The case for allele-specific recognition by the TCR.

There is a sharp difference in how one views TCR structure-function-behaviour dependent on whether its recognition of major histocompatibility complex-encoded restriction elements (R) is germline selected or somatically generated. The generally accepted or Standard model is built on the assumption that recognition of R is by the V regions of the αß TCR, which is not driven by allele specificity, whereas the competing model posits that recognition of R is allele-specific. The establishing of allele-specific recognition of R by the TCR would rule out the Standard model and clear the road to a consideration of a competing construct, the Tritope model. Here, the case for allele-specific recognition (germline selected) is detailed making it obvious that the Standard model is untenable.

Core principles characterizing immune function.

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.

The real "danger" lies in the failure to confront fundamentals.

Can we formulate a framework that would provide an agreed upon basis for discussions of immune behaviour? An attempt to do this is, in the end, the main goal of this essay. If you tell a physicist that you have invented a perpetual motion machine, he would not spend any time trying to reveal the flaw. Rather, he would shrug you off because in his framework, such a machine is an impossibility. However, immunologists lacking an agreed upon, preferably default, framework spend their time chasing into dead-end alleys or take refuge in descriptive empiricism. This will be illustrated using Danger theory, which ignores fundamentals to generate a framework believed to obviate the need for a Self (S)-Nonself (NS) discrimination and which is claimed to be bolstered with monogamous data (observation married to a single explanation). The arguments presented here apply to all NS-marker theories (pathogenicity, discontinuity, localization, danger, etc.).

Exploring the elements for a successful immune offense against cancer.

A successful immune attack on a tumor requires two elements. First, a nonself (NS) epitope that can act as an effective target must be expressed uniquely and uniformly on the tumor. Second, the immune system must be induced to produce an appropriate ridding effector activity specific for the cell expressing that de novo displayed NS-epitope. Today, the major effort is directed toward nonspecifically increasing the horsepower of the immune system by relieving suppressive and resistance factors using checkpoint blockade. This is coupled to the hope that the cancer will display a unique nonself determinant and that tolerance to Self (S) will not be abrogated. Here, these two elements will be explored in order to see what a more defined approach to the immune system treatment of cancer entails. While a Hail Mary approach may, in the end, be our only alternative, defining the elements of a solution, attainable or not, based on basic immunology, can only be salutary.

What would Treg-cell biology look like when viewed from a rationalized perspective?

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).

Rationalizing thymic selection for functional T-cells: A commentary.

What are the minimum specificity requirements of a thymic selective process that establishes (1) restrictive recognition of peptide, (2) the Self (S)-Nonself (NS) discrimination, and (3) the categories of effector function? Given an answer to that question, how well does it fit with the observed selective processes in thymus where T-cells are generated? Any discrepancies between the two must be rationalized. The goal of this essay is to attempt just that.

Autoimmunity: Rationalizing possible pathways from initiation to disease.

Any physiological system that has as its output an activity that is biodestructive and ridding must have a way of distinguishing the host (self) from that which is other (nonself). The setting in which autoimmunity can be analyzed depends, in part and unavoidably, on the way in which the normal self (S)-nonself (NS) discrimination is accomplished. Any discussion of autoimmunity should include one's view of this latter. To this end, a pathway for the normal S-NS discrimination will be proposed. Then, a mechanism for the determination of effector class will be considered as autoimmune disease is consequent to it. Experiments challenging both the proposed model of normal behavior, as well as that of the extrapolation to autoimmunity, will be cited along with a discussion of some of the elements which, if rendered defective, would result in autoimmunity. The goal is to see how far this particular abstraction based largely on the logic of evolutionary biology can meaningfully guide understanding of the disease.

Two unresolved problems facing models of the Self-Nonself discrimination.

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.

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).

The existence of antigen-receptors, BCR, and T cell antigen-receptors, that are "polyreactive", necessitates a rethinking of its effect on two problems faced by the "adaptive" immune system: the self (S)-nonself (NS) discrimination and the determination of effector class. Here, we will concentrate on the impact of polyreactivity on the S-NS discrimination. The anti-S cells interacting with S (i.e., responding to Signal 1) are on the pathway to inactivation. Before irreversibility sets in, these cells can be activated by a second signal (Signal 2) from an effector T-helper (eTh). As these polyreactive anti-S cells express anti-NS specificities, they can be activated by recognition of NS-epitopes in the host's normal immunogenic load with the potential to result in autoimmunity. This problem is delineated using a discrete structural model, the corollaries of which are: (1) a two-step pathway for the purging of anti-S cells (i.e., the S-NS discrimination), and (2) defensible contexts within which to view the phenomena of receptor editing, anergy, and dual receptor cells.

"Allorestriction" should be distinguished from "alloreactivity".

