Identification Of T-cell Epitopes Research Articles

How to find a T cell's 'turn-ons'

A new array-based strategy offers a sensitive, high-throughput tool for identification of T-cell epitopes and monitoring of the cellular immune response to antigen stimulation.

Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles.

We introduced previously an on-line resource, RANKPEP that uses position specific scoring matrices (PSSMs) or profiles for the prediction of peptide-MHC class I (MHCI) binding as a basis for CD8 T-cell epitope identification. Here, using PSSMs that are structurally consistent with the binding mode of MHC class II (MHCII) ligands, we have extended RANKPEP to prediction of peptide-MHCII binding and anticipation of CD4 T-cell epitopes. Currently, 88 and 50 different MHCI and MHCII molecules, respectively, can be targeted for peptide binding predictions in RANKPEP. Because appropriate processing of antigenic peptides must occur prior to major histocompatibility complex (MHC) binding, cleavage site prediction methods are important adjuncts for T-cell epitope discovery. Given that the C-terminus of most MHCI-restricted epitopes results from proteasomal cleavage, we have modeled the cleavage site from known MHCI-restricted epitopes using statistical language models. The RANKPEP server now determines whether the C-terminus of any predicted MHCI ligand may result from such proteasomal cleavage. Also implemented is a variability masking function. This feature focuses prediction on conserved rather than highly variable protein segments encoded by infectious genomes, thereby offering identification of invariant T-cell epitopes to thwart mutation as an immune evasion mechanism.

Identification of T-cell epitopes using ELISpot and peptide pool arrays.

Here we describe a method for T-cell epitope identification using a modified ELISpot assay that is both simple and efficient. By using a carefully constructed array of pools of overlapping peptides spanning the entire antigen sequence to stimulate T-cell responses, we are able to detect antigen-specific cytokine responses by both CD8+ and CD4+ T cells and identify the specific peptides to which the cells are responding. Additionally, by performing magnetic bead depletion of either CD8+ or CD4+ cells prior to the assay, we are able to determine the phenotype of the responding cells to each of the peptide epitopes identified. Use of this method will allow the identification of both CD4+ and CD8+ T-cell epitopes without the need for MHC allele-matched reagents and without the need for highly specialized instrumentation. By using an array of peptide pools, this method also dramatically reduces the number of immune cells required to test the entire antigen sequence, often a limiting factor in vaccine testing and other studies.

Identification of human tumor antigens recognized by T-cells and their use for immunotherapy.

Identification of human tumor antigens led to development of new immunotherapies for patients with cancer. Identification of T-cell epitopes allowed us to monitor antitumor T-cell responses quantitatively and qualitatively during immunotherapy as well as to develop more efficient immunotherapies with sufficient amounts of antigens in more immunogenic forms. Various immunotherapies, passive immunotherapies, including adoptive transfer of tumor reactive T-cells or allogeneic antigen-specific donor T-cells, and active immunization with identified tumor antigens or dendritic cells pulsed with tumor antigens are being evaluated in clinical trials. Although tumor regression has been observed in some patients, further improvement is required.

The use of HPLC-MS in T-cell epitope identification

The hunt for T-cell epitopes is going on because hopes are set on such peptide sequences for diagnosis and vaccine development in the fight against infectious and tumor diseases. In addition to a variety of other techniques used in T-cell epitope identification, mass spectrometers coupled to microcapillary liquid chromatography have now become an important and sensitive tool in separation, detection, and sequence analysis of highly complex natural major histocompatibility complex (MHC) ligand mixtures. In this article, we review the basics of mass spectrometric techniques and their on-line coupling to microcapillary liquid chromatography (μcap-LC). Furthermore, we introduce current strategies for the identification of new T-cell epitopes using microcapillary liquid chromatography–mass spectrometry (μcap-LC-MS).

