The role of peptides in thymic positive selection of class II major histocompatibility complex-restricted T cells

Inactivation of the RB family prevents thymus involution and promotes thymic function by direct control of Foxn1 expression

RB family genes control T cell production and promote thymic involution through reducing Foxn1 expression in thymic epithelial cells.

Thymic involution during aging is a major cause of decreased production of T cells and reduced immunity. Here we show that inactivation of Rb family genes in young mice prevents thymic involution and results in an enlarged thymus competent for increased production of naive T cells. This phenotype originates from the expansion of functional thymic epithelial cells (TECs). In RB family mutant TECs, increased activity of E2F transcription factors drives increased expression of Foxn1, a central regulator of the thymic epithelium. Increased Foxn1 expression is required for the thymic expansion observed in Rb family mutant mice. Thus, the RB family promotes thymic involution and controls T cell production via a bone marrow–independent mechanism, identifying a novel pathway to target to increase thymic function in patients.

An endogenous peptide positively selects and augments the activation and survival of peripheral CD4+ T cells

Although CD4⁺ and CD8⁺ T cells differ in their positively selecting signal strength, endogenous positively selecting ligands have only been identified for MHC class I-restricted T cell receptors (TCRs). Here we screened for ligands that can positively select MHC class II-restricted TCRs, using thymocytes from four I-E^k restricted TCR transgenic mice and a large panel of self peptides. One peptide, gp250, induced positive selection of AND CD4⁺ T cells, had no homology with the AND TCR agonist ligand, and was recognized with a high degree of specificity. gp250 acted as a co-agonist to initiate activation and enhance survival of peripheral AND CD4⁺ T cells. Thus, positively selecting ligands play critical roles in thymocyte development and in the activation and maintenance of peripheral T cells.

How the immune system achieves self-nonself discrimination during adaptive immunity

We propose an "Avidity Model of Self-Nonself Discrimination" in which self-nonself discrimination is achieved by both central thymic selection and peripheral immune regulation. The conceptual framework that links these two events is the understanding that both in the thymus and in the periphery the survival or the fate of T cells is determined by the avidity of the interactions between T cell receptors (TCRs) on T cells, specific to any antigens and MHC/antigen peptides presented by antigen-presenting cells (APCs). We envision that the immune system achieves self-nonself discrimination, during adaptive immunity, not by recognizing the structural differences between self versus foreign antigens, but rather by perceiving the avidity of T cell activation. Intrathymic deletion of high avidity T cell clones responding to the majority of self-antigens generates a truncated peripheral self-reactive repertoire composed of mainly intermediate and low but devoid of high avidity T cells compared with the foreign-reactive repertoire. The existence of intermediate avidity self-reactive T cells in the periphery represents a potential danger of pathogenic autoimmunity inherited in each individual because potentially pathogenic self-reactive T cells are included in the pool of intermediate avidity T cells and can often be functionally activated to elicit autoimmune diseases. The distinct composition of peripheral T cell repertoires to self versus to foreign antigens provides a unique opportunity for the immune system to discriminate self from nonself, in the periphery, by selectively downregulating intermediate avidity T cells to both self and foreign antigens. Selective downregulation of the intermediate avidity T cell populations containing the potentially pathogenic self-reactive T cells enables the immune system to specifically control autoimmune diseases without damaging the effective anti-infection immunity, which is, largely, mediated by high avidity T cells specific to the infectious pathogens. In this regard, it has been recently shown that Qa-1-restricted CD8(+) T cells selectively downregulate intermediate avidity T cells, to both self and foreign antigens, and as a consequence, specifically dampen autoimmunity yet optimize the immune response to foreign antigens. Selective downregulation of intermediate avidity T cells is accomplished via specific recognition, by the Qa-1-restricted CD8(+) T cells, of particular Qa-1/self-peptide complexes, such as Qa-1/Hsp60sp, which function as a common surrogate target structure and preferentially expressed on the activated intermediate avidity T cells. This regulatory pathway thus represents one example of the peripheral mechanisms that the immune system evolved to complete self-nonself discrimination that is achieved, imperfectly, by thymic negative selection, in order to maintain self-tolerance. The conceptual framework of the "Avidity Model" differs from, but contains intellectual wisdom of certain conceptual elements of, the "Tunable Activation Thresholds Hypothesis," the "Danger Model," and the "Ergotypic Regulation Phenomenon." It provides a unified and simple paradigm to explain various seemingly unrelated biomedical problems inherent in immunological disorders that cannot be uniformly interpreted by any currently existing paradigms. The potential impact of the conceptual framework of the "Avidity Model" on our understanding of the development and control of commonly seen autoimmune diseases is also discussed.