Whether or not allorestriction should be distinguished from alloreactivity depends on one's model of the TCR­ligand interaction. If the ligand is viewed as a determinant formed by a meld between peptide and the MHC-encoded restricting element, then the TCR, like the BCR, has a single combining site specific for the composite epitope (the Centric Model). If, however, one views the recognition of peptide and the MHC-encoded restricting element as independent, then interactions at two sites of the TCR must be integrated to signal the T cell (the Tritope Model). As TCR recognition of the MHC-encoded restricting element is, by definition, restricted (allele-specific), then under the Centric Model, all TCR signaling interactions with the composite epitope are due to allorestriction, which is peptide-specific. In contrast, under the Tritope Model, there are two classes of signaling interaction, allorestriction and alloreactivity. Alloreactivity is peptide-unspecific and is triggered by recognition of the allo-MHC-encoded restricting element allele. Alloreactivity is incompatible with the Centric Model, under which one would predict that it does not exist. Selected data are analyzed to illustrate the importance of this distinction.

Ten experiments that would make a difference in understanding immune mechanisms.

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.

What is so special about thinking; after all, we all do it!

Understanding the adaptive immune system can be simplified by treating it as three linked modules, the generation of the recognitive repertoire, the sorting of the repertoire by purging anti-self, and the coupling of the repertoire to appropriate effector mechanisms. Each of these modules has a unique database and a logic that is determined by evolutionary considerations founded on value versus harm. Selection cannot operate to perfection, only to adequacy, meaning not limiting to the procreation of the species. Consequently, this system has limits in that it fails, by human standards, to adequately protect against a variety of pathogens and, even when protecting successfully against others, all too often initiates autoimmunity and innocent bystander pathology. What evolution trivializes defines the subject called clinical immunology. If we wish to deal with the pathology that evolution views to be of an acceptable frequency, then we had best first understand what it did give us as a sufficiently functional system, namely the decision pathways of the three modules and in what ways their protective outputs are limited.

The evolutionary context for a self-nonself discrimination.

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.

Why Aire? Compensating for late bloomers.

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.

How does the immune response get started?

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.

What roles do regulatory T cells play in the control of the adaptive immune response?

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.

The Tritope Model for restrictive recognition of antigen by T-cells II. Implications for ontogeny, evolution and physiology.

Based on the Tritope Model of the TCR [Cohn, M., 2005c. The Tritope Model for restrictive recognition of antigen by T-cells. I. What assumptions about structure are needed to explain function? Mol. Immunol. 42, 1419-1443], a set of functional and evolutionary problems surrounding restrictive recognition of antigen are discussed. These include the origin of allele-specific recognition, the selection pressures for polygeneism and polymorphism, the TCR signaling interactions, the centrality of effector T-helper (eTh)-dependence for activation, the role of haplotype exclusion, "nonclassical" MHC-elements, alloreactivity versus xenoreactivity, etc. Further, a set of observations believed to support the Standard Model are reinterpreted.

What does the T-cell receptor recognize when it docks on an MHC-encoded restricting element?

The postulate is analyzed that single V-gene segments encode recognition of the allele-specific determinants (a) required for the restrictive response of the alphabeta TCR to peptide. The consequence of this is that the positively selected V-domain, Valpha or Vbeta, engages an allele-specific determinant (a) on one subunit or domain of the MHC-encoded restricting element. The entrained V-domain docks on an invariant determinant (i) on the complementing subunit or domain. Consequently, each functional V-domain expresses an anti-a site and an anti-i site, and all subunits or domains of MHC-encoded restricting elements express an a- and i-determinant. The evidence, both biological and structural, discussed here strongly supports this postulate which has far reaching consequences.

An in depth analysis of the concept of "polyspecificity" assumed to characterize TCR/BCR recognition.

A workshop group developed the concept of a "polyspecific" TCR/BCR in the framework of today's consensus model. They argue that the individual TCR/BCR combining site is composed of a packet of specificities randomly plucked from the repertoire, hence it is "polyspecific." This essay analyzes the conclusions of the workshop and suggests an alternative. "Polyspecificity" must be dissected into its two component parts, specificity and degeneracy. The TCR and the BCR must be treated differently because the TCR recognizes allele-specifically the MHC-encoded restricting element (R) that serves as the platform presenting peptide (P). Only the anti-P paratope of the TCR behaves analogously to the BCR paratope. The two paratopes are selected to recognize a shape-determinant referred to as an epitope or ligand. The paratope is functionally unispecific in recognition, not polyspecific, with respect to shape; it is degenerate in recognition with respect to chemistry. The recognized shape-determinant can be the product of many chemically different substances, peptide, carbohydrate, lipid, steroid, nucleic acid, etc. Such a degenerate set is functionally treated by the paratope as one shape/epitope/ligand and, in no sense, can a paratope recognizing such a degenerate set be described as "polyspecific." Degeneracy and specificity are concepts that must be distinguished. The two positions are analyzed in this essay, the experiments used to support the view that the paratope of the TCR/BCR is polyspecific, are reinterpreted, and an alternative framework with its accompanying nomenclature, is presented.

History of the antibody workshops.

At a critical period in the history of contemporary immunology, a handful of biochemists and fringe immunologists formed a group known as the Antibody Workshop. They had a major impact on the field by attracting molecular biologists who worked to reduce the study of cellular and organ level immunology to the molecular level. This had a dramatic effect on the field both conceptually and practically by providing the targets for clinical manipulation. The story of the origin and development of this group over time is recounted here.