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Cohn M. Giving Context to Non-self-marker Theories of Immune Responsiveness. Scand J Immunol 2017; 86:124-129. [DOI: 10.1111/sji.12579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 06/23/2017] [Indexed: 11/30/2022]
Affiliation(s)
- M. Cohn
- Conceptual Immunology Group; The Salk Institute; La Jolla CA USA
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Cohn M. A Commentary on a Workshop ‘To Reveal the Foundational Concepts of Immune Regulation
’ (i.e. Tolerance). Scand J Immunol 2017; 85:312-320. [DOI: 10.1111/sji.12536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 02/01/2017] [Indexed: 01/06/2023]
Affiliation(s)
- M. Cohn
- Conceptual Immunology Group; The Salk Institute; La Jolla CA USA
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Cohn M. Core principles characterizing immune function. Eur J Immunol 2016; 47:35-40. [PMID: 28000923 DOI: 10.1002/eji.201646706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/10/2016] [Accepted: 11/18/2016] [Indexed: 11/07/2022]
Abstract
The immune system is an anticipatory mechanism designed by evolution to protect the individual against noxious agents and harmful cellular debris. In order to recognize substances that it has never encountered, the immune system somatically generates an appropriately sized random (with respect to self and nonself [NS]) recognitive repertoire that is coupled to a biodestructive and ridding output. Consequently, a Self-NS discrimination is required in order to avoid autoimmunity. This essay is an attempt to highlight the core principles upon which this anticipatory mechanism depends in order to function.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute, La Jolla, CA, USA
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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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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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Cohn M. Thoughts engendered by Bretscher's Two-step, Two-signal model for a peripheral self-non-self discrimination and the origin of primer effector T helpers. Scand J Immunol 2015; 81:87-95. [PMID: 25413363 DOI: 10.1111/sji.12255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/27/2014] [Indexed: 01/18/2023]
Abstract
There are three questions under re-examination here that have been inspired by Bretscher's 'Two-step, Two-signal' model. First, what is the nature of the steps required in order for antigen-responsive cells to become effectors? Second, how does the immune system get started? Third and the most troublesome, what is the mechanism that relates the delivery of the two signals? To answer the first question, Bretscher proposes a pathway that I will place in another context by comparing it with what had been envisaged under the Associative Recognition of Antigen (ARA) model. The second question, how does the immune system gets started, is crucial to our understanding of the self-non-self discrimination. This problem boils down to, what is the origin of the first effector T helper (eTh) cells required to activate all antigen-responsive cells including the T helpers themselves (the primer problem)? To deal with this question, I proposed an antigen-independent pathway to primer eTh. Bretscher presents us with an antigen-dependent pathway to primer eTh. As competing models are precious in clarifying thinking and in guiding experimentation, I felt it important to reanalyse the two models and look for ways to decide between them. The third question deals with the requirement for and the mechanism of associative (linked) recognition of antigen (ARA). The concept of ARA is so compelling at both the experimental and theoretical levels that to save it, a new perspective will be introduced.
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute, La Jolla, CA, USA
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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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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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Cohn M. Musings About Regulation by T-Suppressors: A Response to the Commentary by Kristofor Ellestad on ‘Meanderings into the Regulation of Effector Class by the Immune System: Derivation of the Trauma Model’. Scand J Immunol 2012; 76:92-8. [DOI: 10.1111/j.1365-3083.2012.02723.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cohn M. Ten experiments that would make a difference in understanding immune mechanisms. Cell Mol Life Sci 2012; 69:405-12. [PMID: 22042272 PMCID: PMC11115027 DOI: 10.1007/s00018-011-0869-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 09/28/2011] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
Abstract
Jacques Monod used to say, "Never trust an experiment that is not supported by a good theory." Theory or conceptualization permits us to put order or structure into a vast amount of data in a way that increases understanding. Validly competing theories are most useful when they make testably disprovable predictions. Illustrating the theory-experiment interaction is the goal of this exercise. Stated bleakly, the answers derived from the theory-based experiments described here would impact dramatically on how we understand immune behavior.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, San Diego, CA 92037, USA.
