Tritope model of restrictive recognition by the TCR

On integrity in immunity during ontogeny or how thymic regulatory T cells work

The Standard model of T cell recognition asserts that T cell receptor (TCR) specificities are positively and negatively selected during ontogeny in the thymus and that peripheral T cell repertoire has mild self-major histocompatibility complex (MHC) reactivity, known as MHC restriction of foreign antigen. Thus, the TCR must bind both a restrictive molecule (MHC allele) and a peptide reclining in its groove (pMHC ligand) in order to transmit signal into a T cell. The Standard and Cohn's Tritope models suggest contradictory roles for complementarity-determining regions (CDRs) of the TCRs. Here, I discuss both concepts and propose a different solution to ontogenetic mechanism for TCR-MHC-conserved interaction. I suggest that double (CD4+ CD8+ )-positive (DP) developing thymocytes compete with their αβTCRs for binding to self-pMHC on cortical thymic epithelial cells (cTECs) that present a selected set of tissue-restricted antigens. The competition between DPs involves TCR editing and secondary rearrangements, similar to germinal-centre B cell somatic hypermutation. These processes would generate cells with higher TCR affinity for self-pMHC, facilitating sufficiently long binding to cTECs to become thymic T regulatory cells (tTregs). Furthermore, CD4+ Foxp3+ tTregs can be generated by mTECs via Aire-dependent and Aire-independent pathways, and additionally on thymic bone marrow-derived APCs including thymic Aire-expressing B cells. Thymic Tregs differ from the induced peripheral Tregs, which comprise the negative feedback loop to restrain immune responses. The implication of thymocytes' competition for the highest binding to self-pMHC is the co-evolution of species-specific αβTCR V regions with MHC alleles.

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.

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.

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

This essay provides an analysis of the inadequacy of the current view of restrictive recognition of peptide by the T-cell antigen receptor. A competing model is developed, and the experimental evidence for the prevailing model is reinterpreted in the new framework. The goal is to contrast the two models with respect to their consistency, coverage of the data, explanatory power, and predictability.

Basal and antigen-induced exposure of the proline-rich sequence in CD3ε

The CD3ε cytoplasmic tail contains a conserved proline-rich sequence (PRS) that influences TCR-CD3 expression and signaling. Although the PRS can bind the SH3.1 domain of the cytosolic adapter Nck, whether the PRS is constitutively available for Nck binding or instead represents a cryptic motif that is exposed via conformational change upon TCR-CD3 engagement (CD3Δc) is currently unresolved. Furthermore, the extent to which a cis-acting CD3ε basic amino acid-rich stretch (BRS), with its unique phosphoinositide-binding capability, might impact PRS accessibility is not clear. In this study, we found that freshly harvested primary thymocytes expressed low to moderate basal levels of Nck-accessible PRS ("open-CD3"), although most TCR-CD3 complexes were inaccessible to Nck ("closed-CD3"). Ag presentation in vivo induced open-CD3, accounting for half of the basal level found in thymocytes from MHC(+) mice. Additional stimulation with either anti-CD3 Abs or peptide-MHC ligands further elevated open-CD3 above basal levels, consistent with a model wherein antigenic engagement induces maximum PRS exposure. We also found that the open-CD3 conformation induced by APCs outlasted the time of ligand occupancy, marking receptors that had been engaged. Finally, CD3ε BRS-phosphoinositide interactions played no role in either adoption of the initial closed-CD3 conformation or induction of open-CD3 by Ab stimulation. Thus, a basal level of open-CD3 is succeeded by a higher, induced level upon TCR-CD3 engagement, involving CD3Δc and prolonged accessibility of the CD3ε PRS to Nck.

TCR-MHC docking orientation: natural selection, or thymic selection?

T cell receptors (TCR) dock on their peptide-major histocompatibility complex (pMHC) targets in a conserved orientation. Since amino acid sidechains are the foundation of specific protein-protein interactions, a simple explanation for the conserved docking orientation is that key amino acids encoded by the TCR and MHC genes have been selected and maintained through evolution in order to preserve TCR/pMHC binding. Expectations that follow from the hypothesis that TCR and MHC evolved to interact are discussed in light of the data that both support and refute them. Finally, an alternative and equally simple explanation for the driving force behind the conserved docking orientation is described.

On the opposing views of the self-nonself discrimination by the immune system

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.

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.

A hypothesis accounting for the paradoxical expression of the D gene segment in the BCR and the TCR

The D gene segment expressed in both the TCR and the BCR has a challenging behavior that begs interpretation. It is incorporated in three reading frames in the rearranged transcription unit but is expressed in antigen-selected cells in a preferred frame. Why was it so important to waste 2/3 of newborn cells? The hypothesis is presented that the D region is framework playing a role in both the TCR and the BCR by determining whether a signal is transmitted to the cell upon interaction with a cognate ligand. This assumption operates in determining haplotype exclusion for the BCR and in regulating the signaling orientation for the TCR. Relevant data as well as a definitive experiment challenging the validity of this hypothesis, are discussed.

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.

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.

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.

On a key postulate of T-cell receptor restrictive function: the V-gene loci act as a single pool encoding recognition of the polymorphic alleles of the species major histocompatibility complex

The proposition that single Valpha or Vbeta gene segments specify the recognition of the allele-specific determinants expressed on the major histocompatibility complex-encoded restricting elements of the species has as its consequence a totally different picture of the functioning of the T-cell receptor. This commentary justifies this assumption and outlines some of its most important consequences.

On ‘Credo 2004’ as Viewed Under the ‘Development-Context’ Model of Colin Anderson

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'.