Autoimmune regulator initiates the expression of promiscuous genes in thymic epithelial cells

The expression of peripheral antigens in the thymus, known as promiscuous gene expression, has been implicated in T cell tolerance and autoimmunity. Here we identified thymic epithelial cells (TECs) as the main cell type that expresses a diverse range of tissue-restricted antigens (TRAs). The TECs of a common autoimmune (non-obese diabetic [NOD]) mouse model express much lower levels of an autoimmune regulator (Aire) and TRAs than normal (Balb/c) TECs. Transfection of an Aire plasmid led to increased levels of TRA expression in cultured TECs from Balb/c and NOD mice; an increase that was enhanced by the presence of thymocytes. These data show that Aire initiates promiscuous gene expression in TECs, and that this function might be under thymocyte control.

The relationship between immunodominance, DM editing, and the kinetic stability of MHC class II:peptide complexes

Immunodominance refers to the restricted antigen specificity of T cells detected in the immune response after immunization with complex antigens. Despite the presence of many potential peptide epitopes within these immunogens, the elicited T-cell response apparently focuses on a very limited number of peptides. Over the last two decades, a number of distinct explanations have been put forth to explain this very restricted specificity of T cells, many of which suggest that endosomal antigen processing restricts the array of peptides available to recruit CD4 T cells. In this review, we present evidence from our laboratory that suggest that immunodominance in CD4 T-cell responses is primarily due to an intrinsic property of the peptide:class II complexes. The intrinsic kinetic stability of peptide:class II complexes controls DM editing within the antigen-presenting cells and thus the initial epitope density on priming dendritic cells. Additionally, we hypothesize that peptides that possess high kinetic stability interactions with class II molecules display persistence at the cell surface over time and will more efficiently promote T-cell signaling and differentiation than competing, lower-stability peptides contained within the antigen. We discuss this model in the context of the existing data in the field of immunodominance.

Plasticity in the positive selection of T cells: affinity of the selecting antigen and IL-7 affect T cell responsiveness

The current study examines how responsiveness of T cells is affected by the avidity of the peptide/MHC engaged during positive selection of their thymocyte precursors. We used a thymus reaggregate culture system in which CD4(+)CD8(+) thymocytes from AND TCR transgenic mice were induced to undergo positive selection by pigeon cytochrome c (PCC) peptide or its analogs presented by I-E(k) class II MHC on a thymic epithelial cell line. When low-affinity peptide analogs drove positive selection, up to 100 microM was needed to produce >50% CD4(+) T cells, and these cells were highly responsive to PCC. In contrast, <0.2 microM high-affinity peptides was required to achieve similar selection efficiency, but the resultant cells failed to respond to PCC. However, these cells were not dead based on dye exclusion and capacity to respond to phorbal ester and to agonist if IL-2 was also present, supporting the view that non-responsiveness of cells selected on high-affinity peptides is a form of central T cell tolerance distinct from deletion. Cells selected on intermediate-affinity peptides showed variable responsiveness which was suppressed 5- to 10-fold by addition during reaggregate culture of antibody to the IL-7R. Similarly, supplementary IL-7 in the reaggregate culture produced CD4(+) T cells that were promiscuously responsive. Overall, this study demonstrates that the responsiveness of T cells is not rigidly controlled and that the presence of IL-7 during T cell development has the potential to negate central T cell tolerance and produce autoreactive T cells.