Use of combinatorial peptide libraries for T-cell epitope mapping

T lymphocytes play important roles not only in infectious diseases and autoimmunity, but also in immune responses against tumors. For many of these disorders, the relevant target antigens are not known. Designing effective methods that allow the search for T-cell epitopes is therefore an important goal in the areas of infectious diseases, oncology, vaccine development, and numerous other biomedical specialties. So far, the strategies used to examine T-cell recognition have been based largely on mapping T-cell epitopes with overlapping peptides from known proteins or with entire proteins, e.g., from a specific virus, bacterium, or human tissue. These approaches are tedious and have a number of limitations. It is, for example, almost impossible to isolate T cells that infiltrate an organ or infectious site and identify their specificity unless one already has a concept as to which antigens may be relevant. During recent years, a number of laboratories have developed less biased approaches that employ either the selection of putative T-cell epitopes based on the prediction of binding to certain major histocompatibilty complex (MHC) molecules and peptide or protein libraries that have been generated in expression systems, e.g. phage, or rely on combinatorial peptide chemistry. The latter technique has been refined by a number of laboratories including ours. Bead-bound or, preferably, positional scanning synthetic and soluble combinatorial peptide libraries allow the identification of T-cell epitopes within complex mixtures of proteins even for T cells that have been expanded from an organ infiltrate with a polyclonal stimulus. The practical steps that are involved in the latter method are described in this article.

Identification of T-cell epitopes in clotting factor IX and lack of tolerance in inbred mice

Immune responses to the factor IX protein pose problems for hemophilia B patients who develop antibodies against factor IX and for potential future treatment with gene therapy. To better define the response to human factor IX, we analyzed T-cell responses to human factor IX in factor IX knockout mice on BALB/c and C57BL/6 (B6) backgrounds, both strains having CD4+ T cells that proliferate in response to human factor IX. Surprisingly, wild-type mice have similar factor IX-recognizing CD4+ T cells. We defined a dominant CD4+ epitope for each strain (CVETGVKITVVAGEH for BALB/c and LLELDEPLVLNSYVTPIC for B6) that was recognized by both factor IX knockout and wild-type mice. While human factor IX did not cross-react with the mouse homologs of these epitopes, immunization with peptides from murine factor IX stimulated proliferation in factor IX knockout mice and wild-type mice, demonstrating a failure to delete murine factor IX-specific T cells in normal mice.

Identification of T-cell epitopes in the structural and non-structural proteins of classical swine fever virus.

To identify new T-cell epitopes of classical swine fever virus (CSFV), 573 overlapping, synthetic pentadecapeptides spanning 82% of the CSFV (strain Glentorf) genome sequence were synthesized and screened. In proliferation assays, 26 peptides distributed throughout the CSFV viral protein sequences were able to induce specific T-cell responses in PBMCs from a CSFV-Glentorf-infected d/d haplotype pig. Of these 26 peptides, 18 were also recognized by PBMCs from a CSFV-Alfort/187-infected d/d haplotype pig. In further experiments, it could be shown that peptide 290 (KHKVRNEVMVHWFDD), which corresponds to amino acid residues 1446-1460 of the CSFV non-structural protein NS2-3 could induce interferon-gamma secretion after secondary in vitro restimulation. The major histocompatibility complex (MHC) restriction for stimulation of T-cells by this pentadecapeptide was identified as being mainly MHC class II and partially MHC class I. In cytolytic assays, CSFV-specific cytotoxic T-lymphocytes (CTLs) were able to lyse peptide 290-loaded target cells. These findings indicate the existence of a CSFV-specific helper T-cell epitope and a CTL epitope in this peptide.

Update on immunologic basis of celiac disease

During the past few years several seminal studies have greatly expanded our knowledge on celiac disease pathogenesis. This review focuses on aspects that have been most properly addressed and where substantial new information has been gathered include. Topics covered include (a) the identification of T-cell epitopes in gluten and the mechanisms of specific T-cell response in celiac disease small intestine; (b) the mechanisms of induction of mucosal lesion; and (c) the putative role of non-T-cell factors in driving mucosal response to gliadin. After discussing a brief history of the "quest for the cause of celiac disease," we examine the development of the typical celiac lesion (the crypt hyperplastic mucosal atrophy) as it generally unfolds: the increased entry of dietary antigens; the early changes, linked to specific components of the innate immunity rather than to its adaptive branch; the most thoroughly investigated subsequent response, involving a strong T-cell response and cytokines; and the factors responsible for enterocytes' death. The emerging pattern is that of a complex interaction of factors, although far from being completely understood, but fascinating as it opens an incredible window of knowledge on an autoimmune disorder whose environmental factor is known, whose autoantigen is known, whose autoantibodies are known: a truly unique situation in medicine.

