Correlation of structure with T cell responses of the three members of the HLA-DRw52 allelic series

Using DR52c/Ni2+ mimotope tetramers to detect Ni2+ reactive CD4+ T cells in patients with joint replacement failure

T cell mediated hypersensitivity to nickel (Ni²⁺) is one of the most common causes of allergic contact dermatitis. Ni²⁺ sensitization may also contribute to the failure of Ni²⁺ containing joint implants, and revision to non-Ni²⁺ containing hardware can be costly and debilitating. Previously, we identified Ni²⁺ mimotope peptides, which are reactive to a CD4⁺ T cell clone, ANi2.3 (Vα1, Vβ17), isolated from a Ni²⁺ hypersensitive patient with contact dermatitis. This T cell is restricted to the major histocompatibility complex class II (MHCII) molecule, Human Leukocyte Antigen (HLA)-DR52c (DRA, DRB3*0301). However, it is not known if Ni²⁺ induced T cell responses in sensitized joint replacement failure patients are similar to subjects with Ni²⁺ induced contact dermatitis. Here, we generated DR52c/Ni²⁺ mimotope tetramers, and used them to test if the same Ni²⁺ T cell activation mechanism could be generalized to Ni²⁺ sensitized patients with associated joint implant failure. We confirmed the specificity of these tetramers by staining of ANi2.3T cell transfectomas. The DR52c/Ni²⁺ mimotope tetramer detected Ni²⁺ reactive CD4⁺ T cells in the peripheral blood mononuclear cells (PBMC) of patients identified as Ni²⁺ sensitized by patch testing and a positive Ni²⁺ LPT. When HLA-typed by a DR52 specific antibody, three out of four patients were DR52 positive. In one patient, Ni²⁺ stimulation induced the expansion of Vβ17 positive CD4⁺ T cells from 0.8% to 13.3%. We found that the percentage of DR52 positivity and Vβ17 usage in Ni²⁺ sensitized joint failure patients are similar to Ni sensitized skin allergy patients. Ni²⁺ independent mimotope tetramers may be a useful tool to identify the Ni²⁺ reactive CD4⁺ T cells.

Multiple mismatches at the low expression HLA loci DP, DQ, and DRB3/4/5 associate with adverse outcomes in hematopoietic stem cell transplantation

A single mismatch in highly expressed HLA-A, -B, -C, and -DRB1 loci (HEL) is associated with worse outcomes in hematopoietic stem cell transplantation, while less is known about the cumulative impact of mismatches in the lesser expressed HLA loci DRB3/4/5, DQ, and DP (LEL). We studied whether accumulation of LEL mismatches is associated with deleterious effects in 3853 unrelated donor transplants stratified according to number of matches in the HEL. In the 8/8 matched HEL group, LEL mismatches were not associated with any adverse outcome. Mismatches at HLA-DRB1 were associated with occurrence of multiple LEL mismatches. In the 7/8 HEL group, patients with 3 or more LEL mismatches scored in the graft-versus-host vector had a significantly higher risk of mortality (1.45 and 1.43) and transplant-related mortality (1.68 and 1.54) than the subgroups with 0 or 1 LEL mismatches. No single LEL locus had a more pronounced effect on clinical outcome. Three or more LEL mismatches are associated with lower survival after 7/8 HEL matched transplantation. Prospective evaluation of matching for HLA-DRB3/4/5, -DQ, and -DP loci is warranted to reduce posttransplant risks in donor-recipient pairs matched for 7/8 HEL.

