Hindering auxiliary anchors are potent modulators of peptide binding and selection by I-Ak class II molecules

Predicting reverse-bound peptide conformations in MHC Class II with PANDORA

Recent discoveries have transformed our understanding of peptide binding in Major Histocompatibility Complex (MHC) molecules, showing that peptides, for some MHC class II alleles, can bind in a reverse orientation (C-terminus to N-terminus) and can still effectively activate CD4+ T cells. These finding challenges established concepts of immune recognition and suggests new pathways for therapeutic intervention, such as vaccine design. We present an updated version of PANDORA, which, to the best of our knowledge, is the first tool capable of modeling reversed-bound peptides. Modeling these peptides presents a unique challenge due to the limited structural data available for these orientations in existing databases. PANDORA has overcome this challenge through integrative modeling using algorithmically reversed peptides as templates. We have validated the new PANDORA feature through two targeted experiments, achieving an average backbone binding-core L-RMSD value of 0.63 Å. Notably, it maintained low RMSD values even when using templates from different alleles and peptide sequences. Our results suggest that PANDORA will be an invaluable resource for the immunology community, aiding in the development of targeted immunotherapies and vaccine design.

The Molecular and Functional Characteristics of HLA-G and the Interaction with Its Receptors: Where to Intervene for Cancer Immunotherapy?

Human leukocyte antigen G (HLA-G) mediates maternal-fetal immune tolerance. It is also considered an immune checkpoint in cancer since it may mediate immune evasion and thus promote tumor growth. HLA-G is, therefore, a potential target for immunotherapy. However, existing monoclonal antibodies directed against HLA-G lack sufficient specificity and are not suitable for immune checkpoint inhibition in a clinical setting. For this reason, it is essential that alternative approaches are explored to block the interaction between HLA-G and its receptors. In this review, we discuss the structure and peptide presentation of HLA-G, and its interaction with the receptors Ig-like transcript (ILT) 2, ILT4, and Killer cell immunoglobulin-like receptor 2DL4 (KIR2DL4). Based on our findings, we propose three alternative strategies to block the interaction between HLA-G and its receptors in cancer immunotherapy: (1) prevention of HLA-G dimerization, (2) targeting the peptide-binding groove of HLA-G, and (3) targeting the HLA-G receptors. These strategies should be an important focus of future studies that aim to develop immune checkpoint inhibitors to block the interaction between HLA-G and its receptors for the treatment of cancer.

Predicting peptides bound to I-Ag7 class II histocompatibility molecules using a novel expectation-maximization alignment algorithm

The useful structural features of class II MHC molecules are rarely integrated into T-cell epitope predictions. We propose an approach that applies a novel expectation-maximization algorithm to align the naturally processed peptides selected by the class II MHC I-A(g7) molecule - focusing on the five MHC-specific anchor positions. Based on the alignment profile, log of odds (LOD) scores supplemented with the Laplace plus-one pseudocounts method are applied to identify the potential T-cell epitopes. In addition, an innovative computational concept of hindering residues using statistical and structural information is developed to refine the prediction. Performance analysis by receiver operating characteristics statistics and the experimental validation of the LOD scores demonstrate the accuracy of our predictive model. Furthermore, our model successfully predicts T-cell epitopes of hen egg-white lysozyme protein antigen. Our study provides a framework for predicting T-cell epitopes in class II MHC molecules.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide-MHC binding affinity. The ISC-PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide-MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms--q2, SEP, and NC--ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

Identification of naturally processed peptides bound to the class I MHC molecule H-2Kd of normal and TAP-deficient cells

This report details the biochemical features of natural peptides selected by the H-2Kd class I MHC molecule. In normal cell lines, the length of the naturally processed peptides ranged from 8 to 18 amino acids, although the majority were 9-mers (16% were longer than nine residues). The binding motif for the 9-mer peptides was dominated by the presence of a tyrosine at P2 and an isoleucine/leucine at the P9 position. The P2 residue contributed most towards binding; and the short peptides bound better and formed longer-lived cell surface complexes than the long peptides, which bound poorly and dissociated rapidly. The longer peptides did not exhibit this strictly defined motif. Trimming the long peptides to their shorter forms did not enhance binding and conversely, extending the 9-mer peptides did not decrease binding. The long peptides were present on the cell-surface bound to H-2Kd (Kd) and were not intermediate products of the class I MHC processing pathway. Finally, in two different TAP-deficient cells the long peptides were the dominant species, which suggested that TAP-independent pathways selected for long peptides by class I MHC molecules.

