the peptide to be produced by antigen processing pathways. In some instances, the antigen processing components themselves are actually responsible for generating post-translational modifications. Finally, evidence is accumulating that modifications can be altered as a consequence of inflammation, transformation, apoptosis and aging. This leads to altered repertories of MHC-associated peptides, which may be important in immune responses associated with autoimmune diseases, infection and cancer.
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Affiliation(s)
- Victor H Engelhard
- Carter Center for Immunology Research and the Department of Microbiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA.
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17
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Abstract
The relative plasticity of peptide binding to class II major histocompatibility complex (MHC) molecules permits formation of multiple conformational isomers by the same peptide and MHC molecule; such conformers are specifically recognized by distinct subsets of T cells. Here, we review current knowledge and recent advances in our understanding of peptide-class II MHC conformational isomerism and the mechanisms that generate distinct MHC-peptide conformers. We focus on our studies of two T-cell subsets, type A and B, which recognize distinct conformers of the dominant epitope of hen egg white lysozyme presented by I-A(k). These conformers form via different pathways and in distinct intracellular vesicles: the type A conformer forms in late endosomes upon processing of native protein, while the more flexible type B conformer forms in early endosomes and at the cell surface. In this process, H2-DM acts as a conformational editor, eliminating the type B conformer in late endosomes. Type B T cells constitute a significant component of the naïve T-cell repertoire; furthermore, self-reactive type B T cells escape negative selection and are present in abundance in the periphery. Ongoing studies should elucidate the role of type B T cells in immunity to pathogens and in autoimmune pathology.
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Affiliation(s)
- Scott B Lovitch
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
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18
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Li B, O'Meara MH, Lubach JW, Schowen RL, Topp EM, Munson EJ, Borchardt RT. Effects of sucrose and mannitol on asparagine deamidation rates of model peptides in solution and in the solid state. J Pharm Sci 2005; 94:1723-35. [PMID: 15986465 DOI: 10.1002/jps.20372] [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
Asparagine (Asn) degradation kinetics in two model peptides, Gly-Gln-Asn-Gly-Gly (GQNGG) and Val-Tyr-Pro-Asn-Gly-Ala (VYPNGA), were studied at 50 degrees C in pH 7 buffer solutions in the presence and absence of 5% (w/v) sucrose or mannitol and at 50 degrees C and 30% relative humidity in solid samples lyophilized from these solutions. Solid formulations were characterized using Karl Fischer coulometric titration, thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), Fourier-transform infrared spectrometry (FTIR), and solid-state nuclear magnetic resonance (NMR) spectroscopy. GQNGG and VYPNGA showed similar pseudo first-order deamidation rates in solution in the absence of sucrose and mannitol. Adding 5% sucrose or mannitol decreased the rates by no more than 17%. The model peptides degraded 2- to 80-fold more slowly in the solid formulations of sucrose and mannitol than in 5% solutions of these carbohydrates. Ratios of deamidation rates of the model peptides depended upon the solid matrix. In the mannitol solid, the ratio of deamidation rates of GQNGG and VYPNGA (GQNGG:VYPNGA) was approximately 8, while in the sucrose solid, the model peptides deamidated at similar rates (GQNGG:VYPNGA congruent with 1). DSC showed the mannitol formulations to be largely amorphous immediately after lyophilization with some ordered, crystalline-like structure; the extent of ordered structure increased during storage as shown by FTIR and ssNMR. In contrast, the sucrose formulation was largely amorphous after lyophilization and remained so during storage. Together, the results showed that 5% sucrose or mannitol in solution does not significantly change the rates of Asn deamidation of the model peptides, while sucrose stabilizes the model peptides against deamidation more than mannitol in the solid state.