The structure of HLA-DR52c: comparison to other HLA-DRB3 alleles

Class II major histocompatibility complex (MHCII) molecules present antigens to CD4(+) T cells. In addition to the most commonly studied human MHCII isotype, HLA-DR, whose beta chain is encoded by the HLA-DRB1 locus, several other isotypes that use the same alpha chain but have beta chains encoded by other genes. These other DR molecules also are expressed in antigen-presenting cells and are known to participate in peptide presentation to T cells and to be recognized as alloantigens by other T cells. Like some of the HLA-DRB1 alleles, several of these alternate DR molecules have been associated with specific autoimmune diseases and T cell hypersensitivity. Here we present the structure of an HLA-DR molecule (DR52c) containing one of these alternate beta chains (HLA-DRB3*0301) bound to a self-peptide derived from the Tu elongation factor. The molecule shares structurally conserved elements with other MHC class II molecules but has some unique features in the peptide-binding groove. Comparison of the three major HLA-DBR3 alleles (DR52a, b, and c) suggests that they were derived from one another by recombination events that scrambled the four major peptide-binding pockets at peptide positions 1, 4, 6, and 9 but left virtually no polymorphisms elsewhere in the molecules.

Components of the ligand for a Ni++ reactive human T cell clone

The major histocompatibility complex (MHC) restriction element for a human Ni(2+) reactive T cell, ANi-2.3, was identified as DR52c. A series of experiments established that the functional ligand for this T cell was a preformed complex of Ni(2+) bound to the combination of DR52c and a specific peptide that was generated in human and mouse B cells, but not in fibroblasts nor other antigen processing-deficient cells. In addition, ANi-2.3 recognition of this complex was dependent on His81 of the MHC beta chain, suggesting a role for this amino acid in Ni(2+) binding to MHC. We propose a general model for Ni(2+) recognition in which betaHis81 and two amino acids from the NH(2)-terminal part of the MHC bound peptide coordinate Ni(2+) which then interacts with some portion of the Valpha CDR1 or CDR2 region.

Complementarity and redundancy of the binding specificity of HLA-DRB1, -DRB3, -DRB4 and -DRB5 molecules

The second HLA-DR molecules, which are encoded by loci different from HLA-DRB1 are weakly polymorphic. Predominant alleles such as HLA-DRB3*0101, HLA-DRB4*0101 and HLA-DRB5*0101 are therefore interesting targets to define antigenic peptides with major impact for the entire population. Strikingly, they have been poorly investigated. Thus we have characterized peptides from the major bee venom allergen that bind efficiently to these molecules and compared them to peptides specific for preponderant HLA-DRB1 molecules. Interestingly, DRB5*0101 and DRB1*0701 molecules share four binding peptides and use some identical anchor residues. Similarities are also found between DRB3*0101 and its haplotype-associated molecules DRB1*0301 and DRB1*1301. In sharp contrast, DRB4*0101 exhibits a unique binding specificity, which results from particular structural features of its peptide binding site. Ybeta81 seems to alter the amino acid preferences of the P1 pocket, while Rbeta71, Ebeta74, Nbeta26 and Cbeta13 confer to the P4 pocket a unique topology. Our results show that the two HLA-DR molecules expressed in most haplotypes studied here have mostly complementary binding patterns. Only haplotype HLA-DR52 exhibits peptide binding redundancies. Finally our results document functional similarities among HLA-DR molecules and allow us to propose peptide sequences that might be useful for bee venom immunotherapy.

DRB3 alleles with variations in the annealing sites of commonly used amplification primers

New HLA alleles are often identified initially from observing uncommon patterns found in low-resolution typing performed via polymerase chain reaction using sequence-specific oligonucleotide probes (PCR-SSOP). Recently, the HLA-DR oligotyping analysis of two Caucasian, one Caucasian/American Indian and two African American individuals resulted in the identification of three novel DRB3 alleles. Using DRB-specific primer sets commonly employed in amplification-based typing, all four individuals were originally characterized as DRB3 negative. Direct sequencing identified DRB3*0104 (variation at codon 8, TCG instead of TTG), and DRB3*0101202 (variation at intron (-13), G instead of C). One individual appeared to carry a DR52-associated DRB1 allele without an associated DRB3 allele. Lack of conservation at the junction of intron 1 and exon 2 of the DRB3 gene suggests that commonly used DRB-specific primer sets may need to be modified.

