Autologous peptides constitutively occupy the antigen binding site on Ia

The biogenesis of the immunopeptidome

The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.

Autodisplay of streptococcal protein G for construction of an orientation-controlled immunoaffinity layer

An immunoaffinity layer with orientation-controlled antibodies was constructed to express streptococcal protein G in Escherichia coli cells using autodisplay technology. The sequence of protein G, a specific IgG-binding protein, was inserted into the autodisplay vector using recombinant technology and the constructed plasmid vector was transformed into E. coli cells. Protein G was confirmed to be autodisplayed with a high density of 2 × 10⁵ copies per cell by SDS-PAGE analysis, and its IgG-binding affinity was confirmed by fluorescence microscopy. Autodisplayed protein G showed higher affinity than the IgG-binding Z-domain for goat IgG. Immunoassays based on E. coli cells were established to detect horseradish peroxidase (HRP) and C-reactive protein (CRP). Protein G autodisplaying E. coli cells were utilized as a solid support and immunoassays showed improved sensitivity by orientation control of autodisplayed protein G. The outer membrane (OM) of protein G autodisplaying E. coli was isolated and layered to construct an immunoaffinity layer. The OM was coated on a microplate to perform the immunoassays, which showed limits of detection of 5 and 0.2 ng mL^-1 for HRP and CRP, respectively. An OM layer with autodisplayed protein G was applied as the immunoaffinity layer of a surface plasmon resonance (SPR) biosensor. After CRP detection, the SPR responses showed good linearity, with an R² value of 0.99. The immunoaffinity layer with orientation control by autodisplayed protein G was confirmed to be applicable in immunoassays and immunosensors to improve sensitivity.

Mechanism and strategies of immunotherapy resistance in colorectal cancer

Colorectal cancer (CRC) is the third most common cancer in the world. Although there are standard treatment options for CRC, most patients respond poorly to these treatments. Immunotherapies have gradually emerged due to the increasing awareness and understanding of tumor immunity, exhibiting good therapeutic efficacy in various cancers. Immunotherapies include cytokines, immune checkpoint inhibitors (ICIs), and adoptive cell therapies. In particular, ICIs, which are antibodies against cytotoxic T lymphocyte-associated protein 4 (CTLA-4), programmed cell death 1 (PD-1), or its ligand PD-L1, have been successfully applied clinically for solid tumors, relieving the inhibitory effect of the tumor microenvironment on T cells. However, only a minority of patients with cancer achieve a durable clinical response during immunotherapy. Several factors restrict the efficacy of immunotherapy, leading to the development of drug resistance. In this review, we aimed to discuss the current status of immunotherapy for CRC and elaborate on the mechanisms that mediate resistance to immunotherapy and other potential therapeutic strategies.

Immunoinformatics: Predicting Peptide-MHC Binding

Immunoinformatics is a discipline that applies methods of computer science to study and model the immune system. A fundamental question addressed by immunoinformatics is how to understand the rules of antigen presentation by MHC molecules to T cells, a process that is central to adaptive immune responses to infections and cancer. In the modern era of personalized medicine, the ability to model and predict which antigens can be presented by MHC is key to manipulating the immune system and designing strategies for therapeutic intervention. Since the MHC is both polygenic and extremely polymorphic, each individual possesses a personalized set of MHC molecules with different peptide-binding specificities, and collectively they present a unique individualized peptide imprint of the ongoing protein metabolism. Mapping all MHC allotypes is an enormous undertaking that cannot be achieved without a strong bioinformatics component. Computational tools for the prediction of peptide-MHC binding have thus become essential in most pipelines for T cell epitope discovery and an inescapable component of vaccine and cancer research. Here, we describe the development of several such tools, from pioneering efforts to the current state-of-the-art methods, that have allowed for accurate predictions of peptide binding of all MHC molecules, even including those that have not yet been characterized experimentally.

Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

The entirety of human leukocyte antigen (HLA)-presented peptides is referred to as the HLA ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the tumour immunopeptidome by mass spectrometry (MS) comprehensively views the pathophysiologically relevant antigenic signature of human malignancies. MS is an unbiased approach stringently filtering the candidates to be tested as opposed to epitope prediction algorithms. In the setting of peptide-specific immunotherapies, MS-based strategies significantly diminish the risk of lacking clinical benefit, as they yield highly enriched amounts of truly presented peptides. Early immunopeptidomic efforts were severely limited by technical sensitivity and manual spectra interpretation. The technological progress with development of orbitrap mass analysers and enhanced chromatographic performance led to vast improvements in mass accuracy, sensitivity, resolution, and speed. Concomitantly, bioinformatic tools were developed to process MS data, integrate sequencing results, and deconvolute multi-allelic datasets. This enabled the immense advancement of tumour immunopeptidomics. Studying the HLA-presented peptide repertoire bears high potential for both answering basic scientific questions and translational application. Mapping the tumour HLA ligandome has started to significantly contribute to target identification for the design of peptide-specific cancer immunotherapies in clinical trials and compassionate need treatments. In contrast to prediction algorithms, rare HLA allotypes and HLA class II can be adequately addressed when choosing MS-guided target identification platforms. Herein, we review the identification of tumour HLA ligands focusing on sources, methods, bioinformatic data analysis, translational application, and provide an outlook on future developments.

Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture

This unit describes a technique for the direct and quantitative measurement of the capacity of peptide ligands to bind Class I and Class II MHC molecules. The binding of a peptide of interest to MHC is assessed based on its ability to inhibit the binding of a radiolabeled probe peptide to purified MHC molecules. This unit includes protocols for the purification of Class I and Class II MHC molecules by affinity chromatography, and for the radiolabeling of peptides using the chloramine T method. An alternate protocol describes alterations in the basic protocol that are necessary when performing direct binding assays, which are required for (1) selecting appropriate high-affinity, assay-specific, radiolabeled ligands, and (2) determining the amount of MHC necessary to yield assays with the highest sensitivity. After a predetermined incubation period, dependent upon the allele under examination, the bound and unbound radiolabeled species are separated, and their relative amounts are determined. Three methods for separation are described, two utilizing size-exclusion gel-filtration chromatography and a third using monoclonal antibody capture of MHC. Data analysis for each method is also explained.

Functional recombinant MHC class II molecules and high-throughput peptide-binding assays

BACKGROUND

Molecules of the class II major histocompability complex (MHC-II) specifically bind and present exogenously derived peptide epitopes to CD4+ T helper cells. The extreme polymorphism of the MHC-II hampers the complete analysis of peptide binding. It is also a significant hurdle in the generation of MHC-II molecules as reagents to study and manipulate specific T helper cell responses. Methods to generate functional MHC-II molecules recombinantly, and measure their interaction with peptides, would be highly desirable; however, no consensus methodology has yet emerged.

RESULTS

We generated alpha and beta MHC-II chain constructs, where the membrane-spanning regions were replaced by dimerization motifs, and the C-terminal of the beta chains was fused to a biotinylation signal peptide (BSP) allowing for in vivo biotinylation. These chains were produced separately as inclusion bodies in E. coli , extracted into urea, and purified under denaturing and non-reducing conditions using conventional column chromatography. Subsequently, diluting the two chains into a folding reaction with appropriate peptide resulted in efficient peptide-MHC-II complex formation. Several different formats of peptide-binding assay were developed including a homogeneous, non-radioactive, high-throughput (HTS) binding assay. Binding isotherms were generated allowing the affinities of interaction to be determined. The affinities of the best binders were found to be in the low nanomolar range. Recombinant MHC-II molecules and accompanying HTS peptide-binding assay were successfully developed for nine different MHC-II molecules including the DPA1*0103/DPB1*0401 (DP401) and DQA1*0501/DQB1*0201, where both alpha and beta chains are polymorphic, illustrating the advantages of producing the two chains separately.

CONCLUSION

We have successfully developed versatile MHC-II resources, which may assist in the generation of MHC class II -wide reagents, data, and tools.

Measurement of MHC/peptide interactions by gel filtration

This unit describes a technique for the direct and quantitative measurement of the capacity of peptide ligands to bind Class I and Class II MHC molecules. The binding of a peptide of interest to MHC is assessed based on its ability to inhibit the binding of a radiolabeled probe peptide to MHC molecules. The establishment of an MHC/peptide binding assay, and its subsequent use in determining the MHC binding capacities of peptide ligands, requires sufficient stocks of purified MHC and both labeled and unlabeled peptides. Accordingly, this unit includes protocols for the purification of Class I and Class II MHC molecules by affinity chromatography, and for the radiolabeling of peptides using the chloramine T method. A support protocol describes alterations in the basic protocol that are necessary when performing direct binding assays, which are required for (1) selecting appropriate high-affinity, assay-specific, radiolabeled ligands and (2) determining the amount of MHC necessary to yield assays with the highest sensitivity. After a 2-day incubation, the bound and unbound radiolabeled species are separated, and their relative amounts are determined. Two methods for separation by size-exclusion gel-filtration chromatography are described, as is data analysis.

Finding the groove

Envisioning how T cells might recognize antigen presented by major histocompatibility complex molecules proved to be a formidable challenge. Pamela Bjorkman describes her journey to provide structural insights into how such recognition is achieved.

Achieving stability through editing and chaperoning: regulation of MHC class II peptide binding and expression

In antigen-presenting cells (APCs), loading of major histocompatibility complex class II (MHC II) molecules with peptides is regulated by invariant chain (Ii), which blocks MHC II antigen-binding sites in pre-endosomal compartments. Several molecules then act upon MHC II molecules in endosomes to facilitate peptide loading: Ii-degrading proteases, the peptide exchange factor, human leukocyte antigen-DM (HLA-DM), and its modulator, HLA-DO (DO). Here, we review our findings arguing that DM stabilizes a globally altered conformation of the antigen-binding groove by binding to a lateral surface of the MHC II molecule. Our data imply changes in the interactions between specificity pockets and peptide side chains, complementing data from others that suggest DM affects hydrogen bonds. Selective weakening of peptide/MHC interactions allows DM to alter the peptide repertoire. We also review our studies in cells that highlight the ability of several factors to modulate surface expression of MHC II molecules via post-Golgi mechanisms; these factors include MHC class II-associated Ii peptides (CLIP), DM, and microbial products that modulate MHC II traffic from endosomes to the plasma membrane. In this context, we discuss possible mechanisms by which the association of some MHC II alleles with autoimmune diseases may be linked to their low CLIP affinity.

Replacement of the membrane proximal region of I-Ad MHC class II molecule with I-E-derived sequences promotes production of an active and stable soluble heterodimer without altering peptide-binding specificity

The MHC class II molecule I-A is the murine homologue of HLA-DQ in humans. The I-A and DQ heterodimers display considerable heterodimer instability compared with their I-E and HLA-DR counterparts. This isotype-specific behavior makes the production of soluble I-A and DQ molecules very difficult. We have developed a strategy for production of soluble I-A(d) molecules involving expression of I-A(d) as a glycosil phosphatidyl inositol (PI) anchored chimera in Chinese Hamster Ovary (CHO) cells. The regions comprising the membrane proximal segments of I-A(d) alpha and beta chains were substituted for the corresponding regions of I-E, and the derived constructs were expressed in CHO cells. Procedures for purification of the soluble class II molecules were optimized and the WT and chimeric molecule were compared for structure, biochemical stability and functionality. Our analysis revealed that the substitutions in the membrane proximal domains improved cell surface expression and thermal stability of I-A(d) without altering the peptide binding specificity of the class II molecule. The results suggest that similar strategies could be used to increase the stability of other unstable class II molecules for in vitro studies.

