51
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Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, Baker BM. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. THE JOURNAL OF IMMUNOLOGY 2017; 199:2203-2213. [PMID: 28923982 DOI: 10.4049/jimmunol.1700744] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022]
Abstract
T cell specificity emerges from a myriad of processes, ranging from the biological pathways that control T cell signaling to the structural and physical mechanisms that influence how TCRs bind peptides and MHC proteins. Of these processes, the binding specificity of the TCR is a key component. However, TCR specificity is enigmatic: TCRs are at once specific but also cross-reactive. Although long appreciated, this duality continues to puzzle immunologists and has implications for the development of TCR-based therapeutics. In this review, we discuss TCR specificity, emphasizing results that have emerged from structural and physical studies of TCR binding. We show how the TCR specificity/cross-reactivity duality can be rationalized from structural and biophysical principles. There is excellent agreement between predictions from these principles and classic predictions about the scope of TCR cross-reactivity. We demonstrate how these same principles can also explain amino acid preferences in immunogenic epitopes and highlight opportunities for structural considerations in predictive immunology.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Sarah Catherine B Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556; .,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
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52
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Prinz JC. Autoimmune aspects of psoriasis: Heritability and autoantigens. Autoimmun Rev 2017; 16:970-979. [PMID: 28705779 DOI: 10.1016/j.autrev.2017.07.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/10/2017] [Indexed: 12/28/2022]
Abstract
Chronic immune-mediated disorders (IMDs) constitute a major health burden. Understanding IMD pathogenesis is facing two major constraints: Missing heritability explaining familial clustering, and missing autoantigens. Pinpointing IMD risk genes and autoimmune targets, however, is of fundamental importance for developing novel causal therapies. The strongest association of all IMDs is seen with human leukocyte antigen (HLA) alleles. Using psoriasis as an IMD model this article reviews the pathogenic role HLA molecules may have within the polygenic predisposition of IMDs. It concludes that disease-associated HLA alleles account for both missing heritability and autoimmune mechanisms by facilitating tissue-specific autoimmune responses through autoantigen presentation.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig-Maximilian-University of Munich, Munich, Germany.
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53
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Abstract
Alloimmune T cells are central mediators of rejection and graft-versus-host disease in both solid organ and hematopoietic stem cell transplantation. Unique among immune responses in terms of its strength and diversity, the T cell alloresponse reflects extensive genetic polymorphisms between allogeneic donors and recipients, most prominently within the major histocompatibility complex (MHC), which encodes human leukocyte antigens (HLAs) in humans. The repertoire of alloreactive T cell clones is distinct for every donor-recipient pair and includes potentially thousands of unique HLA/peptide specificities. The extraordinary magnitude of the primary alloresponse and diversity of the T cell population mediating it have presented technical challenges to its study in humans. High-throughput T cell receptor sequencing approaches have opened up new possibilities for tackling many fundamental questions about this important immunologic phenomenon.
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54
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Abstract
Alloreactive T lymphocytes are the primary mediators of allograft rejection. The size and diversity of the HLA-alloreactive T cell repertoire has thus far precluded the ability to follow these T cells and thereby to understand their fate in human transplant recipients. This review summarizes the history, challenges, and recent advances in the study of alloreactive T cells. We highlight the historical development of assays to measure alloreactivity and discuss how high-throughput T cell receptor (TCR) sequencing-based assays can provide a new window into the fate of alloreactive T cells in human transplant recipients. A specific approach combining a classical in vitro assay, the mixed lymphocyte reaction, with deep T cell receptor sequencing is described as a tool to track the donor-reactive T cell repertoire for any specific HLA-mismatched donor-recipient pair. This assay can provide mechanistic insights and has potential as a noninvasive, highly specific biomarker for rejection and tolerance.
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55
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56
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Continuous Dual Resetting of the Immune Repertoire as a Basic Principle of the Immune System Function. J Immunol Res 2017; 2017:3760238. [PMID: 28246613 PMCID: PMC5299180 DOI: 10.1155/2017/3760238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/04/2016] [Indexed: 01/01/2023] Open
Abstract
Idiopathic chronic inflammatory conditions (ICIC) such as allergy, asthma, chronic obstructive pulmonary disease, and various autoimmune conditions are a worldwide health problem. Understanding the pathogenesis of ICIC is essential for their successful therapy and prevention. However, efforts are hindered by the lack of comprehensive understanding of the human immune system function. In line with those efforts, described here is a concept of stochastic continuous dual resetting (CDR) of the immune repertoire as a basic principle that governs the function of immunity. The CDR functions as a consequence of system's thermodynamically determined intrinsic tendency to acquire new states of inner equilibrium and equilibrium against the environment. Consequently, immune repertoire undergoes continuous dual (two-way) resetting: against the physiologic continuous changes of self and against the continuously changing environment. The CDR-based dynamic concept of immunity describes mechanisms of self-regulation, tolerance, and immunosenescence, and emphasizes the significance of immune system's compartmentalization in the pathogenesis of ICIC. The CDR concept's relative simplicity and concomitantly documented congruency with empirical, clinical, and experimental data suggest it may represent a plausible theoretical framework to better understand the human immune system function.
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57
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Polyspecificity of Anti-lipid A Antibodies and Its Relevance to the Development of Autoimmunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 966:181-202. [PMID: 28887790 DOI: 10.1007/5584_2017_94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The process of natural selection favours germ-line gene segments that encode CDRs that have the ability to recognize a range of structurally related antigens. This presents an immunological advantage to the host, as it can confer protection against a common pathogen and still cope with new or changing antigens. Cross-reactive and polyspecific antibodies also play a central role in autoimmune responses, and a link has been shown to exist between auto-reactive B cells and certain bacterial infections. Bacterial DNA, lipids, and carbohydrates have been implicated in the progression of autoimmune diseases such as systemic lupus erythematosus. As well, reports of anti-lipid A antibody polyspecificity towards single-stranded DNA together with the observed sequence homology amongst isolated auto- and anti-lipid A antibodies has prompted further study of this phenomenon. Though the lipid A epitope appears cryptic during Gram-negative bacterial infection, there have been several reported instances of lipid A-specific antibodies isolated from human sera, some of which have exhibited polyspecificity for single stranded DNA. In such cases, the breakdown of negative selection through polyspecificity can have the unfortunate consequence of autoimmune disease. This review summarizes current knowledge regarding such antibodies and emphasizes the features of S1-15, A6, and S55-5, anti-lipid A antibodies whose structures were recently determined by X-ray crystallography.
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58
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Van Regenmortel MHV. Structure-Based Reverse Vaccinology Failed in the Case of HIV Because it Disregarded Accepted Immunological Theory. Int J Mol Sci 2016; 17:E1591. [PMID: 27657055 PMCID: PMC5037856 DOI: 10.3390/ijms17091591] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/14/2022] Open
Abstract
Two types of reverse vaccinology (RV) should be distinguished: genome-based RV for bacterial vaccines and structure-based RV for viral vaccines. Structure-based RV consists in trying to generate a vaccine by first determining the crystallographic structure of a complex between a viral epitope and a neutralizing monoclonal antibody (nMab) and then reconstructing the epitope by reverse molecular engineering outside the context of the native viral protein. It is based on the unwarranted assumption that the epitope designed to fit the nMab will have acquired the immunogenic capacity to elicit a polyclonal antibody response with the same protective capacity as the nMab. After more than a decade of intensive research using this type of RV, this approach has failed to deliver an effective, preventive HIV-1 vaccine. The structure and dynamics of different types of HIV-1 epitopes and of paratopes are described. The rational design of an anti-HIV-1 vaccine is shown to be a misnomer since investigators who claim that they design a vaccine are actually only improving the antigenic binding capacity of one epitope with respect to only one paratope and not the immunogenic capacity of an epitope to elicit neutralizing antibodies. Because of the degeneracy of the immune system and the polyspecificity of antibodies, each epitope studied by the structure-based RV procedure is only one of the many epitopes that the particular nMab is able to recognize and there is no reason to assume that this nMab must have been elicited by this one epitope of known structure. Recent evidence is presented that the trimeric Env spikes of the virus possess such an enormous plasticity and intrinsic structural flexibility that it is it extremely difficult to determine which Env regions are the best candidate vaccine immunogens most likely to elicit protective antibodies.
