Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

The cellular immune system screens peptides presented by host cells on MHC molecules to assess if the cells are infected. In this study we examined whether the presented peptides contain enough information for a proper self/nonself assessment by comparing the presented human (self) and bacterial or viral (nonself) peptides on a large number of MHC molecules. For all MHC molecules tested, only a small fraction of the presented nonself peptides from 174 species of bacteria and 1000 viral proteomes (0.2%) is shown to be identical to a presented self peptide. Next, we use available data on T-cell receptor-peptide-MHC interactions to estimate how well T-cells distinguish between similar peptides. The recognition of a peptide-MHC by the T-cell receptor is flexible, and as a result, about one-third of the presented nonself peptides is expected to be indistinguishable (by T-cells) from presented self peptides. This suggests that T-cells are expected to remain tolerant for a large fraction of the presented nonself peptides, which provides an explanation for the “holes in the T-cell repertoire” that are found for a large fraction of foreign epitopes. Additionally, this overlap with self increases the need for efficient self tolerance, as many self-similar nonself peptides could initiate an autoimmune response. Degenerate recognition of peptide-MHC-I complexes by T-cells thus creates large and potentially dangerous overlaps between self and nonself

Revisiting Thymic Positive Selection and the Mature T Cell Repertoire for Antigen

To support effective host defense, the T cell repertoire must balance breadth of recognition with sensitivity for antigen. The concept that T lymphocytes are positively selected in the thymus is well established, but how this selection achieves such a repertoire has not been resolved. Here we suggest that it is direct linkage between self and foreign antigen recognition that produces the necessary blend of TCR diversity and specificity in the mature peripheral repertoire, enabling responses to a broad universe of unpredictable antigens while maintaining an adequate number of highly sensitive T cells in a population of limited size. Our analysis also helps to explain how diversity and frequency of antigen-reactive cells in a T cell repertoire are adjusted in animals of vastly different size scale to enable effective antipathogen responses and suggests a possible binary architecture in the TCR repertoire that is divided between germline-related optimal binding and diverse recognition

Unique pathogen peptidomes facilitate pathogen-specific selection and specialization of MHC alleles

A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7\% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8\% of pathogen pairs shared more than 1\% of their peptides. Indeed, 98.8\% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants

Molecular characterisation of Ovine CD1

The CD1 molecules are a family of ß2microglobulin- associated glycoproteins with strong structural homology, but weaker sequence homology, to the MHC class I antigens. In contrast to the classical class I antigens, CD1 molecules exhibit restricted tissue expression (cortical thymocytes, dendritic cells, a subset of B cells and some intestinal epithelial cells), and are nonpolymorphic. Five CD1 genes have been identified in humans, two in the mouse and several in other mammalian species (Calabi et al, 1991). CD1 expression has also been detected by immunohistological techniques in the cow, sheep and pig.The MHC class I -like structure of CD1 and the expression on classical antigen presenting cells of the immune system has pointed to a role for CD1 in antigen presentation. Indeed, evidence has been accumulating over the past few years to support this view, with several reports suggesting that CD4 -8- T cells in particular may be able to recognise nonclassical presentational elements including MHC class lb molecules such as TLa and Qa, as well as CD1. Most recently, CD1b molecules on human monocytes have been demonstrated to restrict the response of CD4 -8- T cells to antigens derived from M. tuberculosis (Porcelli et al, 1992).Previous studies on the ovine CD1 family have involved the use of monoclonal antibodies to assess tissue expression and distribution, and biochemical analyses of the ovine CD1 antigens. However, no studies have been carried out to investigate ovine CD1 at the molecular level. Therefore, a human CD1 C a3 probe was used to screen several sheep thymocyte cDNA libraries. The HCD1 B -like clone SCD1 A25 was isolated from a foetal thymocyte library. A homologous probe comprising the a3/TM /CYT domains from this clone was derived by PCR amplification and used to identify a further three ovine clones - SCD1 B -42, SCD1 B -52 and SCD1T10. Three of the four clones are truncated at the 5' end, with sequences beginning towards the end of the al domain or the start of the a2 domain. These 5' truncation events probably reflect poor reverse transcriptase activity during library preparation. The fourth clone, SCD1 B -52, represents a transcript containing a precise a3 deletion. The PCR technique was used to amplify the missing 5' ends from two of the three truncated$equences, thus generating full length coding sequence for two of the four ovine CD1's identified.Comparison of the ovine CD1 sequences amongst themselves has shown them to be 81 -96% identical at the nucleotide level and 79 -90% identical at the amino acid level, suggesting that the four clones represent different gene products rather than allelic variants of CD1. The sheep sequences have also been analysed by comparison to the human, mouse and rabbit coding seqences. Perhaps unexpectedly, given the existence of five different human CD1 genes, all of the ovine CD1 sequences are most homologous to human CD1 B at both the nucleotide and amino acid levels. The sheep CD1 sequences also show a high percentage sequence identity to the cottontail rabbit sequence, which is itself most similar to HCD1 B.Southern blot analysis of genomic DNA digested with a variety of enzymes and probed with the homologous a3 probe has indicated the possible existence of up to seven ovine CD1 genes. Further studies are required to determine which of these genes are expressed and to identify the genes encoding the CD1 molecules recognised by the monoclonal antibodies. The significance and implications of these results are discussed and potential further experiments suggested

