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.     

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.     

The Tritope Model for restrictive recognition of antigen by T-cells I. What assumptions about structure are needed to explain function?

Given that the recognition of the allele-specific determinants expressed by MHC-encoded restricting elements (R) is germline encoded and selected, whereas the recognition of peptide (P) is somatically encoded and selected, then two different combining sites must be under selection. This necessitates a multirecognitive-single T-cell antigen-receptor (TCR) with anti-R and anti-P paratopes that function in concert to signal restrictive reactivity. The consequences of this “two repertoire” postulate not only gives us a concept of TCR structure quite distinct from that at present generally accepted, but, in addition, resolves many existent contradictions. The problems of the positive and negative selection, alloreactivity, Self–Nonself (S–NS) discrimination, the nature and size of the repertoire, and the related experimental interpretations, are discussed. Further the Tritope Model is compared with previously proposed models to justify why a competing model is warranted.     

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.     

T cell receptor alpha variable 12‐2 bias in the immunodominant response to Yellow fever virus

The repertoire of human αβ T‐cell receptors (TCRs) is generated via somatic recombination of germline gene segments. Despite this enormous variation, certain epitopes can be immunodominant, associated with high frequencies of antigen‐specific T cells and/or exhibit bias toward a TCR gene segment. Here, we studied the TCR repertoire of the HLA‐A*0201‐restricted epitope LLWNGPMAV (hereafter, A2/LLW) from Yellow Fever virus, which generates an immunodominant CD8⁺ T cell response to the highly effective YF‐17D vaccine. We discover that these A2/LLW‐specific CD8⁺ T cells are highly biased for the TCR α chain TRAV12‐2. This bias is already present in A2/LLW‐specific naïve T cells before vaccination with YF‐17D. Using CD8⁺ T cell clones, we show that TRAV12‐2 does not confer a functional advantage on a per cell basis. Molecular modeling indicated that the germline‐encoded complementarity determining region (CDR) 1α loop of TRAV12‐2 critically contributes to A2/LLW binding, in contrast to the conventional dominant dependence on somatically rearranged CDR3 loops. This germline component of antigen recognition may explain the unusually high precursor frequency, prevalence and immunodominance of T‐cell responses specific for the A2/LLW epitope.     

Role of the MHC restriction during maturation of antigen‐specific human T cells in the thymus

In the thymus, a T‐cell repertoire able to confer protection against infectious and noninfectious agents in a peptide‐dependent, self‐MHC‐restricted manner is selected. Direct detection of Ag‐specific thymocytes, and analysis of the impact of the expression of the MHC‐restricting allele on their frequency or function has never been studied in humans because of the extremely low precursor frequency. Here, we used a tetramer‐based enrichment protocol to analyze the ex vivo frequency and activation‐phenotype of human thymocytes specific for self, viral and tumor‐antigens presented by HLA‐A*0201 (A2) in individuals expressing or not this allele. Ag‐specific thymocytes were quantified within both CD4CD8 double or single‐positive compartments in every donor. Our data indicate that the maturation efficiency of Ag‐specific thymocytes is poorly affected by HLA‐A2 expression, in terms of frequencies. Nevertheless, A2‐restricted T‐cell lines from A2⁺ donors reacted to A2⁺ cell lines in a highly peptide‐specific fashion, whereas their alloreactive counterparts showed off‐target activity. This first ex vivo analysis of human antigen‐specific thymocytes at different stages of human T‐cell development should open new perspectives in the understanding of the human thymic selection process.     

“Allorestriction” should be distinguished from “alloreactivity”

Whether or not allorestriction should be distinguished from alloreactivity depends on one's model of the TCR–ligand 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.     