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Affiliation(s)
- Marc H V Van Regenmortel
- UMR 7242 Biotechnologie et Signalisation Cellulaire, Université de Strasbourg-CNRS, 300, Boulevard Sébastien Brant, CS 10413, 67412 Illkirch Cedex, France.
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59
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Van Regenmortel MHV. Commentary: Basic Research in HIV Vaccinology Is Hampered by Reductionist Thinking. Front Immunol 2016; 7:266. [PMID: 27458032 PMCID: PMC4932109 DOI: 10.3389/fimmu.2016.00266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022] Open
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60
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Lucca LE, Axisa PP, Aloulou M, Perals C, Ramadan A, Rufas P, Kyewski B, Derbinski J, Fazilleau N, Mars LT, Liblau RS. Myelin oligodendrocyte glycoprotein induces incomplete tolerance of CD4(+) T cells specific for both a myelin and a neuronal self-antigen in mice. Eur J Immunol 2016; 46:2247-59. [PMID: 27334749 DOI: 10.1002/eji.201646416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/09/2016] [Accepted: 06/17/2016] [Indexed: 01/28/2023]
Abstract
T-cell polyspecificity, predicting that individual T cells recognize a continuum of related ligands, implies that multiple antigens can tolerize T cells specific for a given self-antigen. We previously showed in C57BL/6 mice that part of the CD4(+) T-cell repertoire specific for myelin oligodendrocyte glycoprotein (MOG) 35-55 also recognizes the neuronal antigen neurofilament medium (NF-M) 15-35. Such bi-specific CD4(+) T cells are frequent and produce inflammatory cytokines after stimulation. Since T cells recognizing two self-antigens would be expected to be tolerized more efficiently, this finding prompted us to study how polyspecificity impacts tolerance. We found that similar to MOG, NF-M is expressed in the thymus by medullary thymic epithelial cells, a tolerogenic population. Nevertheless, the frequency, phenotype, and capacity to transfer experimental autoimmune encephalomyelitis (EAE) of MOG35-55 -reactive CD4(+) T cells were increased in MOG-deficient but not in NF-M-deficient mice. We found that presentation of NF-M15-35 by I-A(b) on dendritic cells is of short duration, suggesting unstable MHC class II binding. Consistently, introducing an MHC-anchoring residue into NF-M15-35 (NF-M15-35 T20Y) increased its immunogenicity, activating a repertoire able to induce EAE. Our results show that in C57BL/6 mice bi-specific encephalitogenic T cells manage to escape tolerization due to inefficient exposure to two self-antigens.
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Affiliation(s)
- Liliana E Lucca
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Pierre-Paul Axisa
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Meryem Aloulou
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Corine Perals
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Abdulraouf Ramadan
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Pierre Rufas
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Bruno Kyewski
- Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, Heidelberg, Germany
| | - Jens Derbinski
- Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, Heidelberg, Germany
| | - Nicolas Fazilleau
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Lennart T Mars
- INSERM, U1043, Toulouse, France.,Centre National de la Recherche Scientifique, U5282, Toulouse, France.,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France
| | - Roland S Liblau
- INSERM, U1043, Toulouse, France. .,Centre National de la Recherche Scientifique, U5282, Toulouse, France. .,Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse, France. .,CHU Toulouse, Département d'Immunologie, Toulouse, France.
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61
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Ramadan A, Lucca LE, Carrié N, Desbois S, Axisa PP, Hayder M, Bauer J, Liblau RS, Mars LT. In situ expansion of T cells that recognize distinct self-antigens sustains autoimmunity in the CNS. Brain 2016; 139:1433-46. [PMID: 27000832 DOI: 10.1093/brain/aww032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/15/2016] [Indexed: 01/22/2023] Open
Abstract
Polyspecific T cells recognizing multiple distinct self-antigens have been identified in multiple sclerosis and other organ-specific autoimmune diseases, but their pathophysiological relevance remains undetermined. Using a mouse model of multiple sclerosis, we show that autoimmune encephalomyelitis induction is strictly dependent on reactivation of pathogenic T cells by a peptide (35-55) derived from myelin oligodendrocyte glycoprotein (MOG). This disease-inducing response wanes after onset. Strikingly, the progression of disease is driven by the in situ activation and expansion of a minority of MOG35-55-specific T cells that also recognize neurofilament-medium (NF-M)15-35, an intermediate filament protein expressed in neurons. This mobilization of bispecific T cells is critical for disease progression as adoptive transfer of NF-M15-35/MOG35-55 bispecific T cell lines caused full-blown disease in wild-type but not NF-M-deficient recipients. Moreover, specific tolerance through injection of NF-M15-35 peptide at the peak of disease halted experimental autoimmune encephalomyelitis progression. Our findings highlight the importance of polyspecific autoreactive T cells in the aggravation and perpetuation of central nervous system autoimmunity.
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Affiliation(s)
- Abdulraouf Ramadan
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Liliana E Lucca
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Nadège Carrié
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Sabine Desbois
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Pierre-Paul Axisa
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Myriam Hayder
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Jan Bauer
- Center for Brain Research, Department of Neuroimmunology, Medical University of Vienna, Vienna, Austria
| | - Roland S Liblau
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Lennart T Mars
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France INSERM UMR995, LIRIC, F-59000 Lille, France Université de Lille, centre d'excellence LICEND and FHU IMMINeNT, F-59000 Lille, France
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62
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Muraille E. The Unspecific Side of Acquired Immunity Against Infectious Disease: Causes and Consequences. Front Microbiol 2016; 6:1525. [PMID: 26793171 PMCID: PMC4707229 DOI: 10.3389/fmicb.2015.01525] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/18/2015] [Indexed: 11/13/2022] Open
Abstract
Acquired immunity against infectious disease (AIID) has long been considered as strictly dependent on the B and T lymphocytes of the adaptive immune system. Consequently, AIID has been viewed as highly specific to the antigens expressed by pathogens. However, a growing body of data motivates revision of this central paradigm of immunology. Unrelated past infection, vaccination, and chronic infection have been found to induce cross-protection against numerous pathogens. These observations can be partially explained by the poly-specificity of antigenic T and B receptors, the Mackaness effect and trained immunity. In addition, numerous studies highlight the importance of microbiota composition on resistance to infectious disease via direct competition or modulation of the immune response. All of these data support the idea that a non-negligible part of AIID in nature can be nonspecific to the pathogens encountered and even of the antigens expressed by pathogens. As this protection may be dependent on the private T and B repertoires produced by the random rearrangement of genes, past immune history, chronic infection, and microbiota composition, it is largely unpredictable at the individual level. However, we can reasonably expect that a better understanding of the underlying mechanisms will allow us to statistically predict cross-protection at the population level. From an evolutionary perspective, selection of immune mechanisms allowing for partially nonspecific AIID would appear to be advantageous against highly polymorphic and rapidly evolving pathogens. This new emerging paradigm may have several important consequences on our understanding of individual infectious disease susceptibility and our conception of tolerance, vaccination and therapeutic strategies against infection and cancer. It also underscores the importance of viewing the microbiota and persisting infectious agents as integral parts of the immune system.