Generation of functional HLA-DR*1101 tetramers receptive for loading with pathogen- or tumour-derived synthetic peptides

BACKGROUND

MHC class I-peptide tetramers are currently utilised to characterize CD8+ T cell responses at single cell level. The generation and use of MHC class II tetramers to study antigen-specific CD4+ T cells appears less straightforward. Most MHC class II tetramers are produced with a homogeneously built-in peptide, reducing greatly their flexibility of use. We attempted the generation of "empty" functional HLA-DR*1101 tetramers, receptive for loading with synthetic peptides by incubation. No such reagent is in fact available for this HLA-DR allele, one of the most frequent in the Caucasian population.

RESULTS

We compared soluble MHC class II-immunoglobulin fusion proteins (HLA-DR*1101-Ig) with soluble MHC class II protein fused with an optimised Bir site for enzymatic biotynilation (HLA-DR*1101-Bir), both produced in insect cells. The molecules were multimerised by binding fluorochrome-protein A or fluorochrome-streptavidin, respectively. We find that HLA-DR*1101-Bir molecules are superior to the HLA-DR*1101-Ig ones both in biochemical and functional terms. HLA-DR*1101-Bir molecules can be pulsed with at least three different promiscuous peptide epitopes, derived from Tetanus Toxoid, influenza HA and the tumour associated antigen MAGE-3 respectively, to stain specific CD4+ T cells. Both staining temperature and activation state of CD4+ T cells are critical for the binding of peptide-pulsed HLA-DR*1101-Bir to the cognate TCR.

CONCLUSION

It is therefore possible to generate a soluble recombinant HLA-DR*1101 backbone that is receptive for loading with different peptides to stain specific CD4+ T cells. As shown for other HLA-DR alleles, we confirm that not all the strategies to produce soluble HLA-DR*1101 multimers are equivalent.

Conformational isomers of a peptide-class II major histocompatibility complex

The relative plasticity of peptide binding to class II major histocompatibility complex (MHC) molecules permits formation of multiple conformational isomers by the same peptide and MHC molecule; such conformers are specifically recognized by distinct subsets of T cells. Here, we review current knowledge and recent advances in our understanding of peptide-class II MHC conformational isomerism and the mechanisms that generate distinct MHC-peptide conformers. We focus on our studies of two T-cell subsets, type A and B, which recognize distinct conformers of the dominant epitope of hen egg white lysozyme presented by I-A(k). These conformers form via different pathways and in distinct intracellular vesicles: the type A conformer forms in late endosomes upon processing of native protein, while the more flexible type B conformer forms in early endosomes and at the cell surface. In this process, H2-DM acts as a conformational editor, eliminating the type B conformer in late endosomes. Type B T cells constitute a significant component of the naïve T-cell repertoire; furthermore, self-reactive type B T cells escape negative selection and are present in abundance in the periphery. Ongoing studies should elucidate the role of type B T cells in immunity to pathogens and in autoimmune pathology.

T Cells Distinguish MHC-Peptide Complexes Formed in Separate Vesicles and Edited by H2-DM

The peptide spanning residues 48-61 of hen egg white lysozyme (HEL) presented by I-A(k) gives rise to two T cell populations, referred to as type A and B, that distinguish the complex generated intracellularly upon processing of HEL from that formed with exogenous peptide. Here, we ascribe this difference to recognition of distinct conformers of the complex and show that formation of the two complexes results from antigen processing in different intracellular compartments and is dependent upon H2-DM. While the type A complex preferentially formed in a lysosome-like late vesicle, the type B complex failed to form in this compartment; this distinction was abolished in antigen-presenting cells lacking DM. Experiments in vitro indicated that H2-DM acts directly on the complex to eliminate the type B conformation. We conclude that different antigen-processing pathways generate distinct MHC-peptide conformers, priming T cells with distinct specificity that may play unique roles in immunity.

Cutting edge: TCR contacts as anchors: effects on affinity and HLA-DM stability

Peptides presented via the class II MHC (MHCII) pathway are selected based on affinity for MHCII and stability in the presence of HLA-DM. Currently, epitope selection is thought to be controlled by the ability of peptide to sequester "anchor" residues into pockets in the MHCII. Residues exhibiting higher levels of solvent accessibility have been shown to contact TCR, but their roles in affinity and complex stability have not been directly studied. Using the HLA-DR1-binding influenza peptide, hemagglutinin (306-318), as a model, we show that side chain substitutions at these positions influence affinity and HLA-DM stability. Multiple substitutions reduce affinity to a greater extent than the loss of the major P1 anchor residue. We propose that these effects may be mediated through the H-bond network. These results demonstrate the importance of solvent-exposed residues in epitope selection and blur the distinctions between anchor and TCR contact residues.

Specificity of peptide selection by antigen-presenting cells homozygous or heterozygous for expression of class II MHC molecules: The lack of competition

We isolated and identified naturally processed peptides selected by antigen-presenting cells homozygous for expression of I-A(g7) or I-A(d) class II MHC molecules, or from heterozygous antigen-presenting cells that express I-A(g7) along with I-A(g7PD) or I-A(d). Identification of large numbers of peptides demonstrated that despite being closely related on a structural level, each class II MHC molecule selected for very unique peptides. The large data sets allowed us to definitively establish the preferred peptide-binding motifs critical for selection of peptides by I-A(g7), I-A(g7PD), and I-A(d). Finally, extensive analyses of peptide families reveals that there was little competition among class II MHC alleles for display of peptides and that presence of one allele had minimal impact on the repertoire of peptides selected by another.

Chemical identification of a low abundance lysozyme peptide family bound to I-Ak histocompatibility molecules

The processing by antigen-presenting cells (APC) of the protein hen egg-white lysozyme (HEL) results in the selection of a number of peptide families by the class II major histocompatibility complex (MHC) molecule, I-A(k). Some of these families are expressed in very small amounts, in the order of a few picomoles/10(9) APC. We detected these peptides from an extract of class II MHC molecules by using monoclonal anti-peptide antibodies to capture the MHC-bound peptides prior to their examination by HPLC tandem mass spectrometry. Here, we have identified several members of a family of peptides encompassing residues 20-35, which represent less than 1% of the total HEL peptides. Binding analysis indicated that the core segment of the family was represented by residues 24-32 (SLGNWVCAA). Asn-27 (shown in boldface) is the main MHC-binding residue, mapped as interacting with the P4 pocket of the I-A(k) molecule. Analysis of several T cell hybridomas indicated that three residues contacted the T cell receptor: Tyr-23 (P-1), Leu-25 (P3), and Trp-28 (P5). The HEL peptides isolated from the APC extract were sulfated on Tyr-23, but further analysis showed that this modification did not occur physiologically but took place during the peptide isolation.

Perspective on antigen processing and presentation

The phenomenon of antigen processing and presentation and the concept that T cells recognize peptides resulting from the partial catabolism of proteins, are relatively new. These concepts were first recognized and developed at a time when lymphocyte immunity - the adaptive system - and cellular immunity, with its major component of activated macrophages, were not perceived as part of one integrated system. To me, it was the fundamental findings on the role of major histocompatibility (MHC) molecules that set the framework for understanding how phagocytes and the antigen presenting cell (APC) system interact with the adaptive cellular system, in a truly symbiotic relationship (1). In this chapter we make a historical review of the developments that, in my biased opinion, led to the understanding of antigen presentation as a central event. I emphasize my own work, placing it in my perspective of how I saw the field moving.

Distinct recognition by two subsets of T cells of an MHC class II-peptide complex

We examine here the nature of the differential recognition by CD4+ T cells of a single peptide from hen-egg white lysozyme (HEL) presented by I-A(k) class II MHC molecules. Two subsets of T cells (called A and B) interact with the same peptide, each in unique ways that reflect the nature of the complex of peptide and MHC. We show that the A and B set of T cells can be distinguished by their functional interaction with the three T cell receptor (TCR) contact residues of the bound peptide. The dominant peptide of HEL selected from processing is bound in a single register where a critical TCR contact residue is situated about the middle of the core segment of the peptide: all T cells establish functional contact with it. Three sets of T cells, however, can be distinguished by their differential recognition of two TCR contacts situated at the amino and carboxyl sides of the central TCR contact residue. Type A T cells, the conventional cells that see the peptide after processing of HEL, need to recognize all three TCR contact residues. In contrast, the type B T cells recognize the peptide given exogenously, but not when processed: these T cells recognize either one of the peripheral TCR contact residues, indicating a much more flexible interaction of peptide with I-A(k) molecules. We discuss the mode of generation of the various T cells and their biological relevance.