Identification of T-cell epitopes of Cry j 1 in dogs sensitive to Japanese cedar (cryptomeria japonica) Pollen

Identification of T-cell epitopes of Cry j 1 in dogs sensitive to Japanese cedar (cryptomeria japonica) Pollen

Peptide-based immunotherapy of autoimmunity: a path of puzzles, paradoxes and possibilities.

Our understanding of the basic mechanisms controlling the generation of productive immunity continues to evolve at a great pace. Models of how the immune response may be diverted from tackling invading pathogens into mounting an inappropriate response towards self tissue antigens also continue to develop. Armed with this knowledge, however, we are yet to develop effective and broadly applicable strategies to prevent or treat autoimmune disorders. This review assesses the prospects for developing antigen-specific therapies through the use of synthetic peptide antigens, and specifically altered peptide ligands (APL), to target pathogenic T-cell autoreactivity. Identification of T-cell epitopes within autoantigens has allowed the development of a minimalist approach to certain experimental models. Thus single peptides can replace purified autoantigen or homogenized tissue as the agents that elicit T-cell autoreactivity and therefore pathology. If we are using peptides to provoke disease, we should also be able to use peptides to prevent disease, and many reports over the last 15 years have confirmed this. But is this applicable to human autoimmune disorders and what is the best approach to use?

Update on immunologic basis of celiac disease

During the past few years several seminal studies have greatly expanded our knowledge on celiac disease pathogenesis. This review focuses on aspects that have been most properly addressed and where substantial new information has been gathered include. Topics covered include (a) the identification of T-cell epitopes in gluten and the mechanisms of specific T-cell response in celiac disease small intestine; (b) the mechanisms of induction of mucosal lesion; and (c) the putative role of non-T-cell factors in driving mucosal response to gliadin. After discussing a brief history of the "quest for the cause of celiac disease," we examine the development of the typical celiac lesion (the crypt hyperplastic mucosal atrophy) as it generally unfolds: the increased entry of dietary antigens; the early changes, linked to specific components of the innate immunity rather than to its adaptive branch; the most thoroughly investigated subsequent response, involving a strong T-cell response and cytokines; and the factors responsible for enterocytes' death. The emerging pattern is that of a complex interaction of factors, although far from being completely understood, but fascinating as it opens an incredible window of knowledge on an autoimmune disorder whose environmental factor is known, whose autoantigen is known, whose autoantibodies are known: a truly unique situation in medicine.

Comparison of phage pIII, pVIII and GST as carrier proteins for peptide immunisation in Balb/c mice

Carrier proteins are important for improving the efficiency of synthetic peptide vaccines. Recently, genetically-based systems such as filamentous phage display or glutathione S-transferase (GST)-fusion proteins have been employed for immunisation. Whilst these carrier systems can facilitate the evaluation of a potential vaccine by reducing the time and cost of production, their relative efficacy and the kinetics of the immune response to each carrier has not been directly compared. In this study, we have displayed the epitopes of the anti-ErbB-2 Mabs N12 (C531–A586, EP531) and N28 (T216–C235, EP216) on phage minor coat protein pIII, major coat protein pVIII and GST. Balb/c H-2 d mice were immunised with the constructs and the sera were tested after the initial, the 3rd, 5th and 6th immunisations for an anti-peptide, an anti-ErbB-2 and an anti-carrier response. The specificity of the antibody response was also mapped using synthetic peptides. It was found that GST was the best of the three carriers, both in terms of the magnitude and the kinetics of the induced anti-peptide and anti-ErbB-2 response. Multiple (five) administrations of the immunogens were necessary to obtain a high titre of antibodies specific for ErbB-2. It was further noted that whilst an anti-EP531 response was induced using all three carriers, EP216 was not immunogenic irrespective of the carrier used. The lack of immunogenicity of EP216 implies it does not contain a H-2 d T cell recognition site. All three carriers provide a useful system for vaccination and consequently facilitate the identification of T-cell epitopes in Balb/c inbred mice.