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Affiliation(s)
- Eric Muraille
- Laboratoire de Parasitologie, Faculté de Médecine, Université Libre de BruxellesBruxelles, Belgium
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63
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Pichler WJ, Adam J, Watkins S, Wuillemin N, Yun J, Yerly D. Drug Hypersensitivity: How Drugs Stimulate T Cells via Pharmacological Interaction with Immune Receptors. Int Arch Allergy Immunol 2015; 168:13-24. [DOI: 10.1159/000441280] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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64
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Bremel RD, Homan EJ. Extensive T-Cell Epitope Repertoire Sharing among Human Proteome, Gastrointestinal Microbiome, and Pathogenic Bacteria: Implications for the Definition of Self. Front Immunol 2015; 6:538. [PMID: 26557118 PMCID: PMC4617169 DOI: 10.3389/fimmu.2015.00538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
T-cell receptor binding to MHC-bound peptides plays a key role in discrimination between self and non-self. Only a subset, typically a pentamer, of amino acids in a MHC-bound peptide form the motif exposed to the T-cell receptor. We categorize and compare the T-cell exposed amino acid motif repertoire of the total proteomes of two groups of bacteria, comprising pathogens and gastrointestinal microbiome organisms, with the human proteome and immunoglobulins. Given the maximum 205, or 3.2 million of such motifs that bind T-cell receptors, there is considerable overlap in motif usage. We show that the human proteome, exclusive of immunoglobulins, only comprises three quarters of the possible motifs, of which 65.3% are also present in both composite bacterial proteomes. Very few motifs are unique to the human proteome. Immunoglobulin variable regions carry a broad diversity of T-cell exposed motifs (TCEMs) that provides a stratified random sample of the motifs found in pathogens, microbiome, and the human proteome. Individual bacterial genera and species vary in the content of immunoglobulin and human proteome matched motifs that they carry. Mycobacteria and Burkholderia spp carry a particularly high content of such matched motifs. Some bacteria retain a unique motif signature and motif sharing pattern with the human proteome. The implication is that distinguishing self from non-self does not depend on individual TCEMs, but on a complex and dynamic overlay of signals wherein the same TCEM may play different roles in different organisms, and the frequency with which a particular TCEM appears influences its effect. The patterns observed provide clues to bacterial immune evasion and to strategies for intervention, including vaccine design. The breadth and distinct frequency patterns of the immunoglobulin-derived peptides suggest a role of immunoglobulins in maintaining a broadly responsive T-cell repertoire.
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65
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Cohn M. Two unresolved problems facing models of the Self-Nonself discrimination. J Theor Biol 2015; 387:31-8. [PMID: 26449741 DOI: 10.1016/j.jtbi.2015.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/07/2015] [Accepted: 09/17/2015] [Indexed: 12/25/2022]
Abstract
Although the Associative (linked) Recognition of Antigen (ARA) model for a Self (S)-Nonself (NS) discrimination, now over 50 years old, is built on a solid conceptual and experimental base, two unsettled questions remain. In examining these questions, unanticipated aspects of the ARA Model itself had to be reconsidered. This essay spells out these problems and suggests possible solutions.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, CA 92037-1099, USA.
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66
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Cohn M. What would Treg-cell biology look like when viewed from a rationalized perspective? Eur J Immunol 2015; 45:3002-9. [PMID: 26256556 DOI: 10.1002/eji.201545799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/25/2015] [Accepted: 08/04/2015] [Indexed: 11/09/2022]
Abstract
The argument that Treg cells play a role in determining the Self (S)-Nonself (NS) discrimination (i.e. tolerance) is challenged based on two theoretical constructs, the two stage-two signal model for the S-NS discrimination and the Tritope model of TCR function. The conclusions are then tested by reinterpreting a published probing set of data purporting to show that Treg cells regulate tolerance. It is concluded that the major role of suppression is to operate as a feedback mechanism modulating the magnitude of the effector response; it is not a determinant of the S-NS discrimination (i.e. tolerance).
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute, La Jolla, CA, USA
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67
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Aas-Hanssen K, Thompson KM, Bogen B, Munthe LA. Systemic Lupus Erythematosus: Molecular Mimicry between Anti-dsDNA CDR3 Idiotype, Microbial and Self Peptides-As Antigens for Th Cells. Front Immunol 2015; 6:382. [PMID: 26284067 PMCID: PMC4517057 DOI: 10.3389/fimmu.2015.00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/13/2015] [Indexed: 11/19/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is marked by a T helper (Th) cell-dependent B cell hyperresponsiveness, with frequent germinal center reactions, and gammaglobulinemia. A feature of SLE is the finding of IgG autoantibodies specific for dsDNA. The specificity of the Th cells that drive the expansion of anti-dsDNA B cells is unresolved. However, anti-microbial, anti-histone, and anti-idiotype Th cell responses have been hypothesized to play a role. It has been entirely unclear if these seemingly disparate Th cell responses and hypotheses could be related or unified. Here, we describe that H chain CDR3 idiotypes from IgG+ B cells of lupus mice have sequence similarities with both microbial and self peptides. Matched sequences were more frequent within the mutated CDR3 repertoire and when sequences were derived from lupus mice with expanded anti-dsDNA B cells. Analyses of histone sequences showed that particular histone peptides were similar to VDJ junctions. Moreover, lupus mice had Th cell responses toward histone peptides similar to anti-dsDNA CDR3 sequences. The results suggest that Th cells in lupus may have multiple cross-reactive specificities linked to the IgVH CDR3 Id-peptide sequences as well as similar DNA-associated protein motifs.
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Affiliation(s)
- Kristin Aas-Hanssen
- Department of Immunology, Centre for Immune Regulation, Institute of Clinical Medicine, University of Oslo , Oslo , Norway
| | - Keith M Thompson
- Department of Immunology, Centre for Immune Regulation, Institute of Clinical Medicine, University of Oslo , Oslo , Norway
| | - Bjarne Bogen
- Department of Immunology, Centre for Immune Regulation, Institute of Clinical Medicine, University of Oslo , Oslo , Norway ; KG Jebsen Centre for Influenza Vaccine Research, Institute of Clinical Medicine, University of Oslo , Oslo , Norway
| | - Ludvig A Munthe
- Department of Immunology, Centre for Immune Regulation, Institute of Clinical Medicine, University of Oslo , Oslo , Norway
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Van Regenmortel MHV. Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition. J Mol Recognit 2015; 27:627-39. [PMID: 25277087 DOI: 10.1002/jmr.2394] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 11/09/2022]
Abstract
The concept of antibody specificity is analyzed and shown to reside in the ability of an antibody to discriminate between two antigens. Initially, antibody specificity was attributed to sequence differences in complementarity determining regions (CDRs), but as increasing numbers of crystallographic antibody-antigen complexes were elucidated, specificity was analyzed in terms of six antigen-binding regions (ABRs) that only roughly correspond to CDRs. It was found that each ABR differs significantly in its amino acid composition and tends to bind different types of amino acids at the surface of proteins. In spite of these differences, the combined preference of the six ABRs does not allow epitopes to be distinguished from the rest of the protein surface. These findings explain the poor success of past and newly proposed methods for predicting protein epitopes. Antibody polyspecificity refers to the ability of one antibody to bind a large variety of epitopes in different antigens, and this property explains how the immune system develops an antibody repertoire that is able to recognize every antigen the system is likely to encounter. Antibody heterospecificity arises when an antibody reacts better with another antigen than with the one used to raise the antibody. As a result, an antibody may sometimes appear to have been elicited by an antigen with which it is unable to react. The implications of antibody polyspecificity and heterospecificity in vaccine development are pointed out.
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Affiliation(s)
- Marc H V Van Regenmortel
- Wallenberg Research Center, Stellenbosch Institute for Advanced Study, Stellenbosch University, Stellenbosch, South Africa
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69
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Autoimmunity: Rationalizing possible pathways from initiation to disease. J Theor Biol 2015; 375:40-51. [DOI: 10.1016/j.jtbi.2014.05.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/12/2014] [Accepted: 05/20/2014] [Indexed: 12/23/2022]
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70
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Van Regenmortel MHV. Why Does the Molecular Structure of Broadly Neutralizing Monoclonal Antibodies Isolated from Individuals Infected with HIV-1 not Inform the Rational Design of an HIV-1 Vaccine? AIMS Public Health 2015; 2:183-193. [PMID: 29546103 PMCID: PMC5690275 DOI: 10.3934/publichealth.2015.2.183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/28/2015] [Indexed: 01/12/2023] Open
Abstract
It is commonly assumed that neutralizing Mabs that bind to the HIV-1 Env glycoprotein are more specific reagents than anti-HIV-1 polyclonal antisera and that knowledge of the structure of these Mabs facilitates the rational design of effective HIV-1 vaccine immunogens. However, after more than ten years of unsuccessful experimentation using the structure-based reverse vaccinology approach, it is now evident that it is not possible to infer from the structure of neutralizing Mabs which HIV immunogens induced their formation nor which vaccine immunogens will elicit similar Abs in an immunized host. The use of Mabs for developing an HIV-1 vaccine was counterproductive because it overlooked the fact that the apparent specificity of a Mab very much depends on the selection procedure used to obtain it and also did not take into account that an antibody is never monospecific for a single epitope but is always polyspecific for many epitopes. When the rationale of the proponents of the unsuccessful rational design strategy is analyzed, it appears that investigators who claim they are designing a vaccine immunogen are only improving the binding reactivity of a single epitope-paratope pair and are not actually designing an immunogen able to generate protective antibodies. The task of a designer consists in imagining what type of immunogen is likely to elicit a protective immune response but in the absence of knowledge regarding which features of the immune system are responsible for producing a functional neutralizing activity in antibodies, it is not feasible to intentionally optimize a potential immunogen candidate in order to obtain the desired outcome. The only available option is actually to test possible solutions by trial-and-error experiments until the preset goal is perhaps attained. Rational design and empirical approaches in HIV vaccine research should thus not be opposed as alternative options since empirical testing is an integral part of a so-called design strategy.