Upregulation of the CLIP self peptide on mature dendritic cells antagonizes T helper type 1 polarization

Dendritic cells (DCs) initiate and regulate immunity against foreign and self antigens. Here we identified more than 200 individual major histocompatibility complex class II-associated peptides on human DCs and found that mature DCs selectively upregulated the self peptide CLIP. CLIP cosegregated together with foreign antigenic peptides in tetraspan microdomains on the surface and localized to DC-T cell synapses. The increased representation of CLIP-major histocompatibility complex class II complexes favored polarization of autologous naive T cells toward the nonpolarized and T helper type 2 (T(H)2) phenotype. There was also a considerably higher T(H)2/T(H)1 ratio in H2-DM-deficient mice, which have a CLIP(hi) phenotype, in contrast to wild-type, CLIP(lo) mice. Thus, the self peptide CLIP on DCs qualifies as an endogenous regulator in priming of T helper cells by antagonizing the polarization toward the T(H)1 phenotype.

Analysis of peptide affinity to major histocompatibility complex proteins for the two-step binding mechanism

A novel approach to the analysis of an equilibrium two-step peptide-protein binding is developed and applied to the experimental data. The first step of the process is the release of an endogenous peptide from a binding groove and the second is the binding of an added peptide. The method developed enables us to determine consequently the maximum protein occupancy level (protein-binding capacity), the dissociation constant of an endogenous peptide, and the dissociation constant of a binding (antigenic) peptide. It is shown and confirmed by experimental data that the value of an equilibrium dissociation constant of a binding peptide could be much less than the experimental value of ED(50) (concentration of added peptide required to bind half of the protein), but not equal to that commonly assumed for major histocompatibility complex (MHC)-peptide binding. The model considered gives a clear understanding of why some peptides may be good binders to MHC protein in vitro, but do not exhibit anticipated activity on the cellular level and vice versa.

Binding interactions between peptides and proteins of the class II major histocompatibility complex

The activation of helper T cells by peptides bound to proteins of the class II Major Histocompatibility Complex (MHC II) is pivotal to the initiation of an immune response. The primary functional requirement imposed on MHC II proteins is the ability to efficiently bind thousands of different peptides. Structurally, this is reflected in a unique architecture of binding interactions. The peptide is bound in an extended conformation within a groove on the membrane distal surface of the protein that is lined with several pockets that can accommodate peptide side-chains. Conserved MHC II protein residues also form hydrogen bonds along the length of the peptide main-chain. Here we review recent advances in the study of peptide-MHC II protein reactions that have led to an enhanced understanding of binding energetics. These results demonstrate that peptide-MHC II protein complexes achieve high affinity binding from the array of hydrogen bonds that are energetically segregated from the pocket interactions, which can then add to an intrinsic hydrogen bond-mediated affinity. Thus, MHC II proteins are unlike antibodies, which utilize cooperativity among binding interactions to achieve high affinity and specificity. The significance of these observations is discussed within the context of possible mechanisms for the HLA-DM protein that regulates peptide presentation in vivo and the design of non-peptide molecules that can bind MHC II proteins and act as vaccines or immune modulators.

Hb(64-76) epitope binds in different registers and lengths to I-Ek and I-Ak

The nature of peptide binding to MHC molecules is intrinsically degenerate, in what, one given MHC molecule can accommodate numerous peptides which are structurally diverse, and one given peptide can bind to different alleles. The structure of the MHC class II molecules allows peptides to extend out of the binding groove at both ends and these residues can potentially influence the stability and persistence of peptide/class II complexes. We have previously shown that both I-E(k) and I-A(k)-restricted T cell hybridomas could be generated against the Hb(64-76) epitope. In this study, we characterized the binding register of the Hb(64-76) epitope to I-A(k), and showed that it was shifted by one residue in comparison to its binding to I-E(k), and did not use a dominant anchor residue at P1. This conclusion was further supported by the modeling of the Hb(64-76) epitope bound to I-A(k), which revealed that all of its putative anchor residues fit into their corresponding pockets. We identified the naturally processed Hb epitopes presented by both I-E(k) and I-A(k), and found that they consisted of different species. Those associated with I-A(k) being 20-22 residues long, whereas, those found to I-E(k) contained 14-16 residues. These findings suggested that the lack of a dominant P1 anchor could be compensated by the selection of longer peptides. Overall, these studies revealed the Hb(64-76) epitope bound to I-E(k) and I-A(k) in distinct registers and lengths, demonstrating the plasticity MHC molecules have in generating distinct TCR ligands from the same amino acid sequence.

The analysis of peptide affinity and its binding kinetics to DR1DW1 major histocompatibility complex protein

The connection between experimentally measured values of ED50 (concentration of added peptide required to bind half of the protein), which characterize peptide-protein binding and the equilibrium dissociation constant of peptide-protein complex Kd (affinity) is considered. It is shown and confirmed by experimental studies that in certain cases, as a result of the absence of equilibrium in the system, the value of Kd could be much less than the experimental value of ED50, but not equal to that as commonly assumed. This is especially applicable to the formation of peptide-MHC complexes with low dissociation rates (strong binding), which may require longer time-intervals to reach equilibrium. Thus the search of the good binding peptides based on finding ones with the smallest measured values' of ED50 may result in missing the best binders with the lowest values of dissociation constant (highest affinity). To analyze the problem we considered the formal chemical kinetics of peptide-protein binding. Experimental studies of peptide binding was performed to obtain the parameters of the kinetic model. According to the predictions of the model, it was confirmed that peptide binding occurs through the preceding step, which is either a release of an endogenous peptide or some conformational change of the molecule. The half decay time for this process was determined to be approximately 3 h. Based on the model developed, a new effective method for determination of the dissociation rates of peptide-MHC complexes and the equilibrium dissociation constants Kd was proposed, which implies the comparison of binding levels (ED50) at different instants of time. This method works especially well for the peptide-MHC complexes with relatively slow dissociation rates (stable complexes), for which the direct off-rate measurements as well as obtaining equilibrium binding data to determine Kd are highly time consuming and not very reliable.

Formation of a highly peptide-receptive state of class II MHC

Peptide binding to class II MHC proteins occurs in acidic endosomal compartments following dissociation of class II-associated invariant chain peptide (CLIP). Based on peptide binding both to empty class II MHC and to molecules preloaded with peptides including CLIP, we find evidence for two isomeric forms of empty MHC. One (inactive) does not bind peptide. The other (active) binds peptide rapidly, with k(on) 1000-fold faster than previous estimates. The active isomer can be formed either by slow isomerization of the inactive molecule or by dissociation of a preformed peptide/MHC complex. In the absence of peptide, the active isomer is unstable, rapidly converting to the inactive isomer. These results demonstrate that fast peptide binding is an inherent property of one isomer of empty class II MHC. Dissociation of peptides such as CLIP yields this transient, peptide-receptive isomer.

Initiation of the Autologous Mixed Lymphocyte Reaction Requires the Expression of Costimulatory Molecules B7-1 and B7-2 on Human Peripheral Blood Dendritic Cells

The human autologous mixed lymphocyte reaction (AMLR) consists of a proliferative response of primarily CD4+ T lymphocytes stimulated by autologous non-T cells expressing class II MHC-encoded gene products and is thought to represent a self-recognitive mechanism that might be important in regulating the cellular interactions involved in the generation of normal immune responses. To further define appropriate stimulator cell populations, as well as the molecular mechanism responsible for the initiation of AMLR, we compared the T cell-stimulatory capacity of highly purified populations of peripheral blood dendritic cells (DCs) and monocytes (Mos) under serum-free conditions, thus carefully avoiding the presence of xenogeneic Ags. Whereas both freshly isolated Mos and DCs were found to be poor stimulators of autologous T cell proliferation, preactivation of DCs, but not of Mos, for 48 h with granulocyte-macrophage CSF led to a 113-fold increase in DC stimulatory capacity. AMLR was inhibited by mAbs against HLA-DR and CD4 molecules, and, in addition, showed a higher dependence on the granulocyte-macrophage CSF-induced up-regulation and/or de novo expression of the costimulatory molecules B7-2 and, in particular, B7-1 as compared with an Ag-specific or allogeneic MLR. Thus, our data suggest that the high density of costimulatory molecules together with MHC class II molecules on competent APCs appear to be the major triggers for the initiation of AMLR.

The structure of HLA-DM, the peptide exchange catalyst that loads antigen onto class II MHC molecules during antigen presentation

The three-dimensional structure of the soluble ecto-domain of HLA-DM has been determined to 2.5 A resolution by X-ray crystallography. HLA-DM has both peptide exchange activity and acts as a chaperone to peptide-free class II MHC molecules. As predicted, the structure is similar to that of classical class II MHC molecules except that the peptide-binding site is altered to an almost fully closed groove. An unusual cavity is found at the center of the region that binds peptides in class II MHC molecules, and a tryptophanrich lateral surface is identified that is a candidate both for binding to HLA-DR, to effect catalysis, and to HLA-DO, an inhibitor.

Contribution of mass spectrometry to contemporary immunology

Mass spectrometry has become an increasingly important tool in the characterization of histocompatibility complex molecule (MHC) bound antigen peptides. It is one of the few technologies capable of identifying minute amounts of peptides in complex (5,000-10,000 constituents) MHC elution mixtures. Currently, the combination of tandem mass spectrometry with electrospray ionization (ESI) and microcapillary liquid chromatography (microLC) has proven to be the more versatile and effective technology. Post-source decay (PSD) and on-slide digestion combined with matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) may be valuable as well in certain circumstances. Recent refinements in the technology, such as the development of the quadrupole ion trap (QIT), Fourier transform ion cyclotron resonance (FTICR), and orthogonal quadrupole-time-of-flight (qToF) mass spectrometers equipped with nanoscale electrospray ionization sources and combined with microscale LC or capillary zone electrophoresis (CZE) yield attomole-range sensitivity in peptide sequencing, a level approaching the immuno-relevant level to a significant extent. In this review, past and ongoing developments in mass spectrometry and analytical separation techniques and their application to contemporary immunology are discussed.