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Affiliation(s)
- Bei Li
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66047, USA
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19
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Abstract
Alterations in amino acid sequence can generate neo-epitopes from self proteins, causing autoaggressive immune attack. There is a range of possible post-translational modifications (PTMs) of mammalian proteins that can allow immune recognition of neo-self epitopes. These effects can vary from overt increase in affinity of MHC or T-cell receptor binding, to more subtle effects on the activity of proteolytic enzymes involved in antigen processing. Furthermore, intriguing insights into how the complex interactions between inflammation, enzyme activity and protein modification can direct self recognition are beginning to be unearthed.
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Affiliation(s)
- Stephen M Anderton
- University of Edinburgh, Institute of Immunology and Infection Research, School of Biological Sciences, Kings Buildings, West Mains Road, Edinburgh, EH9 3JT, UK.
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20
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Moss CX, Matthews SP, Lamont DJ, Watts C. Asparagine deamidation perturbs antigen presentation on class II major histocompatibility complex molecules. J Biol Chem 2005; 280:18498-503. [PMID: 15749706 DOI: 10.1074/jbc.m501241200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational protein modifications can be recognized by B and T lymphocytes and can potentially make "self"-proteins appear foreign to the immune system. Such modifications may directly affect major histocompatibility complex-restricted T cell recognition of processed peptides or may perturb the processing events that generate such peptides. Using the tetanus toxin C fragment protein as a test case, we show that spontaneous deamidation of asparagine residues interferes with processing by the enzyme asparagine endopeptidase (AEP) and contributes to diminished antigen presentation. Deamidation inhibits AEP action either directly, when asparagine residues targeted by AEP are modified, or indirectly, when adjacent Asn residues are deamidated. Thus, deamidation of long-lived self-proteins may qualitatively or quantitatively affect the spectrum of self-peptides displayed to T cells and may thereby contribute to the onset or exacerbation of autoimmune disease.
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Affiliation(s)
- Catherine X Moss
- Division of Cell Biology and Immunology, University of Dundee, Scotland, United Kingdom
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21
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Abstract
The disease mechanisms of complex inflammatory disorders are difficult to define because of extensive interactions between genetic and environmental factors. Coeliac disease is a typical complex inflammatory disorder, but this disease is unusual in that crucial genetic and environmental factors have been identified. This knowledge has allowed functional studies of the predisposing HLA molecules, the identification of antigenic epitopes and detailed studies of disease-relevant T cells in coeliac disease. This dissection of the pathogenic mechanisms of coeliac disease has uncovered principles that are relevant to other chronic inflammatory diseases.
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Affiliation(s)
- Ludvig M Sollid
- Institute of Immunology, Rikshospitalet, University of Oslo, 0027 Oslo, Norway.
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22
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Kumar R, Eastwood AL, Brown ML, Laurie GW. Human genome search in celiac disease: mutated gliadin T-cell-like epitope in two human proteins promotes T-cell activation. J Mol Biol 2002; 319:593-602. [PMID: 12054857 DOI: 10.1016/s0022-2836(02)00366-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Discovery of a number of novel and known human genes whose protein products bear striking similarity to two or more wheat gliadin domains raised the possibility that human intestinal non-HLA peptides homologous to celiac T-cell epitopes could play a role in non-HLA gene specification in celiac disease. Database searching of the entire human genome identified only 11 gut-expressed proteins with high T-cell epitope homology, particularly to the DQ2-gamma-I-gliadin epitope (i.e. TFIIA, FOXJ2 and IgD; mean BestFit quality score=40 versus random value of 24). Others were similar to DQ2-alpha-I-gliadin (i.e. PAX9; BestFit quality 46 versus 20 for random), or DQ2-alpha-II-gliadin (PHLDA1, known in mice as the T-cell death-associated gene; BestFit quality 43 versus 30 for random) epitopes. Among proteins previously screened for gliadin homology, noteworthy was achaete scute homologous protein (DQ2-alpha-I-gliadin; BestFit quality 41 versus 22 for random). With the exception of IgD, all are nuclear factors. Paying particular attention to the position of potential major histocompatibility complex (MHC) anchor residues, several were selected for testing in a DQ2-gamma-I-gliadin-restricted T-cell system. All native 10-mer peptides were inactive, even when deamidated, but V96F substitution of deamidated TFIIA amino acid residues 91-100 stimulated IL-2 release at levels exceeding the wheat gliadin positive control. Also active, but only slightly, was L1009F substitution of AIB3 amino acid residues 1004-1013. PlotSimilarity alignment of TFIIAs from eight species revealed subthreshold similarity score in the peptide region, in contrast to the highly conserved amino and carboxy termini. Molecular modeling of TFIIA[V96F] peptide points to an important juxtaposition of an upwardly projecting phenylalanine residue at peptide position 6 that likely contacts a receptor complementarity-determining region, and a downwardly projecting glutamic acid residue that fits into the shallow MHC P7 pocket. These observations tentatively point to a new multi-gene hypothesis for the initiation of celiac disease in which deamidated free human peptides with T-cell epitope homology (particularly those made more homologous by mutation) escape negative selection, as per deamidation of the HEL(48-62) peptide in the hen egg lysozyme model of autoimmunity. Deamidation following peptide release due to injury triggers inflammation, thereafter repeatedly provoked by dietary gliadin immunodominant peptides concentrated in the proximal small intestine.