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Affiliation(s)
- Marc H V Van Regenmortel
- CNRS, UMR7242 - Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, Illkirch 67400, France ; Tel: +27-793376766
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71
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Van Regenmortel MHV. An Outdated Notion of Antibody Specificity is One of the Major Detrimental Assumptions of the Structure-Based Reverse Vaccinology Paradigm, Which Prevented It from Helping to Develop an Effective HIV-1 Vaccine. Front Immunol 2014; 5:593. [PMID: 25477882 PMCID: PMC4235417 DOI: 10.3389/fimmu.2014.00593] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/05/2014] [Indexed: 01/12/2023] Open
Abstract
The importance of paradigms for guiding scientific research is explained with reference to the seminal work of Karl Popper and Thomas Kuhn. A prevalent paradigm, followed for more than a decade in HIV-1 vaccine research, which gave rise to the strategy known as structure-based reverse vaccinology is described in detail. Several reasons why this paradigm did not allow the development of an effective HIV-1 vaccine are analyzed. A major reason is the belief shared by many vaccinologists that antibodies possess a narrow specificity for a single epitope and are not polyspecific for a diverse group of potential epitopes. When this belief is abandoned, it becomes obvious that the one particular epitope structure observed during the crystallographic analysis of a neutralizing antibody–antigen complex does not necessarily reveal, which immunogenic structure should be used to elicit the same type of neutralizing antibody. In the physical sciences, scientific explanations are usually presented as logical deductions derived from a relevant law of nature together with certain initial conditions. In immunology, causal explanations in terms of a single cause acting according to a law of nature are not possible because numerous factors always play a role in bringing about an effect. The implications of this state of affairs for the rational design of HIV vaccines are outlined. An alternative approach to obtain useful scientific understanding consists in intervening empirically in the immune system and it is suggested that manipulating the system experimentally is needed to learn to control it and achieve protective immunity by vaccination.
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Affiliation(s)
- Marc H V Van Regenmortel
- CNRS, Biotechnologie des Interactions Moleculaires, IREBS, School of Biotechnology, ESBS, University of Strasbourg , Illkirch , France
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72
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Bremel RD, Homan EJ. Frequency Patterns of T-Cell Exposed Amino Acid Motifs in Immunoglobulin Heavy Chain Peptides Presented by MHCs. Front Immunol 2014; 5:541. [PMID: 25389426 PMCID: PMC4211557 DOI: 10.3389/fimmu.2014.00541] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/12/2014] [Indexed: 01/17/2023] Open
Abstract
Immunoglobulins are highly diverse protein sequences that are processed and presented to T-cells by B-cells and other antigen presenting cells. We examined a large dataset of immunoglobulin heavy chain variable regions (IGHV) to assess the diversity of T-cell exposed motifs (TCEMs). TCEM comprise those amino acids in a MHC-bound peptide, which face outwards, surrounded by the MHC histotope, and which engage the T-cell receptor. Within IGHV there is a distinct pattern of predicted MHC class II binding and a very high frequency of re-use of the TCEMs. The re-use frequency indicates that only a limited number of different cognate T-cells are required to engage many different clonal B-cells. The amino acids in each outward-facing TCEM are intercalated with the amino acids of inward-facing MHC groove-exposed motifs (GEM). Different GEM may have differing, allele-specific, MHC binding affinities. The intercalation of TCEM and GEM in a peptide allows for a vast combinatorial repertoire of epitopes, each eliciting a different response. Outcome of T-cell receptor binding is determined by overall signal strength, which is a function of the number of responding T-cells and the duration of engagement. Hence, the frequency of TCEM re-use appears to be an important determinant of whether a T-cell response is stimulatory or suppressive. The frequency distribution of TCEMs implies that somatic hypermutation is followed by T-cell clonal expansion that develops along repeated pathways. The observations of TCEM and GEM derived from immunoglobulins suggest a relatively simple, yet powerful, mechanism to correlate T-cell polyspecificity, through re-use of TCEMs, with a very high degree of specificity achieved by combination with a diversity of GEMs. The frequency profile of TCEMs also points to an economical mechanism for maintaining T-cell memory, recall, and self-discrimination based on an endogenously generated profile of motifs.
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73
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Lucca LE, Desbois S, Ramadan A, Ben-Nun A, Eisenstein M, Carrié N, Guéry JC, Sette A, Nguyen P, Geiger TL, Mars LT, Liblau RS. Bispecificity for myelin and neuronal self-antigens is a common feature of CD4 T cells in C57BL/6 mice. THE JOURNAL OF IMMUNOLOGY 2014; 193:3267-77. [PMID: 25135834 DOI: 10.4049/jimmunol.1400523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The recognition of multiple ligands by a single TCR is an intrinsic feature of T cell biology, with important consequences for physiological and pathological processes. Polyspecific T cells targeting distinct self-antigens have been identified in healthy individuals as well as in the context of autoimmunity. We have previously shown that the 2D2 TCR recognizes the myelin oligodendrocyte glycoprotein epitope (MOG)35-55 as well as an epitope within the axonal protein neurofilament medium (NF-M15-35) in H-2(b) mice. In this study, we assess whether this cross-reactivity is a common feature of the MOG35-55-specific T cell response. To this end, we analyzed the CD4 T cell response of MOG35-55-immunized C57BL/6 mice for cross-reactivity with NF-M15-35. Using Ag recall responses, we established that an important proportion of MOG35-55-specific CD4 T cells also responded to NF-M15-35 in all mice tested. To study the clonality of this response, we analyzed 22 MOG35-55-specific T cell hybridomas expressing distinct TCR. Seven hybridomas were found to cross-react with NF-M15-35. Using an alanine scan of NF-M18-30 and an in silico predictive model, we dissected the molecular basis of cross-reactivity between MOG35-55 and NF-M15-35. We established that NF-M F24, R26, and V27 proved important TCR contacts. Strikingly, the identified TCR contacts are conserved within MOG38-50. Our data indicate that due to linear sequence homology, part of the MOG35-55-specific T cell repertoire of all C57BL/6 mice also recognizes NF-M15-35, with potential implications for CNS autoimmunity.