The multigenic structure of the MHC locus contributes to positive selection efficiency: a role for MHC class II gene-specific restriction

The study of T cell positive selection in the thymus has long been focused on the specificity of the MHC-TCR interactions, making use of genetically manipulated mice that display TCR specificities or selecting peptides of limited diversity. However, little is known on the role of the MHC molecules irrespective of the peptide specificity and the implications of MHC multigenic structure in thymic positive selection have not been addressed. Here, we investigated the effect of MHC class II genetic configuration on the positive selection efficiency of naturally generated pre-selection repertoires in the mouse thymus. Analysis of positively selected thymocyte populations in MHC-congenic and -transgenic mice revealed that expression of I-E molecule in the thymic cortex increases positive selection efficiency of CD4 cells by approximately 50%. We show that increments in positive selection attributable to either the I-A and I-E genes are not due to increased MHC class II expression in the thymic cortex and are not affected by the number of MHC alleles. Collectively, our findings imply that MHC class II gene-restricted TCR specificities significantly contribute to positive selection efficiency, introducing the notion that multigenic structure of the MHC locus serves to increase selection of non-overlapping TCR repertoires.

What are the commonalities governing the behavior of humoral immune recognitive repertoires?

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.

Direct recognition by alphabeta cytolytic T cells of Hfe, a MHC class Ib molecule without antigen-presenting function

Crystallographic analysis of human Hfe has documented an overall structure similar to classical (class Ia) MHC molecules with a peptide binding groove deprived of ligand. Thus, to address the question of whether alphabeta T cells could recognize MHC molecules independently of bound ligands, we studied human and mouse Hfe interactions with T lymphocytes. We provide formal evidence of direct cytolytic recognition of human Hfe by mouse alphabeta T cell receptors (TCR) in HLA-A*0201 transgenic mice and that this interaction results in ZAP-70 phosphorylation. Furthermore, direct recognition of mouse Hfe molecules by cytotoxic T lymphocytes (CTLs) was demonstrated in DBA/2 Hfe knockout mice. These CTLs express predominantly two T cell antigen receptor alpha variable gene segments (AV6.1 and AV6.6). Interestingly, in wild-type mice we identified a subset of CD8+ T cells positively selected by Hfe that expresses the AV6.1/AV6.6 gene segments. T cell antigen receptor recognition of MHC molecules independently of bound ligand has potential general implications in alloreactivity and identifies in the Hfe case a cognitive link supporting the concept that the immune system could be involved in the control of iron metabolism.

Unraveling a hotspot for TCR recognition on HLA-A2: evidence against the existence of peptide-independent TCR binding determinants

T cell receptor (TCR) recognition of peptide takes place in the context of the major histocompatibility complex (MHC) molecule, which accounts for approximately two-thirds of the peptide/MHC buried surface. Using the class I MHC HLA-A2 and a large panel of mutants, we have previously shown that surface mutations that disrupt TCR recognition vary with the identity of the peptide. The single exception is Lys66 on the HLA-A2 alpha1 helix, which when mutated to alanine disrupts recognition for 93% of over 250 different T cell clones or lines, independent of which peptide is bound. Thus, Lys66 could serve as a peptide-independent TCR binding determinant. Here, we have examined the role of Lys66 in TCR recognition of HLA-A2 in detail. The structure of a peptide/HLA-A2 molecule with the K66A mutation indicates that although the mutation induces no major structural changes, it results in the exposure of a negatively charged glutamate (Glu63) underneath Lys66. Concurrent replacement of Glu63 with glutamine restores TCR binding and function for T cells specific for five different peptides presented by HLA-A2. Thus, the positive charge on Lys66 does not serve to guide all TCRs onto the HLA-A2 molecule in a manner required for productive signaling. Furthermore, electrostatic calculations indicate that Lys66 does not contribute to the stability of two TCR-peptide/HLA-A2 complexes. Our findings are consistent with the notion that each TCR arrives at a unique solution of how to bind a peptide/MHC, most strongly influenced by the chemical and structural features of the bound peptide. This would not rule out an intrinsic affinity of TCRs for MHC molecules achieved through multiple weak interactions, but for HLA-A2 the collective mutational data place limits on the role of any single MHC amino acid side-chain in driving TCR binding in a peptide-independent fashion.

A commentary on the Zinkernagel-Hengartner 'Credo 2004'

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.

T cell receptor engagement by peptide-MHC ligands induces a conformational change in the CD3 complex of thymocytes

The T cell receptor (TCR) can recognize a variety of cognate peptide/major histocompatibility complex (pMHC) ligands and translate their affinity into distinct cellular responses. To achieve this, the nonsignaling alphabeta heterodimer communicates ligand recognition to the CD3 signaling subunits by an unknown mechanism. In thymocytes, we found that both positive- and negative-selecting pMHC ligands expose a cryptic epitope in the CD3 complex upon TCR engagement. This conformational change is induced in vivo and requires the expression of cognate MHC. We conclude that TCR engagement with a cognate pMHC ligand induces a conformational change in the CD3 complex of thymocytes and propose that this marks an initial event during thymic selection that signals the recognition of self-antigen.

An alternative to current thinking about positive selection, negative selection and activation of T cells

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.

Whither T-suppressors: if they didn’t exist would we have to invent them?

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.

Does complexity belie a simple decision--on the Efroni and Cohen critique of the minimal model for a self-nonself discrimination

The immune system somatically generates a large and random paratopic repertoire that must be sorted into those specificities (anti-self) which, if expressed, would debilitate the host and those specificities (anti-nonself) which, if not expressed, would leave the host unprotected from infection. The critique of Efroni and Cohen that minimal models are misleading and without heuristic value is evaluated by illustrative examples.