Unraveling features of the natural MHC class II peptidome of skin-migrated dendritic cells

Dendritic cells (DCs) migrating from peripheral tissues at steady state are considered the most efficient antigen-presenting cells (APCs) involved in the induction of peripheral T-cell tolerance via self-antigen presentation on MHC class II molecules. However, difficulties in obtaining sufficient numbers of such DCs have precluded previous analyses of their natural MHC class II peptidome in laboratory animals or humans. Here, we overcome this difficulty by collecting the large quantities of sheep DCs that migrate from the skin via the afferent lymphatics at steady state to the draining lymph node. We compared the repertoire of MHC class II-bound peptides from afferent lymph DCs with autologous APCs derived from peripheral blood. A large fraction of the MHC class II peptidome from skin DCs was derived from membrane-recycling proteins (59%) and from proteins of the antigen presentation machinery (50%), whereas these types of peptides constituted a more limited fraction in blood APCs (21 and 11%, respectively). One sheep cytokeratin peptide was identified in the skin DC peptidome indicating active processing of epithelium-derived antigens. Conversely, peptides derived from cytosolic and soluble antigens of the extracellular milieu were more represented in blood APCs than skin DCs. The biased peptidome of skin-migrated DCs indicates that these cells express a peptide repertoire for the generation of self-reactive and/or regulatory T cells mainly directed toward DC molecules from internal and external membranes and to a lesser extent toward antigens of the extracellular milieu, including some tissue-specific peptides.     

Different affinity windows for virus and cancer‐specific T‐cell receptors: Implications for therapeutic strategies

T‐cell destiny during thymic selection depends on the affinity of the TCR for autologous peptide ligands presented in the context of MHC molecules. This is a delicately balanced process; robust binding leads to negative selection, yet some affinity for the antigen complex is required for positive selection. All TCRs of the resulting repertoire thus have some intrinsic affinity for an MHC type presenting an assortment of peptides. Generally, TCR affinities of peripheral T cells will be low toward self‐derived peptides, as these would have been presented during thymic selection, whereas, by serendipity, binding to pathogen‐derived peptides that are encountered de novo could be stronger. A crucial question in assessing immunotherapeutic strategies for cancer is whether natural TCR repertoires have the capacity for efficiently recognizing tumor‐associated peptide antigens. Here, we report a comprehensive comparison of TCR affinities to a range of HLA‐A2 presented antigens. TCRs that bind viral antigens fall within a strikingly higher affinity range than those that bind cancer‐related antigens. This difference may be one of the key explanations for tumor immune escape and for the deficiencies of T‐cell vaccines against cancer.     

Sculpting MHC class II–restricted self and non‐self peptidome by the class I Ag‐processing machinery and its impact on Th‐cell responses

It is generally assumed that the MHC class I antigen (Ag)‐processing (CAP) machinery — which supplies peptides for presentation by class I molecules — plays no role in class II–restricted presentation of cytoplasmic Ags. In striking contrast to this assumption, we previously reported that proteasome inhibition, TAP deficiency or ERAAP deficiency led to dramatically altered T helper (Th)‐cell responses to allograft (HY) and microbial (Listeria monocytogenes) Ags. Herein, we tested whether altered Ag processing and presentation, altered CD4⁺ T‐cell repertoire, or both underlay the above finding. We found that TAP deficiency and ERAAP deficiency dramatically altered the quality of class II‐associated self peptides suggesting that the CAP machinery impacts class II–restricted Ag processing and presentation. Consistent with altered self peptidomes, the CD4⁺ T‐cell receptor repertoire of mice deficient in the CAP machinery substantially differed from that of WT animals resulting in altered CD4⁺ T‐cell Ag recognition patterns. These data suggest that TAP and ERAAP sculpt the class II–restricted peptidome, impacting the CD4⁺ T‐cell repertoire, and ultimately altering Th‐cell responses. Together with our previous findings, these data suggest multiple CAP machinery components sequester or degrade MHC class II–restricted epitopes that would otherwise be capable of eliciting functional Th‐cell responses.     