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Affiliation(s)
- Liliana E Lucca
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Sabine Desbois
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Abdulraouf Ramadan
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Avraham Ben-Nun
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miriam Eisenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nadège Carrié
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Jean-Charles Guéry
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, San Diego, CA 92109
| | - Phuong Nguyen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Lennart T Mars
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Roland S Liblau
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France; Département d'Immunologie, Centre Hospitalier Universitaire Toulouse, Hôpital Purpan, Toulouse F-31300, France
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74
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Vaz NM, Carvalho CR. On the origin of immunopathology. J Theor Biol 2014; 375:61-70. [PMID: 24937801 DOI: 10.1016/j.jtbi.2014.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 12/19/2022]
Abstract
Stranded between medicine and experimental biology, immunology is buried in its own problems and remains distant from important areas of current biology, such as evolutionary theory, developmental biology and cognitive sciences. Immunology has treated the living system merely as the place or dimension in which immune activity takes place, inserted on a misleading axis (progressive responsiveness versus no response; memory versus tolerance) which neglects the analysis of a robustly stable dynamics which is always present and is neither tolerance nor immunity-a problem currently approached as one of "regulatory" activity. However, a regulatory response also demands regulation, leading to an endless recursion and the adoption of a stimulus-response framework inevitably drives us away from the physiological processes in which lymphocytes are involved. Herein, we propose that immunological physiology, like everything else in the body is dynamic and conservative. Immunopathology, including inherited immunodeficiencies, severe forms of infectious diseases, allergy and autoimmune diseases, are interferences with this stability which frequently include oligoclonal expansions of T lymphocytes. We suggest that this decrease in clonal diversity results from a loss of the stabilizing connectivity among lymphocytes and are not simply markers of immunopathology, but are rather expressions of basic pathogenic mechanisms. The so-called autoimmune diseases are examples of this disequilibrium. In the last decade the characterization of an enormous and diversified commensal microbiota has posed a new and pressing problem: how to explain the harmonic conviviality with trillions of foreign macromolecules. In addition, robustly stable relations towards macromolecular diet can be established by simple ingestion, a state presently labeled as "oral tolerance", a problem that has been buffered for decades as anti-inflammatory protection of the gut. A major change in terminology is necessary to describe this new panorama. We focus on two important gaps in immunological discussions: (a) the organism, seen simultaneously as the medium with which the immune system is constantly in touch and as the entity that mediates the contact with external materials; and (b) the observer, the immunologist, who operates as a human being in human languaging with other human beings, and characterizes immunological specificity. We acknowledge that we are proposing radical departures from current dogma and that we should justify them. Most of what we propose stem form a way of seeing called Biology of Cognition and Language, that derives from ideas of the neurobiologist/philosopher Humberto Maturana, also known as "autopoiesis theory".
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Affiliation(s)
- Nelson M Vaz
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil.
| | - Claudia R Carvalho
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil
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75
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Tauber AI. Reconceiving autoimmunity: An overview. J Theor Biol 2014; 375:52-60. [PMID: 24880023 DOI: 10.1016/j.jtbi.2014.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/13/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
Three interconnected positions are advocated: (1) although serving as a useful model, the immune self does not exist as such; (2) instead of a self/nonself demarcation, the immune system 'sees' itself, i.e., it does not ignore the 'self' or attack the 'other;' but exhibits a spectrum of responses, which when viewed from outside the system appear as discrimination of 'self' and 'nonself' based on certain criteria of reactivity. When immune reactions are conceived in terms of normal physiology and open exchange with the environment, where borders dividing host and foreign are elusive and changing, host defense is only part of the immune system's functions, which actually comprise two basic tasks: protection, i.e., to preserve host integrity, and maintenance of organismic identity. And thus (3) if the spectrum of immunity is enlarged, differentiating low reactive 'autoimmune' reactions from activated immune responses against the 'other' is only a matter of degree. Simply, all immunity is 'autoimmunity,' and the pathologic state of immunity directed at normal constituents of the organism is a particular case of dis-regulation, which appropriately is designated, autoimmune. Other uses of 'autoimmunity' and its congeners function as the semantic remnants of Burnet's original self/nonself theory and should be replaced. A new nomenclature is proposed, concinnity, which more accurately designates the physiology of the animal's ordinary housekeeping economy mediated by the immune system than 'autoimmunity' when used to describe such normal functions.
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Affiliation(s)
- Alfred I Tauber
- Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel.
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76
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Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J, Özkan E, Davis MM, Wucherpfennig KW, Garcia KC. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 2014; 157:1073-87. [PMID: 24855945 PMCID: PMC4071348 DOI: 10.1016/j.cell.2014.03.047] [Citation(s) in RCA: 395] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/17/2014] [Accepted: 03/14/2014] [Indexed: 01/07/2023]
Abstract
In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.
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Affiliation(s)
- Michael E. Birnbaum
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Juan L. Mendoza
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Dhruv K. Sethi
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Shen Dong
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Jacob Glanville
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Jessica Dobbins
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115,Program in Immunology, Harvard Medical School, Boston, MA 02115
| | - Engin Özkan
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Kai W. Wucherpfennig
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115,Program in Immunology, Harvard Medical School, Boston, MA 02115
| | - K. Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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77
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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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78
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Grignolio A, Mishto M, Faria AMC, Garagnani P, Franceschi C, Tieri P. Towards a liquid self: how time, geography, and life experiences reshape the biological identity. Front Immunol 2014; 5:153. [PMID: 24782860 PMCID: PMC3988364 DOI: 10.3389/fimmu.2014.00153] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/24/2014] [Indexed: 01/08/2023] Open
Abstract
The conceptualization of immunological self is amongst the most important theories of modern biology, representing a sort of theoretical guideline for experimental immunologists, in order to understand how host constituents are ignored by the immune system (IS). A consistent advancement in this field has been represented by the danger/damage theory and its subsequent refinements, which at present represents the most comprehensive conceptualization of immunological self. Here, we present the new hypothesis of "liquid self," which integrates and extends the danger/damage theory. The main novelty of the liquid self hypothesis lies in the full integration of the immune response mechanisms into the host body's ecosystems, i.e., in adding the temporal, as well as the geographical/evolutionary and environmental, dimensions, which we suggested to call "immunological biography." Our hypothesis takes into account the important biological changes occurring with time (age) in the IS (including immunosenescence and inflammaging), as well as changes in the organismal context related to nutrition, lifestyle, and geography (populations). We argue that such temporal and geographical dimensions impinge upon, and continuously reshape, the antigenicity of physical entities (molecules, cells, bacteria, viruses), making them switching between "self" and "non-self" states in a dynamical, "liquid" fashion. Particular attention is devoted to oral tolerance and gut microbiota, as well as to a new potential source of unexpected self epitopes produced by proteasome splicing. Finally, our framework allows the set up of a variety of testable predictions, the most straightforward suggesting that the immune responses to defined molecules representing potentials antigens will be quantitatively and qualitatively quite different according to the immuno-biographical background of the host.
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Affiliation(s)
- Andrea Grignolio
- Interdepartmental Center "Luigi Galvani" for Bioinformatics, Biophysics and Biocomplexity, University of Bologna , Bologna , Italy
| | - Michele Mishto
- Centro Interdipartimentale di Ricerca sul Cancro "G. Prodi", University of Bologna , Bologna , Italy ; Institut für Biochemie, Charité - Universitätsmedizin Berlin , Berlin , Germany
| | - Ana Maria Caetano Faria
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte , Brazil
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna , Bologna , Italy
| | - Claudio Franceschi
- Interdepartmental Center "Luigi Galvani" for Bioinformatics, Biophysics and Biocomplexity, University of Bologna , Bologna , Italy ; Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna , Bologna , Italy ; IRCCS of Neurological Science , Bologna , Italy ; Institute of Organic Synthesis and Photoreactivity, National Research Council , Bologna , Italy
| | - Paolo Tieri
- Institute for Applied Mathematics "M. Picone", National Research Council , Rome , Italy
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79
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Abstract
αβ T cells are an integral part of protective immunity against pathogens. After precursor cells arise in the adult bone marrow or fetal liver, they migrate to the thymus where they rearrange their T-cell receptor genes (TCR) and undergo selection on the basis of their interactions with ligands expressed by thymic stroma and other cells. Those that survive then exit the thymus to populate the peripheral immune compartment, where they patrol the blood and lymphoid systems. The composition of this pre-immune peripheral repertoire is critically important in determining the robustness of an immune response. In both mice and humans, the magnitude and diversity of a response are directly correlated with the frequency of precursor T cells. Equally relevant are the functional characteristics of these lymphocytes. Engagement of a specific antigen to the TCR activates signaling pathways in the naive T cell that result in cellular proliferation and the acquisition of particular effector functions. A portion of these persist following the resolution of infection and become memory cells. These memory cells can mount a faster and stronger response when they encounter the same antigen at a later time. As the molecular basis for TCR ligand interaction has become better defined, it is clear that some T cells can recognize multiple distinct ligands and therefore T-cell memory developed by exposure to one ligand may play a significant role in the response to a different antigen. Thus, there is an increasing focus on understanding how exposure to related or unrelated antigens influences the T-cell repertoire and impacts subsequent immunity. In this review, we discuss the issue of TCR cross-reactivity in the development of memory phenotype CD4(+) T cells and the implications for pathogen-specific responses. We review both the human and mouse data and discuss the therapeutic implications of these findings in the contexts of infection and vaccination.