SHP1‐ing thymic selection

Thymocyte development and maintenance of peripheral T‐cell numbers and functions are critically dependent on T‐cell receptor (TCR) signal strength. SHP1 (Src homology region 2 domain‐containing phosphatase‐1), a tyrosine phosphatase, acts as a negative regulator of TCR signal strength. Moreover, germline SHP1 knockout mice have shown impaired thymic development. However, this has been recently questioned by an analysis of SHP1 conditional knockout mice, which reported normal thymic development of SHP1 deficient thymocytes. Using this SHP1 conditional knockout mice, in this issue of the European Journal of Immunology, Martinez et al. [Eur. J. Immunol. 2016. 46: 2103–2110] show that SHP1 indeed does have a role in the negative regulation of TCR signal strength in positively selected thymocytes, and in the final maturation of single positive thymocytes. They report that thymocyte development in such mice shows loss of mature, post‐selection cells. This is due to increased TCR signal transduction in thymocytes immediately post positive‐selection, and increased cell death in response to weak TCR ligands. Thus, SHP1‐deficiency shows strong similarities to deficiency in the T‐cell specific SHP1‐associated protein Themis.     

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.     

Structure of an autoimmune T cell receptor complexed with class II peptide-MHC: insights into MHC bias and antigen specificity

T cell receptor crossreactivity with different peptide ligands and biased recognition of MHC are coupled features of antigen recognition that are necessary for the T cell's diverse functional repertoire. In the crystal structure between an autoreactive, EAE T cell clone 172.10 and myelin basic protein (1-11) presented by class II MHC I-Au, recognition of the MHC is dominated by the Vbeta domain of the TCR, which interacts with the MHC alpha chain in a manner suggestive of a germline-encoded TCR/MHC "anchor point." Strikingly, there are few specific contacts between the TCR CDR3 loops and the MBP peptide. We also find that over 1,000,000 different peptides derived from combinatorial libraries can activate 172.10, yet the TCR strongly prefers the native MBP contact residues. We suggest that while TCR scanning of pMHC may be degenerate due to the TCR germline bias for MHC, recognition of structurally distinct agonist peptides is not indicative of TCR promiscuity, but rather highly specific alternative solutions to TCR engagement.     

Molecular genetic evaluation of NLRP3, MVK and TNFRSF1A associated periodic fever syndromes

Periodic fever syndromes (PFSs) are a family of clinical disorders, which are characterized by recurrent episodes of fever in the absence of microbial, autoimmune or malign conditions. Most common types of PFSs are associated with four genes: MEFV, MVK, TNFRSF1A and NLRP3. This paper aims to add new data to the genotype–phenotype association of MVK-, TNFRSF-1A- and NLRP3‐associated PFSs. A total number of 211 patients were evaluated. Two different approaches were used for the molecular genetic evaluation of MVK-, TNFRSF-1A- and NLRP3‐associated PFSs. For the first 147 patients, Sanger sequence analysis of selected exons of MVK, TNFRSF1A and NLRP3 genes was done. For subsequent 64 patients, targeted NGS panel analysis, covering all exons of MVK, TNFRSF1A and NLRP3 genes, was used. A total number of 48 variants were detected. The “variant detection rate in index patients” was higher in the NGS group than Sanger sequencing group (19% vs. 15,1%). For the variant positive patients, a detailed genotype–phenotype table was built. In PFSs, lack of correlation exists between genotype and phenotype in the general population and even within the families. In some cases, mutations behave differently and yield unexpected phenotypes. In this study, we discussed the clinical effects of eight different variants we have detected in the MVK, TNFRSF1A and NLRP3 genes. Four of them were previously identified in patients with PFS. The remaining four were not reported in patients with PFS. Thus, we had to interpret their clinical effects by analysing their frequencies and in silico analysis predictions. We suggest that new studies are needed to evaluate the effects of these variants more clearly. To be able to demonstrate a clearer genotype–phenotype relationship, all PFS‐related genes should be analysed together and the possibility of polygenic inheritance should be considered.     

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.     