Selective Isolation and Identification of HLA‐DR‐Associated Naturally Processed and Presented Epitope Peptides

Activation of CD4 helper T‐cells is mediated by the presentation of antigenic peptides in context of self‐MHC class II molecules. So far, the rules after which antigen‐presenting cells (APC) select a particular epitope within a given protein antigen have been not fully elucidated. Nevertheless, immunoaffinity purification of APC‐derived MHC class II molecules and the subsequent elutions of their with associated naturally processed and presented peptide epitopes (NPPE) have helped tremendously in understanding the nature of this rather complex process. In the present study, a novel approach for identifying such NPPEs is introduced, which is based on the culture of APCs in a completely protein‐free medium during the antigen presenting process. These APCs do still express a high level of MHC class II as determined by HLA‐DR cell surface staining, but the repertoire of the associated NPPEs is drastically reduced when compared to peptides eluted from cells maintained under normal culture condition. Actually, reverse phase‐high pressure liquid chromatography (RP‐HPLC) revealed that the entire NPPE repertoire consisted of less than ten major peaks, which is more than a 100‐fold reduction of background peptide peaks as seen in cells from serum‐containing culture conditions. Feeding APCs with exogenous antigens further confirmed the advantage of this novel system. While exogenous antigen‐derived peptide peaks in an NPPE‐eluate from RP‐HPLC are hardly to detect by conventional procedures, the very low background of serum‐ and protein‐free cultured APCs immensely facilitated this process, providing an improved tool for the identification and characterization of NPPEs.     

Genomics-based identification of self-ligands with T cell receptor-specific biological activity

Summary: Self‐peptide/major histocompatibility complex (MHC) complexes profoundly influence the biology of T lymphocytes. They promote the selection of the T cell receptor (TCR) repertoire in the thymus, maintain the homeostasis of peripheral T cells prior to encounter with antigen, and modify the responsiveness of T cells to foreign antigens. In addition, they can serve as antigens for autoaggressive T cells that induce autoimmune diseases. The complete sequencing of the genomes of human, mouse, and many pathogenic organisms now provides us with a comprehensive list of all possible proteins that may be the source of foreign antigenic and self‐peptides. A computational approach using profile‐based similarity searches on potential self‐MHC‐binding peptides can be used to efficiently predict self‐peptides with biological activities. The common feature of the identified peptides is similarity to antigen. Thus, self‐peptides may form ‘hazy’ images of the universe of antigens that are used as templates to create and maintain the TCR repertoire.     

T cells compete by cleaving cell surface CD27 and blocking access to CD70‐bearing APCs

T cells compete against each other for access to molecules on APCs in addition to peptide/MHC complexes. However, the identity of cell surface molecules that influence T‐cell competition, other than peptide/MHC, have yet to be defined. Here, we identify CD70, a TNF ligand expressed on activated APCs, as an important mediator of T‐cell competition for APCs. Upon engagement of CD27 by CD70, CD27 is proteolytically cleaved from the surface of the interacting CD8⁺ T cell and captured by CD70 expressing dendritic cells. The capture of CD27 effectively masks CD70 on APCs, disallowing the interaction with CD27 on other competing T cells. Collectively, our data indicate that T cells compete against each other for access to the TNF‐ligand CD70, an interaction that affects the duration and potency of T cell/DC interactions, thus influencing the repertoire of responding CD8⁺ T cells to self or foreign antigens.     

Unconventional T‐cell recognition of an arthritogenic epitope of proteoglycan aggrecan released from degrading cartilage

It has been proposed that peptide epitopes bind to MHC class II molecules to form distinct structural conformers of the same MHC II–peptide complex termed type A and type B, and that the two conformers of the same peptide–MHC II complex are recognized by distinct CD4 T cells, termed type A and type B T cells. Both types recognize short synthetic peptides but only type A recognize endosomally processed intact antigen. Type B T cells that recognize self peptides from exogenously degraded proteins have been shown to escape negative selection during thymic development and so have the potential to contribute to the pathogenesis of autoimmunity. We generated and characterized mouse CD4 T cells specific for an arthritogenic epitope of the candidate joint autoantigen proteoglycan aggrecan. Cloned T‐cell hybridomas specific for a synthetic peptide containing the aggrecan epitope showed two distinct response patterns based on whether they could recognize processed intact aggrecan. Fine mapping demonstrated that both types of T‐cell recognized the same core epitope. The results are consistent with the generation of aggrecan‐specific type A and type B T cells. Type B T cells were activated by supernatants released from degrading cartilage, indicating the presence of antigenic extracellular peptides or fragments of aggrecan. Type B T cells could play a role in the pathogenesis of proteoglycan‐induced arthritis in mice, a model for rheumatoid arthritis, by recognizing extracellular peptides or protein fragments of joint autoantigens released by inflamed cartilage.     