Synergistic effect of IL-2, IL-12, and IL-18 on thymocyte apoptosis and Th1/Th2 cytokine expression

In the periphery, IL-18 synergistically induces the expression of the Th1 cytokine IFN-gamma in the presence of IL-12 and the Th2 cytokines IL-5 and IL-13 in the presence of IL-2. Although the expression of these cytokines has been described in the thymus, their role in thymic development and function remains uncertain. We report here that freshly isolated thymocytes from C57BL/6 and BALB/c mice stimulated in vitro with IL-2-plus-IL-18 or IL-12-plus-IL-18 produce large amounts of IFN-gamma and IL-13. Analysis of the thymic subsets, CD4(-)CD8(-) (DN), CD4(+)CD8(+), CD4(+)CD8(-), and CD4(-)CD8(+) revealed that IL-18 in combination with IL-2 or IL-12 induces IFN-gamma and IL-13 preferentially from DN cells. Moreover, DN2 and DN3 thymocytes contained more IFN-gamma(+) cells than cells in the later stage of maturation. Additionally, IL-18 in combination with IL-2 induces CCR4 (Th2-associated) and CCR5 (Th1-associated) gene expression. In contrast, IL-18-plus-IL-12 specifically induced CCR5 expression. The IL-2-plus-IL-18 or IL-12-plus-IL-18 effect on IFN-gamma and IL-13 expression is dependent on Stat4 and NF-kappaB but independent of Stat6, T-bet, or NFAT. Furthermore, IL-12-plus-IL-18 induces significant thymocyte apoptosis when expressed in vivo or in vitro, and this effect is exacerbated in the absence of IFN-gamma. IL-12-plus-IL-18-stimulated thymocytes can also induce IA-IE expression on cortical and medullary thymic epithelial cells in an IFN-gamma-dependent manner. Thus, the combination of IL-2, IL-12, and IL-18 can induce phenotypic and functional changes in thymocytes that may alter migration, differentiation, and cell death of immature T cells inside the thymus and potentially affect the Th1/Th2 bias in peripheral immune compartments.

Functional reprogramming of the primary immune response by T cell receptor antagonism

The T cell receptor must translate modest, quantitative differences in ligand binding kinetics into the qualitatively distinct signals used to determine cell fate. Here, we use mice that express an endogenous T cell receptor (TCR) antagonist and an adoptive transfer system to examine the influence of TCR signal quality on the development of effector function. We show that activation of antigen-specific T cells in the presence of an antagonist results in a functional reprogramming of the primary immune response, marked by altered T cell homing, a failure to develop effector function, and ultimately clonal elimination by apoptosis. Importantly, antagonism does not block cell division, implying that the signals promoting clonal expansion and effector differentiation are distinct.

Differential roles for Wiskott-Aldrich syndrome protein in immune synapse formation and IL-2 production

Wiskott-Aldrich syndrome protein (WASP)-deficient T cells exhibit defects in IL-2 production that are widely believed to stem from primary defects in actin remodeling and immune synapse formation. Surprisingly, however, we find that WASP-deficient T cells responding to Ag-specific APCs polymerize actin and organize talin and PKC theta normally, forming an immune synapse that is stable for at least 3 h. At low doses of peptide, WASP-deficient T cells show less efficient talin and PKC theta polarization. Thus, although WASP may facilitate immune synapse formation at low peptide concentrations, WASP is not required for this process. Defects in IL-2 production are observed even under conditions in which immune synapse formation proceeds normally, suggesting that the role of WASP in regulating IL-2 production is independent of its role in immune synapse formation.

Self-reactivity in thymic double-positive cells commits cells to a CD8αα lineage with characteristics of innate immune cells

Thymocytes displaying self-reactive T cell receptors usually undergo negative selection in the thymus. Here we demonstrate that agonist peptides can promote positive selection of immature double-positive thymocytes into distinct lineages, varying with the agonist concentration and the animal's age. Microarray gene expression analyses showed broad transcriptional alterations in a set of transcripts associated with the innate immune system, as well as silencing of CD8 beta expression. The resulting CD8 alpha alpha T cells showed a rapid effector cytokine response. Hence, T cells displaying self-reactive receptors can have the gene expression profile and phenotypic characteristics of innate immune cells.

Immature CD4(+)CD8(+) thymocytes form a multifocal immunological synapse with sustained tyrosine phosphorylation

The immunological synapse formed during mature T cell activation consists of a central cluster of TCR and MHC molecules surrounded by a ring of LFA-1 and ICAM-1. We examined synapse formation in thymocytes undergoing activation in a lipid bilayer system by following the movement of fluorescent MHC and ICAM-1 molecules. Immature CD4(+)CD8(+) thymocytes formed a decentralized synapse with multiple foci of MHC accumulation corresponding to areas of exclusion of ICAM-1. The MHC clusters and ICAM-1 holes were mobile and transient and correlated with active and sustained signaling, as shown by staining with antibodies against phosphotyrosine and activated Lck. Our findings show that signaling in immature thymocytes can result from a novel, multifocal pattern of receptor accumulation.