The level of peptide-MHC complex determines the susceptibility to autoimmune diabetes: studies in HEL transgenic mice

We report a mouse model for the spontaneous development of autoimmune diabetes: the 3A9 T cell receptor (TCR) transgenic mouse, which contains T cells that recognize the 52 - 61 family of hen egg-white lysozyme (HEL) peptides in the context of MHC class II I-A(k) molecules, was bred to the ILK3 mouse, that expresses HEL protein via the rat insulin promoter (RIP). Despite partial tolerance of 3A9 T cells in ILK3 mice, spontaneous diabetes developed in 64 % of 3A9xILK3 mice by 20 weeks of age. We provide evidence that APC from peri-pancreatic nodes have a large content of peptide-MHC complex and stimulate 3A9 T cells. We also report that cross presentation of HEL from beta cells to APC is 26-fold more efficient than presentation of soluble HEL. We previously reported on a biochemical margin of safety, based on the observation that activation of naive 3A9 T cells required 100-fold more peptide-MHC complexes than required for deletion of 3A9 thymocytes. We speculate that the high local density of autologous peptide-MHC complexes can be a determining factor that leads to the activation of autoreactive CD4 T cells and, consequently, to the development of autoimmunity.

Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes

The class II major histocompatibility complex (MHC) glycoproteins HLA-DQ8 and HLA-DQ2 in humans and I-A(g7) in nonobese diabetic (NOD) mice are the major risk factors for increased susceptibility to type 1 diabetes. Using X-ray crystallography, we have determined the three-dimensional structure of DQ8 complexed with an immunodominant peptide from insulin. The similarity of the DQ8, DQ2 and I-A(g7) peptide-binding pockets suggests that diabetes is caused by the same antigen-presentation event(s) in humans and NOD mice. Correlating type 1 diabetes epidemiology and MHC sequences with the DQ8 structure suggests that other structural features of the P9 pocket in addition to position 57 contribute to susceptibility to type 1 diabetes.

T cell recognition of the dominant I-A(k)-restricted hen egg lysozyme epitope: critical role for asparagine deamidation

Type-B T cells raised against the immunodominant peptide in hen egg lysozyme (HEL(48-62)) do not respond to whole lysozyme, and this has been thought to indicate that peptide can bind to l-A(k) in different conformations. Here we demonstrate that such T cells recognize a deamidated form of the HEL peptide and not the native peptide. The sequence of the HEL epitope facilitates rapid and spontaneous deamidation when present as a free peptide or within a flexible domain. However, this deamidated epitope is not created within intact lysozyme, most likely because it resides in a highly structured part of the protein. These findings argue against the existence of multiple conformations of the same peptide-MHC complex and have important implications for the design of peptide-based vaccines. Furthermore, as the type-B T cells are known to selectively evade induction of tolerance when HEL is expressed as a transgene, these results suggest that recognition of posttranslationally modified self-antigen may play a role in autoimmunity.

Quantitation of lysozyme peptides bound to class II MHC molecules indicates very large differences in levels of presentation

Knowing the abundance of peptides presented by MHC molecules is a crucial aspect for understanding T cell activation and tolerance. In this report we determined the relative abundance of four distinct peptide families after the processing of the model Ag hen egg-white lysozyme. The development of a sensitive immunochemical approach reported here made it possible to directly quantitate the abundance of these four epitopes presented by APCs, both in vitro and in vivo. We observed a wide range of presentation among these four different epitopes presented on the surface of APCs, with 250-fold differences or more between the most abundant epitope (48-63) and the least abundant epitopes. Importantly, we observe similar ratios of presentation from APCs in vitro as well as from APCs from the spleens and thymi of hen egg-white lysozyme transgenic mice. We discuss the relationship between the amount of peptide presented and their binding to I-A(k) molecules, immunogenicity, and tolerogenicity.