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Cohn M. The evolutionary context for a self-nonself discrimination. Cell Mol Life Sci 2010; 67:2851-62. [PMID: 20585970 PMCID: PMC2956437 DOI: 10.1007/s00018-010-0438-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 06/10/2010] [Indexed: 10/19/2022]
Abstract
This essay was written to illustrate how one might think about the immune system. The formulation of valid theories is the basic component of how-to-think because the reduction of large and complex data sets by the use of logic into a succinct model with predictability and explanatory power, is the only way that we have to arrive at "understanding". Whether it is to achieve effective manipulation of the system or for pure pleasure, "understanding" is a universally agreed upon goal. It is in the nature of science that theories are there to be disproven. An experimentally disproven theory is a successful one. As they fail experimental test one by one, we end up with a default theory, that is, one that has yet to fail. Here, using the self-nonself discrimination as an example, how-to-think as I see it, will be illustrated.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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Abstract
The question under analysis in this commentary is, what was the evolutionary selection pressure that necessitated the ectopic expression of a subset of peripheral self-antigens in the thymus and by peripheral APC? The suggestion is that antigen expression is delayed until after the immune system is responsive.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Cohn M. The discussion with Jacques Miller: illustrating the limitations of pure empiricism. Immunol Cell Biol 2009; 87:435-7. [PMID: 19434068 PMCID: PMC2882186 DOI: 10.1038/icb.2009.34] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA, USA
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Cohn M. On the critique by Colin Anderson of 'A reply to Dembic: on an end to the beginning of mis-understanding the immune response'. Scand J Immunol 2009; 70:1-9. [PMID: 19522761 PMCID: PMC2729654 DOI: 10.1111/j.1365-3083.2009.02264.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
My proposal of a set of postulates that can be used to guide computer modeling has understandably met with significant criticism at two levels, semantic and conceptual. The major source of contention is my assumption that the sorting of the paratopic repertoire is both necessary and sufficient to explain the evolutionarily selected mechanism for the self-nonself discrimination. While 'necessary' is agreed upon, 'sufficient' is debatable as this commentary illustrates. My essay is in defense of 'sufficiency'.
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Bauer AL, Beauchemin CAA, Perelson AS. Agent-based modeling of host-pathogen systems: The successes and challenges. Inf Sci (N Y) 2009; 179:1379-1389. [PMID: 20161146 PMCID: PMC2731970 DOI: 10.1016/j.ins.2008.11.012] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based models relevant to host–pathogen systems and discuss their contributions to our understanding of biological processes. We then point out some limitations and challenges of agent-based models and encourage efforts towards reproducibility and model validation.
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Affiliation(s)
- Amy L Bauer
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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Cohn M. A reply to Dembic: on an end to the beginning of misunderstanding the immune response. Scand J Immunol 2009; 69:302-5. [PMID: 19284493 DOI: 10.1111/j.1365-3083.2009.02230.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We all agree that dealing with the complexity and volume of the data necessitates the use of computer modelling. This in turn requires a heuristic conceptual framework to guide this modelling. The first attempt to do this by Cohn has been criticized by Dembic as being severely lacking. This commentary deals with his criticism of the framework to show why Cohn's postulates, in fact, remain unchallenged.