Grass allergen-specific T-cells of atopic patients.

The prevalence of atopic diseases has increased dramatically in the Western world over the last 20 years. Further insight into the mechanisms of the allergic reaction may help in the development of new more efficient protocols for the specific treatment of allergic diseases. Until a decade ago the major focus in allergy research was on the IgE reactivity of atopic patients and the description of major allergens responsible for the allergic reactions. More recently, the important role of CD4+ T-cells in orchestrating the production of IgE and the maturation of eosinophils through the production of IL-4 (or IL-13) and IL-5 has been clearly established. This has led to the characterization of T-cell responsiveness to numerous major allergens, demonstrating the importance of T-cells for the allergic response of atopic patients and for the specific treatment of allergic diseases. One of the major objectives of allergy research is the development of improved treatment protocols for specific therapy. In this review our results on the T-cell reactivity of grass allergic patients to the group 5 major allergen of the grass Phleum pratense (Phl p 5) are discussed in relation to the literature on allergen-specific T-cell reactivity and the specific treatment of allergic disease. Our investigations focused on three subjects: 1) Grass allergen-specific T-cell reactivity of atopic patients in freshly isolated PBMC cultures, 2) Phl p 5 isoallergen recognition of T-cell lines (TCL) and clones (TCC) established from PBMC of grass allergic patients, and 3) Identification of T-cell epitopes on Phl p 5.

Identification of T-cell epitopes in nonstructural proteins of foot-and-mouth disease virus.

Porcine T-cell recognition of foot-and-mouth disease virus (FMDV) nonstructural proteins (NSP) was tested using in vitro lymphoproliferative responses. Lymphocytes were obtained from outbred pigs experimentally infected with FMDV. Of the different NSP, polypeptides 3A, 3B, and 3C gave the highest stimulations in the in vitro assays. The use of overlapping synthetic peptides allowed the identification of amino acid regions within these proteins that were efficiently recognized by the lymphocytes. The sequences of some of these antigenic peptides were highly conserved among different FMDV serotypes. They elicited major histocompatibility complex-restricted responses with lymphocytes from pigs infected with either a type C virus or reinfected with a heterologous FMDV. A tandem peptide containing the T-cell peptide 3A[21-35] and the B-cell antigenic site VP1[137-156] also efficiently stimulated lymphocytes from infected animals in vitro. Furthermore, this tandem peptide elicited significant levels of serotype-specific antiviral activity, a result consistent with the induction of anti-FMDV antibodies. Thus, inclusion in the peptide formulation of a T-cell epitope derived from the NSP 3A possessing the capacity to induce T helper activity can allow cooperative induction of anti-FMDV antibodies by B cells.

Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta-algorithm.

The identification of T-cell epitopes can be crucial for vaccine development. An epitope is a peptide segment that binds to both a T-cell receptor and a major histocompatibility complex (MHC) molecule. Predicting which peptide segments bind MHC molecules is the first step in epitope prediction. An iterative stepwise discriminant analysis meta-algorithm explores a large molecular database to derive quantitative motifs for peptide binding. The applications presented here demonstrate the algorithm's versatility by producing four closely related models for HLA-DR1. Two models use an expert initial estimate and two do not; two models use amino acid residues as the only predictors and two use amino acid groupings as additional predictors. Each model correctly classifies >90% of the peptides in the database. Software is available commercially; data are free over the Internet.

Computational binding assays of antigenic peptides

Computer models can be combined with laboratory experiments for the efficient determination of (i) peptides that bind MHC molecules and (ii) T-cell epitopes. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures. This requires the definition of standards and experimental protocols for model application. We describe the requirements for validation and assessment of computer models. The utility of combining accurate predictions with a limited number of laboratory experiments is illustrated by practical examples. These include the identification of T-cell epitopes from IDDM-, melanoma- and malaria-related antigens by combining computational and conventional laboratory assays. The success rate in determining antigenic peptides, each in the context of a specific HLA molecule, ranged from 27 to 71%, while the natural prevalence of MHC-binding peptides is 0.1-5%.

