Nomenclature for factors of the HLA system, 1987

A gene feature enumeration approach for describing HLA allele polymorphism

HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences.

The peptide binding specificity of HLA-B27 subtypes

Five HLA-B27 subtypes, B*2701, B*2703, B*2704, B*2705, and B*2706, were tested for direct binding with twenty-six synthetic nonapeptides carrying the primary anchor residue motifs (combination of amino residues at positions 2 and 9) relevant to B*2705. The peptide sequences were derived from human HSP89 alpha, P53 and MBP. The alpha chains were immunospecifically isolated from LH (B*2701), CH (B*2703), WE1 (B*2704), BTB (B*2705), and LIE (B*2706) cells and their peptide binding was measured by the HLA class I alpha chain refolding assay. The data obtained indicated that the B27 subtypes tested can bind a common set of peptides carrying several different anchor residue motifs. The motifs, R-K and R-R, reported for B*2705 and a new motif H-R were accepted by B*2703, B*2704, and B*2706, but not by B*2701. However, other motifs, including known B*2702 and/or B*2705 motifs, R-H, R-L, R-A, and R-F, and a new motif found here, R-G, were apparently accepted by all B27 subtypes tested. The observed cross-peptide binding in the B27 subgroup is compatible with the so-called arthritogenic peptide hypothesis in the pathogenesis of ankylosing spondylitis.

Biological-clinical significance of selective loss of HLA-class-I allelic product expression in squamous-cell carcinoma of the uterine cervix

To determine possible correlations between the selective loss of HLA-class-I allelic forms on neoplastic cells and their biological-clinical characteristics, 89 squamous-cell carcinomas of the uterine cervix were evaluated immunohistochemically using monomorphic and polymorphic antibodies against HLA-A, -B, and -C molecules and analyzed clinico-pathologically. Four of the carcinomas exhibited a lack of detectable class-I heavy-chain expression associated with beta 2-microglobulin. In 19 of 42 HLA-A2-positive patients, tumor cells revealed loss of the HLA-A2 allelic product. Loss of HLA-B7 and/or 40 (B7/40) allelic product(s) on tumor cells was observed in 12 of 25 HLA-B7/40-positive cases. These alterations did not correlate with patient age, clinical stage (FIGO) of the disease, histological sub-type (WHO) or depth of cervical invasion. However, a statistically significant correlation was observed between lymph-node metastases and selective loss of HLA-B7/40 allelic product(s), but not with HLA-A2 allelic product on cancer cells of the primary lesion. Our results indicate that selective loss of certain HLA-class-I alleles on neoplastic cells can influence the nodal metastatic potential and suggest that these 2 class-I molecules may have different immune functions as restriction elements in T-cell-mediated cytotoxicity.

Complexity of the HLA-DP region: RFLP analysis versus PLT typing and oligotyping

A total of 84 individuals were DP typed in parallel with the restriction fragment length polymorphism (RFLP) analysis and the primed lymphocyte test (PLT). Whereas 80% of the cases gave concordant results, the other 20% showed discrepancies for one of the two alleles carried by the typed individuals. Oligotyping, PCR-RFLP and sequencing confirmed the results found by PLT. The 20% discordant results obtained with RFLP led us to conclude that RFLP typing cannot replace PLT typing. From a more general point of view, the RFLP analysis revealed the DP region to be more complex than expected since for each given PLT DP defined specificity, more than one RFLP DP haplotype could be determined. These were possibly induced by crossing-overs or gene conversion events.

Immunogenetic study of three Japanese families with neonatal lupus erythematosus

We encountered three Japanese families with neonatal lupus erythematosus. None of the three fathers showed any signs of collagen disease. The three mothers were found to suffer from Sjögren's syndrome; they all tested positive for anti-SSA and SSB antibodies and had lymphocyte infiltration into the small salivary gland. In two families, one child had neonatal lupus erythematosus while a sibling was normal; in the third family, both children had neonatal lupus erythematosus. Thus, a mother with positive anti-SSA and SSB antibodies can give birth to one infant with and one infant without or have two infants with neonatal lupus erythematosus. We conducted HLA typing of all 12 members of the three families in order to clarify the immunologic factors involved. We found no increased frequency of any HLA phenotype in the three mothers and their four children with neonatal lupus erythematosus; however, HLA-DR4 was present in three of the children with neonatal lupus erythematosus.