Cloning and characterization of murine thyroglobulin cDNA

Thyroglobulin is used to induce in mice experimental autoimmune thyroiditis (EAT), a model for Hashimoto thyroiditis. Because murine thyroglobulin is a more potent inducer of EAT than heterologous thyroglobulins, it has been hypothesized that it contains unique pathogenic epitopes. The validation of this hypothesis has been hampered by the lack of the murine thyroglobulin sequence. To identify murine-specific areas in thyroglobulin, we cloned, by reverse transcriptase PCR, and sequenced the complete murine thyroglobulin cDNA. This encodes a polypeptide of 2748 amino acids that is 73.5 and 71.8% identical to bovine and human thyroglobulin, respectively. Six regions are unique to each species. We also analyzed through EpiMer the sequences able to bind to the I-Ek major histocompatibility allele and, therefore, function as T cell epitopes. EpiMer analysis showed seven murine-specific T cell epitopes in thyroglobulin. The availability of the complete murine thyroglobulin sequence should promote the understanding of the pathogenesis and immunoregulation of EAT.

Immunodominant CD4+ T-cell epitope within nonstructural protein 3 in acute hepatitis C virus infection

In acute hepatitis C virus infection, 50 to 70% of patients develop chronic disease. Considering the low rate of spontaneous viral clearance during chronic hepatitis C infection, the first few months of interaction between the patient's immune system and the viral population seem to be crucial in determining the outcome of infection. We previously reported the association between a strong and sustained CD4+ T-cell response to nonstructural protein 3 (NS3) of the hepatitis C virus and a self-limited course of acute hepatitis C infection. In this study, we identify an immunodominant CD4+ T-cell epitope (amino acids 1248 to 1261) that was recognized by the majority (14 of 23) of NS3-specific CD4+ T-cell clones from four of five patients with acute hepatitis C infection. This epitope can be presented to CD4+ T cells by HLA-DR4, -DR11, -DR12, -DR13, and -DR16. HLA-binding studies revealed a high binding affinity for 10 of 13 common HLA-DR alleles. Two additional CD4+ T-cell epitopes, amino acids 1388 to 1407 and amino acids 1450 to 1469, showed a very narrow pattern of binding to individual HLA-DR alleles. Our data suggest that the NS3-specific CD4+ T-cell response in acute hepatitis C infection is dominated by a single, promiscuous peptide epitope which could become a promising candidate for the development of a CD4+ T-cell vaccine.

Rejection of cardiac allografts by T cells expressing a restricted repertoire of T-cell receptor V beta genes

We have recently shown that T cells infiltrating cardiac allografts early in graft rejection use a limited T-cell receptor (TCR) V beta repertoire. In this study we tested whether this limited repertoire of V beta genes is important for graft rejection. A cell line, AL2-L3, was established from LEW lymphocytes infiltrating ACI heart allografts 2 days after transplantation. This cell line is composed of CD4+ T cells that primarily recognize the class II RTI.B major histocompatibility complex (MHC) molecule expressed by the donor graft. This cell line precipitated acute rejection of donor hearts with a median survival time (MST) of 10.5 days following adoptive transfer to sublethally irradiated LEW recipients. This rate of graft rejection was significantly (P < 0.0007) accelerated when compared with a MST of 60 days for allografts in irradiated control recipients. The AL2-L3-mediated acceleration of graft rejection was donor specific as WF third-party heart allografts were rejected with a delayed tempo (MST = 28.5 days). The V beta repertoire of this cell line was primarily restricted to the expression of V beta 4, 15 and 19 genes. The nucleotide sequence analysis of the beta-chain cDNAs from this cell line demonstrated that the restricted use of the V gene repertoire was not shared with the N, D and J regions. A wide variety of CDR3 loops and J beta genes were used in association with selected V beta genes. These data provide evidence for the role a restricted repertoire of V beta genes plays in cardiac allograft rejection in this model. The restricted usage of the V beta repertoire in an early T-cell response to allografts may provide the opportunity to therapeutically disrupt the rejection reaction by targeting selected T-cell populations for elimination at the time of organ transplantation.

Class I HLA-restricted cytotoxic T lymphocyte responses against malaria--elucidation on the basis of HLA peptide binding motifs

In animal models, CD8+ T cells are a critical effector mechanism in the protective immunity against malaria. Conventional approaches to the development of many vaccines, including those against malaria, have however proved inadequate. In particular, an alternative approach is needed for the development of vaccines designed to induce a cellular immune response mediated by CD8+ T cells. Advances in the field of molecular immunology during the past decade have provided an insight into the presentation of peptides by MHC class I molecules and their recognition by CD8+ T cells. These studies have provided a conceptual basis for the development of efficacious parasitic and viral vaccines. By a combination of immunochemical and cellular immunologic analyses based on specific peptide binding motifs, a subunit malaria vaccine that includes CD8+ T cell epitopes restricted by the most common class I HLA alleles, including HLA-A2, can now be constructed.

The in vitro response to human fibroblast-derived extracellular matrix proteins is restricted by specific HLA class II genes. Relevance for coeliac disease

Coeliac disease is an immunologic disease of the small intestine which is caused by ingestion of wheat gliadin, the disease-promoting agent. The disease associates strongly with the particular HLA type, HLA-DQA1*0501, DQB1*0201 alleles. Further specific autoantibodies against reticulin and endomysium are found in patients; these autoantibodies appear to be disease specific. An extracellular matrix noncollagenous protein reacts specifically with CD patients' serum immunoglobulin A and is the target of antireticulin antibodies. In this study the immune response to this matrix protein was analyzed in vitro in normal, healthy individuals. Our study shows that the immune response to Fb-CDAP is strictly regulated by the HLA-DR3, DQA1*0501, DQB1*0201 alleles, and that only those cells which were positive for these alleles produced an immune response. On the other hand, half of the cells positive for these HLA alleles were responders. Monoclonal antibodies to DR and DQ inhibited the response in an additive way, showing that both DR and DQ can act as an antigen-presenting structure. The immune response to gliadin has been shown to associate with the same HLA type as CD, but the association is not as strong. Our results show that the immune responses to Fb-CDAP can be generated in vitro in genetically predisposed persons in the absence of CD.

