Major histocompatibility complex (MHC) class I multimer technology has become an indispensable immunological assay system to dissect antigen-specific cytotoxic CD8 ؉ T cell responses by flow cytometry. However, the development of high-throughput assay systems, in which T cell responses against a multitude of epitopes are analyzed, has been precluded by the fact that for each T cell epitope, a separate in vitro MHC refolding reaction is required. We have recently demonstrated that conditional ligands that disintegrate upon exposure to long-wavelength UV light can be designed for the human MHC molecule HLA-A2. To determine whether this peptide-exchange technology can be developed into a generally applicable approach for high throughput MHC based applications we set out to design conditional ligands for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Here, we describe the development and characterization of conditional ligands for this set of human MHC molecules and apply the peptide-exchange technology to identify melanoma-associated peptides that bind to HLA-A3 with high affinity. The conditional ligand technology developed here will allow high-throughput MHC-based analysis of cytotoxic T cell immunity in the vast majority of Western European individuals.M HC Class I molecules are heterotrimeric complexes consisting of an invariant light chain called ␤2-microglobulin (␤2m), a polymorphic heavy chain (HC) and an Ϸ8-to 11-aa peptide ligand. These peptide-MHC (pMHC) complexes are recognized by the T cell receptor (TCR) of CD8 ϩ T cells in a peptide-specific fashion, and this interaction forms the molecular basis of antigen recognition by CD8 ϩ T cells. In the past decade, the mapping of pathogen-specific and autoimmune-or cancer-associated T cell epitopes has been a major driving force in the development of assay systems for immunomonitoring. In addition, knowledge of such T cell epitopes forms a cornerstone in the development of vaccine-based or adoptive T cell therapies. As a first step in the mapping of disease-associated T cell epitopes, peptide fragments of disease-associated proteomes may be analyzed for binding to MHC molecules of interest, and subsequent assays can then be used to determine whether T cell reactivity against such pMHC complexes does occur. As demonstrated in a landmark study by Altman and colleagues (1), such antigen-specific T cell reactivity can efficiently be detected by the staining of T cell populations with recombinant fluorescent multimeric MHC molecules.There is an increasing interest in the development of assay systems, such as MHC-based microarrays, that can monitor a multitude of T cell responses in parallel (2-4). Unfortunately, current technology does not allow for the high-throughput generation of different pMHC complexes, thereby limiting the utility of these techniques. Specifically, because MHC class I complexes that are devoid of peptide are markedly unstable (5, 6), current production processes for recombinant MHC complexes require inclusion of a specific T cell epi...

MHC class I molecules present a variable but limited repertoire of antigenic peptides for T-cell recognition. Understanding how peptide selection is achieved requires mechanistic insights into the interactions between the MHC I and candidate peptides. We find that, at first encounter, MHC I H-2K b considers a wide range of peptides, including those with expanded N termini and unfitting anchor residues. Discrimination occurs in the second step, when noncanonical peptides dissociate with faster exchange rates. This second step exhibits remarkable temperature sensitivity, as illustrated by numerous noncanonical peptides presented by H-2K b in cells cultured at 26°C relative to 37°C. Crystallographic analyses of H-2K b -peptide complexes suggest that a conformational adaptation of H-2K b drives the decisive step in peptide selection. We propose that MHC class I molecules consider initially a large peptide pool, subsequently refined by a temperature-sensitive induced-fit mechanism to retain the canonical peptide repertoire.antigen presentation | peptide binding | anchor residues | dynamics | entropy M HC class I molecules present a wide array of peptides to cytotoxic T lymphocytes, allowing the immune system to scan for intracellular pathogens and mutated proteins. These peptides are not chosen at random, but rather are selected for their ability to bind to the polymorphic MHC class I peptidebinding groove. Antigenic peptide precursors are produced by the proteasome and further trimmed by cytosolic aminopeptidases. They are translocated into the endoplasmic reticulum (ER) lumen by the peptide transporter TAP that has broad peptide specificity. Peptides can be further trimmed in the ER lumen by ER aminopeptidases before selection by a defined MHC class I allele (reviewed in ref. 1). Only few peptides from a broad peptidome are presented by a given MHC class I allele. How a defined MHC I allele selects the correct peptides for presentation out of a large and diverse peptide pool is unclear.In principle, MHC class I molecules could consider only "optimal" peptides and ignore the remainder of the TAPtranslocated peptidome. Alternatively, MHC class I could bind all available peptides followed by a selection step for the optimal candidates for presentation. To discriminate between these scenarios, we studied peptide association (on-rates) and dissociation (off-rates) from the mouse MHC class I molecule H-2K b . To characterize the biophysical basis of discrimination between candidate peptides we complemented the kinetic data with five crystal structures of H-2K b with peptide variants. A comprehensive analysis of our in vitro data indicated that discrimination against suboptimal peptides by MHC class I may exhibit a strong temperature dependency, as illustrated by the H-2K b peptidome from cells cultured at 26°C versus 37°C. We thus arrive at a two-step model for peptide selection by MHC class I molecules, which explains how not so "empty MHC class I molecules come out in the cold" (2).