Differential expression of alternative H2-M isoforms in B cells, dendritic cells and macrophages by proinflammatory cytokines

Major histocompatibility (MHC) class II heterodimers bind peptides generated by degradation of endocytosed antigens and display them on the surface of antigen presenting cells (APCs) for recognition by CD4+ T cells. Efficient loading of MHC class II molecules with peptides is catalyzed by the MHC class II-like molecule H2-M. The coordinate regulation of MHC class II and H2-M expression is a prerequisite for efficient MHC class II/peptide assembly in APCs determining both the generation of the T cell repertoire in the thymus and cellular immune responses in the periphery. Here we show that expression of H2-M and MHC class II genes is coordinately and cell type-specific regulated in splenic B cells, splenic dendritic cells (DCs) and peritoneal macrophages (Mphi) in response to proinflammatory and immunoregulatory cytokines, including GM-CSF, IFN-gamma, TGF-beta2, IL-4, IL-10 and viral IL-10. In addition, ratio-RT-PCR expression analysis of the duplicated H2-Mbeta-chain loci demonstrates for the first time that Mbl and Mb2 genes are differentially expressed in individual APC types. Mb2 is preferentially expressed in IL-4, GM-CSF, IL-10, vIL-10 and IFN-gamma stimulated splenic B cells, whereas splenic DCs express both Mb genes at almost equal levels. In contrast, peritoneal Mphi express predominantly Mb2 but stimulation with IFN-gamma induces a switch towards Mb1 expression. These data suggest a common mechanism that regulates coordinate expression of H2-M and MHC class II genes in professional APCs. Differential expression of Mb1 and Mb2, and by consequence alternative H2-M isoforms (Malphabeta1 or Malphabeta2), may influence the nature of the peptide repertoire presented by different APC types.     

Peptide presentation by class-I major histocompatibility complex molecules

MHC class-I molecules express distinct peptide-binding pockets within their antigen-binding groove. These are critically involved in the binding of antigenic peptides. The amino acid composition of a pocket dictates the structure of a peptide which can be bound in it. This is evident as a consensus amino acid motif which has to exist within a peptide in order for it to bind to a particular MHC allele. Perturbation of a MHC pocket by amino acid substitution can result in the abolition of peptide binding. Less drastic mutations of the peptide-binding groove, particularly the ones away from the critical pocket, can subtly alter the conformation of bound peptide. Both types of substitution exert an influence on the TCR recognition of antigenic peptide. Peptides are also critically involved in the positive selection of the class-I-restricted TCR repertoire in the thymus. These self peptides act by mimicking their foreign antigens. This mimicking involves the binding of self peptides and foreign antigenic peptides to the same pockets of the MHC class-I-antigen binding groove. Consequently, MHC class-I polymorphism in the antigen binding groove controls the intrathymic positive selection and peripheral antigen presentation by the same mechanisms. The majority of positively selecting self peptides could well originate from the extracellular processing of circulating self proteins. Using the diverse, extracellularly generated self peptides and the different determinant density requirements for positive versus negative selection, the immune system can ensure the repertoire diversity, avoiding both the massive clonal deletion of the selected repertoire and the autoreactivity of its T cells.     

The effects of thymic selection on the range of T cell cross-reactivity

Based on the results of a computational model of thymic selection, we propose a mechanism that produces the observed wide range of T cell cross-reactivity. The model suggests that the cross-reactivity of a T cell that survives thymic selection is correlated with its affinity for self peptides. In order to survive thymic selection, a T cell with low affinity for all self peptides expressed in the thymus must have high affinity for major histocompatibility complex (MHC), which makes it highly cross-reactive. A T cell with high affinity for any self peptide must have low MHC affinity to survive selection, which makes it highly specific for its cognate peptide. Our model predicts that (1) positive selection reduces by only 17% the number of T cells that can detect any given foreign peptide, even though it eliminates over 95% of pre-selection cells; (2) negative selection decreases the average cross-reactivity of the pre-selection repertoire by fivefold; and (3) T cells responding to foreign peptides similar to self peptides will have a lower average cross-reactivity than cells responding to epitopes dissimilar to self.     

Influence of antigen processing on thymic T-cell selection.