Regulatory mechanisms of antitumor T cell responses in the tumor-bearing state

Tumor-bearing hosts develop antitumor immune responses. However, a number of immunosuppressive mechanisms come into operation with the progression of tumor growth. This article will review the observations regarding the modulation of antitumor immune responses in the tumor-bearing state, and consider the mechanisms underlying tumor-induced immune defects, especially in the light of the induction of an abnormal cytokine network. We will also describe the restoration of suppressed antitumor immune responses by administration of a particular cytokine, interleukin-12.

Self and non-self peptides treat autoimmune encephalomyelitis: T cell anergy or competition for major histocompatibility complex class II binding?

In susceptible strains of mice, myelin basic protein (MBP) peptide Acl-ll induces experimental autoimmune encephalomyelitis (EAE) providing a useful model for human multiple sclerosis. Acl-11 binds major histocompatibility complex (MHC) class II molecules A alpha upsilon A beta upsilon. Here, we show that the Acl-11 peptide, when administered intraperitoneally in incomplete Freund's adjuvant (IFA) emulsion, can effectively treat Acl-11-induced EAE in mice. Treatment with Acl-11/IFA 9 days after initial immunization with Acl-11 in complete Freund's adjuvant (CFA) results in a loss of T cell proliferation to MBP Acl-11. This lack of T cell proliferation is not due to T cell anergy and is not specific. A similar lack of T cell proliferation and inhibition of EAE is observed when an ovalbumin peptide OVA323-339 or a sperm whale myoglobin peptide SWM110-121 are used to treat mice immunized with Acl-11. Interestingly, we show that previously unresponsive lymph node cells from treated mice respond normally if Acl-11 is presented by fresh antigen-presenting cells taken from normal mice. These results argue that the lack of T cell proliferation and inhibition of EAE is not due to specific T cell anergy as suggested by others. Instead this appears to be due to blocking of MHC class II molecules A alpha upsilon A beta upsilon by the treating peptides.

Impaired antigen presentation by splenocytes of ethanol-consuming C57BL/6 mice

Excessive alcohol consumption impairs T-cell-dependent immune function. Whether this impairment results from the direct inhibition of helper T (Th) cells or from inhibition of the cells that process and present antigen to Th cells is unclear. The present study examines the effect of dietary alcohol on the ability of spleen cells from C57BL/6 mice to present antigen to T-cell hybridomas. We find that ethanol consumption impairs the ability of spleen cells to present hen egg lysozyme (HEL) in vitro. This impairment was seen for native HEL protein, a hapten-modified HEL, and a peptide bearing a minimal T-cell epitope (HEL 51-60) that requires no additional enzymatic processing. These results suggest that deficiencies in immune responsiveness in alcohol-consuming individuals may include antigen presentation.

Kinetics of chlamydial antigen processing and presentation to T cells by paraformaldehyde-fixed murine bone marrow-derived macrophages

Macrophages are potential candidates for antigen presentation to chlamydial-specific CD4+ T cells. We have studied the kinetics of chlamydial antigen processing and presentation by using paraformaldehyde-fixed bone marrow-derived macrophages (BMDM) and splenic T cells isolated from chlamydia-infected mice. BMDM were inoculated with different multiplicities of heat-killed chlamydial elementary bodies, and at different times postingestion, the macrophages were fixed with paraformaldehyde and used as antigen-presenting cells in T-cell proliferation assays. T-cell proliferative responses were shown to be dependent on the chlamydial inoculum size, with a multiplicity of 10 chlamydiae per macrophage producing optimum T-cell proliferation. Temporal experiments showed that peak T-cell proliferative responses occurred between 4 and 12 h postingestion of chlamydiae by BMDM. T cells proliferated strongly to antigen when presented by H-2-matched BMDM but not when presented by H-2-disparate BMDM, demonstrating that T-cell recognition of processed chlamydial antigen was major histocompatibility complex restricted. BMDM inoculated with 10 chlamydiae per cell and fixed at 8 h postinoculation were shown to be as stimulatory to T cells as conventional splenic antigen-presenting cells. Because large numbers of BMDM can be propagated in vitro, and experimental conditions that provide optimum presentation of processed chlamydial antigen to chlamydia-specific CD4+ T cells can be defined, BMDM may be a potentially useful source for the isolation of naturally processed parasite antigen from major histocompatibility complex class II molecules.

Endogenous antigen presentation by MHC class II molecules

T cell recognition of antigen requires that a complex form between peptides derived from the protein antigen and cell surface glycoproteins encoded by genes within the major histocompatibility complex (MHC). MHC class II molecules present both extracellular (exogenous) and internally synthesized (endogenous) antigens to the CD4 T cells subset of lymphocytes. The mechanisms of endogenous antigen presentation are the subject of this review. Isolation and amino acid sequencing of peptides bound to the class II molecule indicate that a very high proportion (70-90%) of the total peptides presented by the class II molecule are in fact derived from the pool of proteins that are synthetized within the antigen-presenting cell (APC). This type of sequence information as well as the study of model antigens has indicated that proteins expressed in a diversity of intracellular sites, including the cell surface, endoplasmic reticulum and cytosol can gain access to the class II molecule, albeit with different efficiencies. The main questions that remain to be answered are the intracellular trafficking patterns that allow colocalization of internally synthesized antigens with the class II molecule, the site(s) within the cell where peptide:class II molecule complex formation can take place and whether presentation of 'foreign' as well as 'self' antigens takes place by mechanisms that vary from one cell type to another or that vary with the metabolic state of the APC. If such variability exists, is would imply that the array of peptides displayed by class II molecules at the cell surface has similar variability, a possibility that would impact on self tolerance and autoimmunity.