Mapping of T-cell epitopes of Phl p 5: evidence for crossreacting and non-crossreacting T-cell epitopes within Phl p 5 isoallergens.

Group 5 allergens represent major grass pollen allergens because of their high sensitization indices. The identification of T-cell epitopes of these allergens is a prerequisite for the design of immunotherapeutic strategies based on peptide vaccination or modified allergens with conserved T-cell epitopes. This study was undertaken to determine T-cell epitopes on Phl p 5 major pollen allergen of timothy grass (Phleumn pratense). T-cell lines (TCLs) and T-cell clones (TCCs), specific to Phl p 5, were established from the peripheral blood of 18 patients allergic to grass pollen. All TCCs were mapped for epitope specificities using 178 overlapping dodecapeptides representing the primary structures of two isoforms of Phl p 5 (Phl p 5a and Phl p 5b). Phenotype and cytokine production profiles of TCCs were tested. Selected TCCs were analysed for HLA class II restriction. A total of 82 TCCs were isolated. All TCCs displayed the helper cell (TH) phenotype. Their reactivity with two recombinant expressed isoforms of Phl p 5a and Phl p 5b was heterogeneous. The epitope specificity of the TCCs was then revealed. Nineteen T-cell epitopes could be identified on Phl p 5. Eighty-one percent of mapped TCCs recognized three T-cell reactive regions on the Phl p 5 allergen. Some TCCs were reactive with isoepitopes presenting on Phl p 5a as well as Phl p 5b. Allergen-specific stimulation induced a TH0-like type of cytokine production in 25 of 50 TCCs. Almost all TCCs secreted high concentrations of interleukin-13. Phl p 5, a major grass pollen allergen, contains several T-cell epitopes. Some epitope regions were recognized by several patients. Epitope recognition pattern could not be correlated with special HLA class II haplotypes. T-cell stimulating isoepitopes were found at corresponding regions of Phl p 5a and Phl p 5b isoforms.

Neural network-based prediction of candidate T-cell epitopes.

Activation of T cells requires recognition by T-cell receptors of specific peptides bound to major histocompatibility complex (MHC) molecules on the surface of either antigen-presenting or target cells. These peptides, T-cell epitopes, have potential therapeutic applications, such as for use as vaccines. Their identification, however, usually requires that multiple overlapping synthetic peptides encompassing a protein antigen be assayed, which in humans, is limited by volume of donor blood. T-cell epitopes are a subset of peptides that bind to MHC molecules. We use an artificial neural network (ANN) model trained to predict peptides that bind to the MHC class II molecule HLA-DR4(*0401). Binding prediction facilitates identification of T-cell epitopes in tyrosine phosphatase IA-2, an autoantigen in DR4-associated type1 diabetes. Synthetic peptides encompassing IA-2 were tested experimentally for DR4 binding and T-cell proliferation in humans at risk for diabetes. ANN-based binding prediction was sensitive and specific, and reduced the number of peptides required for T-cell assay by more than half, with only a minor loss of epitopes. This strategy could expedite identification of candidate T-cell epitopes in diverse diseases.

Strategies for tumor elimination by cytotoxic T lymphocytes.

Despite differences in their tissue of origin, many tumors share high level expression of certain tumor-associated proteins. Our laboratory has focused on the possibility of utilizing antigenic components of these proteins as a focus for T-cell immunotherapy of cancer. The advantage of targeting such commonly expressed proteins is the fact that such therapy could be of value in eliminating many different types of tumors. A potential barrier in the identification of T-cell epitopes derived from these proteins and presented by tumor cells is the fact that these proteins are also expressed at low levels in some normal tissues, and therefore, self-tolerance may eliminate T cells that are capable of recognizing these epitopes with high avidity. We have utilized two different murine model systems to explore the extent to which self-tolerance may limit the immune response to a tumor-specific antigen. The first compared the ability of mice deficient in expression of murine p53 (p53 knock-out mice) and normal mice, to respond against several epitopes of the p53 protein. The second model compares the ability of conventional mice with transgenic mice that express the influenza hemagglutinin in the periphery to respond to a dominant antigenic peptide of this transgene product. In both models we have investigated the effect self-tolerance has on elimination of tumors expressing the toleragen.