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Cohn M. On the opposing views of the self-nonself discrimination by the immune system. Immunol Cell Biol 2009; 87:113-9, discussion 120-1. [PMID: 19048020 PMCID: PMC2880885 DOI: 10.1038/icb.2008.96] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Today's generally accepted view of the self-nonself discrimination was voiced by Miller(1) in 2004 in a thought-provoking essay. In spite of its popularity, this position has its limitations, which are analyzed here with a view toward establishing an interactive discussion that hopefully will culminate in agreed upon decisive experiments. The inadequacies of Miller's view of the self-nonself discrimination and their resolution under the associative recognition of antigen model are analyzed.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Cohn M. How does the immune response get started? Cell Immunol 2008; 254:91-3. [PMID: 19022423 PMCID: PMC2637764 DOI: 10.1016/j.cellimm.2008.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 07/28/2008] [Accepted: 10/09/2008] [Indexed: 11/30/2022]
Abstract
An effective adaptive immune response requires the prior induction of the regulatory effector T-helper (eTh). There are two competing models of how this cell is induced to effectors. Under the Associative Recognition of Antigen (ARA) or "two signal" model, the T-helper requires eTh in order to be induced to eTh, an "autocatalytic" process. Under the "costimulation" model eTh are induced by an antigen-unspecific signal derived from an "activated" APC. Under the ARA model the problem of the origin of the primer eTh is posed. A nonself antigen-independent pathway to eTh is proposed as well as an experiment to reveal its existence. In the costimulation framework no primer eTh need be postulated but it lacks a mechanism that, in the absence of ARA, accounts for the self-nonself discrimination and the determination of effector class.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Cohn M. A rationalized set of default postulates that permit a coherent description of the immune system amenable to computer modeling. Scand J Immunol 2008; 68:371-80. [PMID: 18782265 PMCID: PMC2581492 DOI: 10.1111/j.1365-3083.2008.02158.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This discussion delineates and rationalizes a set of postulates that permit a coherent understanding of immune function. Although analytical tools such as mathematics and computer modeling have become very popular, simulation and data mining in the absence of a conceptual framework cannot increase understanding. The goal of this essay is to provide the foundation for a discussion that has as its goal the formulation of an agreed upon set of default postulates. Such a set is required to guide the algorithms needed to analyze complex immune behavior.
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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Cohn M. What roles do regulatory T cells play in the control of the adaptive immune response? Int Immunol 2008; 20:1107-18. [PMID: 18658168 PMCID: PMC2733841 DOI: 10.1093/intimm/dxn088] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 07/09/2008] [Indexed: 12/21/2022] Open
Abstract
The immune system, like many systems responsive to specific stimuli, requires feedback regulation. The key regulatory element determining antigen-specific responsiveness is the effector T helper. As the response tends to overshoot, a feedback control of the magnitude of the response is critical to avoid immunopathology. This is the proposed role of the effector T suppressor (T(s)). The reasons for this interpretation of the data are discussed as are the reasons that the competing postulate is ruled out, namely that T(s) function in determining the self-non-self-discrimination. The regulatory T cell family consists of two lineages, T helpers and T(s). Differentiated derivatives of the T helper lineage drive the expression and amplification of specific classes of defensive effector cells. T(s) feedback to limit the magnitude of the process so that debilitating immunopathology is acceptably infrequent.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Cohn M. A biological context for the self-nonself discrimination and the regulation of effector class by the immune system. Immunol Res 2008; 31:133-50. [PMID: 15778511 DOI: 10.1385/ir:31:2:133] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An effective immune response to an antigen requires two sets of decisions: Decision 1, the sorting of the repertoire, and Decision 2, the regulation of effector class. The repertoire, because it is somatically generated, large, and random, must be sorted by a somatic mechanism that subtracts those specificities (anti-self) that, if expressed, would debilitate the host, leaving a residue (anti-nonself) that, if not expressed, would result in the death of the host by infection. The self-nonself discrimination is the metaphor used to describe Decision 1, the sorting of the repertoire. In order to be functional, the sorted repertoire must be coupled to a set of biodestructive and ridding effector functions, such that the response to each antigen is treated in a coherent and independent manner. Although a reasonably complete framework for Decision 1 exists, Decision 2 lacks conceptualization. The questions that must be considered to arrive at a proper framework are posed. It should be emphasized that manipulation at the level of Decision 2 is where clinical applications are likely to be found.