A combination of two distinct in vitro amplification procedures for DNA typing of HLA-DRB and -DQB 1 alleles

The differential hybridisation of oligonucleotide probes to polymerase chain reaction (PCR)-amplified DNA has become a standard procedure for tissue typing. We describe a typing method in which differential ligation replaces differential hybridisation, which is a significant simplification of this strategy. After amplification by the PCR two labelled, sequence-specific oligonucleotides hybridise, in the fluid phase, to one strand of heat-denatured amplification product in juxtaposition. In the case of perfectly complementary sequences surrounding the gap, a thermostable ligase catalyses the ligation of the two oligonucleotides, otherwise they stay separated. The use of heat-resistant ligase enables easy repetition of the denaturation-annealing-ligation cycle in a thermocycler. The ligation products are detected by an enzyme linked immunosorbent assay. We tested this typing approach in a model system, the characterisation of three functional alleles of HLA-DRB3 using three probe pairs. No discrepancies were observed in typing 100 individuals of known genotypes. A total of 33 probe pairs combined with generic and group-specific amplification allowed the typing of alleles of HLA-DRB and -DQB1 loci at low resolution. We confirmed ligation-based typing results of 259 individuals with sequence-based HLA-DRB1 typing and HLA-DQB1 typing using PCR with sequence-specific primers (SSPs). In addition, more than 1,500 ligation-based HLA-DRB1 typings were concordant with SSP typing. Excellent signal-to-noise ratios in the enzyme-linked immunosorbent assay make ligation-based typing remarkably robust. The time requirement of 2.5 h post-PCR enables practicable typing of putative organ donors. The whole procedure is more easily amenable to automation than methods based on differential hybridisation requiring additional incubators and extra handling for hybridisation and washing.

HLA-DR polymorphism affects the interaction with CD4

Major histocompatibility complex (MHC) class II molecules are highly polymorphic and bind peptides for presentation to CD4+ T cells. Functional and adhesion assays have shown that CD4 interacts with MHC class II molecules, leading to enhanced responses of CD4+ T cells after the activation of the CD4-associated tyrosine kinase p56lck. We have addressed the possible contribution of allelic polymorphism in the interaction between CD4 and MHC class II molecules. Using mouse DAP-3-transfected cells expressing different isotypes and allelic forms of the HLA-DR molecule, we have shown in a functional assay that a hierarchy exists in the ability of class II molecules to interact with CD4. Also, the study of DR4 subtypes minimized the potential contribution of polymorphic residues of the peptide-binding groove in the interaction with CD4. Chimeras between the DR4 or DR1 molecules, which interact efficiently with CD4, and DRw53, which interacts poorly, allowed the mapping of polymorphic residues between positions beta 180 and 189 that can exert a dramatic influence on the interaction with CD4.

Linkage between HLA-DRB1 and -DRB3 types in the Japanese population analyzed by oligonucleotide genotyping

We analyzed linkage between HLA-DRB1 and -DRB3 types in 219 Japanese donors by oligonucleotide genotyping. In the Japanese population, DRB1*1201 was linked with DRB3*0101 in all donors analyzed; in contrast, most Caucasian DRB1*1201 is known to be linked with DRB3*02(01/02) (*0201 or *0202). However, most DRB1*1202 was linked with DRB3*0301. Thus, the two DRw12-related DRB1 types are linked with DRB3 types distinct from each other. All the three DRw14-related DRB1 types, DRB1*1401, DRB1*1402, and DRB1*1405, were linked with DRB3*02(01/02) in the Japanese population, contrasting with the known linkage between DRB1*1402 and DRB3*0101 in other ethnic populations. The serologically "blank" DR type, DRB1*1403, was linked with DRB3*0101. Other DRB1 types, DRB1*0301, DRB1*11(01/04) (*1101 or *1104), and DRB1*13(01/02) (*1301 or *1302) in the Japanese population were linked mostly with the same DRB3 types, like those known in other ethnic populations.