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Affiliation(s)
- Rajesh Kumar
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908-0732, USA
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23
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Manoury B, Mazzeo D, Fugger L, Viner N, Ponsford M, Streeter H, Mazza G, Wraith DC, Watts C. Destructive processing by asparagine endopeptidase limits presentation of a dominant T cell epitope in MBP. Nat Immunol 2002; 3:169-74. [PMID: 11812994 DOI: 10.1038/ni754] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Little is known about the processing of putative human autoantigens and why tolerance is established to some T cell epitopes but not others. Here we show that a principal human HLA-DR2-restricted epitope--amino acids 85-99 of myelin basic protein, MBP(85-99)--contains a processing site for the cysteine protease asparagine endopeptidase (AEP). Presentation of this epitope by human antigen-presenting cells is inversely proportional to the amount of cellular AEP activity: inhibition of AEP in living cells greatly enhances presentation of the MBP(85-99) epitope, whereas overexpression of AEP diminishes presentation. These results indicate that central tolerance to this encephalitogenic MBP epitope may not be established because destructive processing limits its display in the thymus. Consistent with this hypothesis, AEP is expressed abundantly in thymic antigen-presenting cells.
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Affiliation(s)
- Bénédicte Manoury
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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24
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Eckels DD, Bian T, Gill JC, Sønderstrup G. Epitopes of the NS3 protein of hepatitis C virus: recognition in HLA-DR4 transgenic mice. Immunol Cell Biol 2002; 80:106-12. [PMID: 11869368 DOI: 10.1046/j.1440-1711.2002.01053.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hepatitis C virus (HCV) infects more than 180 million of the world's population and causes a persistent infection that over decades can result in cirrhosis and hepatocellular carcinoma. Treatment is only partially effective and control is likely only with the development of effective vaccines. Currently, only chimpanzees can be infected with HCV and alternative animal and tissue culture models are badly needed. We have used mice transgenic for HLA-DR and human CD4 to analyse the specificity of murine responses to the HCV NS3 antigen in an effort to determine whether the epitopes recognized correspond to those recognized by human T cells. Indeed, determinants mapped in transgenic mice overlap with those in a patient exposed to HCV through infection. This result provides hope that such an animal model may be a useful tool with which to analyse particular aspects of immune responses to HCV in vivo.
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Affiliation(s)
- David D Eckels
- Blood Research Institute, The Blood Center, Milwaukee, Wisconsin 53201-2178, USA.
