An HLA-binding-motif-aided peptide epitope library: a novel library design for the screening of HLA-DR4-restricted antigenic peptides recognized by CD4+T cells

Identification of human T-cell epitopes and highly immunogenic analog peptides on the non-typeable Haemophilus influenzae P6 outer membrane protein

P6 outer membrane protein is one of the candidates for a vaccine formulation against non-typeable Haemophilus influenzae (NTHi) infection. However, otitis-prone children who have recurrent episodes of acute otitis media due to NTHi fail to respond adequately to P6. An innovative approach to vaccination is therefore required to augment such children's immune response. To develop an effective peptide vaccine, we established P6-specific CD4(+) T-cell lines (TCLs) restricted by the human histocompatibility leukocyte antigen (HLA)-DR9 molecule, and revealed a human T-cell epitope on P6 and its core peptide sequence (p77-85; EYNIALGQR). Furthermore, we found that 3 analog peptides, E77D (the substitution of E at position 77 with D), N79G, and R85K, induced high proliferative responses as well as marked cytokine production when compared to the T-cell epitope peptide. These peptides may be candidates for a peptide vaccine formulation effective against NTHi infections, even in otitis-prone children.

Model-fitting and linkage analysis of sodium–lithium countertransport

Increased sodium-lithium countertransport activity (SLC) associates with hypertension and is highly heritable, yet the underlying genes remain unknown. SLC, measured on 1113 and remeasured 2-3 years later on 675 adult members of 48 Utah pedigrees, was tested for candidate gene association, major locus inheritance, and linkage to genome scan markers using a bivariate model with genotype-specific effects of age, body mass index (BMI), and triglycerides level (TG). No effect of the alpha-adducin Gly460Trp polymorphism on SLC was found. In contrast, SLC increased with age in carriers of apolipoproteinE varepsilon2 (85 individuals; 8.7% of the sample) and decreased in noncarriers. Model-fitting analyses inferred two additional loci with genotype-specific responses to BMI and TG. Using the inferred model, lod scores >2 were obtained for D3S3038, D11S4464, and D10S677 for the BMI-responsive locus, and for D8S1048 for the TG-responsive locus.

A simple screening method for detecting bindings between oligopeptides and HLA-DR molecules on filter papers: possible application for mapping of putative helper T-cell epitopes on MSP1 of Plasmodium falciparum

Binding capacities of synthetic peptides to HLA-DR molecules were tested on filter papers to identify putative helper T-cell epitopes on a malarial protein. The antigen tested was the merozoite surface glycoprotein 1 (MSP1) of Plasmodium falciparum, a vaccine candidate targeting the asexual erythrocytic stage. Bindings between synthetic oligopeptides and HLA-DR molecules were tested. Such bindings were not non-specific, and a known helper T-cell epitope peptide showed positive binding to the restricting HLA-DR molecule. By using this screening system, we observed the unequal distribution of HLA-DR-binding peptides in 10 out of 17 MSP1 blocks tested. Block #6 of MSP1 seemed to show the highest frequency in the positive binding; on the other hand, blocks #1 and #17, both of which were thought to be vaccine candidate regions, contained fewer HLA-DR binding peptides. This was not inconsistent with the results that block #17 was less stimulatory to peripheral T cells than block #6. The peptides with positive binding to HLA-DR showed actual epitope activities when we tested peptide-driven proliferation of human bulk T-cell lines, and association between the two parameters was statistically significant (P<0.001). For more detailed information for vaccine development, peptides with both IgG- and HLA-DR binding activities were mapped in block #17 of MSP1. Together with these results, we demonstrate that our simple screening system seems to provide essential information for vaccine development through uncovering locations of putative epitopes for human helper T cells.