Localization and characterization of serologic epitopes on HLA-A2

A panel of cells expressing 68 different mutant HLA-A2 genes was generated by site-directed mutagenesis and DNA-mediated gene transfer in order to define the regions of class I MHC molecules that contribute to the epitopes recognized by mAb. Each of the variant HLA-A2 molecules differed from HLA-A2.1 by a single amino acid substitution. The substitutions were located in both the alpha-helices and beta-strands of the alpha 1 and alpha 2 domains, and included residues that are highly polymorphic and that are conserved. All but five of the variant HLA-A2 molecules were expressed at levels that ranged from approximately 25%-100% the levels found for HLA-A2.1. The remaining five variants had no detectable expression and all involved substitutions at highly conserved residues. Eleven mAbs with specificities that ranged from highly HLA-A2 specific to monomorphic were analyzed for their ability to bind the variant HLA-A2 molecules. The results demonstrate that the binding of five of 11 mAbs could be mapped to the alpha 1 and alpha 2 domains. MA2.1 was the only antibody mapped to the alpha 1 domain. CR11-351 and A2,A28M1 recognized an overlapping epitope at the amino terminal end of the alpha 2-helix, and PA2.1 and BB7.2 recognized an overlapping epitope that includes the carboxy terminus of the alpha 2-helix and a turn on one of the underlying beta-strands. These results demonstrate that positions located on the surface of the molecule, but not within the peptide-binding cleft of the molecule, are important in serological specificities.

[HLA class II DP antigens and bone marrow transplantation]

The biochemical structure of the HLA class II DP antigens is close to that of the remainder DR and DQ isotypes. Nevertheless, they may play a peculiar functional role. Their importance in bone marrow transplantation, where a complete HLA class II identity between graft donor and recipient is requested, is not yet known. The detection of a DP mismatch by using the mixed lymphocyte reaction is quite difficult. The role of such a mismatch in the incidence of graft versus host disease (GVHD) or graft rejection has to be defined. Studies on large series of recombinant families, using oligotyping, are necessary.

Linkage disequilibrium between the HLA-DQA2 alleles and the HLA/DR/DQ complex

A statistically significant association was observed between alleles of the HLA-DQA2 and of the DR/DQ complex in a DNA-restriction fragment length polymorphism study of 219 members from 21 multiplex families of patients with hyperthyroid Graves' disease and 773 unrelated individuals selected for homozygosity of the HLA-DQA2 alleles. This data provides evidence for linkage disequilibrium rather than for a hot spot of recombination within the HLA-DQ subregion.

Major histocompatibility complex genes and susceptibility to systemic lupus erythematosus

Susceptibility to systemic lupus erythematosus is associated with major histocompatibility complex (MHC)--encoded genes. We have used nucleotide sequence analysis to better define the disease-associated MHC alleles. HLA-DR2, DQw1, and especially the rare allele DQ beta 1. AZH confer high relative risk (RR = 14) for lupus nephritis in a Caucasian population of patients. Pilot studies using historical controls suggest that these genes also confer a high risk in non-Caucasian ethnic groups (RR = 24-78). We have found that DR4 is significantly decreased in patients with lupus nephritis. Fifty percent of the patients with lupus nephritis had either the DQ beta 1.1, the DQ beta 1.AZH, or the DQ beta 1.9 alleles. These alleles share amino acid residues that have been predicted to be the contact points for antigen and the T cell receptor. These HLA alleles appear to have a direct role in the predisposition to lupus nephritis, whereas DR4 may have a "protective" effect.

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.

The relationship between bovine major histocompatibility complex class II polymorphism and disease studied by use of bull breeding values

The predictive value of class II DQ and DYA polymorphisms of the bovine major histocompatibility (MHC) complex (BoLA) for the incidence of disease in dairy cattle was estimated in a sample of 196 progeny-tested AI bulls of the Swedish Red and White breed. The BoLA DQ and DYA types of the bulls were determined by analysing restriction fragment length polymorphisms (RFLPs). Breeding values of bulls for clinical mastitis, all diseases including clinical mastitis and diseases other than clinical mastitis were used as measures of disease resistance or susceptibility. The relationship between MHC polymorphism and bull breeding values for disease resistance was evaluated statistically by linear regression analysis. A significant association between the haplotype DQ1A and susceptibility to clinical mastitis was revealed. No other DQ haplotype nor the DYA locus has a significant effect on any of the disease traits studied.