Virus or tumor Ag–derived peptides that are displayed by MHC class I molecules are attractive starting points for vaccine development because they induce strong protective and therapeutic cytotoxic T cell responses. In thus study, we show that the MHC binding and consequent T cell reactivity against several HLA-A*02 restricted epitopes can be further improved through the incorporation of nonproteogenic amino acids at primary and secondary anchor positions. We screened more than 90 nonproteogenic, synthetic amino acids through a range of epitopes and tested more than 3000 chemically enhanced altered peptide ligands (CPLs) for binding affinity to HLA-A*0201. With this approach, we designed CPLs of viral epitopes, of melanoma-associated Ags, and of the minor histocompatibility Ag UTA2-1, which is currently being evaluated for its antileukemic activity in clinical dendritic cell vaccination trials. The crystal structure of one of the CPLs in complex with HLA-A*0201 revealed the molecular interactions likely responsible for improved binding. The best CPLs displayed enhanced affinity for MHC, increasing MHC stability and prolonging recognition by Ag-specific T cells and, most importantly, they induced accelerated expansion of antitumor T cell frequencies in vitro and in vivo as compared with the native epitope. Eventually, we were able to construct a toolbox of preferred nonproteogenic residues with which practically any given HLA-A*02 restricted epitope can be readily optimized. These CPLs could improve the therapeutic outcome of vaccination strategies or can be used for ex vivo enrichment and faster expansion of Ag-specific T cells for transfer into patients.

T cells are essential players in the defense against infection. By targeting the MHC class I antigen-presenting pathway with peptide-based vaccines, antigen-specific T cells can be induced. However, low immunogenicity of peptides poses a challenge. Here, we set out to increase immunogenicity of influenza-specific CD8+ T cell epitopes. By substituting amino acids in wild type sequences with non-proteogenic amino acids, affinity for MHC can be increased, which may ultimately enhance cytotoxic CD8+ T cell responses. Since preventive vaccines against viruses should induce a broad immune response, we used this method to optimize influenza-specific epitopes of varying dominance. For this purpose, HLA-A*0201 epitopes GILGFVFTL, FMYSDFHFI and NMLSTVLGV were selected in order of decreasing MHC-affinity and dominance. For all epitopes, we designed chemically enhanced altered peptide ligands (CPLs) that exhibited greater binding affinity than their WT counterparts; even binding scores of the high affinity GILGFVFTL epitope could be improved. When HLA-A*0201 transgenic mice were vaccinated with selected CPLs, at least 2 out of 4 CPLs of each epitope showed an increase in IFN-γ responses of splenocytes. Moreover, modification of the low affinity epitope NMLSTVLGV led to an increase in the number of mice that responded. By optimizing three additional influenza epitopes specific for HLA-A*0301, we show that this strategy can be extended to other alleles. Thus, enhancing binding affinity of peptides provides a valuable tool to improve the immunogenicity and range of preventive T cell-targeted peptide vaccines.

Incorporation of cleavable linkers into peptides and proteins is of particular value in the study of biological processes. Here we describe the synthesis of a cleavable linker that is hypersensitive to oxidative cleavage as the result of the periodate reactivity of a vicinal amino alcohol moiety. Two strategies directed towards the synthesis of a building block suitable for solid-phase peptide synthesis were developed: a chemoenzymatic route, involving l-threonine aldolase, and an enantioselective chemical route; these led to α,γ-diamino-β-hydroxybutanoic acids in diastereoisomerically mixed and enantiopure forms, respectively. Incorporation of the 1,2-amino alcohol linker into the backbone of a peptide generated a conditional peptide that was rapidly cleaved at very low concentrations of sodium periodate. This cleavable peptide ligand was applied in the generation of MHC exchange reagents for the detection of antigen-specific T cells in peripheral blood cells. The extremely low concentration of periodate required to trigger MHC peptide exchange allowed the co-oxidation of methionine and disulfide residues to be avoided. Conditional MHC reagents hypersensitive to periodate can now be applied without limitations when UV irradiation is undesired or less practical.