Interactions between double positive thymocytes and high affinity ligands presented by cortical epithelial cells generate double negative thymocytes with T cell regulatory activity

Previous studies on thymocyte differentiation by using reaggregate cultures (RC) of double positive T cell receptor (TCR) transgenic thymocytes and the thymic epithelial cell line ANV indicated that low concentrations of high affinity ligands for the TCR were efficient inducers of thymocyte maturation to CD4 single positive (SP) functional cells. In this study, it is demonstrated that, when high concentrations of high affinity ligands are used in this RC system, double positive (DP) cells down-modulate expression of both coreceptors and that, as a result, large numbers of double negative (DN) cells are generated. These DN cells proliferated modestly in response to stimulation by antigen, and this response was considerably augmented by the addition of IL-2 to the cultures. Notably, these antigen-stimulated DN cells produced large amounts of IL-10. When the DN cells generated in RC were cocultured with naive TCR transgenic T cells in the presence of antigen, they suppressed the proliferative response of the naive T cells. Thus, high affinity ligands, when presented to DP thymocytes by cortical thymic epithelial cells in reaggregate cultures, rather than causing deletion of the immature thymocytes, induce their differentiation into immunoregulatory DN cells, suggesting a distinct mechanism by which self tolerance may be maintained.

Autoreactivity, dynamic tuning and selectivity

The immune system adjusts its response to the context in which antigens, including self-antigens, are recognized. Recent observations support a conceptual framework for understanding how this may be achieved at the cellular and cell-population levels. At both levels, 'perturbations' elicit competition between excitation and de-excitation, resulting either in adaptation or in various responses. The responsiveness of individual cells is dynamically tuned, reflecting their recent experience. The tuning of T-cell activation thresholds by self-ligands facilitates positive selection and continuously regulates the level of autoreactivity in the periphery. Autoreactivity appears to be involved in regulation of the immune response, homeostasis, maintaining of the functional integrity of naïve and memory cells, and in other physiological functions.

T cell selection and differential activation on structurally related HLA-DR4 ligands

Plasticity of TCR interactions during CD4(+) T cell activation by an MHC-peptide complex accommodates variation in the peptide or MHC contact sites in which recognition of an altered ligand by the T cell can modify the T cell response. To explore the contribution of this form of TCR cross-recognition in the context of T cell selection on disease-associated HLA molecules, we have analyzed the relationship between TCR recognition of the DRB1*0401- and DRB1*0404-encoded HLA class II molecules associated with rheumatoid arthritis. Thymic reaggregation cultures demonstrated that CD4(+) T cells selected on either DRB1*0401 or DRB1*0404 could be subsequently activated by the other MHC molecule. Using HLA tetramer technology we identify hemagglutinin residue 307-319-specific T cells restricted by DRB1*0401, but activated by hemagglutinin residues 307-319, in the context of DRB1*0404. One such clone exhibits an altered cytokine profile upon activation with the alternative MHC ligand. This altered phenotype persists when both class II molecules are present. These findings directly demonstrate that T cells selected on an MHC class II molecule carry the potential for activation on altered self ligands when encountering Ags presented on a related class II molecule. In individuals heterozygous for these alleles the possibility of TCR cross-recognition could lead to an aberrant immune response.

Positive selection of CD4(+) T cells is induced in vivo by agonist and inhibited by antagonist peptides

The nature of peptides that positively select T cells in the thymus remains poorly defined. Here we report an in vivo model to study the mechanisms of positive selection of CD4(+) T cells. We have restored positive selection of TCR transgenic CD4(+) thymocytes, arrested at the CD4(+)CD8(+) stage, due to the lack of the endogenously selecting peptide(s), in mice deficient for H2-M and invariant chain. A single injection of soluble agonist peptide(s) initiated positive selection of CD4(+) transgenic T cells that lasted for up to 14 days. Positively selected CD4(+) T cells repopulated peripheral lymphoid organs and could respond to the antigenic peptide. Furthermore, coinjection of the antagonist peptide significantly inhibited agonist-driven positive selection. Hence, contrary to the prevailing view, positive selection of CD4(+) thymocytes can be induced in vivo by agonist peptides and may be a result of accumulation of signals from TCR engaged by different peptides bound to major histocompatibility complex class II molecules. We have also identified a candidate natural agonist peptide that induces positive selection of CD4(+) TCR transgenic thymocytes.