HLA-D region genomic polymorphism associated with Takayasu's arteritis

Takayasu's arteritis, with a strong predilection for women and particular geographic areas, has revealed significant association with human lymphocyte antigens (HLA) specificities. In the present study, the authors investigated for the first time the association of Takayasu's arteritis and HLA at the genomic level. By use of a restriction endonuclease Taq-I and a DQA cDNA probe, HLA-D region restriction fragment length polymorphism was examined in 32 Japanese patients. It was revealed that 65.6% of the patients shared a 6.6 kb fragment, although this fragment was found in 35.3% of the healthy Japanese (Chi square: 6.07, p less than 0.02). This finding suggest that HLA-D region gene variations determine susceptibility to Takayasu's arteritis.

HLA-DP, -DQ and -DR RFLP types in south Indian insulin-dependent diabetes mellitus patients

The frequencies of HLA-DP, DQ and DR RFLP types are compared between insulin-dependent diabetes mellitus (IDDM) patients and healthy controls in the South Indian population. There are no significant differences in the frequencies of any of the DPA. DPB haplotypes, when allowance is made for multiple comparisons. The individual frequencies of two novel alleles, designated "DPA*B" and "DPB*B", however, are significantly higher in controls than in patients, suggesting that these alleles are protective against IDDM. A negative association with DRw15 (DR2). Dw12 is also observed. The positive association with DPw3/6 RFLPs previously observed in White Australians is not present in South Indians. This difference may be due either to undetected heterogeneity within allelic classes or to different linkage disequilibrium patterns between the populations.

A T-cell clone recognizing an MLC stimulating epitope located on the DRw11 beta 1 chain

An alloreactive proliferative T-cell clone, 6065 WS, was obtained in an intrafamilial cell combination where the stimulator was a homozygous DRw11, DRw52, DQw3 son and the responder his haploidentical mother. Proliferation assays on eight local DRw11 families, 75 homozygous B-cell lines (Tenth Histocompatibility Workshop panel) and blocking assays with monoclonal antibodies showed that clone 6065 WS recognizes an epitope on the DRw11 beta 1 chain. Comparison of the reactivity of clone 6065 WS with cells expressing the three known DRw11 beta 1 amino acid sequences identified two unique amino acids at positions 71 and 86 which contribute to determining the specific recognition by the T-cell clone 6065 WS. Our data suggest that one or both of these amino acids can either be directly involved in the recognition by the T-cell receptor or responsible for critical conformation of the determinants on the DR molecule. Alternatively, they could affect recognition of a self peptide bound to the major histocompatibility complex class II molecule.

Characterization of three functional sites in alpha beta 1 DR of DRw13. All three sites are potentially involved in major histocompatibility complex-peptide interaction

An HLA-DR product encoded by the HLA-DRw13/Dw19 haplotype has been identified as the HLA class II molecule involved in antigen presentation to several influenza-specific helper T cell clones. Three different functional sites were identified on this molecule by comparing the structure of HLA-DR products of known sequences and their ability to efficiently present foreign antigen to the T cell clones. These functional sites were mapped on the recently proposed three-dimensional structure of HLA class II molecules. From their position, these sites are all potentially involved in HLA-peptide interaction and capable of affecting the binding and/or the conformation of the foreign peptide. This suggests that polymorphic residues essential in major histocompatibility complex restriction are mostly involved in peptide binding.

HLA-DR and -DQ epitopes and monoclonal antibody specificity

The polymorphism of the HLA system-originally studied serologically using antisera from multiparous women and cellularly using the mixed lymphocyte reaction-has now been further revealed by the use of monoclonal antibodies and, at the most basic level, by the nucleotide and amino acid sequences of the different alleles. In this article, Steven Marsh and Julia Bodmer examine the specificity of mainly well-known HLA-DR and HLA-DQ monoclonal antibodies and postulate the positions of their binding sites, or at least of the polymorphic sites determining their patterns of reactivity. The publication together of all available amino acid sequences of the first domain of the DR beta and DQ alpha and the DQ beta chains (updated and corrected where necessary in collaboration with their authors) provides a useful tool with which to identify binding sites of other antibodies and perhaps to attempt to correlate their position in the structure with their function. Outlines of strategies to produce a wider range of polymorphic antibodies are discussed.