The TCR is an allosterically regulated macromolecular machinery changing its conformation while working

The αβ T‐cell receptor (TCR) is a multiprotein complex controlling the activation of T cells. Although the structure of the complete TCR is not known, cumulative evidence supports that the TCR cycles between different conformational states that are promoted either by thermal motion or by force. These structural transitions determine whether the TCR engages intracellular effectors or not, regulating TCR phosphorylation and signaling. As for other membrane receptors, ligand binding selects and stabilizes the TCR in active conformations, and/or switches the TCR to activating states that were not visited before ligand engagement. Here we review the main models of TCR allostery, that is, ligand binding at TCRαβ changes the structure at CD3 and ζ. (a) The ITAM and proline‐rich sequence exposure model, in which the TCR's cytoplasmic tails shield each other and ligand binding exposes them for phosphorylation. (b) The membrane‐ITAM model, in which the CD3ε and ζ tails are sequestered inside the membrane and again ligand binding exposes them. (c) The mechanosensor model in which ligand binding exerts force on the TCR, inducing structural changes that allow signaling. Since these models are complementary rather than competing, we propose a unified model that aims to incorporate all existing data.     

TCR diversity and Treg cells, sometimes more is more

Treg cells are critical for the maintenance of immune homeostasis and suppression of naturally occurring self‐reactive T cells; however, in order to induce suppression Treg cells must first be activated via their T‐cell receptor by recognition of specific antigen–MHC complexes. In this issue of the European Journal of Immunology, Föhse et al. [ Eur. J. Immunol. 2011. 41: 3101–3113 .] shed light on the important question of the role of TCR diversity on Treg‐cell function by demonstrating that high TCR diversity is crucial for optimal Treg‐cell expansion, peripheral reshaping of the Treg‐cell TCR repertoire and in vivo suppressive capacity. In this Commentary, we discuss these findings and also propose a simple mathematical model to aid in the understanding of the relationship between Treg‐cell TCR diversity and the level of suppression delivered by Treg cells in vivo.     

T cell receptor beta diversity and joining segments in the NOD mouse.

Pancreatic beta-cell autoantigen recognition by the immune system appears to be a critical event in the evolution of insulin dependent diabetes. Immune recognition involves antigen presentation by macrophages and subsequent antigen-peptide-class II MHC recognition by T cell receptors (TCR). Using the NOD mouse as a model for human IDD, we hypothesized that germline variability in the D beta nod and/or J beta nod segments could contribute to beta cell autoimmunity by influencing the specific peptides that are recognized. As an initial approach to our hypothesis, we sought to compare these segments to other strains of mice in search of genetic polymorphisms as reported in NZW mice. The germ line TCR beta nod gene did not display evidence of an expansion or contraction in the number of D beta nod or J beta nod segments at the level of resolution provided by restriction fragment length polymorphism analysis. The absence of such polymorphisms suggests that D beta nod or J beta nod segments are not different from nonautoimmune strains of mice.     

Is the +405 G/C single nucleotide polymorphism of the vascular endothelial growth factor (VEGF) gene associated with late‐onset vitiligo?

The increasing body of evidence for the relationship between the vascular endothelial growth factor (VEGF) polymorphism and autoimmune disorders combined with the enhanced expression of this angiogenic factor in vitiligo makes VEGF a very interesting candidate gene to be investigated in vitiligo. The aim of this study was to evaluate the possible associations between the +405 G/C single nucleotide polymorphisms (SNP) of the VEGF gene (rs2010963) and vitiligo. The independent case–control population sample of 152 patients with vitiligo and 152 matched controls was evaluated in this study. A questionnaire was completed for each vitiligo patient to document the demographic and clinical characteristics of the patients. All enrolled individuals had a venous blood sample collected. Genotype frequencies for +405 G/C VEGF gene polymorphism were determined using polymerase chain reaction (PCR) amplification and restriction fragment length polymorphism (RFLP) analysis. There were no significant differences in genotype or allele distributions for this SNP between cases and controls. However, we observed a significant association between GG genotype and higher age at onset of vitiligo (p = 0.04). Moreover, patients stratification revealed a significant increase in the frequency of GG genotype compared to CC + CG genotypes in patients with the late onset (≥20 years) vitiligo (p = 0.05). Although these results are not conclusive, they could potentially lead to considering the angiogenic factors as a potential target for therapy in late‐onset vitiligo.     

The flexibility of the TCR allows recognition of a large set of naturally occurring epitope variants by HIV-specific cytotoxic T lymphocytes.