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Affiliation(s)
- Melvin Cohn
- The Salk Institute for Biological Studies, Conceptual Immunology Group, La Jolla, CA 92037, USA.
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Shapiro M, Duca KA, Lee K, Delgado-Eckert E, Hawkins J, Jarrah AS, Laubenbacher R, Polys NF, Hadinoto V, Thorley-Lawson DA. A virtual look at Epstein-Barr virus infection: simulation mechanism. J Theor Biol 2008; 252:633-48. [PMID: 18371986 DOI: 10.1016/j.jtbi.2008.01.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 01/09/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
Abstract
Epstein-Barr virus (EBV) is an important human pathogen that establishes a life-long persistent infection and for which no precise animal model exists. In this paper, we describe in detail an agent-based model and computer simulation of EBV infection. Agents representing EBV and sets of B and T lymphocytes move and interact on a three-dimensional grid approximating Waldeyer's ring, together with abstract compartments for lymph and blood. The simulation allows us to explore the development and resolution of virtual infections in a manner not possible in actual human experiments. Specifically, we identify parameters capable of inducing clearance, persistent infection, or death.
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Affiliation(s)
- M Shapiro
- Department of Pathology, Jaharis Building, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
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Cohn M, Mitchison NA, Paul WE, Silverstein AM, Talmage DW, Weigert M. Reflections on the clonal-selection theory. Nat Rev Immunol 2007; 7:823-30. [PMID: 17893695 DOI: 10.1038/nri2177] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
How do we account for the immune system's ability to produce antibodies in response to new antigens? It has been 50 years since F. Macfarlane Burnet published his answer to this question: the clonal-selection theory of antibody diversity. The idea that specificity for diverse antigens exists before these antigens are encountered was a radical notion at the time, but one that became widely accepted. In this article, Nature Reviews Immunology asks six key scientists for their thoughts and opinions on the clonal-selection theory, from its first proposal to their views of it today.
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Abstract
The types of mathematical models used in immunology and their scope have changed drastically in the past 10 years. Classical models were based on ordinary differential equations (ODEs), difference equations, and cellular automata. These models focused on the 'simple' dynamics obtained between a small number of reagent types (e.g. one type of receptor and one type of antigen or two T-cell populations). With the advent of high-throughput methods, genomic data, and unlimited computing power, immunological modeling shifted toward the informatics side. Many current applications of mathematical models in immunology are now focused around the concepts of high-throughput measurements and system immunology (immunomics), as well as the bioinformatics analysis of molecular immunology. The types of models have shifted from mainly ODEs of simple systems to the extensive use of Monte Carlo simulations. The transition to a more molecular and more computer-based attitude is similar to the one occurring over all the fields of complex systems analysis. An interesting additional aspect in theoretical immunology is the transition from an extreme focus on the adaptive immune system (that was considered more interesting from a theoretical point of view) to a more balanced focus taking into account the innate immune system also. We here review the origin and evolution of mathematical modeling in immunology and the contribution of such models to many important immunological concepts.
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Affiliation(s)
- Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel.
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Abstract
This article describes the functionality of a cellular automata-based immune system simulator, which we call SIS (synthetic immune system). SIS is based on descriptive cellular states and rules that define transitions between these states to model an entire immune system. Through the use of this program, an immunologist can test the validity of a proposed model by observing how it responds to self and non-self antigen. The output is then compared with the behavior of a real protective immune system, and the model can then be ruled as being adequate or inadequate. SIS-I, the first version of SIS written, has been modified through the years and is now available on our Web site: (http://www.cig.salk.edu/sis-I/sis.html). Although SIS-I has some flexibility, it has many hardwired values as well as a predefined keyword language for writing immune system rules. SIS-II was developed from SIS-I and allows the user to change more variables and to define keywords used within the program. Herein, we give an overview on how to use SIS-I and SIS-II, along with a future direction, SIS-III.