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Affiliation(s)
- Laura F Su
- The Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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80
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Nikoopour E, Cheung R, Bellemore S, Krougly O, Lee-Chan E, Stridsberg M, Singh B. Vasostatin-1 antigenic epitope mapping for induction of cellular and humoral immune responses to chromogranin A autoantigen in NOD mice. Eur J Immunol 2014; 44:1170-80. [DOI: 10.1002/eji.201343986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/08/2013] [Accepted: 12/18/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Enayat Nikoopour
- Department of Microbiology and Immunology and Centre for Human Immunology; Robarts Research Institute; University of Western Ontario; London Ontario Canada
| | - Rebecca Cheung
- Department of Microbiology and Immunology and Centre for Human Immunology; Robarts Research Institute; University of Western Ontario; London Ontario Canada
| | - Stacey Bellemore
- Department of Microbiology and Immunology and Centre for Human Immunology; Robarts Research Institute; University of Western Ontario; London Ontario Canada
| | - Olga Krougly
- Department of Microbiology and Immunology and Centre for Human Immunology; Robarts Research Institute; University of Western Ontario; London Ontario Canada
| | - Edwin Lee-Chan
- Department of Microbiology and Immunology and Centre for Human Immunology; Robarts Research Institute; University of Western Ontario; London Ontario Canada
| | - Mats Stridsberg
- Department of Medical Sciences; Uppsala University; Uppsala Sweden
| | - Bhagirath Singh
- Department of Microbiology and Immunology and Centre for Human Immunology; Robarts Research Institute; University of Western Ontario; London Ontario Canada
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81
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Cohn M. A stepwise model of polyreactivity of the T cell antigen-receptor (TCR): its impact on the self–nonself discrimination and on related observations (receptor editing, anergy, dual receptor cells). Cell Mol Life Sci 2013; 71:2033-45. [DOI: 10.1007/s00018-013-1540-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/06/2013] [Accepted: 12/02/2013] [Indexed: 12/01/2022]
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82
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Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol 2013; 4:413. [PMID: 24348479 PMCID: PMC3841818 DOI: 10.3389/fimmu.2013.00413] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023] Open
Abstract
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.
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Affiliation(s)
- Adrien Six
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Maria Encarnita Mariotti-Ferrandiz
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Wahiba Chaara
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Susana Magadan
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
| | - Hang-Phuong Pham
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2 , Montpellier , France
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS and Ecole Normale Supérieure , Paris , France
| | - Véronique Thomas-Vaslin
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure , Paris , France
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
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83
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Finton KAK, Larimore K, Larman HB, Friend D, Correnti C, Rupert PB, Elledge SJ, Greenberg PD, Strong RK. Autoreactivity and exceptional CDR plasticity (but not unusual polyspecificity) hinder elicitation of the anti-HIV antibody 4E10. PLoS Pathog 2013; 9:e1003639. [PMID: 24086134 PMCID: PMC3784475 DOI: 10.1371/journal.ppat.1003639] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/04/2013] [Indexed: 01/19/2023] Open
Abstract
The broadly-neutralizing anti-HIV antibody 4E10 recognizes an epitope in the membrane-proximal external region of the HIV envelope protein gp41. Previous attempts to elicit 4E10 by vaccination with envelope-derived or reverse-engineered immunogens have failed. It was presumed that the ontogeny of 4E10-equivalent responses was blocked by inherent autoreactivity and exceptional polyreactivity. We generated 4E10 heavy-chain knock-in mice, which displayed significant B cell dysregulation, consistent with recognition of autoantigen/s by 4E10 and the presumption that tolerance mechanisms may hinder the elicitation of 4E10 or 4E10-equivalent responses. Previously proposed candidate 4E10 autoantigens include the mitochondrial lipid cardiolipin and a nuclear splicing factor, 3B3. However, using carefully-controlled assays, 4E10 bound only weakly to cardiolipin-containing liposomes, but also bound negatively-charged, non-cardiolipin-containing liposomes comparably poorly. 4E10/liposome binding was predominantly mediated by electrostatic interactions rather than presumed hydrophobic interactions. The crystal structure of 4E10 free of bound ligands showed a dramatic restructuring of the combining site, occluding the HIV epitope binding site and revealing profound flexibility, but creating an electropositive pocket consistent with non-specific binding of phospholipid headgroups. These results strongly suggested that antigens other than cardiolipin mediate 4E10 autoreactivity. Using a synthetic peptide library spanning the human proteome, we determined that 4E10 displays limited and focused, but unexceptional, polyspecificity. We also identified a novel autoepitope shared by three ER-resident inositol trisphosphate receptors, validated through binding studies and immunohistochemistry. Tissue staining with 4E10 demonstrated reactivity consistent with the type 1 inositol trisphosphate receptor as the most likely candidate autoantigen, but is inconsistent with splicing factor 3B3. These results demonstrate that 4E10 recognition of liposomes competes with MPER recognition and that HIV antigen and autoepitope recognition may be distinct enough to permit eliciting 4E10-like antibodies, evading autoimmunity through directed engineering. However, 4E10 combining site flexibility, exceptional for a highly-matured antibody, may preclude eliciting 4E10 by conventional immunization strategies.
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Affiliation(s)
- Kathryn A K Finton
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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84
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Myelin recovery in multiple sclerosis: the challenge of remyelination. Brain Sci 2013; 3:1282-324. [PMID: 24961530 PMCID: PMC4061877 DOI: 10.3390/brainsci3031282] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 12/26/2022] Open
Abstract
Multiple sclerosis (MS) is the most common demyelinating and an autoimmune disease of the central nervous system characterized by immune-mediated myelin and axonal damage, and chronic axonal loss attributable to the absence of myelin sheaths. T cell subsets (Th1, Th2, Th17, CD8+, NKT, CD4+CD25+ T regulatory cells) and B cells are involved in this disorder, thus new MS therapies seek damage prevention by resetting multiple components of the immune system. The currently approved therapies are immunoregulatory and reduce the number and rate of lesion formation but are only partially effective. This review summarizes current understanding of the processes at issue: myelination, demyelination and remyelination—with emphasis upon myelin composition/architecture and oligodendrocyte maturation and differentiation. The translational options target oligodendrocyte protection and myelin repair in animal models and assess their relevance in human. Remyelination may be enhanced by signals that promote myelin formation and repair. The crucial question of why remyelination fails is approached is several ways by examining the role in remyelination of available MS medications and avenues being actively pursued to promote remyelination including: (i) cytokine-based immune-intervention (targeting calpain inhibition), (ii) antigen-based immunomodulation (targeting glycolipid-reactive iNKT cells and sphingoid mediated inflammation) and (iii) recombinant monoclonal antibodies-induced remyelination.
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85
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Levin MC, Lee S, Gardner LA, Shin Y, Douglas JN, Cooper C. Autoantibodies to Non-myelin Antigens as Contributors to the Pathogenesis of Multiple Sclerosis. JOURNAL OF CLINICAL & CELLULAR IMMUNOLOGY 2013; 4:10.4172/2155-9899.1000148. [PMID: 24363960 PMCID: PMC3866957 DOI: 10.4172/2155-9899.1000148] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For years, investigators have sought to prove that myelin antigens are the primary targets of autoimmunity in multiple sclerosis (MS). Recent experiments have begun to challenge this assumption, particularly when studying the neurodegenerative phase of MS. T-lymphocyte responses to myelin antigens have been extensively studied, and are likely early contributors to the pathogenesis of MS. Antibodies to myelin antigens have a much more inconstant association with the pathogenesis of MS. Recent studies indicate that antibodies to non-myelin antigens such as neurofilaments, neurofascin, RNA binding proteins and potassium channels may contribute to the pathogenesis of MS. The purpose of this review is to analyze recent studies that examine the role that autoantibodies to non-myelin antigens might play in the pathogenesis of MS.