The design of a specific blocking peptide for the immunosuppressive therapy of an autoimmune disease requires the identification of peptides of an autoantigen that are physiologically processed in vivo and bind to MHC-encoded membrane glycoproteins. However, knowledge of how an antigen is physiologically processed by antigen-presenting cells (APC) in vivo, particularly in the thymus, is lacking. It is also unknown whether the processing of an antigen by different APC in the thymus can influence thymic T-cell selection. This is an important consideration for attempts to delete or inactivate autoreactive T cells that elicit autoimmune disease. To address these issues, we investigated the processing of biosynthetically labelled recombinant human insulin (rHI), a model autoantigen, injected into mice and characterized the insulin peptides associated with MHC class II molecules on thymic epithelial cells and dendritic cells. These APC were found to differ in the way they process insulin. The detection of MHC-class-II-bound insulin peptides on the surface of the epithelial cells but not the dendritic cells correlated with their capacity to either present or not present insulin to T cells, respectively. Thus, antigen processing may control the appearance of different peptide-MHC class II complexes on thymic APC that mediate positive and negative selection, and thereby influence the development of the T-cell repertoire. Our findings could have important bearing on the future design of synthetic blocking peptides that reduce or eliminate the onset of autoimmune disease.     

Self determinant selection and acquisition of the autoimmune T cell repertoire

Autologous proteins are continuously processed and presented in the form of peptides associated with self major histocompatibility (MHC) molecules at the surface of antigen-presenting cells for interaction with autoreactive T cells. During thymic selection, the presentation of self peptides is an essential element in the establishment of the T cell repertoire. Developing T cells which recognize self peptide/self MHC complexes with sufficient affinity are clonally deleted. However, we and others have recently demonstrated that a variety of self peptides, despite their high binding affinity to MHC molecules, never reach the threshold of presentation to ensure negative selection (cryptic self peptides). This mechanism may have been selected to avoid excessive purging of T cell repertoire during ontogeny. However, T cells directed to cryptic self determinants represent a continuous threat for the initiation of autoimmunity in adults. Supporting this view, recent studies have documented the involvement of cryptic self peptide presentation in different autoimmune diseases. In this article, we examine the factors that govern the selection of self peptides for presentation to autoreactive T cells in vivo and discuss their contribution to both the induction and the maintenance of self tolerance. In addition, we analyze the mechanisms by which the hierarchy of determinants on a self protein can be disrupted, thereby leading to the presentation of previously cryptic self peptides and the induction of an autoimmune T-cell-mediated process.     

On the role of self-recognition in T cell responses to foreign antigen

The key role of the thymus in shaping the peripheral T cell receptor (TCR) repertoire has been appreciated for nearly a quarter of a century. For most of that time, a single model has dominated thinking about the physiological role of the positive selection process mediated by TCR recognition of self‐peptides and major histocompatibility complex (MHC) molecules. This developmental filter was believed to populate secondary lymphoid tissues with T cells bearing receptors best able to recognize unknown foreign peptides associated with the particular allelic forms of the MHC molecules present in an individual. More recently, self‐recognition has been suggested to regulate the viability of naïve T cells. Here we focus on new results indicating that a critical contribution of positive selection to host defense is insuring that each peripheral T cell can use self‐recognition to (i) enhance TCR signaling sensitivity upon foreign antigen recognition and (ii) augment the clonal expansion that accompanies limiting foreign antigen display at early points in an infectious process. We also detail new insights into the intracellular signaling circuitry that underlies the effective discrimination between low‐ and high‐quality ligands of the TCR and speculate on how this design might facilitate an additional contribution of self‐recognition to T cell activation in the presence of foreign stimuli.     

The ternary complex: T cell receptor, MHC protein, and immunogenic peptide

The identification and sequencing of the antigen receptor of T cells coupled with the demonstration that MHC proteins specifically bind immunogenic peptides, and the solution of the crystal structure of HLA A2 and Aw68 collectively have led to a working model of how T cells recognize protein antigens. In contrast with many other known receptor-ligand interactions, this unique recognition mechanism has evolved to allow receptors on two separate cells to contact a common peptide ligand. To accomplish this, MHC proteins and the T cell receptor both differ from previously defined biological receptors in many respects. The MHC class I and II molecules are membrane glycoproteins that have evolved the remarkable capacity to bind and display on the surface of cells an extremely large number of structurally diverse peptides, while the antigen specific receptors of T cells are positively selected to specifically interact with the MHC protein alleles of the individual and only some of the repertoire of self peptides.     