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25
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26
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Foucras G, Gallard A, Coureau C, Kanellopoulos JM, Guéry JC. Chronic soluble antigen sensitization primes a unique memory/effector T cell repertoire associated with th2 phenotype acquisition in vivo. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 168:179-87. [PMID: 11751961 DOI: 10.4049/jimmunol.168.1.179] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although much progress has been made in characterization of the signaling pathways that control Th cell commitment, little is known about the early events that govern differentiation of IL-4-producing T lymphocytes in vivo. We have previously shown that chronic administration of low dose, soluble hen egg white lysozyme (HEL) induced the selective development of Ag-specific Th2 in genetically predisposed BALB/c mice. Here, we show that these memory/effector Th2 cells express a unique TCR Vbeta repertoire, different from the TCR Vbeta profile of primary effector cells from HEL-adjuvant-primed mice. This Th2-associated repertoire contains a highly frequent public clonotype characterized by preferred TCR AV and BV gene segment usage along with conserved sequences in the third hypervariable regions of both TCR chains. This Th2 clonotype, which is not recruited in primary effector T cells from HEL-adjuvant-immunized mice, recognized an IA(d)-restricted HEL determinant, preferentially processed by dendritic cells, but not by B cells. Thus, IL-4-producing CD4 T cells that expand following chronic Ag sensitization emerge from a distinct pool of precursors, supporting the hypothesis that ligand-TCR interactions play a crucial role in the regulation of Ag-specific Th2 cell development in vivo.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens/administration & dosage
- Antigens/immunology
- Base Sequence
- Cells, Cultured
- Epitopes, T-Lymphocyte/immunology
- Female
- Gene Rearrangement, T-Lymphocyte
- Genes, T-Cell Receptor beta
- Histocompatibility Antigens Class II/immunology
- Immunologic Memory
- Interleukin-4/biosynthesis
- Lymphocyte Activation
- Mice
- Mice, Inbred BALB C
- Molecular Sequence Data
- Muramidase/administration & dosage
- Muramidase/immunology
- Phenotype
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Sequence Homology, Amino Acid
- Th2 Cells/immunology
- Time Factors
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Affiliation(s)
- Gilles Foucras
- Institut National de la Santé et de la Recherche Médicale, Unité 28, Institut Fédératif de Recherche 30, Hôpital Purpan, place du Dr. Baylac, 31059 Toulouse, France
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27
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Schmid DG, von der Mülbe FD, Fleckenstein B, Weinschenk T, Jung G. Broadband detection electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to reveal enzymatically and chemically induced deamidation reactions within peptides. Anal Chem 2001; 73:6008-13. [PMID: 11791573 DOI: 10.1021/ac0104274] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among the numerous forms of chemical degradation of peptides or proteins, deamidation is one of the alterations observed most frequently. In this irreversible reaction, a glutamine or an asparagine side chain is hydrolyzed to glutamic acid or aspartic acid, respectively (conversion of NH2 to OH). Besides its influence in the deterioration of biotechnological and food products, deamidation represents a defined posttranslational modification reaction with respect to proteomics. Here mass spectrometric techniques play a leading role in determining posttranslational modifications. However, not all mass spectrometers are able to resolve signal differences of 0.0193 Da (mass difference of 12CO vs 13CNH) for singly charged molecules, the mass difference between the first isotopic signal of an asparagine/glutamine-containing peptide and the monoisotopic signal of the corresponding partially deamidated aspartate/glutamate derivative. To detect partial deamidation within peptides, advantage has been taken of the ability of Fourier transform ion cyclotron resonance mass spectrometry to perform very high mass resolution. In this work, we investigated up to triply charged ions produced by electrospray ionization using direct infusion. Although the special heterodyne detection mode enables higher mass resolution than the routinely used broadband detection, often only a small mass window can be investigated. Using broadband detection, we were able to resolve ions with a difference of m/z 0.0064 to detect partially deamidated peptides formed either enzymatically or under acidic and basic conditions.