Self-mediated positive selection of T cells sets an obstacle to the recognition of nonself

Adaptive immune recognition is mediated by the binding of peptide–human leukocyte antigen complexes by T cells. Positive selection of T cells in the thymus is a fundamental step in the generation of a responding T cell repertoire: only those T cells survive that recognize human peptides presented on the surface of cortical thymic epithelial cells. We propose that while this step is essential for optimal immune function, the process results in a defective T cell repertoire because it is mediated by self-peptides. To test our hypothesis, we focused on amino acid motifs of peptides in contact with T cell receptors. We found that motifs rarely or not found in the human proteome are unlikely to be recognized by the immune system just like the ones that are not expressed in cortical thymic epithelial cells or not presented on their surface. Peptides carrying such motifs were especially dissimilar to human proteins. Importantly, we present our main findings on two independent T cell activation datasets and directly demonstrate the absence of naïve T cells in the repertoire of healthy individuals. We also show that T cell cross-reactivity is unable to compensate for the absence of positively selected T cells. Additionally, we show that the proposed mechanism could influence the risk for different infectious diseases. In sum, our results suggest a side effect of T cell positive selection, which could explain the nonresponsiveness to many nonself peptides and could improve the understanding of adaptive immune recognition

The two-faced T cell epitope: Examining the host-microbe interface with JanusMatrix

Advances in the field of T cell immunology have contributed to the understanding that cross-reactivity is an intrinsic characteristic of the T cell receptor (TCR), and that each TCR can potentially interact with many different T cell epitopes. To better define the potential for TCR cross-reactivity between epitopes derived from the human genome, the human microbiome, and human pathogens, we developed a new immunoinformatics tool, JanusMatrix, that represents an extension of the validated T cell epitope mapping tool, EpiMatrix. Initial explorations, summarized in this synopsis, have uncovered what appear to be important differences in the TCR cross-reactivity of selected regulatory and effector T cell epitopes with other epitopes in the human genome, human microbiome, and selected human pathogens. In addition to exploring the T cell epitope relationships between human self, commensal and pathogen, JanusMatrix may also be useful to explore some aspects of heterologous immunity and to examine T cell epitope relatedness between pathogens to which humans are exposed (Dengue serotypes, or HCV and Influenza, for example). In Hand-Foot-Mouth disease (HFMD) for example, extensive enterovirus and human microbiome cross-reactivity (and limited cross-reactivity with the human genome) seemingly predicts immunodominance. In contrast, more extensive cross-reactivity with proteins contained in the human genome as compared to the human microbiome was observed for selected Treg epitopes. While it may be impossible to predict all immune response influences, the availability of sequence data from the human genome, the human microbiome, and an array of human pathogens and vaccines has made computationally–driven exploration of the effects of T cell epitope cross-reactivity now possible. This is the first description of JanusMatrix, an algorithm that assesses TCR cross-reactivity that may contribute to a means of predicting the phenotype of T cells responding to selected T cell epitopes. Whether used for explorations of T cell phenotype or for evaluating cross-conservation between related viral strains at the TCR face of viral epitopes, further JanusMatrix studies may contribute to developing safer, more effective vaccines

Smarter Vaccine Design Will Circumvent Regulatory T Cell-Mediated Evasion in Chronic HIV and HCV Infection

Despite years of research, vaccines against HIV and HCV are not yet available, due largely to effective viral immunoevasive mechanisms. A novel escape mechanism observed in viruses that cause chronic infection is suppression of viral-specific effector CD4(+) and CD8(+) T cells by stimulating regulatory T cells (Tregs) educated on host sequences during tolerance induction. Viral class II MHC epitopes that share a T cell receptor (TCR)-face with host epitopes may activate Tregs capable of suppressing protective responses. We designed an immunoinformatic algorithm, JanusMatrix, to identify such epitopes and discovered that among human-host viruses, chronic viruses appear more human-like than viruses that cause acute infection. Furthermore, an HCV epitope that activates Tregs in chronically infected patients, but not clearers, shares a TCR-face with numerous human sequences. To boost weak CD4(+) T cell responses associated with persistent infection, vaccines for HIV and HCV must circumvent potential Treg activation that can handicap efficacy. Epitope-driven approaches to vaccine design that involve careful consideration of the T cell subsets primed during immunization will advance HIV and HCV vaccine development

Mechanistic diversity in MHC class I antigen recognition

Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells