Serological and immunochemical analysis of the products of a single HLA DR-alpha and DR-beta chain gene expressed in a mouse cell line after DNA-mediated cotransformation reveals that the beta chain carries a known supertypic specificity

The different level of expression of HLA-DRB1 and -DRB3 genes is controlled by conserved isotypic differences in promoter sequence

HLA-DRB1 and -DRB3 are two genes encoding two distinct HLA-DR beta chains in the DRw52 family of haplotypes (DR3, DR5, DR13, and DR14). These beta chains determine the structural and functional identity of the two kinds of HLA-DR molecules expressed. The highly polymorphic HLA-DRB1 locus is always expressed at a higher level than the HLA-DRB3 locus, and functional assays indicate that the proximal promoter of DRB1 is indeed more active than that of DRB3. The DNA sequence of the two promoters in nine different DRw52 haplotypes has revealed a stricking allelic conservation as well as characteristic, isotype-specific, conserved-sequence motifs. These isotype-specific differences concern the functionally essential X and Y box motifs of HLA class II promoters, and they do indeed affect binding of specific nuclear factors to the X and Y boxes of DRB1 or DRB3 promoters. Finally, analysis of the activity of various normal and mutated DRB1 or DRB3 promoters indicates that the X box region of these promoters plays a dominant role in controlling the relative levels of HLA-DRB1 and -DRB3 gene expression.

Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution

Class II genes of the human major histocompatibility complex (MHC) are polymorphic. Allelic variation of the coding region of these genes is involved in the antigen presentation and is associated with susceptibility to certain autoimmune diseases. The DR region is unique among human class II regions in that multiple DRB genes are expressed. Differential expression of the different DRB loci has been demonstrated, and we sequenced the proximal promoter region of the HLA-DRB genes, known to be involved in the regulation of these genes. We found locus-specific and allele-specific nucleotide variations in their regulatory regions and we determined the relationship between the regulatory regions of HLA-DRB genes. This polymorphism found in the regulatory conserved boxes could be involved in the observed differential expression of DRB loci. In addition, we found a polymorphism between the regulatory regions of DRB1 alleles which might be involved in an allele-specific regulation and therefore could be considered as an additional factor in susceptibility to autoimmune diseases.

Multiplication of Mhc-DRB5 loci in the orangutan: implications for the evolution of DRB haplotypes

The beta chain-encoding (B) class II genes of the primate major histocompatibility complex belong to several families. The DRB family of class II genes is distinguished by the occurrence of haplotype polymorphism--the existence of multiple chromosomal forms differing in length, gene number, and gene combinations, each form occurring at an appreciable frequency in the population. Some of the haplotypes, or fragments thereof, are shared by humans, chimpanzees, and gorillas. In an effort to follow the DRB haplotype polymorphism further back in time, we constructed DRB contig maps of the two chromosomes present in the orangutan cell line CP81. Two types of genes were found in the two haplotypes, Popy-DRB5 and Popy-DRB1*03, the former occurring in two copies and one gene fragment in each haplotype, so that the CP81 cell line contains four complete DRB5 genes and two DRB5 fragments altogether. Since the four genes are more closely related to one another than they are to other DRB5 genes, they must have arisen from a single ancestral copy by multiple duplications. At the same time, however, the two CP81 haplotypes differ considerably in their restriction enzyme sites and in the presence of Alu elements at different positions, indicating that they have been separated for a length of time that exceeds the lifespan of a primate species. Moreover, a segment of about 100 kilobase pairs is shared between the orangutan CP81-1 and the human HLA-DR2 haplotype. These findings indicate that part of the haplotype polymorphism may have persisted for more than 13 million years, which is the estimated time of human-orangutan divergence.

Trans-species evolution of Mhc-DRB haplotype polymorphism in primates: organization of DRB genes in the chimpanzee

The DRB region of the human major histocompatibility complex displays length polymorphism: Five major haplotypes differing in the number and type of genes they contain have been identified, each at appreciable frequency. In an attempt to determine whether this haplotype polymorphism, like the allelic polymorphism, predates the divergence of humans from great apes, we have worked out the organization of the DRB region of the chimpanzee Hugo using a combination of chromosome walking, pulsed-field gel electrophoresis, and sequencing. Hugo is a DRB homozygote whose single DRB haplotype is some 440 kilobases (kb) long and contains five genes. At least one and possibly two of these are pseudogenes, while three are presumably active genes. The genes are designated DRB*A0201, DRB2*0101, DRB3*0201, DRB6*0105, and DRB5*0301, and are arranged in this order on the chromosome. The DRB2 and DRB3 genes are separated by approximately 250 kb of sequence that does not seem to contain any additional DRB genes. The DRB*A0201 gene is related to the DRB1 gene of the human DR2 haplotype; the DRB2*0101 and DRB3*0201 genes are related to the DRB2 and DRB3 genes of the human DR3 haplotype, respectively; the DRB6*0105 and DRB5*0301 genes are related to the DRBVI and DRB5 genes of the human DR2 haplotype, respectively. Thus the Hugo haplotype appears to correspond to the entire human DR2 haplotype, into which a region representing a portion of the human DR3 haplotype has been inserted. Since other chimpanzees have their DRB regions organized in different ways, we conclude that, first, the chimpanzee DRB region, like the human DRB region, displays length polymorphism; second, some chimpanzee DRB haplotypes are longer than the longest known human DRB haplotypes; third, in some chimpanzee haplotypes at least, the DRB genes occur in combinations different from those of the human haplotypes; fourth, and most importantly, certain DRB gene combinations have been conserved in the evolution of chimpanzees and humans from their common ancestors. These data thus provide evidence that not only allelic but also haplotype polymorphism can be passed on from one species to another in a given evolutionary lineage.

The evolutionary origin of the HLA-DR3 haplotype

The human HLA-DR3 haplotype consists of two functional genes (DRB1*03 and DRB3*01) and one pseudogene (DRB2), arranged in the order DRB1...DRB2...DRB3 on the chromosome. To shed light on the origin of the haplotype, we sequenced 1480 nucleotides of the HLA-DRB2 gene and long stretches of two other genes, Gogo-DRB2 from a gorilla, "Sylvia" and Patr-DRB2 from a chimpanzee, "Hugo". All three sequences (HLA-DRB2, Gogo-DRB2, Patr-DRB2) are pseudogenes. The HLA-DRB2 and Gogo-DRB2 pseudogenes lack exon 2 and contain a twenty-nucleotide deletion in exon 3, which destroys the correct translational reading frame and obliterates the highly conserved cysteine residue at position 173. The Patr-DRB2 pseudogene lacks exons 1 and 2; it does not contain the twenty-nucleotide deletion, but does contain a characteristic duplication of that part of exon 6 which codes for the last four amino acid residues of the cytoplasmic region. When the nucleotide sequences of these three genes are compared to those of all other known DRB genes, the HLA-DRB2 is seen as most closely related to Gogo-DRB2, indicating orthologous relationship between the two sequences. The Patr-DRB2 gene is more distantly related to these two DRB2 genes and whether it is orthologous to them is uncertain. The three genes are in turn most closely related to HLA-DRBVI (the pseudogene of the DR2 haplotype) and Patr-DRB6 (another pseudogene of the Hugo haplotype), followed by HLA-DRB4 (the functional but nonpolymorphic gene of the DR4 haplotype). These relationships suggest that these six genes evolved from a common ancestor which existed before the separation of the human, gorilla, and chimpanzee lineages. The DRB2 and DRB6 have apparently been pseudogenes for at least six million years (myr). In the human and the gorilla haplotype, the DRB2 pseudogene is flanked on each side by what appear to be related genes. Apparently, the DR3 haplotype has existed in its present form for more than six myr.

Efficient cDNA expression vectors for stable and transient expression of HLA-DR in transfected fibroblast and lymphoid cells

cDNA expression vectors with several useful features were constructed. First, the long terminal repeat of Rous sarcoma virus was used as a promoter to obtain high levels of expression in various cells of human and mouse origin. Second, cis-linked expression units that confer resistance either to mycophenolic acid or the neomycin analog G418 were inserted to facitate the isolation of transfected cells expressing the cDNA of interest. Third, by replicating in simian COS cells, these vectors can be used for efficient transient expression. cDNA fragments encoding the DR alpha or DR beta chains of human class II major histocompatibility complex antigens were inserted into these vectors and high levels of cell surface HLA-DR antigen were obtained after cotransfection into mouse and human fibroblasts. These vectors were also successfully used to correct the inability of a class II-negative B cell line, derived from a patient with a congenital immunodeficiency, to present peptide antigen to DR-restricted T cells.

An in vitro model of peptide-mediated immunomodulation of the human T cell response to Dermatophagoides spp (house dust mite)

Allergic sensitivity of Dermatophagoides spp (house dust mites) is mediated by specific IgE antibody, the production of which requires the presence of CD4+ helper T cells. Attempts to hyposensitize this response in allergic individuals have depended on the administration of extracts of specific allergen. However, the ability of peptides derived from unrelated antigens to inhibit specific immune responses offers an alternative approach to therapy. We have addressed this question by examining the ability of a nonstimulatory peptide analogue derived from influenza virus hemagglutinin to modulate T cell recognition of house dust mite. The peptide inhibited the response of mite-specific CD4+ T cell clones restricted by either the HLA-DRAB1 or DRAB3 gene products. Furthermore, mite-induced polyclonal T cell responses were negatively modulated by the peptide, whereas recognition of common recall antigens remained intact. The inhibitory effects were mediated at the level of the antigen-presenting cell, since no inhibition of mitogen or anti-CD3 antibody-driven T cell proliferation was observed. In direct binding assays, the peptide analogue bound to selected HLA-DR molecules expressed on the membrane of antigen-presenting cells, with specificity predominantly for those class II proteins capable of restricting house dust mite-allergen T cell recognition.

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.

Mapping of an HLA-DRw52-associated determinant on DR beta 1 molecules

The molecular reaction patterns of the DRw52-specific mouse monoclonal antibodies UL-52 and 7.3.19.1 were investigated. Upon immunoprecipitation and two-dimensional IEF-SDS polyacrylamide gel electrophoresis analysis (2D-PAGE) mAb UL-52 selectively isolated DR beta 1 molecules from DRw52-positive cell lines, whereas mAb 7.3.19.1 predominantly precipitated DR beta 3 molecules. Reduced mAb UL-52 binding affinity was observed to DRw8- and DRw12-positive cells, potentially resulting from structural modifications within the antibody binding site. Comparison of mAb UL-52 reactivity with published DR beta chain amino acid sequences demonstrates that the amino acid residues -S- in positions 11 and 13 on DR beta 1 molecules essentially contribute to the formation of the antibody binding site. mAb 7.3.19.1 reactivity, on the other hand, correlates with the expression of DR beta 3 chain amino acid residues K, G and N, in positions 71, 73 and 77, respectively. In contrast to other DRw52 monoclonal antibodies described so far, mAb UL-52 demonstrates a similar reactivity to DRw52 allosera, suggesting that mAb UL-52 and DRw52 allosera possibly recognize the same or a similar determinant on DR beta 1 molecules.

Polymorphism of DRw52 and its association with DRw11 and DRw12 in South African blacks (Negroes) and individuals of mixed ancestry (Cape coloreds)

The HLA-DRB3 gene, which encodes the supertypic HLA-DRw52 antigen, has been shown to have limited polymorphism. The alleles at this locus are also in linkage disequilibrium with the alleles at the DRB1 locus. We have studied 16 DRw11 and three DRw12 haplotypes in the South African populations. Five of the DRw11,DQw7 haplotypes were associated with a TaqI restriction fragment length polymorphism which has not been previously described and which correlated with the DRB3 gene. This new variant, which has been called DRw52d, is confined to individuals of black or mixed ancestry. Two of the DRw11,DQw7 haplotypes were also associated with DRw52a or DRw52c and not with DRw52b as has always been observed in white populations. The less common DRw11,DQw6 haplotype, observed in four individuals, also revealed different allelic associations with the DRB3 gene, together with an unusual DQA association. None of the three DRw12,DQw7 haplotypes had the usual association with the DRw52b allele and also demonstrated two distinct DQA associations. The pattern of linkage disequilibrium of the HLA-D region loci in the South African black populations is more complex than in other populations. These findings may be of significance for the matching of unrelated donors for organ transplantation, as well as the study of disease association with HLA.

A new HLA-DRB1 allele within the DRw52 supertypic specificity (DRw13-DwHAG): sequencing and direct identification by oligonucleotide typing

Molecular analysis of HLA class II polymorphism represents a crucial parameter for HLA matching in transplantation immunology, for the study of HLA-disease association and for the understanding of major histocompatibility complex (MHC)-restricted antigen presentation. We report here the DNA sequence and the deduced amino acid sequence of the polymorphic first domain exon of the DRB1 and DRB3 alleles of the homozygous cell line HAG (DRw13-DwHAG-DQw7). The DRB1 sequence represents a new DRB allele, which clearly shows a close relationship to other DRB1 genes from the DRw52 group and is now officially named DRB1* 1303. The DRB1* 1303 allele is very similar to the two DRw13 alleles we have described earlier, with only five amino acid differences at positions 32, 37, 47, 57 and 71. Furthermore, its sequence in the third hypervariable region is unique among all known DRB1 and DRB3 alleles. The sequence of the DRB3 gene of HAG shows that it corresponds to the previously described DRB3* 0101 (DRw52a) allele. In addition we present analyses of a panel of healthy blood donors and leukemic patients by oligonucleotide typing showing that this new HLA-DR specificity can now be unequivocally identified in routine oligotyping with an allele-specific oligonucleotide probe.

CD4+ cytolytic T cell clones restricted to HLA class II, DR beta I, and DR beta III chains

We have investigated the functional polymorphism of HLA class II antigens using CD4+ CTL clones. Seven CD4+ CTL clones were isolated from a healthy donor (HLA A2 A24; B8 B27; DRw17 DRw52a) by repeated stimulation with irradiated autologous EBV-transformed B cell lines (EBV-B). According to the HLA restriction specificity we divided CD4+ CTL clones into three subgroups: (i) DRw17-restricted CD4+ CTL clones; (ii) DRw52a-restricted CD4+ CTL clones; and (iii) the CD4+ CTL clones, of which the restriction specificity could not be assigned to products of a single HLA locus. Interestingly, DRw17-restricted CD4+ CTL clones distinguished between DRw17 and DRw18. Similarly, DRw52a-restricted CD4+ CTL clones distinguished between DRw52a, w52b, and w52c. There are four amino acids which differ between DRw17 and DRw18, whereas five differ between DRw52a and the other two alleles (DRw52b and DRw52c). The recent elucidation of the crystal structure of a human class I MHC molecule has identified the probable peptide binding site to be a cleft on the outer surface of the molecule, between two alpha-helices. On the basis of the theoretical model for HLA class II molecules, amino acid positions 26 and 28 (DRw17 vs DRw18) and amino acid positions 26, 28, and 74 (DRw52a vs the other two alleles) lie within the "cleft." We propose that amino acid positions 26 and 28 are very important sites with regard to the recognition of antigen-MHC complex by the TCR.

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.

The DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci

The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population, in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a DQw4 allelic product. This study characterizes the DR subregion of that haplotype. cDNA sequence analysis has revealed a DR beta gene which differs at several positions from previously described DR3 beta 1 genes. It is postulated that a gene-conversion-like event with a DRw52 beta gene as donor has generated some of these differences. The haplotype carries a DRw52a allele as defined by oligonucleotide hybridization studies. DNA restriction fragment analysis using a family and several unrelated individuals has allowed us to identify DR alpha and beta fragments associated with the DR3(w18),DQw4 haplotype. The most striking observation is that the DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci. Several genetic mechanisms including reciprocal recombination, gene conversion, and point mutation were involved in generating the differences between these haplotypes. Once established, the DR3(w18),DQw4 haplotype appears to be relatively stable in the population.

Population genetics and molecular biology of the childhood chronic arthropathies

Recent immunogenetic studies of JRA patients have both helped to clarify subdivision into distinctive subtypes and identified those subtypes which may be related to adult rheumatic disease. Despite the variability of HLA associations from different geographic sources, a consensus appears to be emerging as to the most important associations. In addition to the HLA-DR locus, distinct associations with the HLA-DP and HLA-DQ loci have been described. Family studies have suggested an increased risk with certain haplotypes, particularly in the EOPA JRA population. Although inheritance patterns remain to be defined, recent studies with monoclonal antibodies, alloreactive T cell clones, and DNA have identified the existence of specific epitopes encoded by a variety of Ia molecules which may be more directly related to disease susceptibility. The concept of an epitope dose effect is put forward to account for the variable HLA association with disease, particularly with regard to EOPA JRA. Further developments in the definition of micropolymorphisms of Ia molecules at the genomic level as well as the possible involvement of other genetic loci, in particular T cell receptor variable gene products, should help clarify our understanding of the role of genetic factors in the aetiology of JRA. The studies of the last two decades indicate that inferences made by Carter (1969) on the 'polygenic, weakly penetrant genetic effect' in autoimmune disease are indeed applicable to JRA.

The single DR beta gene of the DRw8 haplotype is closely related to the DR beta 3III gene encoding DRw52

In most individuals two HLA-DR beta genes are expressed from each chromosome. One of these genes encodes one of the classical DR specificities, while the other encodes either of the supertypic DRw52/DRw53 specificities. In addition to these genes usually one or two DR beta pseudogenes are present. In contrast, the DRw8 chromosomal region only contains a single DR beta gene. To determine the relationship of this single gene to the multiple DR beta genes of other DR specificities, comparisons of Southern genomic blots were carried out. In this analysis genomic clones for each individual DR beta chain locus were included. The DR beta w8 gene was indistinguishable from the DR beta III gene of DR3 cells (encoding DRw52), suggesting that it is closely related to the latter gene. The functional implications of this finding are discussed.

The molecular basis of susceptibility to rheumatoid arthritis: the conformational equivalence hypothesis

This is an interpretive review of recent immunologic and molecular biologic data concerning the molecular basis of susceptibility to rheumatoid arthritis. The central point of view was taken that the major histocompatibility complex (MHC) class II molecules encoding disease susceptibility function in an immune recognition event involving an antigen "X" that currently eludes characterization. The problem of understanding the meaning of the association of susceptibility with diverse MHC alleles such as DR4 (Dw4 and Dw14), DR1, and DRw10 is approached by detailed biochemical analysis that led to the identification of common stretches of amino acid sequence, presumably encoding conformationally equivalent structures. Non-classic MHC polymorphisms related to disease susceptibility but not associated with particular alleles such as identified by Ab 109d6 proved especially valuable in suggesting new directions for attempting to understand the significance of these associations. Consideration is given to the possibility that a family of either slightly different or identical conformations encoded in either cis or trans cumulatively confer the liability to develop rheumatoid arthritis, and implying a highly non-classic mode of inheritance. The available data do not permit a distinction between the possibilities that an antigen "X" was being presented to T cells or whether the distinctive conformations of the MHC class II molecule serve the same role as antigen "X" but are directly recognized by T cells. However, with additional data, some limited insight should be able to be inferred about the nature of an antigen "X" that specifically binds to the MHC conformation with a complementary interaction. It seems reasonable to consider the pathogenesis of rheumatoid arthritis as a typical immune response resulting from a simple immune recognition event of a single antigenic molecule.

Analysis of HLA-DR glycoproteins by DNA-mediated gene transfer. Definition of DR2 beta gene products and antigen presentation to T cell clones from leprosy patients

We have used DNA-mediated gene transfer to express HLA class II molecules in mouse L cells for serological, biochemical, and functional analysis. cDNA clones encoding the DR2 beta a and DR2 beta b products of the DR2Dw2 haplotype were subcloned into a mouse Moloney leukemia virus-based expression vector (pJ4) and transfected separately into mouse L cells together with a HLA-DR alpha/pJ4 construct. These transfectants have allowed differential analysis of the two DR2 beta products in a manner normally prohibited by the concomitant expression seen in B cells. Two-dimensional SDS-PAGE analysis of the transfectants defines the more acidic beta chain as the product of the DR2 beta a sequence, and the more basic chain as the product of the DR2 beta b sequence. The LDR2a transfectants present antigen efficiently to M.leprae-specific T cell clones and are capable of presenting synthetic peptide, 65-kD recombinant mycobacterial antigen and M.leprae. Of the DR2Dw2-restricted T cell clones we have tested, all use the DR2 beta a chain as their restriction element. Inhibition studies with mAbs demonstrate the dependence of presentation by the transfectant on class II and CD4, while mAbs against LFA-1, which substantially inhibit presentation by B-lymphoblastoid cell lines, do not inhibit transfectant presentation.

Serological recognition of HLA-DR allodeterminant corresponding to DNA sequence involved in gene conversion

HLA class II molecules were isolated from mouse L cells transfected with a DR alpha gene and an allele, 52a, of locus DR beta III from an HLA-homozygous cell line, AVL, of the DR3 haplotype. The isolated molecules were found to possess a new allospecificity, named TR81. This specificity behaved allelic to the previously described specificity TR22 encoded by another allele, 52b, of the DR beta III locus. The TR81 specificity was also present on the DR beta I gene product of the DR3 haplotype. The nucleotide sequence of the gene encoding TR81 differs from TR81-negative DR beta genes of the DRw52 family in only two codons, both located in the regions known to be involved in a gene conversion event. Consequently, the following conclusions can be formulated. (a) TR81 is a bi-locus specificity and allelic to TR22 only in its DR beta III locus localization. (b) The TR81 specificity is the phenotypic counterpart of the gene conversion event which led to the generation of the DR beta I gene of the DR3 haplotype. (c) One or both individual amino acid substitutions in the first domain of the DR beta chain are responsible for the TR81 allospecificity. (d) Since TR81 is expressed on the DR beta I chain of the DR3 haplotype, it is possible that TR81 and DR3 represent the same serological specificity.

Functional polymorphism of each of the two HLA-DR beta chain loci demonstrated with antigen-specific DR3- and DRw52-restricted T cell clones

HLA-DR3- and HLA-DRw52-associated functional polymorphism was investigated with selected tetanus toxoid (TT)-specific T cell clones. We have shown earlier that HLA-DR antigens are encoded by two distinct loci, DR beta I and DR beta III. The alloantigenic determinant(s) defined by the serological HLA-DR3 specificity map to the former, while the supratypic HLA-DRw52 determinants map to DR beta III. Furthermore, we have recently recognized by DNA sequencing three alleles of HLA-DRw52 at locus DR beta III, referred to as 52 a, b, and c. Our objective was to correlate the pattern of T cell restriction with the gene products of individual DR beta chain loci and with the three newly described alleles of locus DR beta III. Among the selected T cell clones, 5 reacted exclusively when TT was presented by HLA-DR3+ APCs (TT-DR3-APC). In contrast, two T cell clones were stimulated by TT-DRw52-APC. More specifically, these two T cell clones (Clones 10 and 16) were stimulated by different subsets of TT-DRw52-APC. Clone 16 responded to some DR3 and TT-DRw6-APC, while clone 10 was stimulated by other TT-DR3 and TT-DRw6, and all TT-DR5-APC. This same pattern of DRw52 restriction was found in panel, as well as in family studies. Because this suggested a correlation with the pattern of DRw52 polymorphism observed earlier by DNA sequencing and oligonucleotide hybridization, the APC used in these experiments were typed for the 52 a, b, and c alleles of locus DR beta III by allele-specific oligonucleotide probes. This distribution overlapped exactly with the stimulation pattern defined by the T cell clones. Clone 16 responded to TT-52a-APC, clone 10 to TT-52b-APC, and both clones to a TT-52c-APC. The response of the T cell clones was inhibited differentially by mAbs to DR. Raising TT concentration, or increasing HLA-class II expression with INF-gamma both affected the magnitude of response of the TT-specific clones but did not modify their specificities. These results demonstrate that a restriction specificity can be attributed to the DR beta III locus and illustrate the functional relevance of the polymorphism observed at this locus. This is of special interest in view of the striking difference in the pattern of structural diversity among alleles of DR beta I and DR beta III.

A cytotoxic human-human hybridoma antibody (TrH6) specific for HLA-DRw52

TrH6 is a new human-human hybridoma antibody (Ab) of IgM, lambda isotype. At concentrations of 17-5000 ng IgM/ml, TrH6 killed twelve out of fourteen lymphoblastoid cell lines that expressed DRw52, but none of the nine DRw53 homozygous lines. Both DRw52+ cells (LUY, TAB) not killed by TrH6 were DR8+, suggesting that these lines express a structural variant of DRw52 linked to DR8. The murine cytotoxic DRw52-specific mAb 7.3.19.1 (Koning et al. 1984) exhibited the same pattern of reactivity with DRw52+ cells as TrH6. However, unlike TrH6, 7.3.19.1 cross-reacted weakly with two DR7+DRw53+ homozygous cell lines, suggesting that the TrH6 epitope has a more limited distribution. The reactions with a panel of cells with known deletions in the HLA-region supported the conclusion that TrH6 is specific for DRw52. Further evidence was obtained in a competition RIA, where the murine mAbs L243 (anti-DR monomorphic) and 7.3.19.1 (anti-DRw52) inhibited binding of radiolabeled TrH6 to DRw52 homozygous cells. TrH6-coated magnetic beads provided a simple rosette-assay for typing of "buffy-coat" leukocytes for the TrH6 epitope.

Identification and distribution of three serologically undetected alleles of HLA-DR by oligonucleotide.DNA typing analysis

Recent progress in the molecular biology of human major histocompatibility complex class II genes (HLA-DP, -DQ, -DR) have shown that the genetic complexity and allelic polymorphism are greater than expected. In the case of HLA-DR, three DR beta-chain loci have been identified and linked, two of which (DR beta I and DR beta III, now assigned names HLA-DRIB and HLA-DR3B) are functional. We have shown that the HLA micropolymorphism detected at the DNA sequence level can easily be analyzed by hybridization with allele-specific oligonucleotides (HLA "oligotyping"). In the case of the HLA DRw52 supertypic specificity, which includes the DR3, DR5, DRw6, and DRw8 haplotypes, three alleles, referred to as DRw52a, DRw52b, and DRw52c, have recently been identified at the HLA-DR3B locus by DNA sequencing. Hybridization with locus- and allele-specific oligonucleotide probes (designated 52a, 52b, and 52c) has been performed on DNA from normal individuals forming a panel of 82 haplotypes to establish the distribution of these three alleles. Individuals of the DR3 haplotype had either the DRw52a or DRw52b allele, and individuals of extended haplotype HLA-A1,B8,DR3 had only the DRw52a allele. DR5 individuals all had the DRw52b allele, while individuals of DRw6 haplotype had the DRw52a, -52b, or -52c allele. None of these three alelles are found in DRw8 individuals. Analysis of this micropolymorphism, undetectable by common typing procedures, is therefore now operational for more accurate HLA matching for transplantation and for improving correlations between HLA and disease susceptibility.

Allelic variation in the DR subregion of the human major histocompatibility complex

Allelic variation in the DR subregion of the human major histocompatibility complex has been analyzed by nucleic acid sequencing of cDNA clones obtained from cell lines homozygous by consanguinity for all the common serological types DR1-9. Two expressed loci were identified in the haplotypes DR2, -3, -4, -7, and -9; one locus being present at a much lower frequency (4-7%) than the other. The low-frequency allele was highly conserved between each of the DRw53 (DR4, -7, -9) and the DRw52 (DR3, -5, -6) haplotypes. Analysis of the variation between alleles confirms the presence of three allelic hypervariable regions. At each variable residue, a limited range of amino acid substitutions are found, distinguishing them from immunoglobulin hypervariable regions. Dinucleotide substitutions are extremely common. Individual hypervariable regions are often shared between haplotypes. Much of the variation in these alleles can be attributed to the shuffling of these regions between haplotypes, possibly by the mechanism of gene conversion.

Molecular localization of LB-Q1, a DRw52-like T-cell recognition epitope and identification at the genomic level of associated shared hybridizing fragments

In this paper we report on the molecular localization of LB-Q1, a supertypic HLA class II determinant which we previously identified by the use of proliferative T cells. The population distribution shows that each of the DRw52 associated specificities DR3, DR5, and DRw6 may occur with and without LB-Q1. DNA from nine DR3, six DR5, and 14 DRw6 homozygous B-cell lines were digested with the enzymes TaqI, EcoRI, and PvuII. Using a DR beta cDNA probe, shared hybridizing fragments were observed that correlate completely with the presence or absence of LB-Q1. T-cell recognition of LB-Q1 can be blocked with a monoclonal antibody (7.3.19.1) which in some haplotypes selectively reacts with the DR beta III chains, but cannot be blocked with a monoclonal antibody (I-LR2) reacting in those same haplotypes exclusively with DR beta I chains. Therefore, LB-Q1 maps to the DR beta III molecule. These data suggest the occurrence of relatively frequent previous recombinations between the two DR beta chain genes present in DRw52 haplotypes.

HLA-D region epitopes associated with juvenile arthritis. Recognition by alloreactive T cell clones and alloantisera

The HLA-D region antigens DR5 (w11,w12), DRw6 (w13,w14), DRw8, DRw52, and DQw1 have previously been shown to be increased in frequency in subsets of patients with juvenile arthritis. Since the HLA-D region is complex (composed of at least 3 subregions encoding multiple molecules, each in turn presenting multiple alloantigenic epitopes), we sought to clarify whether one strongly associated factor might explain the previous findings. To search for the pertinent HLA-D region stimulatory epitopes, alloreactive T cells were primed against DR5 and DRw6 haplotypes and cloned by limiting dilution. Three T cell clones and 1 alloantiserum met the criteria for significant association with juvenile arthritis on patient testing, including DR5, DRw6, and DRw8 haplotypes. Monoclonal antibody blocking revealed that all 4 recognized epitopes on DR subregion products. For 2 of the clones, the relative risks for JA (10.5 and 9.4) were higher than the risks with any other previously described typing reagents.

Structural comparison of the genes of two HLA-DR supertypic groups: the loci encoding DRw52 and DRw53 are not truly allelic

The organization and sequence of the HLA-DR beta chain genes are compared in the two supertypic groups, DRw52 and DRw53, which together account for more than 80% of HLA-DR alleles. From the structural data, we conclude that these two groups represent distinct lineages which have followed different patterns of evolution. The fine structure of the beta chain locus encoding the DRw53 specificity corresponds most closely to the DR beta II pseudogene in the DRw52 haplotypes. Concomitantly, the DR beta I locus in DRw53 haplotypes is more closely related to both of the two expressed DR beta loci of the DRw52 haplotypes (DR beta I and DR beta III). These two loci are the result of a recent duplication. This leads to the proposal that both expressed DR beta chain genes in the DRw52 haplotypes (DR beta I and DR beta III) are derived from a single precursor locus, while the two loci expressed in the DRw53 haplotypes are derived from distinct ancestral loci. The genes encoding DRw52 and DRw53 are therefore not true alleles of the same original locus. A scheme is proposed that accounts for the evolution of DR specificities within the DRw52 and DRw53 groups of haplotypes. It is evident that the different HLA-DR alleles are not structurally equidistant and that one must take into consideration different degrees of heterozygosity or mismatch among the DR alleles.

Analysis of the DR beta chains from two DRw6 cell lines (WT46 and WT52): recombination in vivo may have generated new haplotypes

The HLA-DRw6 haplotype of the class II major histocompatibility complex (MHC) antigens exhibits unusual complexity and cannot be uniquely typed serologically. The DR beta chains expressed by consanguineous homozygous DRw6 typing cells WT46 and WT52 were biochemically analyzed using three monoclonal antibodies (mAb) that recognize denatured DR beta chains. The results of isoelectric focusing and N-terminal sequencing demonstrate that each DRw6 B-cell line expresses two DR beta chains. Evidence of an exchange of mAb epitopes involving the two DR beta chains of one of these cell lines was obtained and may be explained by a recombinational mechanism involving reciprocal exchange of genetic segments of the DR beta chains, one of which may encode the putative DRw6 chain and the other the chain carrying the MT2 allotypic determinant. Since a recombinational hot spot has been shown to occur uniquely in the mouse MHC within the E beta gene, the occurrence of a recombination within the human homolog, DR(MT2) beta, could reflect some specific feature of this MHC region. Comparison of the DR beta chains of the WT46 and WT52 cell lines with those of a third DRw6 cell line, LB, suggests that two alleles of MT2 occur.

Oligonucleotide genotyping shows that alleles at the HLA-DR beta III locus of the DRw52 supertypic group segregate independently of known DR or Dw specificities

Using locus- and allele-specific oligonucleotide probes, we have studied the polymorphism of the HLA-DR beta III locus within the haplotypes of the DRw52 supertypic group. DNA from a number of homozygous typing cells typed for both Dw and DR was used. The DR beta III polymorphisms, DRw52a and DRw52b, do not segregate with Dw typing, or with DR typing, indicating that the determinants responsible for Dw-defined T-cell response and for DR haplotypic recognition are not encoded by the DR beta III locus. Hence, we can conclude that these DR specificities are encoded by the other functional DR locus, DR beta I, while the DR beta III locus encodes only the supertypic product.

Immunochemical analysis of a cell transfected with an HLA-DR gene reveals a new alloantigenic specificity within HLA-DRw52

The HLA-DR antigen has been prepared from the surface of a mouse fibroblast cell line transfected with a single HLA-DR beta-chain gene as well as single HLA-DR alpha and invariant chain gene. Since the HLA-DR beta chain gene studied corresponds to the DR beta III locus, the DR serological specificities detected on the transformed cells can be assigned to this locus. The use of the HLA-DR-producing mouse cell line has led to the identification of a new serological specificity included within DRw52 and associated with some DR3, some DRw6 and all DR5 haplotypes studied. Most likely this new specificity corresponds to an allelic polymorphism at the DR beta III locus of DRw52 individuals and can serve as a new serological marker for this subset of DR3, DR5 and DRw6 haplotypes.

Human allospecific TLCs generated against HLA antigens associated with DR1 through DRw8. II. Population analyses and blocking studies with monoclonal antibodies

Serologic, cellular, and molecular evidence supports the concept of extreme complexity within the HLA-D region. To study the complexity and fine specificity of the HLA-D region at the level of T-cell recognition, a panel of T-cell clones was generated against alloantigens associated with HLA-DR1 through -DRw8. After initial screening of more than 800 clones, 89 representative lines were selected for extensive testing against 204 unrelated stimulator cells. Clone-by-clone correlation analyses were performed to test whether any clones recognized similar or identical epitopes. In addition, clonal reactivity patterns were correlated with known HLA specificities. Twelve clusters of clones were identified with similar reactivity patterns using clone-by-clone correlation analysis. Some groups were significantly correlated with specificities associated with various D-region haplotypes; others had no significant correlation with any defined D-region specificity. Five general types of clones obtained in our study can be categorized as follows: Those recognizing epitopes clearly demonstrating a primary association with the classically defined D-region molecules against which the clones were primed. Clones recognizing epitopes associated with one of the priming antigens and also with another unrelated D-region specificity. Clones detecting epitopes which showed significant correlation with D-region molecules totally different from those against which they were originally primed. Clones with limited reactivity in population studies and no correlation with defined D-region molecules. Clones recognizing class I-associated epitopes.

Two DR beta allelic series defined by exon II-specific synthetic oligonucleotide genomic hybridization: a method of HLA typing?

Comparisons of exon II HLA-DR beta sequences have shown that nucleotide variations are principally clustered within the following three regions: V1 (amino acid 8-15), V2 (25-32), and V3 (70-77). V1, V2, and V3-derived 24-mers have been synthesized, the DR beta sequences coming from DR1, DR3, Drw6, DR4, DR5, and DRw53 haplotypes. Each oligonucleotide was hybridized to Pvu II-digested DNA samples from 13 HLA genotyped families; therefore, 52 haplotypes have been investigated. Six polymorphic Pvu II fragments were detected, constituting two allelic series probably corresponding to the beta 1 and beta 2 locus of the DR region. The first series (beta 1) comprises a minimum of nine alleles while the second series (beta 2), which is less polymorphic, comprises at least four alleles. Certain patterns correlate perfectly with certain DR specificities, whereas other patterns define new subdivisions as in DR3 and DRw6 haplotypes. Although it appears that some mismatches do not always prevent hybridization in the conditions used in this work, this method will provide in many instances a convenient tool for HLA-DR typing.

Polymorphism of human Ia antigens: gene conversion between two DR beta loci results in a new HLA-D/DR specificity

The polymorphic HLA-DR beta-chains are encoded within the human major histocompatibility complex (MHC) by multiple loci resulting from gene duplications. Certain DR haplotypes can be grouped into families based on shared structural factors. We have studied the molecular basis of HLA-DR polymorphism within such a group which includes the haplotypes DR3, DR5 and DRw6. Molecular mapping of the DR beta-chain region allows true allelic comparisons of the two expressed DR beta-chain loci, DR beta I and DR beta III. At the more polymorphic locus, DR beta I, the allelic differences are clustered and may result from gene conversion events over very short distances. The gene encoding the HLA-DR3/Dw3 specificity has been generated by a gene conversion involving the DR beta I and the DR beta III loci of the HLA-DRw6/Dw18 haplotype, as recipient and donor gene, respectively. Based on which allele is found at DR beta III, the less polymorphic locus, two groups of haplotypes can be defined: DRw52a and DRw52b. The generation of HLA-DR polymorphism within the DRw52 supertypic group can thus be accounted for by a succession of gene duplication, divergence and gene conversion.

Molecular analysis of HLA class I and class II antigen loss mutants reveals a homozygous deletion of the DR, DQ, and part of the DP region: implications for class II gene order

The mutant human B-lymphoblastoid cell lines, 721.174 and 721.180, previously reported to exhibit greatly reduced expression of human HLA class I and II antigens (DeMars et al., Hum Immunol 11:77, 1984), were analyzed by Southern blotting using class II cDNA and genomic clones as hybridization probes. All genomic sequences complementary to DR alpha, DR beta, DQ alpha, and DQ beta probes were absent from these mutants. DZ alpha genomic sequences were deleted as were the DP alpha 1 and DP beta 1 loci but the DP beta 2 and most, if not all, of the DP alpha 2 locus were retained. However, no RNA transcripts for either DP alpha 2 or DP beta 2 could be detected. The mapping of the deletion breakpoint within the DP cluster allows the orientation of the loci in the DP region with respect to the centromere as follows: centromere, DP beta 2, DP beta 1, DP alpha 1, (DQ, DR). In addition, the analysis of a set of DR-, DQ-, DP+ homozygous deletion mutants (721.82, 721.84, and 721.101) reveals a deletion breakpoint between the DQ alpha 1/DQ beta 1 loci and the DQ alpha 2/DQ beta 2 loci. These mutants retain DZ alpha genomic sequences, tentatively mapping the DZ alpha locus between the DQ and the DP region. The residual ability of the DR-, DQ-, DP- mutants (174 and 180)* to stimulate allogeneic and autologous lymphoproliferative responses must be attributed to expression of as yet unidentified class II antigens, or to non-class II antigens.

Recognition of class II molecules by human T cells. I. Analysis of epitopes of DR and DQ molecules in a DRw11, DRw52, DQw3 haplotype

The HLA-D region of individuals with the DRw11, w52, DQw3 haplotype encodes multiple molecular products of three distinct subregions, DR, DP, and DQ. Since each molecule can carry multiple stimulatory epitopes, the repertoire of allogeneic T-cell responses to determinants of this haplotype can be quite large. In the present experiments, alloreactive cloned T-cell lines recognized six distinct epitopes associated with DRw11, DRw52, DQw3 haplotypes. Panel studies established that three epitopes were DRw11-like and three were DRw52-like. Blocking with monoclonal antibodies showed that two DRw11-like epitopes were carried by DR-subregion products and one DRw11-like epitope was carried by DQ-subregion molecules. DRw52-like epitopes were detected on separate DR subregion-encoded molecules. One of them carried both DRw11- and DRw52-like epitopes, the other carried two of the DRw52-like epitopes. These epitopes, which represent functional units that trigger T-cell responses, can be detected at the present time only with the methods used in this report. Conventional allogeneic T-cell responses represent the summation of responses to multiple epitopes encoded by different D-subregion genes.

Linkage map of three HLA-DR beta-chain genes: evidence for a recent duplication event

The predominant class II, or Ia, antigen of the human major histocompatibility complex is HLA-DR. It consists of an alpha and a beta chain, the latter being responsible for the remarkable polymorphism of these Ia antigens. Studies with cloned genes had shown the existence of more than one DR beta-chain locus. We have isolated about 100 kilobases of the HLA-DR beta-chain gene region from a cosmid library generated from a consanguineous homozygous B-cell line of the DR3 haplotype. Three HLA-DR beta-chain genes have been characterized. They are arranged in a head-to-tail orientation. One of the genes lacks the region encoding the first domain of the DR beta chain. The two other genes are transcribed, as shown by RNA blot hybridization analysis. A striking restriction site homology has been found within the DR beta-chain gene cluster, suggesting a recent duplication event involving at least 25 kilobases of DNA. Moreover, the molecular map of DR beta chain genes cloned from B-cell lines of two other HLA-DR haplotypes shows extensive homology between alleles of a given DR beta-chain locus.