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Affiliation(s)
- D G Schmid
- Institut für Organische Chemie, Universität Tübingen, Germany
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28
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Wucherpfennig KW. Insights into autoimmunity gained from structural analysis of MHC-peptide complexes. Curr Opin Immunol 2001; 13:650-6. [PMID: 11677085 DOI: 10.1016/s0952-7915(01)00274-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The structural and functional properties of HLA-DQ and -DR molecules that confer susceptibility to several common autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis and multiple sclerosis, have been defined. The relevant polymorphisms directly affect interaction with peptides, which provides strong support for the hypothesis that these diseases are peptide-antigen driven. Several studies indicate that structural modifications of peptides can affect MHC class II binding and/or TCR recognition and should be considered in the analysis of T cell responses in autoimmune diseases.
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Affiliation(s)
- K W Wucherpfennig
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Room D1410, 44 Binney Street, Boston, MA 02115, USA.
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29
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Chen W, Bergerot I, Elliott JF, Harrison LC, Abiru N, Eisenbarth GS, Delovitch TL. Evidence that a peptide spanning the B-C junction of proinsulin is an early Autoantigen epitope in the pathogenesis of type 1 diabetes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:4926-35. [PMID: 11673498 DOI: 10.4049/jimmunol.167.9.4926] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The expression of pro(insulin) in the thymus may lead to the negative selection of pro(insulin) autoreactive T cells and peripheral tolerance to this autoantigen in type 1 diabetes (T1D). We investigated whether proinsulin is expressed in the thymus of young nonobese diabetic (NOD) mice, whether T cells from naive NOD female mice at weaning are reactive to mouse proinsulin, and the role of proinsulin as a pathogenic autoantigen in T1D. Proinsulin II mRNA transcripts were detected in the thymus of 2-wk-old NOD mice at similar levels to other control strains. Despite this expression, proinsulin autoreactive T cells were detected in the periphery of 2- to 3-wk-old naive NOD mice. Peripheral T cells reactive to the insulin, glutamic acid decarboxylase 65 (GAD65), GAD67, and islet cell Ag p69 autoantigens were also detected in these mice, indicating that NOD mice are not tolerant to any of these islet autoantigens at this young age. T cell reactivities to proinsulin and islet cell Ag p69 exceeded those to GAD67, and T cell reactivity to proinsulin in the spleen and pancreatic lymph nodes was directed mainly against a p24-33 epitope that spans the B chain/C peptide junction. Intraperitoneal immunization with proinsulin perinatally beginning at 18 days of age delayed the onset and reduced the incidence of T1D. However, s.c. immunization with proinsulin initiated at 5 wk of age accelerated diabetes in female NOD mice. Our findings support the notion that proinsulin p24-33 may be a primary autoantigen epitope in the pathogenesis of T1D in NOD mice.
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Affiliation(s)
- W Chen
- Autoimmunity/Diabetes Group, The John P. Robarts Research Institute and Department of Microbiology, University of Western Ontario, London, Ontario, Canada
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30
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Cirrito TP, Pu Z, Deck MB, Unanue ER. Deamidation of asparagine in a major histocompatibility complex-bound peptide affects T cell recognition but does not explain type B reactivity. J Exp Med 2001; 194:1165-70. [PMID: 11602644 PMCID: PMC2193507 DOI: 10.1084/jem.194.8.1165] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We have analyzed a panel of T cell hybridomas specific for the chemically dominant epitope of hen egg-white lysozyme 48-61 which has asparagine 59 as an important T cell receptor contact residue. A number of T cells recognize 48-61 with asparagine at position 59, but not the aspartic acid or isoaspartic acid derivatives. Conversely, we find T cells that specifically recognize 48-61 bearing an isoaspartic acid at residue 59, but not asparagine. For other T cells, asparagine, aspartic acid, or isoaspartic acid at residue 59 is irrelevant. We present evidence that our previous distinction between type A and type B T cells is not explained by asparagine deamidation at residue 59.
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Affiliation(s)
- Thomas P. Cirrito
- Department of Pathology and Immunology, and Center for Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Zheng Pu
- Department of Pathology and Immunology, and Center for Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - M. Brian Deck
- Department of Pathology and Immunology, and Center for Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Emil R. Unanue
- Department of Pathology and Immunology, and Center for Immunology, Washington University School of Medicine, St. Louis, MO 63110
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