Monoclonal antibody definition of the DRB3 allele, HLA-Dw25

Monoclonal antibodies are powerful tools for analyzing HLA antigen polymorphism. We have investigated the serological and biochemical nature of the DRw52-related antigen defined by the monoclonal antibody NDS10. A detailed analysis of the population distribution of NDS10 reactivity revealed that the epitope was present on a subpopulation of DRw52 positive cells. A distinct pattern of reactivity was found within DR3 individuals: all of the B18,DR3 cells were NDS10 positive, whereas the A1,B8,DR3 cells were negative. All of the DR5(w11) cells and two of three DRw12 cells reacted with NDS10. NDS10 reactivity with DRw6 was not restricted to either of the serologically defined subtypes; three of 17 DRw13 and nine of 10 DRw14 cells were NDS10 positive. NDS10 was unreactive with all of the DRw8 cells tested. Two-dimensional gel analyses revealed that the NDS10 molecule precipitated from DR3, DR5(w11) and DRw6(w14) cell lines had an identical beta chain profile. These data indicate that NDS10 recognises the Dw25 allele of the DRw52 complex.

Immune responses to the circumsporozoite protein of Plasmodium falciparum in relation to HLA-DR type

Associations between HLA-DR/DQ phenotypes and immune responses to the circumsporozoite (CS) protein of the human malaria parasite, Plasmodium falciparum, were investigated in Thai adults. The frequency of DR and DQ types did not differ between 15 high antibody responders and 16 antibody non-responders. Initial results which suggested that lymphocyte responses to a CS-derived peptide (R32tet32) might be HLA-DR associated were not confirmed by subsequent extension of the study. Thus, MHC restriction appears not to be a major factor in the frequently observed unresponsiveness of the immune system to the P. falciparum sporozoite. Based on these results, it is expected that MHC restriction will not be a major obstacle to the application of a malaria vaccine in outbred human populations.

The rat as an experimental animal

The development and characterization of many inbred, congenic, and recombinant strains of rats in recent years has led to the detailed genetic description of this species, especially in regard to its major histocompatibility complex. This information has contributed substantially to the study of comparative genetics and has greatly enhanced the utility of the rat in a variety of areas of biomedical research. This article focuses on the use of the rat in immunogenetics, transplantation, cancer-risk assessment, cardiovascular diseases, and behavior.

HLA-B27 and HLA-A2 subtypes: structure, evolution and function

Beyond the resolution of tissue typing serology, HLA class I antigens display a certain level of structural microheterogeneity, that allows their subdivision into subtypes. The structure of these subtypes shows that multiple mechanisms operate in the generation of HLA polymorphism and suggests possible evolutionary pathways for subtype diversification. In addition, subtype polymorphism critically affects cellular allorecognition and antigen presentation to self-restricted T cells. These properties are used to define the structure and diversity of T-cell epitopes. In this review, José López de Castro discusses the nature and evolution of this polymorphism and its modulation of antigen recognition by cytolytic T lymphocytes.

Class I cross-restricted T cells reveal low responder allele due to processing of viral antigen

Cytotoxic T lymphocytes (CTL) recognize protein antigens which have been processed by the target cell and then presented in association with the relevant class I molecule of the major histocompatibility complex (MHC). Short synthetic peptides, which are able to associate directly with target cells, may substitute for these processed fragments in stimulating antigen-specific CTL responses. Using this approach, a dominant HLA-A2-restricted epitope has previously been mapped to residues 58-68 of influenza A virus matrix protein. Here we report HLA-A2-restricted CTL which are also able to recognize this short synthetic peptide in association with HLA-Aw69, but which fail to recognize HLA-Aw69 expressing cells infected with influenza A virus. Furthermore, individuals possessing HLA-Aw69 who respond to influenza A virus, do not respond to M58-68. These results imply that the low response to this epitope on infection of HLA-Aw69 individuals with influenza A is due to failure of the naturally processed product of matrix protein to associate with Aw69.