A physiological ligand of positive selection is recognized as a weak agonist

Positive selection is a process that ensures that peripheral T cells express TCR that are self-MHC restricted. This process occurs in the thymus and requires both self-MHC and self-peptides. We have recently established a TCR transgenic (TCR(trans)(+)) mouse model using the C10.4 TCR restricted to the MHC class Ib molecule, H2-M3. Having defined H2-M3 as the positively selecting MHC molecule, the severely limited number of H2-M3 binding peptides allowed us to characterize a mitochondrial NADH dehydrogenase subunit 1-derived 9-mer peptide as the physiological ligand of positive selection. Here, we demonstrate that the NADH dehydrogenase subunit 1 self-peptide is seen by mature C10.4 TCR(trans)(+) T cells as a weak agonist and induces positive selection at a defined concentration range. We also found that the full-length cognate peptide, a strong agonist for mature C10.4 TCR(trans)(+) T cells, initiated positive selection, albeit at significantly lower concentrations. At increased peptide concentrations, and thus increased epitope densities, either peptide only induced the development of partially functional T cells. We conclude that successful positive selection only proceeded at a defined, yet fairly narrow window of avidity.

TCR signaling for initiation and completion of thymocyte positive selection has distinct requirements for ligand quality and presenting cell type

Thymocyte selection involves signaling by TCR engaging diverse self-peptide:MHC molecule ligands on various cell types in the cortex and medulla. Here we separately analyze early and late stages of selection to better understand how presenting cell type, ligand quality, and the timing of TCR signaling contribute to intrathymic differentiation. TCR transgenic CD4+CD8+ thymocytes (double positive (DP)) from MHC-deficient mice were stimulated using various presenting cells and ligands. The resulting CD69high cells were isolated and evaluated for maturation in reaggregate cultures with wild-type or MHC molecule-deficient thymic stroma with or without added hemopoietic dendritic cells (DC). Production of CD4+ T cells required TCR signaling in the reaggregates, indicating that transient recognition of self-ligands by DP is inadequate for full differentiation. DC bearing a potent agonist ligand could initiate positive selection, producing activated thymocytes that matured into agonist-responsive T cells in reaggregates lacking the same ligand. DC could also support the TCR signaling necessary for late maturation. These results argue that despite the negative role assigned to DC in past studies, neither the peptide:MHC molecule complexes present on DC nor any other signals provided by these cells stimulate only thymocyte death. These findings also indicate that unique epithelial ligands are not necessary for positive selection. They provide additional insight into the role of ligand quality in selection events and support the concept that following initiation of maturation from the DP state, persistent TCR signaling is characteristic of and perhaps required by T cells.

Ligand-specific selection of MHC class II-restricted thymocytes in fetal thymic organ culture

Positive and negative selection of thymocytes is determined by the specificity of the TCR and signaling through its associated molecules. We have studied selection of thymocytes bearing a MHC class II-restricted TCR using fetal thymic organ culture. This system allows the addition of peptides to the already diverse panoply of endogenous peptide ligands and is useful for analyzing ligand-specific negative selection of CD4 single positive (CD4SP) thymocytes. The data reveal that the ability of a given ligand to mediate negative selection is related to its dissociation rate from the TCR. We find that negative selection is very sensitive, and only the weakest ligand that we can identify fails to induce negative selection. None of the numerous peptides tested were able to induce an increase in CD4SP thymocytes. In addition, the ligands that induce negative selection of CD4SP thymocytes also cause an increase in numbers of CD8SP thymocytes bearing high levels of the class II-restricted TCR. Although these cells have a cell surface phenotype consistent with positive selection, they most likely represent cells in the process of negative selection. Further analysis reveals that these cells are not induced by these ligands in intact adult animals and that their induction is probably only revealed in the organ culture system.