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Affiliation(s)
- James Mata
- The Salk Institute, Conceptual Immunology Group, San Diego, CA 92186, USA.
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Does the signal for the activation of T cells originate from the antigen-presenting cell or the effector T-helper? Cell Immunol 2006; 241:1-6. [PMID: 16963007 DOI: 10.1016/j.cellimm.2006.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 07/31/2006] [Indexed: 01/28/2023]
Abstract
The present view is that the antigen-presenting cell (APC) processes and presents simultaneously on its surface several different antigens that are displayed randomly (with respect to their being Self or Nonself) as peptide-MHC complexes. The naive T-cell interacting with its ligand on the APC is activated by "co-stimulation," the first step on the pathway to effectors. This view ignores the requirement for associative recognition of antigen (ARA) in mediating both the Self-Nonself discrimination and the regulation of effector class. The introduction of ARA as a requirement for these two decision functions highlights a critical role for the effector T-helper (eTh) and necessitates rethinking the contribution of the APC.
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Abstract
In analysing the Zinkernagel and Hengartner's 'Credo 2004,' Anderson introduces his 'development-context model' for the immunity-tolerance discrimination. He compares this model with the 'geographical model of Credo 2004' and our 'time-based two-signal model'. The discussion here deals with the advantages and limitations of the Anderson model considered largely at the level of principle. A meaningful discussion requires that we agree on the principle which separates the pathway of the effector output into two decision steps, the sorting of the repertoire and the regulation of effector class. The mechanism for the sorting of the repertoire is what might be referred to as the Self-Nonself discrimination. The black box approach, antigen-in, effector response-out, is what is referred to as the immunity-tolerance discrimination which includes the sorting of the repertoire. If this point of principle is accepted then we are left with a 'time-based two signal default model'.
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Cohn M. What are the commonalities governing the behavior of humoral immune recognitive repertoires? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:19-42. [PMID: 16139887 DOI: 10.1016/j.dci.2005.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The humoral repertoire of immune systems is large, random and somatically selected. It is derived from a germline selected repertoire by a variety of diversification mechanisms, complementation of subunits, mutation and gene conversion. However derived, the end-product must be able to recognize and rid a vast variety of pathogens. This is accomplished by viewing antigens as combinatorials of epitopes, an astuce that permits a small repertoire to respond sufficiently rapidly to a vast antigenic universe. A somatically generated repertoire, however, requires a solution to two problems. First, a somatic mechanism for a self-nonself discrimination has to be put in place. Second, the repertoire has to be coupled to the effector mechanisms in a coherent fashion. The rules governing these two mechanisms are species-independent and delineate the parameters of all immune repertoires, whatever the somatic mechanism used to generate them.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Cohn M. On the Responses of Zinkernagel and Hengartner: An Invitation to Join the Fray. Scand J Immunol 2005. [DOI: 10.1046/j.0300-9475.2001.01019.x-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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Abstract
In 'Credo 2004', Zinkernagel and Hengartner give us a food-for-thought analysis of immune responsiveness based on a 'pragmatic and empiric point of view.' The Credo 2004 postulates derived by inductive extrapolation from observation to generalization do not satisfactorily account for immune behaviour because they lack a conceptualization as illustrated here. Nevertheless, Credo 2004 is certainly valuable in a limited framework because it is based on the most likely of assumptions namely that the immune system was evolutionarily selected to protect against infectious agents, and therefore the study of pathogens will most accurately reveal how the immune system responds normally to protect. After reformulating them, the postulates of Credo 2004 are analysed with respect to their generality.