Common west African HLA antigens are associated with protection from severe malaria

A large case-control study of malaria in West African children shows that a human leucocyte class I antigen (HLA-Bw53) and an HLA class II haplotype (DRB1*1302-DQB1*0501), common in West Africans but rare in other racial groups, are independently associated with protection from severe malaria. In this population they account for as great a reduction in disease incidence as the sickle-cell haemoglobin variant. These data support the hypothesis that the extraordinary polymorphism of major histocompatibility complex genes has evolved primarily through natural selection by infectious pathogens.

HLA-DRB3 typing by restriction digestion of locus-specific amplified DNA

Locus HLA-DRB3 codes for the serologically defined supertypic specificity DRw52 in HLA-DR3, -5 and -w6 haplotypes. Three specificities of DRw52 (DRw52a, -b and -c) can further be distinguished by cellular techniques or by DNA typing with allele-specific oligonucleotide probes. These specificities were recently reported to have significant importance in antigen presentation. To avoid a time-consuming hybridization procedure, we have developed a simple typing system using PCR and subsequent digestion by allele-specific restriction endonucleases. A system was established with locus-specific amplification of HLA-DRB3 and digestion by the enzymes KpnI, ScaI and HinfI which recognize unique restriction sites within the amplified region. This allowed HLA-DRB3 typing on agarose gel by determining whether the amplification product has been digested or not. This typing system was compared to conventional oligotyping by analyzing 145 RFLP-typed individuals for their DRw52 specificity using both methods. Agarose typing correlated well with oligotyping and was shown to be more simple and practical even in heterozygous individuals.

RFLP analysis of HLA-DR5 haplotypes

The analysis of HLA-DR5 haplotypes unravelled a new DRB3 polymorphism and permitted the identification of various associations between alleles of the DRB1 and DRB3 loci. This new polymorphism consists of a 10.5 kb Taq1 restriction fragment which was encountered in an African-American family (JS). In Caucasoids, the DRw11 allele has been previously observed only in association with the DRw52b allele. RFLP and oligonucleotide typing of HLA-DRw52 alleles associated with DRw11 showed, however, that 4 Caucasoid individuals from our panel carried the DRw52a allele and 1 the DRw52c allele. Similarly, DRw12, which is usually associated with DRw52b, was encountered with DRw52a in 1 Chinese and with DRw52c in an African-American and a Chinese panel member. The study of DRB3 alleles associated with DRw11 and DRw12 indicates that, similar to serology, RFLP studies become particularly informative when individuals of different races and ethnic origins are studied.

Detection of complex alleles by direct analysis of DNA heteroduplexes

DNA molecules derived from three alleles of the HLA-DRB3 locus and differing from each other at several nucleotide sites were denatured and cross-hybridized. Each allelic combination was found to generate a pair of heteroduplexes of different mobility. Their retardation as compared to homoduplexes was proportional to the number of mismatches. In each heteroduplexes pair the component possessing the highest number of Pyr-Pyr oppositions was the most retarded. The results are those predicted by a theoretical model implying a correlation between base-pair opening and bending of the DNA double helix. These observations introduce a new HLA typing method at the genomic level and indicate an experimental approach to the analysis of the superhelical DNA conformation as related to different types of base oppositions.