Kinetic intermediates in the reactions between peptides and proteins of major histocompatibility complex class II

The kinetics of the reactions between fluorescently labeled sperm whale myoglobin-(110-121) peptide and the murine major histocompatibility complex class II protein I-Ed have been analyzed. The presence in solution of both short- and long-lived protein-peptide complexes is demonstrated by the biphasic dissociation of the myoglobin peptide from I-Ed. The formation of the long-lived terminal complex is preceded by a characteristic induction phase. It is shown that the initially formed complex of the myoglobin peptide and I-Ed is a kinetic intermediate that undergoes a unimolecular reaction to form the terminal complex. Reactions between peptides and the class II proteins thus involve an intermediate structurally distinct from the terminal complex. The terminal complex presumably has a structure that is biologically active and similar to the published class II protein-peptide crystal structure.

T cell epitope recognition involved in the low-responsiveness to a region of hen egg lysozyme (46-61) in C57BL/6 mice

The predominant T cell epitope of hen egg lysozyme (HEL) in high-responder C3H mice has been previously identified as the HEL 46-61 region. In contrast, this region is poorly recognized by T cells from low-responder C57BL/6 mice upon immunization with HEL. In previous studies, we have demonstrated that several C57BL/6 derived T cell hybridomas reactive to this epitope and other HEL epitopes preferentially recognize phosphorylcholine (PC)-conjugated HEL over unconjugated HEL. To understand the mechanisms involved in this difference of T cell recognition, we have further analysed the reactivity of T cells and T cell hybridomas from low-responder C57BL/6 mice. T cells from HEL-immunized mice were preferentially reactive to HEL 47-60. These results suggest a potential deficiency in generating an appropriate T cell epitope from the 46-61 region of native HEL in low-responder C57BL/6 mice. The minimal T cell epitope of this region was defined as HEL 51-60 using the PCH4.1 T hybridoma clone. This minimal epitope represents a single amino acid shift from the minimal epitope of HEL high-responder C3H mice (HEL 52-61). Various peptides representing this region were synthesized with single alanine substitutions at each position. The residues at positions 51, 52, 53 and 57 of HEL appear to be involved in Ia binding and the residues at 55 and 56 in contracting the TCR. T cell reactivity to HEL 51-61 peptides with various substitutions at position 61 strongly suggest that primarily the size of the C-terminal residue interferes with binding to the Ia molecules of low-responder mice. In addition, substitutions of the TCR contacting residues at positions 55 and 56 with similar residues (isoleucine-->leucine or leucine-->isoleucine) significantly increased the T cell reactivity, suggesting a low reactivity with the native residues. Therefore, the requirement of many residues in the T cell epitope for interaction with Ia, the necessity for additional Ag processing to facilitate Ia binding, and the low affinity of the TCR contacting residues may together render C57BL/6 mice unresponsive to the HE 46-61 region.

Inhibition of class II MHC-peptide complex formation by protease inhibitors

Studies on the kinetics of antigenic peptide binding to major histocompatibility complex class II molecules have been used extensively to probe major histocompatibility complex (MHC) structure as well as to investigate the molecular mechanism of peptide recognition. Previous experiments have frequently been carried out in the presence of a cocktail of protease inhibitors to inhibit the proteolysis of MHC heterodimers. By using high performance size exclusion chromatography to measure fluorescent peptide binding to MHC protein, we have found that the addition of a commonly used mixture of protease inhibitors leads to a significant reduction in peptide binding to the class II heterodimer.

Analysis of MHC-presented peptides: applications in autoimmunity and vaccine development

T cells recognize antigenic peptides presented on the cell surface by major histocompatibility complex (MHC) molecules. Here, Roman Chicz and Robert Urban describe the features of peptides bound to MHC molecules and the mechanism by which these surface proteins bind diverse peptide ligands with high affinity. In addition, they discuss the application of new technologies to the identification of MHC-associated peptides.

Characterization of T-helper epitopes of the glycoprotein of vesicular stomatitis virus

The T-helper (Th) cell epitopes in the glycoprotein (GP) of vesicular stomatitis virus serotype Indiana (VSV-IND) were analyzed with a complete panel of overlapping synthetic peptides. Three Th-cell epitopes in C57BL/6 (H-2b) mice and two epitopes in BALB/c (H-2d) mice were defined by their ability to stimulate in vitro proliferation of virus-primed, CD8+ T-cell-depleted spleen cells in a class II-restricted manner. A series of CD4+, I-Ab-restricted T-cell hybridomas from VSV-primed C57BL/6 mice were characterized by their production of interleukin-2 and interleukin-3 upon stimulation with VSV-IND or purified VSV GP in vitro. Of nine hybridomas derived from three independent fusions, five were specific for amino acids (aa) 415 to 433 (p8) of VSV-IND GP, three recognized aa 52 to 71 (p41), and one reacted against aa 316 to 335 (p17). Fluorocytometric analysis of Th hybridomas or VSV-stimulated T-cell lines with monoclonal antibodies specific for the T-cell receptor V beta chain did not reveal obvious correlations between the T-cell receptor V beta gene segment used and the epitope recognized. All three peptides recognized by H-2b mice and both epitopes recognized by H-2d mice which were characterized in primed T-cell populations were capable of activating specific Th cells in vivo as measured by the induction of antibody class switch from immunoglobulin M (IgM) to IgG. Thus, the epitopes are relevant for VSV GP-specific Th response in vivo and are able to provide functional help for the production of anti-VSV-specific neutralizing IgG antibodies.

