On the logic of restrictive recognition of peptide by the T-cell antigen receptor

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 αβ 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.

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.

TCR-pMHC interactions: Two peptide repertoires-one signal

The peptide (P) ligand seen by the TCR is presented by an MHC-encoded restricting element (R). Peptide is viewed from two perspectives, that of the TCR and that of R. The TCR looks at P using an anti-P site that is somatically generated and selected, whereas R looks at P using a binding site that is germline generated and selected. The two segments of P, the one viewed by the TCR, the other viewed by R divide P into two repertoires, Ptcr and Pr that are recognized independently but function cooperatively. The consequences of this for an understanding of TCR specificity and signalling as well as the role of differential processing are analysed. It is ironic that from the point of view of the immunologist, the TCR is highly polyreactive recognizing over a million peptides, whereas from the point of view of the immune system, the TCR is highly specific recognizing essentially only one epitope.

An observation that illustrates most T cell receptor structure-function relationships

The Standard model of the T cell receptor (TCR) structure-function relationships is based on an analogy with the B cell receptor. Here a single observation is analyzed to show why this appears to be untenable. The Standard model cannot account for allele-specific recognition of theMHC-encoded presenter of peptide (R) by the TCR nor can it adequately explain alloreactivity. The competing framework is based on the assumptions that (1) single V-domains recognize the alleles of R, (2) restrictive reactivity is peptide specific, whereas alloreactivity is peptide unspecific, and (3) the TCR is born in two conformations, which display reciprocal behaviors (see text). In any case, whatever position one takes regarding these two models, competing conceptualizations are of crucial value in guiding experimentation, not to mention creative thinking.

Signaling interactions predicted by the Tritope model of the TCR

As the data accumulates, it becomes obvious that the Standard Model of TCR structure-function relationships is in jeopardy. The proposed Tritope model has become more meaningful and, in any case, is richer in prediction and explanation. This is illustrated here by using the signaling interactions of the TCR as examples. An unsuspected signaling pathway for positive selection, and for alloreactivity, is predicted. Further, crucial data needed to elucidate the structural elements that distinguish signaling for restrictive- versus allo-reactivity are identified.

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.

Contemplating Bretscher's View that the Tritope Model is 'Implausible'

There is, at present, only two models of the TCR structure-function relationship. These are referred to here as the Standard (Centric) model and the Tritope model. While I have argued that the Standard model is untenable and proposed the Tritope to replace it, Bretscher has argued that the Tritope model is 'implausible' and throws his support for the Standard model. This essay analyses the implausibility argument concluding that it is unfounded.

Is the Framework of Cohn's 'Tritope Model' for How T Cell Receptors Recognize Peptide/Self-MHC Complexes and Allo-MHC Plausible?

Cohn has developed the tritope model to describe how distinct domains of the T cell receptor (TcR) recognize peptide/self-MHC complexes and allo-MHC. He has over the years employed this model as a framework for considering how the TcR might mediate various signals [1-5]. In a recent publication [5], Cohn employs the Tritope Model to propose a detailed mechanism for the T cell receptor's involvement in positive thymic selection [5]. During a review of this proposal, I became uneasy over the plausibility of the underlying framework of the Tritope Model. I outline here the evolutionary considerations making me question this framework. I also suggest that the proposed framework underlying the Tritope Model makes strong predictions whose validity can most probably be assessed by considering observations reported in the literature.

Analysis of Paris meeting redefining the "self" of the immune system

Some ideas because of their intuitive appeal never die by neglect and survive because they are not amenable to experimental disproof. They can only be evaluated by weighing them against competing ideas and by invoking a credibility factor when used to explain observation. Most scientists would recommend ignoring such ideas, yet there is much to be learned by engaging their proponents in debate. The immune system viewed as an idiotype network, and its tweaking by the new school of "contextualists" is an example of such an idea. As chance would have it, the supporters of this idea gathered in a meeting, thereby permitting a cumulative analysis of this conceptualization. The goal of this essay is to compare the views of each of the speakers in light of a competing theory with the hope that a better understanding of immune responsiveness will emerge.

Thoughts on Positive Selection in Thymus

Any analysis of the mechanism of signalling during positive selection in the thymus is dependent on one's model of the TCR-ligand interaction. To date, thinking about mechanism has been dominated by what might be termed the Standard (or Centric) model, which is based on analogy between the BCR and the TCR. As the present analysis is an independent rationalized view of the TCR-ligand interactions, it permits a more balanced view of positive selection. The goal here was to explore this alternative to the Standard model.

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.

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.

On recognizing 'shades-of-gray' (self-nonself discrimination) or 'colour' (Integrity model) by the immune system

The aim is to discuss Cohn's T-cell receptor (TCR) Tritope model of recognition, propose a novel suggestion for prior-to-positive selection of thymocytes contributing to inherent major histocompatibility complex (MHC) reactivity of a T-cell repertoire and clarify the Integrity model about the function of the immune system. If we compare the perception of light with the recognition of nonself, we could imagine that the opacity might be a measure of docking interaction between specific receptors for antigen on T or B cells (TCR/peptide-MHC or BCR/antigen). From this viewpoint, the self-nonself discrimination (S-NS) metaphor would be perception of black (self) versus white (nonself). However, whereas detection of shades-of-gray suffices to describe S-NS discrimination principle, colour vision of the antigenic world portrays best the Integrity model. In concert with recognition of opacity, the Integrity model proposes detection of at least three colours (signals): red (harmful), blue (useful) and yellow (the rest, including homoeostatic ones). As a result, recognition of nonself is transferred into communication within self while deciding on type of the immune response. Hence, the S-NS discrimination model seems to be an oversimplification, because it fails to see colours and consequently lacks the need for suppressor/regulatory function. Similarly, the Danger model stops short of detecting being useful signals that confer immune asylum to helpful micro-organisms like commensals. I suggest that the immune system's repertoire for recognition, in general, has evolved by a novel drive called 'natural integrity' alongside natural selection, thus facilitating communication between cells of the immune system.

Challenging the Tritope Model of T cell receptor structure-function relationships with classical data on 'super' and 'allo-MHC' antigens

The response of the immune system to allo-MHC-encoded antigens and Mls 'superantigens' has been experimentally analysed in detail, but the data have not been coupled to a theoretical framework. It should therefore be instructive to see how well the newly proposed Tritope Model of TCR structure-function relationships deals with the signalling interactions between the TCR and the above antigens. We will pay heed to William Bateson's admonition, 'treasure the exceptions', by showing how a meaningful theory interrogates the data with the same validity that the data interrogate the theory. The concordances, as well as the contradictions, with the Tritope Model are a test of its heuristic value.

Alloreactivity: an old puzzle revisited

Alloreactivity, defined as a strong primary T cell response against allelic variants of major histocompatibility complex (MHC) molecules in the species, has been a long-standing puzzle in immunology with some of its details remaining unclear up to now. Here I shall provide a historical overview of how our understanding of alloreactivity has evolved and propose an interpretation that considers alloreactivity to be a mixture of four mechanistically distinct prototypes of T cell response, namely, self-restricted peptide specific, allorestricted peptide specific, alloreactive peptide dependent and alloreactive peptide independent. The relative contribution of each prototype to a given alloresponse is dependent on the extent of disparity (i.e. the number and nature of amino acid substitutions in the docking surface for T cell receptor) between the MHC molecule that the T cell recognizes as self and the stimulating MHC molecule.

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.