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Affiliation(s)
- Michael C. Levin
- Veterans Administration Medical Center, Memphis, TN, USA
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Neuroscience, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sangmin Lee
- Veterans Administration Medical Center, Memphis, TN, USA
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lidia A. Gardner
- Veterans Administration Medical Center, Memphis, TN, USA
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yoojin Shin
- Veterans Administration Medical Center, Memphis, TN, USA
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joshua N. Douglas
- Veterans Administration Medical Center, Memphis, TN, USA
- Department of Neuroscience, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Chelsea Cooper
- Veterans Administration Medical Center, Memphis, TN, USA
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA
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86
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Eckle SBG, Rossjohn J, McCluskey J. Alloreactivity. Methods Mol Biol 2013; 1034:3-39. [PMID: 23775729 DOI: 10.1007/978-1-62703-493-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The alloimmune response between individuals genetically disparate for antigens encoded within the major histocompatibility complex (MHC) remains a substantial barrier to transplantation of solid organs, tissues, and hematopoietic stem cells. Alloreactivity has been an immunological paradox because of its apparent contradiction to the requirement of MHC restriction for the induction of normal T lymphocyte mediated immune responses. Through crystallographic analyses and experimental systems utilizing murine CD8(+) cytolytic T cell clones, major advances have been achieved in understanding the molecular and structural basis of T cell receptor recognition of MHC-peptide complexes and the basis of T cell mediated alloreactivity. These studies have further provided an explanation for the relatively high frequencies of alloreactive T cells compared to the frequencies of T cells for microbial derived antigens.
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Affiliation(s)
- Sidonia B G Eckle
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC, Australia
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87
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Knapp B, Dorffner G, Schreiner W. Early relaxation dynamics in the LC 13 T cell receptor in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PLoS One 2013; 8:e64464. [PMID: 23762240 PMCID: PMC3675092 DOI: 10.1371/journal.pone.0064464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/15/2013] [Indexed: 01/24/2023] Open
Abstract
The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology. Although several different models for the activation process of the T cell via the T cell receptor have been proposed, it could not be shown that a structural mechanism, which discriminates between peptides of different immunogenicity levels, exists within the T cell receptor. In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system. Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.
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Affiliation(s)
- Bernhard Knapp
- Center for Medical Statistics, Informatics and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria.
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88
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Madura F, Rizkallah PJ, Miles KM, Holland CJ, Bulek AM, Fuller A, Schauenburg AJA, Miles JJ, Liddy N, Sami M, Li Y, Hossain M, Baker BM, Jakobsen BK, Sewell AK, Cole DK. T-cell receptor specificity maintained by altered thermodynamics. J Biol Chem 2013; 288:18766-75. [PMID: 23698002 PMCID: PMC3696650 DOI: 10.1074/jbc.m113.464560] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The T-cell receptor (TCR) recognizes peptides bound to major histocompatibility molecules (MHC) and allows T-cells to interrogate the cellular proteome for internal anomalies from the cell surface. The TCR contacts both MHC and peptide in an interaction characterized by weak affinity (KD = 100 nM to 270 μM). We used phage-display to produce a melanoma-specific TCR (α24β17) with a 30,000-fold enhanced binding affinity (KD = 0.6 nM) to aid our exploration of the molecular mechanisms utilized to maintain peptide specificity. Remarkably, although the enhanced affinity was mediated primarily through new TCR-MHC contacts, α24β17 remained acutely sensitive to modifications at every position along the peptide backbone, mimicking the specificity of the wild type TCR. Thermodynamic analyses revealed an important role for solvation in directing peptide specificity. These findings advance our understanding of the molecular mechanisms that can govern the exquisite peptide specificity characteristic of TCR recognition.
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Affiliation(s)
- Florian Madura
- Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
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89
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Abstract
Using a dynamic model we study the adaptive immune response to a sequence of two infections. We incorporate lymphocyte diversity by modeling populations as continuous distributions in a multi-dimensional space. As expected, memory cells generated by the primary infection invoke a rapid response when the secondary infection is identical (homologous). When the secondary infection is different (heterologous), the memory cells have a positive effect or no effect at all depending on the similarity of the infections. This model displays 'original antigenic sin' where the average effector affinity for the heterologous infection is lower than it would be for a naive response, but in cases with original antigenic sin we see a reduction in pathogen density. We model pathology resulting from the immune system itself (immunopathology) but find that in cases of original antigenic sin, immunopathology is still reduced. Average effector affinity is not an accurate measure of the quality of an immune response. The effectivity, which is the total pathogen killing rate, provides a direct measure of quality. This quantity takes both affinity and magnitude into account.
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Affiliation(s)
- Sean P Stromberg
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, USA.
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90
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Abstract
Natural killer (NK) cells are key components of innate immune responses, providing surveillance against cells undergoing tumorigenesis or infection, by viruses or internal pathogens. NK cells can directly eliminate compromised cells and regulate downstream responses of the innate and acquired immune systems through the release of immune modulators (cytokines, interferons). The importance of the role NK cells play in immune defense was demonstrated originally in herpes viral infections, usually mild or localized, which become severe and life threatening in NK-deficient patients . NK cell effector functions are governed by balancing opposing signals from a diverse array of activating and inhibitory receptors. Many NK receptors occur in paired activating and inhibitory isoforms and recognize major histocompatibility complex (MHC) class I proteins with varying degrees of peptide specificity. Structural studies have made considerable inroads into understanding the molecular mechanisms employed to broadly recognize multiple MHC ligands or specific pathogen-associated antigens and the strategies employed by viruses to thwart these defenses. Although many details of NK development, signaling, and integration remain mysterious, it is clear that NK receptors are key components of a system exquisitely tuned to sense any dysregulation in MHC class I expression, or the expression of certain viral antigens, resulting in the elimination of affected cells.
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Affiliation(s)
- Kathryn A Finton
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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91
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Lewis JE, Fu SM, Gaskin F. Autoimmunity, end organ damage, and the origin of autoantibodies and autoreactive T cells in systemic lupus erythematosus. DISCOVERY MEDICINE 2013; 15:85-92. [PMID: 23449110 PMCID: PMC3725807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototype of systemic autoimmunity affecting many systems. Both antibodies and autoreactive T cells play significant roles in its pathogenesis. Experimental data and clinical observations indicate that autoimmunity and end organ damage are under separate genetic controls and that there are significant interactions between these two pathways. Experimental evidence has been obtained to support the hypothesis that autoantibodies and autoreactive T effector cells may be initiated by environmental factors through molecular mimicry and the inherent polyreactive nature of antigen receptors. A unified hypothesis has been postulated for the pathogenesis of SLE that has practical implications.
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Affiliation(s)
- Janet E Lewis
- Division of Rheumatology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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92
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Hogan EL, Podbielska M, O'Keeffe J. Implications of Lymphocyte Anergy to Glycolipids in Multiple Sclerosis (MS): iNKT Cells May Mediate the MS Infectious Trigger. ACTA ACUST UNITED AC 2013; 4. [PMID: 26347308 PMCID: PMC4557814 DOI: 10.4172/2155-9899.1000144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Immunogenic lipids may play key roles in host defenses against infection and in generating autoimmune inflammation and organ-specific damage. In multiple sclerosis (MS) there are unequivocal autoimmune features and vulnerability to aggravation or induction by microbial or viral infection. We have found glycolipid-driven anergy of circulating lymphocytes in MS indicating that this immune response is affected in MS and the robust effects of iNKT activation with potent cellular and cytokine activities emphasizes its potential importance. Diverse glycolipids including the endogenous myelin acetylated-galactosylceramides (AcGalCer) can drive activation that could be critical to the inflammatory demyelination in the central nervous system and clinical consequences. The iNKT cells and their invariant or iTCR (Vα24Jα18Vβ11) receptor an innate defense–a discrete immune arm that is separate from peptide-driven acquired immune responses. This offers new possibilities for insight including a likelihood that the pattern recognition of exogenous microbial and myelin immunogens can overlap and cross-react especially in an inflammatory milieu.