Formation and dissociation of short-lived class II MHC-peptide complexes

The incubation of a detergent-solubilized class II MHC protein with excess peptide at 37 degrees C leads to the formation of long-lived protein-peptide complexes (alpha beta P*), which have reported dissociation half-times at 37 degrees C from 30 to 100 h (alpha beta P*-->alpha beta + P*). Here we report an unexpected temperature effect on the reaction between class II MHC and added peptide. When the detergent-solubilized mouse class II MHC protein I-Ad is incubated with excess labeled peptide at 4 degrees C, a large fraction of the resultant complexes are relatively short-lived, with dissociation half-times at 40 degrees C from 2 to 0.2 h. Short-lived complexes formation and dissociation are both characterized by nonexponential kinetics. Short-lived I-A(d)-peptide complexes may contain two peptides, where the second, added fluorescent peptide is prevented from utilizing all the potential intermolecular interactions in the binding site due to the prior partial occupation of the binding site by a prebound peptide.

Determinant capture as a possible mechanism of protection afforded by major histocompatibility complex class II molecules in autoimmune disease

How peptide-major histocompatibility complex (MHC) class II complexes are naturally generated is still unknown, but accumulating evidence suggests that unfolding proteins or long peptides can become bound to class II molecules at the dominant determinant before proteolytic cleavage. We have compared the immunogenicity of hen egg-white lysozyme (HEL) in nonobese diabetic (NOD), (NOD x BALB/c)F1, and E(d) alpha transgenic NOD mice. We find that a response to the subdominant ANOD-restricted determinant disappears upon introduction of an E(d) molecule, and is restored when scission of HEL separates this determinant from its adjoining, competitively dominant, E(d)-restricted determinant. This suggests that the E(d) molecule binds and protects its dominant determinant on a long peptide while captured neighboring determinants are lost during proteolysis. These results provide clear evidence for "determinant capture" as a mechanism of determinant selection during antigen processing and a possible explanation for MHC-protective effects in insulin-dependent diabetes mellitus.

Enhancement of peptide antigen presentation by a second peptide

The influence of nonstimulatory "competitor" peptides on the binding of an antigenic peptide to a major histocompatibility complex (MHC) class II molecule was investigated. Using high-performance size-exclusion chromatography and fluorescein-labeled peptides, we show that the presence of the peptides dynorphin A-(1-13) and poly(L-lysine) results in enhancement rather than inhibition of the binding of hen egg lysozyme peptide-(107-116) [HEL-(107-116)] to the detergent-solubilized mouse class II molecule IEd. In parallel, dynorphin A-(1-13) and poly(L-lysine) were found to enhance the specific activation of an IEd-restricted T-cell hybridoma by HEL-(107-116). A molecular mechanism involving an intermediate two peptide-MHC class II protein complex is proposed to explain the enhancement of peptide binding to class II molecules by an irrelevant second peptide.

The involvement of antigen processing in determinant selection by class II MHC and its relationship to immunodominance

The T cell response in vivo to many whole proteins is focused on a limited number of possible determinants which can be termed immunodominant. Antigen processing for class II antigen presentation appears to play a major role in this selective process. With experimental evidence accumulated in our laboratory as well as others, we review several possible mechanisms involved in antigen processing responsible for selective or differential determinant expression. In particular, we discuss the determinant capture model in which MHC class II molecules initially capture large antigen fragments, such that bound determinants are protected from proteolysis by the MHC molecules and eventually become dominant while the flanking determinants are trimmed away. Such flanking determinants therefore become subdominant or cryptic. This mechanism underlies the capturing role of MHC molecules in the physiological processing of antigens.

The set of naturally processed peptides displayed by DR molecules is tuned by polymorphism of residue 86

The response to tetanus toxoid (TT) was studied in immune donors that carry two alleles of DR5 that differ only at DR beta residue 86: DRB1*1101 (G86, abbreviated 1101) and DRB1*1104 (V86, abbreviated 1104). A large number of TT-specific T cell clones was isolated and the epitopes recognized in association with 1101 and 1104 were mapped. We found that two epitopes (p2 and p32) can be recognized in association with both 1101 and 1104 while three epitopes (p23, p27 and p30) are recognized in association with 1101, but never in association with 1104. The sets of naturally processed self peptides displayed by 1101 and 1104 were characterized using alloreactive T cell clones. We found that all 1104 alloreactive clones recognize both 1104 and 1101, while approximately 30% of the alloreactive 1101 clones fail to recognize 1104. Thus it is apparent that both naturally processed TT and self peptides displayed on 1104 molecules represent a fraction of those displayed on 1101 molecules. The mechanism responsible for this differential presentation was investigated by comparing the capacity of 1101 and 1104 antigen-presenting cells to present TT or synthetic peptides to specific T cells and by measuring the binding of these peptides to DR molecules. Three sets of results suggest that V86 acts as a constraint to the binding of naturally processed peptides: (i) all 1104-restricted or alloreactive T cell clones recognize TT- or allo-epitopes presented by 1101 as well, thus ruling out a major effect of V86 as a residue determining T cell restriction specificity; (ii) presentation of naturally processed peptides correlates in general with the capacity of long synthetic peptides to bind to 1101 or 1104 and (iii) while the naturally processed p30 epitope discriminates between 1101 and 1104, a short synthetic peptide binds equally well to and is comparably recognized in association with both 1101 and 1104. Taken together these results suggest that the natural polymorphism at residue 86 might be a molecular switch that finely tunes the complexity of the peptide collection presented on DR molecules.