The complexity of DRw6 and DR5 haplotypes in American blacks demonstrated by serology, cellular typing, and restriction fragment length polymorphism analysis

This study describes the diversity of DRw6 and DR5 haplotypes in the American black population using serology, cellular typing, and restriction fragment length polymorphism (RFLP) analysis. DRw6 (DRw13 and DRw14) and DR5 (DRw11 and DRw12) haplotypes are observed at a high frequency in this population (DRw6: 32%, DR5: 30%). Many of these haplotypes express undefined HLA-D specificities and unusual DQ and DRw52 associations which previously have not been well characterized or reported (e.g., DRw13, DQw5, DRw52c, D-; DRw13, DQw2, DRw52a, D-; DRw11, DQw5, DRw52c, D-). Serologic analysis of class II alleles in American blacks suggests the presence of DRw13, DRw11 and DQw6 allelic variants and demonstrates the difficulty in defining DRw6 and DR5 in this population. The class II genes from four American black families expressing many of the novel DRw13, DRw14, DRw11, and DRw12 haplotypes defined by serology and mixed leukocyte culture were further characterized by RFLP analysis. The data presented here along with other published data identify at least eight DRw13 haplotypes (DRw13A-DRw13H) in the human population. Five of these haplotypes exhibit an undefined HLA-D specificity. Three DRw14 haplotypes (DRw14A-DRw14C) and eight DR5 haplotypes (DRw11A-DRw11E and DRw12A-DRw12C) were also identified. The novel DRw6 and DR5 haplotypes observed in American blacks may arise from differences in DRB1, DQA1, and DQB1 genes as well as from differences in the combinations of alleles of these genes encoded by a haplotype. The serologic and RFLP analyses suggest that some DRw13 and DRw11 haplotypes represent transitional steps between DRw13 and DRw11 in the evolutionary pathway which generated the DRw52 family.

Sequence analysis and HLA-DR genotyping of a novel HLA-DRw14 allele

Analysis of a Japanese population by oligonucleotide genotyping revealed that one Japanese HLA-DRw14 allele had a DRB1 genotype different from that of the known HLA-DRw14-related alleles, DRB1*1401 (DRw14-Dw9) and DRB1*1402 (DRw14-Dw16). The second exon of the DRB1 gene of the novel DRw14 allele (designated DRB1-14c) was amplified enzymatically and sequenced after cloning into a plasmid vector. The amino acid sequence of the first domain in the DR beta 1 chain encoded in the DRB1-14c allele was more similar to that of the DRB1*1401 allele (three amino acid substitutions) than to that of the DRB1*1402 allele (six amino acid substitutions). No polymorphic amino acid residue that could explain the common serologic HLA-DRw14 specificity was identified among the sequences of the three DRw14-related alleles. Sequence-specific oligonucleotides (SSOs) were synthesized on the basis of the DRB1-14c nucleotide sequence and used for genotyping of the Japanese population. These SSOs served as useful probes for identifying the DRB1-14c allele in a wide range of donors.

DR-restricted T-cell reactivities associated with the Dw19 specificity can be directed against the products of either locus DRB3 (DRw52c) or locus DRB1

HLA-Dw 19 antigen presenting cells express two different DR beta chains encoded respectively by DRB1 and DRB3 genes. In the present study we determined which of these two DR beta chains is recognized by DR-restricted T-cell clones. First we selected influenza-specific, DR-restricted T-cell clones of which restriction is strictly associated with the Dw19 specificity. Then we characterized by oligonucleotide typing one antigen presenting cell (HC12M) which exhibits a new haplotype associating a DRB1 gene highly related or identical to that from Dw 18 haplotypes with a DRB3 gene highly related or identical to that from Dw19 haplotypes. Finally, by testing the reactivity of the selected T-cell clones against Dw18, Dw19, and HC12M antigen presenting cells, we show that these DR-restricted "Dw19-specific" effectors can recognize either the DRB1-encoded chain present only on Dw19 antigen presenting cell or the DRB3-encoded chain shared by Dw19 and HC12M antigen presenting cells. Interestingly, our results show that DRB1 chains from Dw19 and Dw18 which differ by a single amino acid substitution at position 86 may be distinguished by T cells, implicating that this residue plays a role in T-cell recognition of HLA-DR-antigen complex. The implication of our results with regard to the new nomenclature of HLA specificities defined by T-cell clones will be discussed.