Positive selection of self‐antigen‐specific CD8+ T cells by hematopoietic cells

In contrast to thymic epithelial cells, which induce the positive selection of conventional CD8⁺ T cells, hematopoietic cells (HCs) select innate CD8⁺ T cells whose Ag specificity is not fully understood. Here we show that CD8⁺ T cells expressing an H‐Y Ag‐specific Tg TCR were able to develop in mice in which only HCs expressed MHC class I, when HCs also expressed the H‐Y Ag. These HC‐selected self‐specific CD8⁺ T cells resemble innate CD8⁺ T cells in WT mice in terms of the expression of memory markers and effector functions, but are phenotypically distinct from the thymus‐independent CD8⁺ T‐cell population. The peripheral maintenance of H‐Y‐specific CD8⁺ T cells required presentation of the self‐Ag and IL‐15 on HCs. HC‐selected CD8⁺ T cells in mice lacking the Tg TCR also showed these features. Furthermore, by using MHC class I tetramers with a male Ag peptide, we found that self‐Ag‐specific CD8⁺ T cells in TCR non‐Tg mice could develop via HC‐induced positive selection, supporting results obtained from H‐Y TCR Tg mice. These findings indicate the presence of self‐specific CD8⁺ T cells that are positively selected by HCs in the peripheral T‐cell repertoire.     

The immune system victorious: Selective preservation of self

How the body successfully distinguishes its own tissue cells from those that are foreign and genetically nonidentical to it has been a focus of much research. Clonal deletion maintains that immune system cells with the potential to injure self constituents are eliminated during development, thereby neutralizing their capacity to induce self injury. Selected self-reactive maturing T cell clones undergo deletion in the thymus. A two-step selection process affects immature T cells that enter the thymus. Positive selection makes certain that all surviving cells are able to identify major histocompatibility complex (MHC) proteins present on all body cells. These MHC proteins interact with antigens and present them to T lymphocytes. Negative selection is essential for self-tolerance. It eliminates potentially injurious self-reactive T cells by placing them in contact with a mixture of self antigens in the thymus. Clonal anergy might act together with clonal deletion to maintain self tolerance. Self-reactive T cells in the blood of healthy subjects could represent cells whose affinities for antigen are too weak to initiate an immunologic disease. The fate of T cells reacting to a specific antigen has been traced in transgenic mice. Class I MHC molecules present peptides manufactured within the cell, whereas class II MHC molecules present peptides from extracellular proteins. Interaction of a T cell receptor with its homologous antigen associated with MHC molecules leads to proliferation of that T cell in the presence of costimulatory signals. Investigations elucidating the role of T cell receptors, MHC molecules and antigen peptides in self-nonself discrimination are discussed. The article concludes with an introductory summary of the remaining articles in the issue that address selected topics in self-nonself discrimination.     

Peptidomic analysis of type 1 diabetes associated HLA‐DQ molecules and the impact of HLA‐DM on peptide repertoire editing

HLA‐DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII‐bound peptides in human embryonic kidney 293T cells expressing HLA‐DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM‐resistant, DM‐dependent, or DM‐sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ‐peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T‐cell epitopes to DM editing.     

Role of self-major histocompatibility complex/peptide ligands in selection and maintenance of a diverse T cell repertoire

Positive selection has long been thought to be a devise for producing a repertoire of T cells that can efficiently recognize foreign peptides in the context of self-major histocompatibility complex (MHC) molecules. However, in the light of recent evidence that long-term survival of mature T cells requires continuous contact with self-MHC molecules, the possibility for an additional role for positive selection has emerged: to generate a repertoire of T cells that can be maintained in the periphery through contact with self-MHC/peptide ligands. In support of this idea, our recent work suggests that positive selection is highly peptide specific and, more important, that mature T cells require extrathymic contact with the same MHC/peptide ligands that initially induced positive selection in the thymus in order for prolonged survival and to undergo homeostatic proliferation in response to T cell deficiency.     

Thymus‐specific serine protease regulates positive selection of a subset of CD4+ thymocytes

Thymus‐specific serine protease (TSSP) was initially reported as a putative protease specifically expressed in the endosomal compartment of cortical thymic epithelial cells (cTEC). As such, TSSP is potentially involved in the presentation of the self‐peptides that are bound to MHC class II molecules expressed at the cTEC surface and are involved in the positive selection of CD4⁺ thymocytes. We tested this hypothesis by generating mutant mice deprived of Prss16, the gene encoding TSSP. TSSP‐deficient mice produced normal numbers of T cells, despite a decrease in the percentage of cTEC expressing high surface levels of MHC class II. By using sensitive transgenic models expressing MHC class II‐restricted TCR transgenes (Marilyn and OT‐II), we showed that the absence of TSSP markedly impaired the selection of Marilyn and OT‐II CD4⁺ T cells. In contrast, selection of CD8⁺ T cells expressing an MHC class I‐restricted TCR transgene (OT‐I) was unaffected. Therefore, TSSP is involved in the positive selection of some CD4⁺ T lymphocytes and likely constitutes the first serine protease to play a function in the intrathymic presentation of self‐peptides bound to MHC class II complexes.     

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.