Molecular basis for degenerate T-cell recognition of one peptide in the context of several DR molecules

A human CD4+ T cell epitope in the influenza hemagglutinin is cross-reactive to influenza A virus subtypes and to influenza B virus

The hemagglutinin protein (HA) of the influenza virus family is a major antigen for protective immunity. Thus, it is a relevant target for developing vaccines. Here, we describe a human CD4(+) T cell epitope in the influenza virus HA that lies in the fusion peptide of the HA. This epitope is well conserved in all 16 subtypes of the HA protein of influenza A virus and the HA protein of influenza B virus. By stimulating peripheral blood mononuclear cells (PBMCs) from a healthy adult donor with peptides covering the entire HA protein based on the sequence of A/Japan/305/1957 (H2N2), we generated a T cell line specific to this epitope. This CD4(+) T cell line recognizes target cells infected with influenza A virus seasonal H1N1 and H3N2 strains, a reassortant H2N1 strain, the 2009 pandemic H1N1 strain, and influenza B virus in cytotoxicity assays and intracellular-cytokine-staining assays. It also lysed target cells infected with avian H5N1 virus. We screened healthy adult PBMCs for T cell responses specific to this epitope and found individuals who had ex vivo gamma interferon (IFN-γ) responses to the peptide epitope in enzyme-linked immunospot (ELISPOT) assays. Almost all donors who responded to the epitope had the HLA-DRB1*09 allele, a relatively common HLA allele. Although natural infection or standard vaccination may not induce strong T and B cell responses to this highly conserved epitope in the fusion peptide, it may be possible to develop a vaccination strategy to induce these CD4(+) T cells, which are cross-reactive to both influenza A and B viruses.

DRB1*12:01 presents a unique subset of epitopes by preferring aromatics in pocket 9

This study characterized the unique peptide-binding characteristics of HLA-DRB1*12:01 (DR1201), an allele studied in the context of various autoimmune diseases, using a peptide competition assay and structural modeling. After defining Influenza A/Puerto Rico/8/34 Matrix Protein M1 (H1MP) 40-54 as a DR1201 restricted epitope, the critical anchor residues within this sequence were confirmed by measuring the relative binding of peptides with non-conservative substitutions in competition with biotin labeled H1MP(40-54) peptide. Based on this information, a set of peptides was designed with single amino acid substitutions at these anchor positions. The overall peptide binding preferences for the DR1201 allele were deduced by incubating these peptides in competition with the reference H1MP(40-54) to determine the relative binding affinities of each to recombinant DR1201 protein. As expected, pocket 1 preferred methionine and aliphatic residues, and tolerated phenylalanine. Pocket 4 was mostly composed of hydrophobic residues, thereby preferentially accommodating aliphatic residues, but could also weakly accommodate lysine due to its slightly acidic environment. Pocket 6 accepted a wide range of amino acids because of the diverse residues that comprise this pocket. Pocket 9 accepted aliphatic and negatively charged amino acids, but showed a remarkable preference for aromatic residues due to the conformation of the pocket, which lacks the typical salt bridge between β57Asp and α76Arg. These binding characteristics contrast with the closely related DR1104 allele, distinguishing DR1201 among the alleles of the HLA-DR5 group. These empirical results were used to develop an algorithm to predict peptide binding to DR1201. This algorithm was used to verify T cell epitopes within novel antigenic peptides identified by tetramer staining and within peptides from published reports that contain putative DR1201 epitopes.

Reverse immunogenetic and polyepitopic approaches for the induction of cell-mediated immunity against bovine viral pathogens

The control of several infectious diseases of animals by vaccination is perhaps the most outstanding accomplishment of veterinary medicine in the last century. Even the eradication of some pathogens is in sight, at least in some parts of the world. However, infectious diseases continue to cost millions of dollars to the livestock industry. One of the reasons for the failure to control certain pathogens is the limited emphasis placed on cell-mediated immunity (CMI) in the design of vaccines against these pathogens. Traditionally, vaccine-induced immunity has been studied in relation to antibody-mediated protection. More recent studies, however, have focused on understanding CMI and developing means of inducing CMI. This review focuses on recent advances made in the study of CMI in general and of cytotoxic T lymphocytes in particular. Parallels from studies in human and mouse immunology are drawn in order to point out implications to bovine immunology, specifically for immunity against bovine herpesvirus 1.

Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1

An alphabeta T-cell receptor (alphabetaTCR)/hemagglutinin (HA) peptide/human leukocyte antigen (HLA)-DR1 complex was stabilized by flexibly linking the HA peptide with the human HA1.7 alphabetaTCR, to increase the local concentration of the interacting proteins once the peptide has been loaded onto the major histocompatibility complex (MHC) molecule. The structure of the complex, determined by X-ray crystallography, has a binding mode similar to that of the human B7 alphabetaTCR on a pMHCI molecule. Twelve of the 15 MHC residues contacted are at the same positions observed earlier in class I MHC/peptide/TCR complexes. One contact, to an MHC loop outside the peptide-binding site, is conserved and specific to pMHCII complexes. TCR gene usage in the response to HA/HLA-DR appears to conserve charged interactions between three lysines of the peptide and acidic residues on the TCR.

Identification of CD4+ T cell epitopes from NY-ESO-1 presented by HLA-DR molecules

In previous studies, the shared cancer-testis Ag, NY-ESO-1, was demonstrated to be recognized by both Abs and CD8+ T cells. Gene expression of NY-ESO-1 was detected in many tumor types, including melanoma, breast, and lung cancers, but was not found in normal tissues, with the exception of testis. In this study, we describe the identification of MHC class II-restricted T cell epitopes from NY-ESO-1. Candidate CD4+ T cell peptides were first identified using HLA-DR4 transgenic mice immunized with the NY-ESO-1 protein. NY-ESO-1-specific CD4+ T cells were then generated from PBMC of a patient with melanoma stimulated with the candidate peptides in vitro. These CD4+ T cells recognized NY-ESO-1 peptides or protein pulsed on HLA-DR4+ EBV B cells, and also recognized tumor cells expressing HLA-DR4 and NY-ESO-1. A 10-mer peptide (VLLKEFTVSG) was recognized by CD4+ T cells. These studies provide new opportunities for developing more effective vaccine strategies by using tumor-specific CD4+ T cells. This approach may be applicable to the identification of CD4+ T cell epitopes from many known tumor Ags recognized by CD8+ T cells.

A new categorization of HLA DR alleles on a functional basis

In this analysis, we introduce a new categorization of HLA DR alleles which are important members of HLA class II genes encoding cell surface glycoproteins that function to present antigenic peptides to T cells. We have grouped all HLA DR molecules into seven different functional categories on the basis of their ability to bind and present antigenic peptides to T cells and their association with susceptibility or resistance to disease. This novel categorization of DR alleles on the basis of function allows for the prediction of seven similar subregion structures (supertypes or supermotifs) within pocket 4 of HLA DR peptide binding groove as the molecular basis for grouping these alleles. The physicochemical characteristics of HLA DR supertype residues, charge in particular, may influence the selectivity for binding peptide, dominate promiscuous T-cell recognition of antigenic peptides, and affect HLA DR disease associations. To rationalize the functional categories of DR alleles, we have further combined the seven DR supertype patterns into three groups based on the charges of residues within the supertypes. Grouping HLA DR alleles into functional categories may assist in understanding the mechanistic basis of autoimmunity, resolving current paradoxes in HLA disease associations, and developing new immunotherapy strategies.

Binding analysis of 95 HIV gp120 peptides to HLA-DR1101 and -DR0401 evidenced many HLA-class II binding regions on gp120 and suggested several promiscuous regions

To identify HLA-DR-binding peptides within the human immunodeficiency virus (HIV)-1 proteins. 95 overlapping synthetic peptides representing the entire sequence of gp120-LAI were screened for their capacity to bind to two HLA-DR molecules with distant sequences (DR0401 and DR1101). By using a cell surface competitive binding assay, 56 DR-binding peptides were identified, of which 35 bound to both DR1101 and DR0401. A highly significant concordance was evidenced by statistical analysis between binding of peptides to one and to the other DR molecule, suggesting a high proportion of promiscuity among gp120 peptides, even though no clear sequence pattern accounting for such promiscuity was found. DR-binding peptides were located along the entire gp120 sequence. Yet, the majority of them (42 among 56) were concentrated in seven multiagretopic regions that were arbitrarily defined as regions containing four or more overlapping continuous peptides binding to DR1011 and/or DR0401. A good correlation was found between DR-binding regions or DR-binding peptides defined in this study and promiscuous T helper gp120 epitopes previously described in seropositive individuals. All these results suggest that the identification of multiagretopic DR-binding regions may be a great help for the predicition of protein determinants that have the likelihood of being promiscuous T helper epitopes in humans.