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Affiliation(s)
- Edward L Hogan
- Georgia Regents University, Institute of Molecular Medicine and Genetics, Department of Neurology, 1120 15 Street, Augusta, 30912-2620 GA, USA ; National University of Ireland Galway, Department of Microbiology, University Road, Galway, Ireland ; Medical University of South Carolina, Department of Neurosciences, 173 Ashley Avenue, Charleston, SC 29401, USA
| | - Maria Podbielska
- Georgia Regents University, Institute of Molecular Medicine and Genetics, Department of Neurology, 1120 15 Street, Augusta, 30912-2620 GA, USA ; Ludwik Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences, Laboratory of Signaling Proteins, R. Weigla Street 12, 53-114 Wrocław, Poland
| | - Joan O'Keeffe
- Department of Life and Physical Sciences, School of Science, Galway-Mayo Institute of Technology, Galway, Ireland
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93
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Kieber-Emmons T, Monzavi-Karbassi B, Pashov A, Saha S, Murali R, Kohler H. The promise of the anti-idiotype concept. Front Oncol 2012; 2:196. [PMID: 23267437 PMCID: PMC3526099 DOI: 10.3389/fonc.2012.00196] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/01/2012] [Indexed: 11/13/2022] Open
Abstract
A basic tenet of antibody-based immunity is their specificity to antigenic determinates from foreign pathogen products to abnormal cellular components such as in cancer. However, an antibody has the potential to bind to more than one determinate, be it an antigen or another antibody. These observations led to the idiotype network theory (INT) to explain immune regulation, which has wax and waned in enthusiasm over the years. A truer measure of the impact of the INT is in terms of the ideas that now form the mainstay of immunological research and whose roots are spawned from the promise of the anti-idiotype concept. Among the applications of the INT is understanding the structural implications of the antibody-mediated network that has the potential for innovation in terms of rational design of reagents with biological, chemical, and pharmaceutical applications that underlies concepts of reverse immunology which is highlighted herein.
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Affiliation(s)
- Thomas Kieber-Emmons
- Winthrop P. Rockefeller Cancer Institute, Department of Pathology, University of Arkansas for Medical Sciences Little Rock, AR, USA
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94
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Viral antigen density and confinement time regulate the reactivity pattern of CD4 T-cell responses to vaccinia virus infection. Proc Natl Acad Sci U S A 2012; 110:288-93. [PMID: 23248307 DOI: 10.1073/pnas.1208328110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
T-cell recognition of ligands is polyspecific. This translates into antiviral T-cell responses having a range of potency and specificity for viral ligands. How these ligand recognition patterns are established is not fully understood. Here, we show that an activation threshold regulates whether robust CD4 T-cell activation occurs following viral infection. The activation threshold was variable because of its dependence on the density of the viral peptide (p)MHC displayed on infected cells. Furthermore, the activation threshold was not observed to be a specific equilibrium affinity (K(D)) or half-life (t(1/2)) of the TCR-viral pMHC interaction, rather it correlated with the confinement time of TCR-pMHC interactions, i.e., the half-life (t(1/2)) of the interaction accounting for the effects of TCR-pMHC rebinding. One effect of a variable activation threshold is to allow high-density viral pMHC ligands to expand CD4 T cells with a variety of potency and peptide cross-reactivity patterns for the viral pMHC ligand, some of which are only poorly activated by infections that produce a lower density of the viral pMHC ligand. These results argue that antigen concentration is a key component in determining the pattern of K(D), t(1/2) and peptide cross-reactivity of the TCRs expressed on CD4 T cells responding to infection.
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95
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Abstract
T cells must recognize a vast array of potential foreign peptide–MHC complexes. Comprehensive immune cover can only be provided if each T cell recognizes numerous peptides. The implications of this T cell cross-reactivity include autoimmune disease but also provide opportunities for multiple therapeutic interventions. 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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96
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What is so special about thinking; after all, we all do it! Exp Mol Pathol 2012; 93:354-64. [DOI: 10.1016/j.yexmp.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 08/17/2012] [Indexed: 12/24/2022]
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97
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Garcia KC. Reconciling views on T cell receptor germline bias for MHC. Trends Immunol 2012; 33:429-36. [PMID: 22771140 PMCID: PMC3983780 DOI: 10.1016/j.it.2012.05.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/13/2012] [Accepted: 05/13/2012] [Indexed: 01/25/2023]
Abstract
Whether MHC restriction by the T cell receptor (TCR) is a product of evolutionary pressures leading to germline-encoded 'rules of engagement' remains avidly debated. Structural results derived from analysis of TCR-peptide-MHC complexes appear to support a model of physical specificity between TCR germline V regions and MHC. Yet, some recent evidence suggests that thymic selection, and co-receptors may have misled us into thinking the TCR is exclusively MHC-specific, when in fact, TCRs can robustly engage non-MHC ligands when given the chance. Here, I propose that seemingly contradictory data and hypotheses for, and against, germline bias are, in fact, compatible and can be reconciled into a unifying model.
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Affiliation(s)
- K Christopher Garcia
- Howard Hughes Medical Institute, Department of Molecular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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98
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Unbiased identification of target antigens of CD8+ T cells with combinatorial libraries coding for short peptides. Nat Med 2012; 18:824-8. [PMID: 22484809 DOI: 10.1038/nm.2720] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/03/2011] [Indexed: 12/13/2022]
Abstract
Cytotoxic CD8(+) T cells recognize the antigenic peptides presented by class I major histocompatibility complex (MHC) molecules. These T cells have key roles in infectious diseases, autoimmunity and tumor immunology, but there is currently no unbiased method for the reliable identification of their target antigens. This is because of the low affinities of antigen-specific T cell receptors (TCR) to their target MHC-peptide complexes, the polyspecificity of these TCRs and the requirement that these TCRs recognize protein antigens that have been processed by antigen-presenting cells (APCs). Here we describe a technology for the unbiased identification of the antigenic peptides presented by MHC class I molecules. The technology uses plasmid-encoded combinatorial peptide libraries and a single-cell detection system. We validated this approach using a well-characterized influenza-virus–specific TCR, MHC and peptide combination. Single APCs carrying antigenic peptides can be detected among several million APCs that carry irrelevant peptides. The identified peptide sequences showed a converging pattern of mimotopes that revealed the parent influenza antigen. This technique should be generally applicable to the identification of disease-relevant T cell antigens.
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99
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Cohn M. Meanderings into the Regulation of Effector Class by the Immune System: Derivation of the Trauma Model. Scand J Immunol 2012; 76:77-88. [DOI: 10.1111/j.1365-3083.2012.02721.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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100
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Van Regenmortel MHV. Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol 2012; 3:194. [PMID: 22787464 PMCID: PMC3391733 DOI: 10.3389/fimmu.2012.00194] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/21/2012] [Indexed: 01/05/2023] Open
Abstract
This review describes the structure-based reverse vaccinology approach aimed at developing vaccine immunogens capable of inducing antibodies that broadly neutralize HIV-1. Some basic principles of protein immunochemistry are reviewed and the implications of the extensive polyspecificity of antibodies for vaccine development are underlined. Although it is natural for investigators to want to know the cause of an effective immunological intervention, the classic notion of causality is shown to have little explanatory value for a system as complex as the immune system, where any observed effect always results from many interactions between a large number of components. Causal explanations are reductive because a single factor is singled out for attention and given undue explanatory weight on its own. Other examples of the negative impact of reductionist thinking on HIV vaccine development are discussed. These include (1) the failure to distinguish between the chemical nature of antigenicity and the biological nature of immunogenicity, (2) the belief that when an HIV-1 epitope is reconstructed by rational design to better fit a neutralizing monoclonal antibody (nMab), this will produce an immunogen able to elicit Abs with the same neutralizing capacity as the Ab used as template for designing the antigen, and (3) the belief that protection against infection can be analyzed at the level of individual molecular interactions although it has meaning only at the level of an entire organism. The numerous unsuccessful strategies that have been used to design HIV-1 vaccine immunogens are described and it is suggested that the convergence of so many negative experimental results justifies the conclusion that reverse vaccinology is unlikely to lead to the development of a preventive HIV-1 vaccine. Immune correlates of protection in vaccines have not yet been identified because this will become feasible only retrospectively once an effective vaccine exists. The finding that extensive antibody affinity maturation is needed to obtain mature anti-HIV-1 Abs endowed with a broad neutralizing capacity explains why antigens designed to fit matured Mabs are not effective vaccine immunogens since these are administered to naive recipients who possess only B-cell receptors corresponding to the germline version of the matured Abs.
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Affiliation(s)
- Marc H. V. Van Regenmortel
- Stellenbosch Institute of Advanced Study, Wallenberg Research Center at Stellenbosch University,Stellenbosch, South Africa
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