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Affiliation(s)
- M Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Cohn M. The common sense of the self-nonself discrimination. ACTA ACUST UNITED AC 2005; 27:3-17. [PMID: 15711952 DOI: 10.1007/s00281-005-0199-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 12/15/2004] [Indexed: 11/28/2022]
Abstract
The vertebrate immune system was evolutionarily selected to express a large random somatically generated paratopic repertoire coupled to effector mechanisms invented, in large measure, by non-vertebrates. The self-nonself discrimination is determined by Decision 1, the sorting of this repertoire into those specificities (anti-self) which, if expressed, would debilitate the host and those specificities (anti-nonself) which, if not expressed, would result in the death of the host by infection. Decision 1, the sorting of the repertoire, is mediated by a somatic learning process operating epitope-by-epitope that deletes anti-self specificities leaving the residue as anti-nonself. The activation of anti-nonself is the first step on entry into Decision 2, which optimizes the choice and magnitude of the effector class that rids the pathogen without significantly debilitating the host. The principles governing Decision 1, the self-nonself discrimination are analyzed here.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Chao DL, Davenport MP, Forrest S, Perelson AS. A stochastic model of cytotoxic T cell responses. J Theor Biol 2004; 228:227-40. [PMID: 15094017 DOI: 10.1016/j.jtbi.2003.12.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Accepted: 12/31/2003] [Indexed: 10/26/2022]
Abstract
We have constructed a stochastic stage-structured model of the cytotoxic T lymphocyte (CTL) response to antigen and the maintenance of immunological memory. The model follows the dynamics of a viral infection and the stimulation, proliferation, and differentiation of naïve CD8(+) T cells into effector CTL, which can eliminate virally infected cells. The model is capable of following the dynamics of multiple T cell clones, each with a T cell receptor represented by a digit string. MHC-viral peptide complexes are also represented by strings and a string match rule is used to compute the affinity of a T cell receptor for a viral epitope. The avidities of interactions are also computed by taking into consideration the density of MHC-viral peptides on the surface of an infected cell. Lastly, the model allows the probability of T cell stimulation to depend on avidity but also incorporates the notion of an antigen-independent programmed proliferative response. We compare the model to experimental data on the cytotoxic T cell response to lymphocytic choriomeningitis virus infections.
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Affiliation(s)
- Dennis L Chao
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
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Cohn M. An alternative to current thinking about positive selection, negative selection and activation of T cells. Immunology 2004; 111:375-80. [PMID: 15056372 PMCID: PMC1782432 DOI: 10.1111/j.0019-2805.2004.01830.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Given that recognition by the T-cell receptor (TCR) of allele-specific determinants on major histocompatibility complex (MHC)-encoded restricting elements (Rs) is germline encoded, whereas recognition of peptide (P) is somatically encoded, two combining site repertoires, anti-R and anti-P, are implied. As a consequence, the three pathways of T cells, positive selection, negative selection and activation, must be signalled by qualitatively distinct interactions engaging the TCR. These are spelled out as they provide an alternative to the current thinking that these pathways depend on affinity-based quantitatively distinguishable interactions.
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Affiliation(s)
- Melvin Cohn
- The Salk Institute for Biological Studies, Conceptual Immunology Group, La Jolla, CA 92037-1099, USA.
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Cohn M. Whither T-suppressors: if they didn’t exist would we have to invent them? Cell Immunol 2004; 227:81-92. [PMID: 15135290 DOI: 10.1016/j.cellimm.2004.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 02/03/2004] [Indexed: 10/26/2022]
Abstract
Arriving at an understanding of the role of suppressor T-cells (regulatory T-cells, CD4(+)CD25+) depends on whether their functional repertoire is somatically selected to be anti-Self or anti-Nonself. Immunologists are ambivalent; often publications espousing opposite views share an author. Here the arguments are detailed that the suppressor repertoire is not somatically selected to be anti-Self, but rather it is anti-Nonself. Therefore, suppression cannot regulate the Self-Nonself discrimination; its function is to regulate the magnitude and class of the anti-Nonself effector response.
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Affiliation(s)
- Melvin Cohn
- Gulbenkian Science Institute, Oeiras, Portugal.
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