HLA-DP4, the Most Frequent HLA II Molecule, Defines a New Supertype of Peptide-Binding Specificity

Abstract

Among HLA-DP specificities, HLA-DP4 specificity involves at least two molecules, HLA-DPA1*0103/DPB1*0401 (DP401) and HLA-DPA1*0103/DPB1*0402 (DP402), which differ from each other by only three residues. Together, they are present worldwide at an allelic frequency of 20–60% and are the most abundant human HLA II alleles. Strikingly, the peptide-binding specificities of these molecules have never been investigated. Hence, in this study, we report the peptide-binding motifs of both molecules. We first set up a binding assay specific for the immunopurified HLA-DP4 molecules. Using multiple sets of synthetic peptides, we successfully defined the amino acid preferences of the anchor residues. With these assays, we were also able to identify new peptide ligands from allergens and viral and tumor Ags. DP401 and DP402 exhibit very similar patterns of recognition in agreement with molecular modeling of the complexes. Pockets P1 and P6 accommodate the main anchor residues and interestingly contain only two polymorphic residues, β86 and β11, respectively. Both positions are almost dimorphic and thus produce a limited number of pocket combinations. Taken together, our results support the existence of three main binding supertypes among HLA-DP molecules and should significantly contribute to the identification of universal epitopes to be used in peptide-based vaccines for cancer, as well as for allergic or infectious diseases.

Adenovirus hexon T-cell epitope is recognized by most adults and is restricted by HLA DP4, the most common class II allele

“…Further analysis of the hexon peptide reveals a motif consistent with the HLA DP4-binding motif described by Castelli et al 10 Comparison of PBMC responses to a panel of overlapping peptides and single residue mutations in the IFN-g ELISPOT assay identified Leu 914 and Phe 919 as the major anchors at P1 and P6, respectively. Competition studies confirmed that peptides with Ser substitutions at either P1 or P6 did not bind to HLA DP4.…”

“…This data is consistent with the analysis of the model HLA DP4 peptide Oxy 271-287 : the P1 and P6 anchors were critical for peptide binding, whereas deletion of the minor P9 anchor did not eliminate binding. 10 Deletion of the hexon peptide Cterminal 6 residues, which includes the P6 and P9 anchors from both motifs, completely eliminated the PBMC response (H910-918). Additionally, PBMC did not recognize H916-925, a peptide with a deletion of the Nterminal 6 residues that deletes the motif 1 P1 anchor but retains the entire motif 2.…”

HLA-associated susceptibility to childhood B-cell precursor ALL: definition and role of HLA-DPB1 supertypes

“…Furthermore, grouping amino-acid polymorphisms at positions 36, 56, and 76 failed to define recognised supertypes, and were not associated with leukaemia (data not shown). Clustering of DP alleles into six supertypes based on amino acid dimorphisms at positions 84 (P1 pocket), 69 (P4 pocket), and 11 (P6 pocket) represents an expanded version of the scheme proposed by Castelli et al (2002) based on peptide binding, and a slightly modified version of the hierarchical clustering scheme proposed by Doytchinova and Flower (2005). We have provisionally denoted the six supertypes DP1 (GKD), DP2 (GEG), DP3 (LKD), DP4 (GKG), DP6 (LED), and DP8 (GED) since they broadly resemble those defined in the primed lymphocyte test (PLT) as DPw specificites (De Koster et al, 1991).…”

“…Since different alleles can have overlapping peptide-binding properties, depending on the number of PBP that they share (Southwood et al, 1998), this has permitted DR alleles with the same amino acid polymorphisms lining specific peptidebinding pockets to be clustered into supertypes Southwood et al, 1998;Doytchinova and Flower, 2005). Using a similar approach, Castelli et al (2002) defined three DP supertype clusters with shared amino acid residues in the P1 (b84) and P6 (b11) PBP. However, the P4 peptide-binding pocket, at position b69, also makes an important contribution to antibody and peptide-binding (Arroyo et al, 1995;Chicz et al, 1997), T-cell responses (Berretta et al, 2003;Diaz et al, 2003) and disease susceptibility (Potolicchio et al, 1999;Wang et al, 1999).…”

Recent advances in tumour antigen‐specific therapy: In vivo veritas

“…10,11 Moreover, detailed analysis of HLA-DP4 peptide binding may facilitate future searches of novel tumour antigenic peptides restricted by this frequently occurring class II MHC allele. 12 Another favourable trait is the "degenerate" DR binding of certain antigenic peptides, i.e., various TA-derived antigenic peptides have been reported to bind to diverse HLA-DR molecules. 13,14 The identification of TA-derived epitopes presented by MHC class II molecules is complicated by the lack of effective screening methods.…”