Identification of T cell ligands in a library of peptides covalently attached to HLA-DR4

While T cells have been clearly implicated in a number of disease processes including autoimmunity, graft rejection, and atypical immune responses, the precise Ags recognized by the pathogenic T cells have often been difficult to identify. This has particularly been true for MHC class II-restricted CD4+ T cells. Although such cells can be demonstrated to have undergone clonal expansion at sites of pathology, they are frequently difficult to establish as stable T cell clones. Furthermore, in general, larger peptides in higher concentrations are required to stimulate CD4+ T cells than CD8+ T cells, which makes some of the techniques developed to identify CD8+ T cell Ags impractical. To circumvent some of these problems, we developed a model system consisting of two parts. The first part involves the construction of an indicator T cell hybridoma expressing a chimeric TCR comprised of murine constant regions and human variable regions specific for influenza hemagglutinin 307-319 presented by DR4. The second part consists of a library of fibroblasts each expressing multiple peptides as amino terminal covalent extensions of the beta-chain of HLA-DR4 (DRA1*0101, DRB1*0401). Using this model system, we screened approximately 100, 000 peptides and identified three novel peptides stimulatory for the HA1.7 TCR. While there is some convergence at residues known to be important for T cell recognition, all three peptides differ markedly from each other and bear little resemblance to wild-type hemagglutinin 307-319.

Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide

In our model system, we generated T cell clones specific for the HLA-DR4 (DRB1*0405)-index peptide (YWALEAAAD) complex. Based on response patterns of the T cell clones, analogue peptides containing single amino acid substitutions of the index peptide were classified into three types, agonists, antagonists or null peptides (non-agonistic and non-antagonistic peptides). Subtle structural changes induced by the antagonists in the T-cell receptor (TCR) binding regions have already been explained using the root mean square (r.m.s.) deviations from the DR4-index peptide complex in the molecular dynamics (MD) trajectory. In this work, we performed additional MD simulations at 300 K with explicit solvent molecules to reveal the structural character of the HLA-DR4 complexed with the analogue peptides. We examined the r.m.s. deviations of the TCR-binding sites and the exposed areas of the bound peptides. Remarkable differences of the r.m.s. deviations among the DR4-antagonist complexes, together with our previous data, suggest that the magnitude of structural changes of TCR-binding regions would determine the strength of TCR antagonism. The simulations also indicate that TCR could discriminate null peptides from other ligands mainly through the changes of exposed side chains of the bound peptide, rather than the conformational changes of TCR-binding surfaces on HLA molecule.

Quantitative analysis of peptide-MHC class II interaction

The tremendous progress in the field of basic immunology and immunochemistry made in the last decade has significantly advanced our understanding of antigen processing and presentation by MHC class I and II proteins. In this review different techniques to study peptide interaction with MHC class II molecules are summarized and their impact on the elucidation of quantitative parameters, like affinities or kinetic data, is discussed. A recently introduced method based on synthetic combinatorial peptide libraries allows to quantify the binding contribution of each amino acid residue in a class II ligand and is presented in more detail. As this knowledge is fundamental for current investigations in modern medicine, e.g. for novel immune system based therapy concepts, further aspects like the design of new high affinity MHC class II ligands and the prediction of peptide antigens are discussed.

Physico-chemical and biological analysis of true combinatorial libraries

Combinatorial libraries offer new sources of compounds for the research of pharmacological agents such as receptor ligands, enzyme inhibitors or substrates and antibody-binding epitopes. The present review stresses the main roles played by both physico-chemical analysis, particularly when complex mixture of compounds are synthesized as libraries, and biological analysis from which active compounds are identified. After a brief discussion of semantic problems related to the designation of the product mixtures, the physico-chemical analysis of mixtures is reviewed with special emphasis on mass spectrometric techniques. These methods are able both to give a representative view of a library composition and to identify single critical compounds in large libraries. Then the biological screening of such combinatorial libraries is critically discussed with respect to the power and limitations of the methods used for the identification of the active components. Special attention is given to the complex process of library deconvolution. It is pointed out that while combinatorial techniques have evolved towards sophisticated high-tech methods, simple and robust biochemical tests should be used to deconvolute. From a large panel of published examples, a set of trends are identified which should help investigators to choose the most appropriate assay for the discovery of new entities.