Binding of ALA-substituted analogs of HA306-320 to DR1101, DR1301, and DR0402 molecules: correlation of DR-peptide interactions with recognition by a single TCR

We tested the hypothesis that a cross-reactive T-cell clone could recognize HA306-320 peptide complexed to autologous HLA-DR1101, and also to allogenic HLA-DR0402 and HLA-DR1301 molecules, because of similar orientations of HA306-320 side chains in the groove of the three DR molecules. To approach peptide orientations in each HLA groove we compared the capacity of Ala-monosubstituted analogs to bind and be presented by DR1101, DR0402, and DR1301. Results indicated that the orientation of HA306-320 in DR1101 was grossly similar to the known orientation of HA307-319 in DR0101. Data suggested many similarities in peptide orientations in DR0402 and DR1301 as well. However, differences in binding were also observed. Ala substitution of Y309 had much less effect on peptide binding to DR1301 and DR0402 than to DR1101 and Ala-substitution of T314 increased affinity for DR1301 but not for DR1101 and DR0402. These alterations of peptide-DR interactions were probably communicated to the upper peptide surface. Indeed, the levels of T-cell clone reactivities against analogs mutated at positions predicted to face the TCR were lower when complexed to allogeneic DR molecules than when complexed to DR1101. Yet these epitopic alterations are likely subtle, since the decreased reactivity of the clone to allogeneic molecules could be compensated by peptide substitution at Y309, predicted to face the MHC.

The relative importance of individual DR binding motif positions as defined by peptide anchor analysis of influenza hemagglutinin peptide 306-318 and human myelin basic protein peptide 152-165 binding to several DR molecules: definition of a common extended DR binding motif

Definition of peptide binding motifs for DR molecules has proven difficult as the peptides that bind to a DR molecule have shown extensive variability at putative motif positions. Recent studies suggest that specific peptide anchor residues (motif positions) and specific DR residues can differ in importance for peptide binding to a DR molecule. To assess further the relevance of individual peptide anchor residues, the binding of serial alanine-substituted analogs of influenza virus hemagglutinin (HA) 306-318 and human myelin basic protein (MBP) 152-165 to a panel of transfected wild-type DR molecules was examined. This analysis included DR molecules from a wide range of allelic families and, unlike most earlier studies, multiple members of single DR allelic families. The data show that different peptide residues serve as critical anchors for binding to different DR molecules. For example, MBP binding to DR(alpha, beta 1*0303) required peptide residues F154 (i), R159 (i + 5) and R162 (i + 8). In contrast, MBP binding to DR(alpha, beta 1*0102) required peptide residues I153 (i) and L156 (i + 3). More importantly, the combination of critical anchor residues in HA and MBP differed for binding to a single DR molecule [e.g. V309 (i) for HA and I153 (i) and L156 (i + 3) for MBP binding to DR(alpha, beta 1*0102)]. Although the location of the binding pocket in each DR molecule compared to the DR (alpha, beta 1 *0101) crystal is expected to be similar and suggests a common extended DR binding motif, the present results suggest that the relative importance of individual peptide anchor residues and of the corresponding DR binding pockets will differ for each DR/peptide complex.

Modulation of promiscuous T cell receptor recognition by mutagenesis of CDR2 residues

The T cell receptor (TCR) recognizes a ligand composed of a major histocompatibility complex (MHC) molecule and a peptide antigen. Prior studies of murine T cell clones have demonstrated that residues in the CDR3 region of TCR interact with amino acids in the peptide during MHC-restricted antigen recognition. However, the questions of whether direct TCR MHC contacts are made and where such contact sites might map in the TCR have not been resolved. In this study, we have taken advantage of the promiscuous recognition of a peptide from influenza virus (HA 307-319) by human T cell clones to map sites in the TCR that mediate differences in human leukocyte antigen-D related (HLA-DR) restriction in the presence of a common peptide antigen. Site-specific mutagenesis of cloned TCR genes and transfection into Jurkat cells were used to demonstrate that single amino acid substitutions in CDR2 of the TCR-alpha chain controlled whether a T cell was restricted by the product of a single DR allele (DR7) or would respond to the HA 307-319 peptide when presented by the products of one of several different DR alleles (DR1, DR4, DR5, or DR7). Because the relevant DR alleles are defined by polymorphism in the DR-beta chain, these results also suggest a rotational orientation for recognition in which TCR-alpha interacts with DR beta.