MHC-peptide ligand interactions establish a functional threshold for antigen-specific T cell recognition

Antigen-specific T cell recognition is dependent on the functional density of the TCR-ligand, which consists of specific MHC molecules and a specifically bound peptide. We have examined the influence of the affinity and concentration of exogenous peptide and the density of specific MHC molecules on the proliferation of a CD4+, DQA1*0501/DQB1*0201 (DQ2.1)-restricted, HSV-2-specific T cell clone. Using antigen peptide analogs with different mutations of known DQ2-anchor residues, T cell response was reduced in an peptide-affinity and - concentration specific manner. The decrease using weaker binding peptides was gradual as stimulation with a peptide with intermediate affinity yielded intermediate T cell proliferation and the poorest binding peptide induced an even weaker T cell response. MHC class II density on the APC was modified using DQ2 homo- and heterozygous B-LCLs as APCs, however this variation of MHC concentration had no effect on T cell proliferation. We interpret this as a reflection of a low threshold for activation of the T cell clone, in which peptide-MHC avidity is the over-riding determinant of the strength of ligand signal.

Immunological self/nonself discrimination: integration of self vs nonself during cognate T cell interactions with antigen-presenting cells

The hypothesis is presented that immunological integration of nonefficacious vs efficacious T cell antigen receptor (TCR) signals are foundational for self/nonself discrimination and that multiple integrative mechanisms are intrinsic to the molecular to molar organization of an adaptive immune response. These integrative mechanisms are proposed to adaptively regulate expression of costimulatory signals, such that foreign proteins are associated with the expression of costimulatory signals, whereas self-proteins are associated with the lack of costimulatory signaling. Overall, this model offers several unique contributions to the study of immunology. First, this model postulates that cognate TCR/major histocompatibility complex (MHC) interactions are sufficient to adaptively mediate immunological self/nonself discrimination. This model thereby offers a unique alternative to models that largely rely on innate immunity to prime immune discrimination. Second, the integrative model argues that the immune system can simultaneously reinforce self-tolerance and promote immunity to foreign organisms at the same time and in the same location. Many alternative models presume that pathogenic self-reactive T cells do not exist at the outset of an immune response against foreign agents. Third, the integrative model uniquely predicts relationships between immunodeficiency and autoimmune pathogenesis. Fourth, this model illustrates the regulatory advantages of cognate antigen presenting cell (APC) systems (i.e., T cell or B cell APC) compared to nonspecific APC. Cognate APC systems together with the respective clonotypic responders may comprise a fundamental "network" of lymphoid cells. Such networks would have clone-specific regulatory capabilities and may be central for immunological self/nonself discrimination. Fifth, this model provides an explanation for "infectious" tolerance without creating specialized subsets of "suppressor" or "regulatory" T cells. Each mature T cell retains the potential to reinforce tolerance or mediate immunity, depending on the specific antigenic cues present in the immediate environment.

Selection of the T cell repertoire

Advances in gene technology have allowed the manipulation of molecular interactions that shape the T cell repertoire. Although recognized as fundamental aspects of T lymphocyte development, only recently have the mechanisms governing positive and negative selection been examined at a molecular level. Positive selection refers to the active process of rescuing MHC-restricted thymocytes from programmed cell death. Negative selection refers to the deletion or inactivation of potentially autoreactive thymocytes. This review focuses on interactions during thymocyte maturation that define the T cell repertoire, with an emphasis placed on current literature within this field.

Degree of TCR Internalization and Ca2+ Flux Correlates with Thymocyte Selection

Recent evidence suggests that TCR down-regulation directly reflects the number of TCRs that have engaged MHC/peptide ligand complexes. Here, we examined the influence of defined peptides on thymic selection based on their ability to induce differential TCR internalization. Our results demonstrate that there is a direct correlation: peptides that induce strong TCR down-regulation are most efficient at mediating negative selection, whereas peptides that induce suboptimal TCR internalization are more efficient at triggering positive selection. As a consequence of suboptimal TCR internalization, a proportion of TCR complexes that remain on the cell surface may be able to relay continual signals required for survival and differentiation. In addition, we show that the magnitude of Ca2+ influx set by these peptides reflects the hierarchy of TCR down-regulation and correlates with positive vs negative selection of transgenic thymocytes. Together, our data suggest that T cell selection is mediated by differing intensities of the same TCR-mediated signal, rather than by distinct signals.