Pathogens attempt to evade immune recognition by expressing mutated antigens. The present study shows that two mechanisms happen in vivo during the course of HIV infection to limit the escape of antigenic variants from cytotoxic T lymphocyte (CTL) recognition: recognition of several epitope variants by the same TCR and generation of several CTL populations specific for a single epitope but recognizing different variant sequences. We have studied two CTL populations directed towards the HIV-p24gag amino acids 176--184 QASQEVKNW epitope, presented by HLA-B5301. Both CTL populations were derived from a long-term asymptomatic HIV-infected child and they express different TCR. Each of the two CTL recognizes five of the 10 naturally occurring variants. These variants are distinct for both CTL and thus a total of eight variants are recognized. Thus, polyclonality of CTL specific for the same epitope but differing in variant sequences recognized may improve the control of variant viruses' replication in vivo. In addition to cross-recognition of several variant epitopes, promiscuous recognition of exogenous peptides complexed to allogeneic HLA-B molecules occurs, showing that the TCR can tolerate amino acid changes on both the peptide and the MHC molecule. This flexibility of the TCR is probably of great importance for control of viruses with high genetic variability, such as HIV.     

Regulatory T cells and co-evolution of allele-specific MHC recognition by the TCR

What is the evolutionary mechanism for the TCR-MHC-conserved interaction? We extend Dembic's model (Dembic Z. In, Scand J Immunol e12806, 2019) of thymus positive selection for high-avidity anti–self-MHC Tregs among double (CD4 + CD8+)-positive (DP) developing thymocytes. This model is based on competition for self-MHC (+ Pep) complexes presented on cortical epithelium. Such T cells exit as CD4 + CD25+FoxP3 + thymic-derived Tregs (tTregs). The other positively selected DP T cells are then negatively selected on medulla epithelium removing high-avidity anti–self-MHC + Pep as T cells commit to CD4 + or CD8 + lineages. The process is likened to the competitive selection and affinity maturation in Germinal Centre for the somatic hypermutation (SHM) of rearranged immunoglobulin (Ig) variable region (V[D]Js) of centrocytes bearing antigen-specific B cell receptors (BCR). We now argue that the same direct SHM processes for TCRs occur in post-antigenic Germinal Centres, but now occurring in peripheral pTregs. This model provides a potential solution to a long-standing problem previously recognized by Cohn and others (Cohn M, Anderson CC, Dembic Z. In, Scand J Immunol e12790, 2019) of how co-evolution occurs of species-specific MHC alleles with the repertoire of their germline TCR V counterparts. We suggest this is not by ‘blind’, slow, and random Darwinian natural selection events, but a rapid structured somatic selection vertical transmission process. The pTregs bearing somatic TCR V mutant genes then, on arrival in reproductive tissues, can donate their TCR V sequences via soma-to-germline feedback as discussed in this journal earlier. (Steele EJ, Lindley RA. In, Scand J Immunol e12670, 2018) The high-avidity tTregs also participate in the same process to maintain a biased, high-avidity anti–self-MHC germline V repertoire.     

Recent advances in the pathology of heritable gastric cancer syndromes

Despite the relative rarity of hereditary gastric cancer syndromes, the prompt recognition of their specific clinical features and histopathological characteristics is pivotal in offering patients the most appropriate treatment. In this article, we address the three major inherited syndromes that primarily affect the stomach: hereditary diffuse gastric cancer (HDGC), caused by germline variants in CDH1 and CTNNA1; gastric adenocarcinoma and proximal polyposis of the stomach, caused by germline mutations in promoter 1B of APC; and familial intestinal gastric cancer, which has a poorly defined genetic cause. The main focus will be on HDGC, in light of the recent publication of updated clinical practice guidelines and emerging concepts regarding HDGC histopathology. In particular, we describe the broad morphological spectrum of HDGC lesions, stressing the importance of recognising indolent and aggressive phenotypes. Moreover, we discuss the increased risk of gastric (pre)malignancies developing in patients with other well‐defined hereditary cancer syndromes, such as familial adenomatous polyposis, Lynch syndrome, Peutz–Jeghers syndrome, juvenile polyposis, Li–Fraumeni syndrome, and hereditary breast and ovarian cancer syndrome.